commit bfec8775a9c903ca8b464a26b2b1ce2b16b0cb75 Merge: 2a3b085e c84dea5a Author: jbbel Date: Tue Sep 15 17:04:52 2026 -0700 Merge pull request #241 from jbbel/deankow_helfrich_interaction src_deankow/{helfrich_membrane,interaction}: port the src_deankow bug… commit c84dea5a39e6203f7341eb741dfcb6765f837e31 Author: jbb Date: Tue Sep 15 16:59:56 2026 -0700 src_deankow/{helfrich_membrane,interaction}: port the src_deankow bug fixes helfrich_membrane/ and interaction/ were created by copying multilevel/, surface/ and moving/ after issues #207-#230 were filed, so they were never covered by the fixes in #238, #239 and #240. This ports the ones that apply. Each directory was audited against every fix rather than patched wholesale; the two directories do NOT carry the same set. helfrich_membrane/ (a copy of moving/) -- #208, #209, #210, #211, #213, #214, #216, #217, #218, #219, #222, #223, #228: #208 new_dk_metric built the new inverse-square-root metric from the OLD determinant; detg holds the previous time level at that point. #209 the init loop filled newgmetric/newsqrgmetric/newdetg but FillBoundary'd gmetric/sqrgmetric/detg, which had not been written at all. Seed the old metric from the new one, fill all six, and fill the new trio after new_dk_metric in AdvancePhiAtLevel too. #210 the num_flux == 4 noise terms for sub-fluxes 2 and 3 took phi/det/metric from the opposite cell to their deterministic and drift terms. #211 leftover mult(1./cell_vol) on the fine->coarse reflux path. This one applies here because helfrich_membrane uses the particle-count convention, like surface/ and moving/ (see below for interaction/). #213 update_phi's num_flux == 4 branch was still the static-metric version. #214 compute_flux_z gated the physical-boundary branch on the box bounds rather than the face index -- the bug #231 fixed everywhere else. Also setVal the flux MultiFabs, as #231 did, so an unwritten component is a reproducible zero. #216 ColorParticlesWithPhi computed the cell index without prob_lo and truncated instead of flooring. #217 members read/accumulated inside device lambdas via a captured `this`. #218 init_dk_metric/new_dk_metric neither AMREX_GPU_DEVICE nor inline. #219 unguarded amrex::Print() inside device lambdas (all three sites). #222 amrex::IntVect(1,1) has no 3D overload; drop the debug print_state. #223 bare `elseif` in a preprocessor block, plus the unbalanced braces around it; replaced with a DK_EXT_POT_FORM selector. All three forms compile. #228 phi_old seeded with one component when phi may have two. helfrich_membrane/update_metric.H was never added to the repo even though AdvancePhiAtLevel.cpp #includes it, so the directory did not build from a clean checkout. It is added here (with the #208 and #218 fixes applied) and registered in Make.package. interaction/ -- #212, #216, #219, #228 only: #212 the closing parenthesis of the amp*amp*(...) group in the on-surface drift was misplaced, folding the geometric factor into the sum, which leaves a spurious drift where the Ito drift must vanish by symmetry. Present at two sites. Also adopt the numerically stable cfac: (1 - 1/sqrt(det))/(det-1) is exactly 1/(det + sqrt(det)) but is 0/0 as det -> 1. #216, #219 (the AdvectWithRandomWalk site only -- AddParticles was already guarded here), #228, and the flux setVal from #231. #211 deliberately NOT applied to interaction/: it uses the particle-density convention (AddParticles takes int(num_part*phi*cell_vol+rannum)) and all three of its mult(1./cell_vol) calls are consistently active, exactly like multilevel/. Removing the scaling there would have broken conservation. #222 and #223 do not apply either -- interaction/ kept multilevel's correct IntVect::TheUnitVector() and dimension-guarded print_state, and has no `elseif`. Both exec/dean_kow/helfrich and exec/dean_kow/interaction build clean and run on multiple ranks with amrex.fpe_trap_invalid=1; interaction conserves mass to round-off. The only remaining implicit-`this` capture in either directory is the host-side plotfile-header I/O lambda, which is not a device kernel. DK_EXT_POT_FORM 1, 2 and 3 all compile in helfrich_membrane. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/helfrich_membrane/AdvancePhiAtLevel.cpp src_deankow/helfrich_membrane/AmrCoreAdv.cpp src_deankow/helfrich_membrane/Make.package src_deankow/helfrich_membrane/ParticleData.H src_deankow/helfrich_membrane/StochasticPC.cpp src_deankow/helfrich_membrane/init_metric.H src_deankow/helfrich_membrane/mykernel.H src_deankow/helfrich_membrane/update_metric.H src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/StochasticPC.cpp commit 2a3b085e3470f792522e6fed93d698a3b9b83d10 Merge: 24a5e905 3a11c140 Author: jbbel Date: Tue Sep 15 16:48:44 2026 -0700 Merge pull request #240 from jbbel/deankow_1d_stats_bc src_deankow/1d_stats: test bc_hi, not bc_lo, at the high-x boundary commit 3a11c140ba00f6918bf5500b3683593d8114f076 Author: jbb Date: Tue Sep 15 16:46:53 2026 -0700 src_deankow/1d_stats: test bc_hi, not bc_lo, at the high-x boundary Fixes #207. The two branches of compute_flux_x that handle the high-x domain boundary tested bc_lo rather than bc_hi -- a copy/paste slip from the two low-x branches just above. bc_lo and bc_hi are passed in independently from bc.lo(0) and bc.hi(0) (myfunc.cpp), so whenever the two ends of the domain use different boundary conditions the high end was handled with the low end's rule: - bc_lo = foextrap, bc_hi = ext_dir: the high face took the zero-flux branch instead of the Dirichlet branch, so phiright was never applied and no boundary noise was injected; - bc_lo = int_dir (periodic) with bc_hi = ext_dir/foextrap: neither high-x branch fired, so i == dom_hi+1 fell through to the interior else and read phi(i,j,k,...) -- the ghost cell one past the last valid cell. The case that works today is bc_lo == bc_hi, which is presumably why this went unnoticed. compute_flux_y and compute_flux_z in the same file already test the matching bc. Verified against the pre-change build (inputs_neq, phileft=320, phiright=0, nsteps=20, fixed seed): - bc_lo = bc_hi = ext_dir: plotfiles bit-identical, so existing runs are unaffected; - bc_lo = foextrap, bc_hi = ext_dir: the last cell of the mean profile goes from 5.30754 (old, not draining -- the zero-flux branch) to 5.07299 (new), which is exactly the value the bc_lo = bc_hi = ext_dir run gives. The high end now depends only on bc_hi, and the difference decays into the interior. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/1d_stats/mykernel.H commit 24a5e905ceca219f0d51c5ccc51c02a1bbdec477 Merge: 963cfb02 95523e32 Author: jbbel Date: Tue Sep 15 16:23:03 2026 -0700 Merge pull request #239 from jbbel/deankow_portability Deankow portability commit 95523e32e6b632b476aa537c55d347bc03b20918 Author: jbb Date: Tue Sep 15 16:17:45 2026 -0700 src_deankow: fix ColorParticlesWithPhi cell index and the phi_old seed copy Fixes #216, #228. These two are plain correctness bugs rather than portability ones; they are in a separate commit so they can be dropped independently. #216 {multilevel,surface,moving,ensemble}/StochasticPC.cpp: ColorParticlesWithPhi converted a particle position to a cell index with a raw divide and a static_cast. That omits the prob_lo offset (correct only when prob_lo == 0 in every direction, which nothing enforces), omits domain.smallEnd(), and truncates toward zero instead of flooring, so static_cast(-0.3) is 0 rather than -1. Negative indices are reachable in normal operation: AddParticles grows the domain by one cell in each periodic direction and this routine runs on phi_grown. Use amrex::getParticleCell, the same helper getNewCell/getOldCell already use. The effect was a wrong phi "colour" in the particle plotfile -- a silent diagnostic error, not a solver one. #228 {multilevel,ensemble,surface,moving}/AmrCoreAdv.cpp: InitData seeded phi_old from phi_new copying exactly one component, but phi has two whenever alg_type != 0. Component 1 of phi_old stayed uninitialized until the first std::swap in timeStepNoSubcycling, and WriteCheckpointFile on the very next line writes both components -- so a restart from that checkpoint started from garbage. Copy phi_new[0].nComp() components, as the rest of these files already do. All four directories build; moving runs clean on 4 ranks with num_flux=4 and amrex.fpe_trap_invalid=1. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/ensemble/AmrCoreAdv.cpp src_deankow/ensemble/StochasticPC.cpp src_deankow/moving/AmrCoreAdv.cpp src_deankow/moving/StochasticPC.cpp src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/StochasticPC.cpp src_deankow/surface/AmrCoreAdv.cpp src_deankow/surface/StochasticPC.cpp commit f8f7940fc7cfe02a5d6863872f98fe29ccf6e9f2 Author: jbb Date: Tue Sep 15 16:11:46 2026 -0700 src_deankow: GPU/3D portability fixes, and make the ensemble drift consistent Fixes #217, #218, #219, #222, #223, #226, #227. #217 {surface,moving}/AmrCoreAdv.cpp: several AMREX_GPU_DEVICE lambdas read AmrCoreAdv data members directly. A [=] lambda captures `this`, so the member access dereferences a host pointer from device code -- illegal on GPU. Copy the members into locals first (multilevel/ already uses this idiom). The worst case was surf_area, which was *accumulated* inside the metric-init kernel: that is also an unsynchronised read-modify-write across OpenMP threads. Replace it with detg.sum(1)*dx*dy (newdetg in moving/), which reduces over the valid region across ranks and needs no reduction in the kernel at all. moving/ additionally indexed the host Vector t_new[0] from two device lambdas; that is now hoisted. #218 {surface,moving}/init_metric.H, moving/update_metric.H: init_dk_metric and new_dk_metric are called from device lambdas but were neither AMREX_GPU_DEVICE nor inline -- the first breaks GPU builds, the second makes a second include site a duplicate-symbol link error. Decorate them like every other pointwise kernel. Also drop the never-referenced TWOPI and the unused sig11..sig22 from the active declarations. #219 {surface,moving}/StochasticPC.cpp: restore the #ifndef AMREX_USE_GPU guards around the two debug amrex::Print() calls in AddParticles, which were dropped when the file was copied from multilevel/. amrex::Print is host-only, so GPU builds fail to compile here. The same pattern in AdvectWithRandomWalk was never guarded in any directory (multilevel/ included) and is guarded now too. #222 {surface,moving}/ParticleData.H: amrex::IntVect(1,1) has no 3D overload, so it is a hard compile error with DIM=3; use IntVect::TheUnitVector() as multilevel/ does. Delete the accompanying print_state() of a hard-coded cell (31,16) -- it is unguarded debug output in a per-timestep path and that cell need not be in the domain. #223 {surface,moving}/mykernel.H: the external-potential block selected between three forms with #if 1 / #else / `elseif`. `elseif` is not a preprocessor directive, and the C++ `if(num_flux == 1){` opener sat inside the #if while its matching brace sat outside, so selecting any branch but the first gave both a syntax error and unbalanced braces. Replace with a named DK_EXT_POT_FORM selector and proper #elif, and hoist the opener and the shared caps/capsy/capr/ caprx declaration (the num_flux == 4 branch uses them too) out of the #if. All three forms now compile in both directories. #226 ensemble/: the grid and the particles disagreed along an ensemble direction. advance_phi skipped the entire flux computation there, while AdvectWithRandomWalk applied the external-potential drift unconditionally and only zeroed the random increment. Per the choice recorded on the issue, the grid is the side that changes: compute_flux_x/y are now always called and take an a_ensemble_dir argument, suppressing the diffusive and stochastic terms themselves while keeping the drift. With ext_pot == 0 this leaves the flux at zero, exactly as skipping the call did, so existing ensemble runs are unaffected. compute_flux_z has no drift term, so its guard is left alone. a_ensemble_dir is also hoisted out of the lambdas -- it is a host Vector. #227 singlelevel/main.cpp: the variance normalisation n_cell*n_cell is the cell count only in 2D, and the int*int product overflows for n_cell >= 46341. Use geom.Domain().numPts(), which is exact and dimension-agnostic. Builds verified for surface, moving, ensemble and multilevel (gnu, MPI, 2D); singlelevel/main.cpp syntax-checked (that exec dir has a stale hard-coded AMREX_HOME, unrelated to this change). DK_EXT_POT_FORM 1, 2 and 3 all compile. ensemble runs clean with ext_pot off (mass conserved to round-off) and on. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/ensemble/myfunc.cpp src_deankow/ensemble/mykernel.H src_deankow/moving/AmrCoreAdv.cpp src_deankow/moving/ParticleData.H src_deankow/moving/StochasticPC.cpp src_deankow/moving/init_metric.H src_deankow/moving/mykernel.H src_deankow/moving/update_metric.H src_deankow/multilevel/StochasticPC.cpp src_deankow/singlelevel/main.cpp src_deankow/surface/AmrCoreAdv.cpp src_deankow/surface/ParticleData.H src_deankow/surface/StochasticPC.cpp src_deankow/surface/init_metric.H src_deankow/surface/mykernel.H commit 963cfb02146747411dd5ce5bdc0fda30194d736f Merge: e3d62e50 6b7b766e Author: jbbel Date: Tue Sep 15 15:44:19 2026 -0700 Merge pull request #238 from jbbel/deankow_moving_metric_fixes src_deankow/{surface,moving}: fix moving-metric and reflux bugs commit 6b7b766e4a7af3a2bd393b95bce6d97cb6af335c Author: jbb Date: Tue Sep 15 15:41:23 2026 -0700 src_deankow/{surface,moving}: fix moving-metric and reflux bugs Fixes #208, #209, #210, #211, #213. #208 moving/update_metric.H: new_dk_metric built the new inverse-square-root metric from the OLD determinant. The routine is a copy of init_dk_metric in which only the left-hand sides were renamed to new*, so newdetg(...,2) and every occurrence of s = sqrt(det) in newsqrmet still read detg, which at that point holds the previous time level. Since (I + v v^T)^(-1/2) = I - v v^T/(s(s+1)), mixing the old s with the new v = (p,q) gives a matrix that is not g^(-1/2), so the stochastic flux amplitude has the wrong covariance for as long as the surface is moving. Verified: with the fix g^(-1/2).g^(-1/2) reproduces g^(-1) to round-off, and the expressions are unchanged for a frozen surface. #209 moving/: the metric ghost cells were never valid. MakeNewLevelFromScratch filled newgmetric/newsqrgmetric/newdetg but then FillBoundary'd gmetric/sqrgmetric/detg, which had not been written at all. Seed the old metric from the new one and fill the ghost cells of all six, and likewise fill the new trio after new_dk_metric in AdvancePhiAtLevel, which writes both over validbox only. compute_flux_x/y read the old metric at (i-1,j)/(i,j-1), which lands in the ghost region on the low faces of every box. #210 {surface,moving}/mykernel.H: in the num_flux == 4 scheme the noise terms for sub-fluxes 2 and 3 took phi, det and the metric from the wrong cell. The deterministic and drift terms agree that comp 2 belongs to (i,j) and comp 3 to (i-1,j) in compute_flux_x (and comp 2 to (i,j-1), comp 3 to (i,j) in compute_flux_y); the stochastic block had the two interchanged, so two of the four sub-fluxes paired a gradient evaluated in one cell with a noise amplitude from its neighbour and the discrete fluctuation-dissipation balance did not hold. Components 0 and 1 were already consistent. #211 {surface,moving}/ParticleData.H: drop the leftover mult(1./cell_vol) on the fine->coarse reflux path. phi is a raw particle count in these two directories (AddParticles uses int(phi_arr(i,j,k,0))) and RefluxFineToCrse deposits +1 per particle, so the contribution is already in the units of phi_crse_new; the other four scalings were commented out when the convention changed but this one was left active, making the fine->coarse correction smaller than the coarse->fine one by a factor of cell_vol. #213 moving/mykernel.H: update_phi's num_flux == 4 branch was still the static metric version -- it did not weight phiold by the old det and divided by the old det instead of the new one. The conserved quantity on a moving surface is phi*sqrt(g), so the update must read phi^{n+1} sqrt(g^{n+1}) = phi^n sqrt(g^n) + dt div(F), which is what the num_flux == 1 branch already does. Both exec/dean_kow/surface and exec/dean_kow/moving build, and moving runs clean on 4 ranks with num_flux=4 and amrex.fpe_trap_invalid=1. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/moving/AdvancePhiAtLevel.cpp src_deankow/moving/AmrCoreAdv.cpp src_deankow/moving/ParticleData.H src_deankow/moving/mykernel.H src_deankow/moving/update_metric.H src_deankow/surface/ParticleData.H src_deankow/surface/mykernel.H commit e3d62e505cc84e0aa78ed472163415cfcd6ae02c Merge: f8e52246 3efa798e Author: jbbel Date: Tue Sep 15 15:18:09 2026 -0700 Merge pull request #232 from chrisriv10/main fix: correct CEXE_headers typo in Make.package files commit f8e5224616f76a342a9701fdd4ec23d43a6fcf65 Merge: 9fcd6fda acbf6013 Author: jbbel Date: Tue Sep 15 12:30:50 2026 -0700 Merge pull request #237 from jbbel/bugfix untangle includes to separate out flory huggins stuff commit acbf6013a8e82f68ab0003de1d6215c596c6d6de Author: jbb Date: Tue Sep 15 11:55:31 2026 -0700 untangle includes to separate out flory huggins stuff exec/hydro/GNUmakefile exec/multispec/GNUmakefile exec/multispec/Init.cpp src_common/InhomogeneousBCVal.H src_common/MultiFabPhysBC.cpp src_common/common_namespace.H src_deankow/interaction/mykernel.H src_gmres/gmres_namespace.H src_multispec/ComputeDivReversibleStress.cpp src_multispec/FluidCharge.cpp src_multispec/multispec_namespace.H commit 9fcd6fda9edcf2f754e47580a37899dfa79ce838 Merge: 313c0a38 463ce968 Author: Ishan Srivastava Date: Mon Sep 14 21:33:09 2026 -0700 Merge pull request #202 from AMReX-FHD/surfchemtest Add restart for nspec_mui and update surfchemtest commit 463ce96870ff5059037228f5eb5f350d367b4633 Merge: 38b59bf8 313c0a38 Author: HyuntaeJung Date: Tue Sep 15 09:53:23 2026 +0900 Merge branch 'main' into surfchemtest commit 313c0a3878f0f488fad1e94b2556759ce81bc60f Merge: 5e475338 6e483694 Author: jbbel Date: Mon Sep 14 14:46:04 2026 -0700 Merge pull request #235 from jbbel/fix add .dat to ignore commit 6e483694ffa38ad1b1516fbeb6acf8952c28323a Author: jbb Date: Mon Sep 14 14:45:13 2026 -0700 add .dat to ignore .gitignore commit 5e4753380dca022bb2d3ea26cc47f574043875a8 Merge: 4275f842 ca98d484 Author: jbbel Date: Mon Sep 14 14:38:09 2026 -0700 Merge pull request #234 from jbbel/cleanup Cleanup commit ca98d484c805688e3657916d30e963cd316cc49c Merge: f0f91eb0 4275f842 Author: jbbel Date: Mon Sep 14 14:37:47 2026 -0700 Merge branch 'main' into cleanup commit 4275f8423f3998ceb24f871b424861382e0f28d2 Merge: 71c7e8f5 f94fc192 Author: Ishan Srivastava Date: Mon Sep 14 14:27:46 2026 -0700 Merge pull request #233 from AMReX-FHD/high_order_bc_stag Dirichlet boundary conditions options in Compressible Staggered Code commit f94fc192c7e45217c66d5768c3b26d6d63e9138c Merge: 54348e01 71c7e8f5 Author: isriva Date: Mon Sep 14 14:13:47 2026 -0700 Merge remote-tracking branch 'origin/main' into high_order_bc_stag commit 71c7e8f5a5d41d43e38e952766532826435a9def Author: isriva Date: Mon Sep 14 14:13:06 2026 -0700 fix trailing whitespace exec/multispec/Init.cpp src_deankow/helfrich_membrane/AmrCoreAdv.cpp src_deankow/helfrich_membrane/StochasticPC.cpp src_deankow/helfrich_membrane/init_metric.H src_deankow/helfrich_membrane/mykernel.H src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/StochasticPC.cpp src_deankow/interaction/myfunc.cpp src_deankow/interaction/mykernel.H src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit 8feb44b510a19c2137add3b7f198fe88e534bd03 Author: isriva Date: Mon Sep 14 14:12:41 2026 -0700 fix tabs exec/multispec/Init.cpp src_deankow/helfrich_membrane/mykernel.H commit f0f91eb06d4f24a40b4ca95907bdd8d05c81489f Author: jbb Date: Mon Sep 14 14:02:28 2026 -0700 more cleanup of code exec/dean_kow/ensemble/Make.Adv exec/dean_kow/helfrich/Make.Adv exec/dean_kow/interaction/Make.Adv exec/dean_kow/moving/Make.Adv exec/dean_kow/multilevel/Make.Adv exec/dean_kow/surface/Make.Adv exec/hydro/GNUmakefile exec/multispec/GNUmakefile src_common/MultiFabPhysBC.cpp src_deankow/ensemble/Kernels.H src_deankow/ensemble/StochasticPC.cpp src_deankow/helfrich_membrane/Kernels.H src_deankow/helfrich_membrane/StochasticPC.cpp src_deankow/interaction/Kernels.H src_deankow/moving/Kernels.H src_deankow/moving/StochasticPC.cpp src_deankow/multilevel/Kernels.H src_deankow/multilevel/StochasticPC.cpp src_deankow/surface/Kernels.H src_deankow/surface/StochasticPC.cpp commit dcfa1d429fb5ff57486de48cb23ced52048a5bdd Author: jbb Date: Mon Sep 14 14:00:29 2026 -0700 clean our unused Src_K code exec/multispec/Init.cpp src_deankow/ensemble/Src_K/Adv_K.H src_deankow/ensemble/Src_K/Make.package src_deankow/ensemble/Src_K/compute_flux_2D_K.H src_deankow/ensemble/Src_K/compute_flux_3D_K.H src_deankow/ensemble/Src_K/slope_K.H src_deankow/helfrich_membrane/Src_K/Adv_K.H src_deankow/helfrich_membrane/Src_K/Make.package src_deankow/helfrich_membrane/Src_K/compute_flux_2D_K.H src_deankow/helfrich_membrane/Src_K/compute_flux_3D_K.H src_deankow/helfrich_membrane/Src_K/slope_K.H src_deankow/interaction/Src_K/Adv_K.H src_deankow/interaction/Src_K/Make.package src_deankow/interaction/Src_K/compute_flux_2D_K.H src_deankow/interaction/Src_K/compute_flux_3D_K.H src_deankow/interaction/Src_K/slope_K.H src_deankow/multilevel/Src_K/Adv_K.H src_deankow/multilevel/Src_K/Make.package src_deankow/multilevel/Src_K/compute_flux_2D_K.H src_deankow/multilevel/Src_K/compute_flux_3D_K.H src_deankow/multilevel/Src_K/slope_K.H commit 54348e01095ff602a34a279511edcdf71ae94da8 Author: isriva Date: Mon Sep 14 13:50:48 2026 -0700 fix styling exec/multispec/Init.cpp src_compressible/compressible_functions.H src_compressible_stag/fluxStag.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit fc3484475789dedb87c6075492a3206a0c27c7a9 Merge: f234e39f ff742471 Author: jbb Date: Mon Sep 14 12:48:26 2026 -0700 Merge branch 'main' into dk_interaction commit 160ff868273cf8b71438cffa333fcb699bb1b6eb Merge: 169effb2 ff742471 Author: isriva Date: Mon Sep 14 12:45:52 2026 -0700 Merge remote-tracking branch 'origin/main' into high_order_bc_stag commit ff742471959c11f6d76eebb9cb6216f634f12251 Merge: a1ae4100 f11cf3a5 Author: jbb Date: Mon Sep 14 12:36:59 2026 -0700 Merge branch 'main' into flory_huggins_diag commit a1ae41003d08a4a1eb12eb9924392f474a1a69a2 Merge: 2db6b164 6dd28ea0 Author: jbb Date: Mon Sep 14 10:20:21 2026 -0700 Merge branch 'flory_huggins_diag' of github.com:AMReX-FHD/FHDeX into flory_huggins_diag commit 3efa798edc38b627bd8ff76b73cbbca41fce781e Author: Chris <185133702+chrisriv10@users.noreply.github.com> Date: Sat Sep 12 22:12:04 2026 -0500 fix: correct CEXE_headers typo in Make.package files src_deankow/1d_stats/Make.package src_deankow/singlelevel/Make.package commit f11cf3a54be369a20b7feb50785d50d64fc9d55b Merge: cd8dbf41 6d7a6bc9 Author: jbbel Date: Fri Sep 11 05:26:49 2026 -0700 Merge pull request #231 from AMReX-FHD/deankow_bdry_flux_index src_deankow: test the face index, not the box bounds, at physical bou… commit 6d7a6bc9921b097fc755c9f29e050563a748160a Author: jbb Date: Fri Sep 11 05:15:18 2026 -0700 src_deankow: test the face index, not the box bounds, at physical boundaries Fixes #214. The compute_flux_* routines gated the physical-boundary branch on the box extents (lo/hi from lbound/ubound of mfi.validbox()) instead of on the index of the face being processed, so every face of a box that touches the domain boundary took the boundary branch. Two consequences, both only visible with foextrap/ext_dir BCs (a fully periodic run always lands in the else branch): - the stochastic flux, which is only added in the else branch, was dropped for those faces -- on a single-grid run that removes the noise from the whole domain; - for Ncomp == 2 (alg_type != 0) the boundary branch never wrote flux(i,j,k,1), so update_phi consumed uninitialized data. Compare against the face index instead (i == dom_lo / i == dom_hi+1, and likewise for j and k), which collapses the nested conditional, and write component 1 in the boundary branch as well. Also zero the flux MultiFabs where they are allocated so that any component left unwritten is a reproducible zero rather than garbage; ensemble already did this. 1d_stats' compute_flux_z was additionally missing the Ncomp parameter its caller passes, so it could not have compiled in 3D. Co-Authored-By: Claude Opus 5 (1M context) src_deankow/1d_stats/main.cpp src_deankow/1d_stats/mykernel.H src_deankow/ensemble/mykernel.H src_deankow/moving/AdvancePhiAtLevel.cpp src_deankow/moving/mykernel.H src_deankow/multilevel/AdvancePhiAtLevel.cpp src_deankow/multilevel/mykernel.H src_deankow/singlelevel/main.cpp src_deankow/singlelevel/mykernel.H src_deankow/surface/AdvancePhiAtLevel.cpp src_deankow/surface/mykernel.H commit cd8dbf41bc3defd3169e87b830dff39adf832a18 Merge: 86e3de32 baf9535e Author: Andy Nonaka Date: Thu Sep 3 16:07:07 2026 -0700 Merge pull request #200 from AMReX-FHD/FPU_chain Fpu chain commit baf9535e76d75f8cd337bf52b74999d5e923a0bb Author: Andy Nonaka Date: Thu Sep 3 16:06:48 2026 -0700 whitespace exec/FPU_FHD_stag/FPU.H exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/main_driver.cpp commit 9a3e95fea13f614695f6fe0c324e018610f9fef6 Merge: 1c94000f 86e3de32 Author: Andy Nonaka Date: Thu Sep 3 16:02:31 2026 -0700 Merge branch 'main' into FPU_chain commit 38b59bf89e47ce0d24140340a2f65d66b95826d8 Author: HyuntaeJung Date: Fri Aug 28 13:19:37 2026 +0900 Use ads_wall_dir for exec/compressible_stag_mui/SPPARKS_MUI/ and fix small typo exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.h exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit 91863a38db1a26fea2e470d1627a67cbeb7fbabc Author: HyuntaeJung Date: Fri Aug 28 10:30:22 2026 +0900 Use ads_wall_dir for surfchem_amrex src_surfchem_amrex/surfchem_mui_functions.cpp commit cbe55a046d50e53f0976becadaec554e128d4c8c Merge: 9fb7370e 86e3de32 Author: HyuntaeJung Date: Fri Aug 28 10:27:47 2026 +0900 Merge branch 'main' into surfchemtest commit 169effb2773a309d14059e61fc3e5f034ba459c9 Author: isriva Date: Fri Aug 21 10:37:57 2026 -0700 fixed bugs for Dirichlet 2 - wrong gradients at the walls src_compressible_stag/fluxStag.cpp commit 39f26af118aeea1354ae57ebab3e3354eda24a24 Author: isriva Date: Fri Aug 21 10:37:09 2026 -0700 support for constant transport coefficients src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible/transCoeffs.cpp commit abca9a75515f6dec1ca09cc4dea3abad27fbaa73 Author: isriva Date: Thu Aug 13 14:06:56 2026 -0700 Roll back to 0dfe3b8f with substantial changes to dirichlet handling of fluxes src_compressible_stag/fluxStag.cpp commit 0dfe3b8f80da6941b2daf1e5b688e10bb52871a2 Merge: 8505d38c 86e3de32 Author: isriva Date: Mon Aug 3 11:58:22 2026 -0700 Merge remote-tracking branch 'origin/main' into high_order_bc_stag commit f234e39f3a82ba04b1ce30277f68421308d3880f Author: jbb Date: Wed Jul 15 10:30:04 2026 -0700 fix particles to reflect update to AMReX particles src_deankow/interaction/StochasticPC.cpp commit 005bc09fceea3b5580a3c630bad2026b64dfa6d2 Author: jbb Date: Fri Jul 10 14:41:32 2026 -0700 added particle input file exec/dean_kow/interaction/inputs_part commit 86e3de32203c657c94d98935dc924ec1bbd2061f Author: Andy Nonaka Date: Mon Jul 6 15:54:38 2026 -0700 fix runtime issue with non-periodic FFT stokes solve exec/hydro/advance.cpp commit 64dd05633c487eddd849d8a5c25a046dd8af29e1 Merge: e6b1b7d4 6555adb9 Author: jbbel Date: Tue Jun 30 09:07:50 2026 -0700 Merge pull request #206 from AMReX-FHD/fft_stokes hook in fft-based stokes solver to hydro commit 6555adb906d9eb92cd1a2be53a33c26c33f6abc9 Author: Andy Nonaka Date: Tue Jun 30 09:01:59 2026 -0700 hook in fft-based stokes solver to hydro exec/hydro/advance.cpp src_common/common_functions.cpp src_common/common_namespace.H commit 6dd28ea06539fbd45feb982a818ae8afedb73a56 Merge: 2b0631ab 55070b68 Author: John Bell Date: Wed Jun 24 16:06:11 2026 -0700 ZZMerge branch 'flory_huggins_diag' of github.com:AMReX-FHD/FHDeX into flory_huggins_diag commit 2b0631abb1a25aaea71b67f3f6202465bb483da2 Author: John Bell Date: Wed Jun 24 15:52:49 2026 -0700 syncing exec/multispec/Init.cpp src_common/common_namespace.H src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MultiFabPhysBC_FH.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit e6b1b7d4f1245351c9d92c9b4bf8c6e927a0ba26 Author: Andy Nonaka Date: Mon Jun 22 12:35:05 2026 -0700 tabs and whitespace exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/compressible_stag/test_GF_reactivesurface/run_2D.sh exec/compressible_stag/test_GF_reactivesurface/run_3D.sh src_deankow/moving/AmrCoreAdv.cpp src_deankow/moving/StochasticPC.cpp src_deankow/moving/init_metric.H src_deankow/moving/mykernel.H src_deankow/multilevel/StochasticPC.cpp src_deankow/surface/AmrCoreAdv.cpp src_deankow/surface/StochasticPC.cpp src_deankow/surface/init_metric.H src_deankow/surface/mykernel.H commit 2db6b16433d64fd31aaf7e95ce5323a2659dbf4d Merge: 31e60221 55070b68 Author: jbb Date: Thu Jun 18 10:32:01 2026 -0700 Merge branch 'flory_huggins_diag' of https://github.com/AMReX-FHD/FHDeX into flory_huggins_diag commit bb84621b9b95bd9ce002cdd75720df09a75f7b42 Author: jbb Date: Thu Jun 18 10:09:57 2026 -0700 debugged DK with particle interaction and added O(N**2) particle method exec/dean_kow/helfrich/GNUmakefile exec/dean_kow/helfrich/inputs_fv exec/dean_kow/interaction/GNUmakefile exec/dean_kow/interaction/inputs_fv src_deankow/helfrich_membrane/AmrCoreAdv.cpp src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/ParticleData.H src_deankow/interaction/StochasticPC.H src_deankow/interaction/StochasticPC.cpp src_deankow/interaction/mykernel.H commit 1c94000f9cdc9b1ce97765a221c1f4ae89482bfa Author: isriva Date: Wed Jun 10 09:54:29 2026 -0700 nonlinear FHD seems to work now for parameters in inputs file exec/FPU_FHD_stag/FPU.H exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/inputs exec/FPU_FHD_stag/main_driver.cpp commit 62bd28e1bca285250d4469d860d22a2830fa02e2 Author: HyuntaeJung Date: Wed Jun 10 07:22:27 2026 +0900 exec/compressible_stag/test_GF_reactivesurface: GF reactive surface example added exec/compressible_stag/test_GF_reactivesurface/README exec/compressible_stag/test_GF_reactivesurface/inputs_GF_reactivesurface_3D exec/compressible_stag/test_GF_reactivesurface/inputs_GF_reactivesurface_quasi2D exec/compressible_stag/test_GF_reactivesurface/run_2D.sh exec/compressible_stag/test_GF_reactivesurface/run_3D.sh commit 2b25f7a0fdb7a64f7cd70790f3fdeed2f37ba4b0 Author: isriva Date: Mon Jun 8 17:35:30 2026 -0700 nonlinear FHD exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/FPU_namespace.H exec/FPU_FHD_stag/flux.cpp exec/FPU_FHD_stag/inputs commit 273400692301a60d8b67fd533e7e47f517999be3 Author: isriva Date: Mon Jun 8 13:19:14 2026 -0700 change output format exec/FPU_FHD_stag/main_driver.cpp commit a67b8b33c158c7c73ef58f3b308a250fb073e188 Author: isriva Date: Thu Jun 4 23:26:56 2026 -0700 C_alphaalpha calculations exec/FPU_FHD_stag/FPU.H exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/FPU_namespace.H exec/FPU_FHD_stag/inputs exec/FPU_FHD_stag/main_driver.cpp commit 989b1c85bd554fe6ca76d7f0631f20c9ddc53717 Author: isriva Date: Thu Jun 4 22:29:43 2026 -0700 more changes exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/FPU_namespace.H exec/FPU_FHD_stag/flux.cpp exec/FPU_FHD_stag/inputs exec/FPU_FHD_stag/main_driver.cpp commit 9d8e0878240d22e5da7a997674d71f61d1dbcf17 Author: Andy Nonaka Date: Thu Jun 4 17:01:50 2026 -0700 re-org, bring in the staggered FHD FPU chain code exec/FPU_FHD_cc/FPU.H exec/FPU_FHD_cc/FPU.cpp exec/FPU_FHD_cc/FPU_namespace.H exec/FPU_FHD_cc/GNUmakefile exec/FPU_FHD_cc/Make.package exec/FPU_FHD_cc/inputs exec/FPU_FHD_cc/inputs_phi exec/FPU_FHD_cc/main.cpp exec/FPU_FHD_stag/FPU.H exec/FPU_FHD_stag/FPU.cpp exec/FPU_FHD_stag/FPU_namespace.H exec/FPU_FHD_stag/GNUmakefile exec/FPU_FHD_stag/Make.package exec/FPU_FHD_stag/flux.cpp exec/FPU_FHD_stag/flux_refactor_plan.md exec/FPU_FHD_stag/inputs exec/FPU_FHD_stag/inputs_phi exec/FPU_FHD_stag/main_driver.cpp exec/FPU_FHD_stag/main_old.cpp exec/FPU_FHD_stag/timeStep.cpp commit 0a40f5d2f1d35e233b48fcb19c8dd0d61f7d4f7d Merge: 7f889da6 55b2fcb6 Author: Andy Nonaka Date: Thu Jun 4 13:14:31 2026 -0700 Merge branch 'main' into FPU_chain commit f7eef16b7d0b2f699eca773b288e71ed632fe72a Author: jbb Date: Tue May 26 10:32:59 2026 -0700 fix flux limiting and removing diagnostic print exec/dean_kow/interaction/inputs_fv src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/mykernel.H src_deankow/multilevel/mykernel.H commit 5661a3c9d60dd2acc8e88f1cbf4f7377e4d7805c Author: jbb Date: Thu Apr 16 13:26:17 2026 -0700 minor change to inputs exec/dean_kow/helfrich/inputs_fv commit f3711019ed39bec5f710497634cc140d84933d0c Author: jbb Date: Wed Apr 15 15:08:25 2026 -0700 debugged Helfrich membrane implementation exec/dean_kow/helfrich/GNUmakefile exec/dean_kow/helfrich/Make.Adv exec/dean_kow/helfrich/Make.package exec/dean_kow/helfrich/inputs_fv exec/dean_kow/moving/inputs_move_debug src_deankow/helfrich_membrane/AdvancePhiAtLevel.cpp src_deankow/helfrich_membrane/AmrCoreAdv.H src_deankow/helfrich_membrane/AmrCoreAdv.cpp src_deankow/helfrich_membrane/Kernels.H src_deankow/helfrich_membrane/Make.package src_deankow/helfrich_membrane/ParticleData.H src_deankow/helfrich_membrane/Src_K/Adv_K.H src_deankow/helfrich_membrane/Src_K/Make.package src_deankow/helfrich_membrane/Src_K/compute_flux_2D_K.H src_deankow/helfrich_membrane/Src_K/compute_flux_3D_K.H src_deankow/helfrich_membrane/Src_K/slope_K.H src_deankow/helfrich_membrane/StochasticPC.H src_deankow/helfrich_membrane/StochasticPC.cpp src_deankow/helfrich_membrane/Tagging.H src_deankow/helfrich_membrane/bc_fill.H src_deankow/helfrich_membrane/init_metric.H src_deankow/helfrich_membrane/main.cpp src_deankow/helfrich_membrane/myfunc.H src_deankow/helfrich_membrane/myfunc.cpp src_deankow/helfrich_membrane/mykernel.H src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/mykernel.H src_deankow/moving/AdvancePhiAtLevel.cpp commit 9ea88573d72784bcff7fb8438544dc76a1b803b8 Author: jbb Date: Fri Apr 10 10:57:27 2026 -0700 added src_k. needed for some bizarre reason src_deankow/interaction/Src_K/Adv_K.H src_deankow/interaction/Src_K/Make.package src_deankow/interaction/Src_K/compute_flux_2D_K.H src_deankow/interaction/Src_K/compute_flux_3D_K.H src_deankow/interaction/Src_K/slope_K.H commit d0a7ad7036bad51f7b1178c09c8703b4ccade7da Author: jbb Date: Fri Apr 10 10:23:41 2026 -0700 converted interation potential to compute measure exec/dean_kow/interaction/GNUmakefile exec/dean_kow/interaction/inputs_fv src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/AmrCoreAdv.H src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/myfunc.H src_deankow/interaction/myfunc.cpp src_deankow/interaction/mykernel.H commit 5484261a02553a3af6296f8c3327b59df0eb8eb6 Author: jbb Date: Thu Apr 9 16:44:26 2026 -0700 initial working version of DK with interaction potential exec/dean_kow/interaction/GNUmakefile exec/dean_kow/interaction/Make.Adv exec/dean_kow/interaction/inputs_fv exec/dean_kow/multilevel/GNUmakefile src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/AmrCoreAdv.H src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/myfunc.H src_deankow/interaction/myfunc.cpp src_deankow/interaction/mykernel.H src_deankow/multilevel/mykernel.H commit 8c065ca30c8375ed38d0c32f04004ef597d90e68 Author: jbb Date: Wed Apr 8 11:22:28 2026 -0700 started flat surface dean kawasaki with particle interactions src_deankow/interaction/AdvancePhiAtLevel.cpp src_deankow/interaction/AmrCoreAdv.H src_deankow/interaction/AmrCoreAdv.cpp src_deankow/interaction/Kernels.H src_deankow/interaction/Make.package src_deankow/interaction/ParticleData.H src_deankow/interaction/StochasticPC.H src_deankow/interaction/StochasticPC.cpp src_deankow/interaction/Tagging.H src_deankow/interaction/bc_fill.H src_deankow/interaction/main.cpp src_deankow/interaction/myfunc.H src_deankow/interaction/myfunc.cpp src_deankow/interaction/mykernel.H commit 55b2fcb6a257fa2804c84916908fb3248cc67f8e Author: jbb Date: Wed Apr 8 10:33:28 2026 -0700 resolved conflicts exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/_1d_dk_hybrid/_ensemble/particles.f exec/dean_kow/multilevel/GNUmakefile exec/dean_kow/multilevel/amrvis.defaults exec/dean_kow/surface/inputs_pp commit a4509799bae2924684a5cc77741b7abda9992377 Merge: 5f5a6aaa d4366f7a Author: jbb Date: Wed Apr 8 10:18:28 2026 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX commit 5f5a6aaac815afbbd9917b7e947affd7e6cf54ab Author: jbb Date: Wed Apr 8 10:11:47 2026 -0700 added support for dean kawasaki on a moving surface exec/dean_kow/moving/GNUmakefile exec/dean_kow/moving/Make.Adv exec/dean_kow/moving/inputs_move_debug src_deankow/moving/AdvancePhiAtLevel.cpp src_deankow/moving/AmrCoreAdv.H src_deankow/moving/AmrCoreAdv.cpp src_deankow/moving/Kernels.H src_deankow/moving/ParticleData.H src_deankow/moving/StochasticPC.H src_deankow/moving/StochasticPC.cpp src_deankow/moving/Tagging.H src_deankow/moving/bc_fill.H src_deankow/moving/init_metric.H src_deankow/moving/main.cpp src_deankow/moving/myfunc.H src_deankow/moving/myfunc.cpp src_deankow/moving/mykernel.H src_deankow/moving/update_metric.H commit d8b7ae80f113570f14c48baa3bf53a4b460268d0 Author: jbb Date: Wed Apr 8 10:09:14 2026 -0700 updated surface dean kawasaki exec/dean_kow/surface/GNUmakefile exec/dean_kow/surface/Make.Adv exec/dean_kow/surface/Make.package exec/dean_kow/surface/inputs_pp src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/mykernel.H src_deankow/surface/AdvancePhiAtLevel.cpp src_deankow/surface/AmrCoreAdv.H src_deankow/surface/AmrCoreAdv.cpp src_deankow/surface/Kernels.H src_deankow/surface/Make.package src_deankow/surface/ParticleData.H src_deankow/surface/StochasticPC.H src_deankow/surface/StochasticPC.cpp src_deankow/surface/Tagging.H src_deankow/surface/bc_fill.H src_deankow/surface/init_metric.H src_deankow/surface/main.cpp src_deankow/surface/myfunc.H src_deankow/surface/myfunc.cpp src_deankow/surface/mykernel.H commit 9fb7370e27c59222bb8143d7474e0276cebfaa2a Author: HyuntaeJung Date: Sun Mar 29 23:58:28 2026 +0900 Update ads_wall_dir for surfchem_amrex src_surfchem_amrex/surfchem_mui_functions.H src_surfchem_amrex/surfchem_mui_functions.cpp commit 7f889da660ed72969b99e7e08add4f79bc2e5e20 Author: Andy Nonaka Date: Sat Mar 28 20:40:15 2026 -0700 reduce sampling number in init exec/FPU_chain/FPU.cpp commit 95bfc538278a0abad0518ebc663a69cff463d210 Author: Andy Nonaka Date: Sat Mar 28 20:18:10 2026 -0700 add n_steps_skip and some timers exec/FPU_chain/main.cpp commit 85b82e9e7e1fe423af44f0a2ff8d8d24e44919d1 Author: Andy Nonaka Date: Fri Mar 27 10:26:41 2026 -0700 fix gpu compile exec/FPU_FHD/FPU.cpp exec/FPU_FHD/FPU_namespace.H commit 2792b9e37a2b29ba2a24569528fe57fab6d216f7 Author: Andy Nonaka Date: Thu Mar 26 10:02:21 2026 -0700 whitespace exec/FPU_FHD/FPU.cpp exec/FPU_FHD/main.cpp commit ee5416c7de267d676ad1147f0caf9f625f103ae8 Author: Andy Nonaka Date: Thu Mar 26 09:59:10 2026 -0700 create namespace exec/FPU_FHD/FPU.H exec/FPU_FHD/FPU.cpp exec/FPU_FHD/FPU_namespace.H exec/FPU_FHD/Make.package exec/FPU_FHD/inputs exec/FPU_FHD/inputs_phi exec/FPU_FHD/main.cpp exec/FPU_chain/inputs commit 09fb1612896b00e910332a10825df05e47ba565a Author: Andy Nonaka Date: Tue Mar 24 15:39:35 2026 -0700 fix the sign convention on advection and stochastic term exec/FPU_FHD/main.cpp commit d0e8b830360cae70a61ac0fb53ffea28d665c9b5 Author: Andy Nonaka Date: Mon Mar 16 16:11:58 2026 -0700 flag to quickly enable/disable fluctuations exec/FPU_FHD/inputs exec/FPU_FHD/inputs_phi exec/FPU_FHD/main.cpp commit b1b2f180aa94c57fbb52d5961fe9eb2665d19bc2 Author: Andy Nonaka Date: Mon Mar 16 16:07:20 2026 -0700 more details in inputs file exec/FPU_FHD/inputs exec/FPU_FHD/inputs_phi commit 1f30ea401b08be58336a9a52f8bb6b72304f197f Author: Hyun Tae Jung Date: Tue Mar 10 11:34:46 2026 +0900 exec/SPPARKS_MUI - tabs exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.cpp commit b7d5b9c53d3828d380a8d4b1f4b6770429e2ecef Author: Hyun Tae Jung Date: Tue Mar 10 11:31:38 2026 +0900 exec/SPPARKS_MUI - whitespace and tabs exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.cpp commit fd4e3590fd75cdc242df3877ea0936972ec30fd3 Author: Andy Nonaka Date: Mon Mar 9 14:52:48 2026 -0700 cleanup. n_particles -> n_cells to avoid confusion exec/FPU_FHD/inputs exec/FPU_FHD/inputs_phi exec/FPU_FHD/main.cpp commit b4ea858d63e82fa0cd2177a98e7a4864ac57856e Author: Andy Nonaka Date: Mon Mar 9 10:08:41 2026 -0700 updates exec/FPU_FHD/inputs_phi commit 2b760360bff1439e1ab34c3cb1e2a2340feddd69 Merge: 5fb0a1c7 d6e3feac Author: Andy Nonaka Date: Mon Mar 9 10:02:04 2026 -0700 Merge branch 'FPU_chain' of github.com:AMReX-FHD/FHDeX into FPU_chain commit 5fb0a1c73ad960dba5230ba0597c35532223b155 Author: Andy Nonaka Date: Mon Mar 9 10:01:56 2026 -0700 phi space exec/FPU_FHD/inputs_phi commit d004b2dd3db94dfb7f76b32221618564269c4826 Author: Hyun Tae Jung Date: Mon Mar 9 22:21:56 2026 +0900 exec/SPPARKS_MUI - implement Lotka-Volterra model exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_lotkavolterra.h exec/compressible_stag_mui/SPPARKS_MUI/diag_lotkavolterra.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_lotkavolterra.h exec/compressible_stag_mui/SPPARKS_MUI/input.cpp exec/compressible_stag_mui/SPPARKS_MUI/spparks.cpp exec/compressible_stag_mui/SPPARKS_MUI/style_diag.h commit 93eb77a755ccfdf31e4016c08c874cdbf6d12696 Author: HyuntaeJung Date: Mon Mar 9 22:14:46 2026 +0900 Update exec/compressible_stag_mui/test_ files exec/compressible_stag_mui/test_COAr_eq/in.kmc exec/compressible_stag_mui/test_COAr_eq/in.kmc_amrex exec/compressible_stag_mui/test_COAr_eq/params_COAr_eq.py exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc_amrex exec/compressible_stag_mui/test_COO2Ar_eq_slurm/in.kmc_amrex exec/compressible_stag_mui/test_COO2Ar_eq_slurm/params_COO2Ar_eq.py exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/event_rate_FHD.py exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/in.kmc_amrex exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_O2Ar_eq_slurm/in.kmc_amrex exec/compressible_stag_mui/test_O2Ar_eq_slurm/params_O2Ar.py commit 2b6855cb87d9d9cf526230abf49a7a4086dc5ad3 Author: Hyun Tae Jung Date: Mon Mar 9 21:58:49 2026 +0900 Replace number density with partial pressure exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h src_surfchem_amrex/surfchem_mui_functions.cpp commit a7c75ebdd38c9a89c473aafd3a379717a68f70fe Author: Hyun Tae Jung Date: Mon Mar 9 21:54:06 2026 +0900 Restart for nspec_mui src_compressible_stag/Checkpoint.cpp src_compressible_stag/main_driver.cpp commit d6e3feaca7a0927e7dcb9464d96c7d45320a79e2 Author: Andy Nonaka Date: Thu Mar 5 08:43:55 2026 -0800 tweak problem exec/FPU_FHD/inputs commit 16e82d45cc090ab98899697e23295624e487f9b6 Author: Andy Nonaka Date: Wed Mar 4 11:56:30 2026 -0800 add diag_int exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp commit d9ad4febb4c9d5efaa4d9aadf8a6cfe72df1580c Author: Andy Nonaka Date: Wed Mar 4 09:10:57 2026 -0800 diag_int for correlation diagnostics exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp commit e84d5832af383807730b304e74943e0ba3bf0006 Author: Andy Nonaka Date: Mon Mar 2 17:28:28 2026 -0800 FPU updates and diags exec/FPU_FHD/FPU.H exec/FPU_FHD/FPU.cpp exec/FPU_FHD/Make.package exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit c223fcbf503b34c44b83a3f444367eca7a2e5b5d Author: Andy Nonaka Date: Mon Mar 2 14:11:11 2026 -0800 new inputs exec/FPU_FHD/inputs commit b6d2eeeb355fc309eb7b93a52ca0745f0f531cd3 Merge: 08bd4dc0 4323d04e Author: Andy Nonaka Date: Mon Mar 2 14:10:54 2026 -0800 Merge branch 'FPU_chain' of github.com:AMReX-FHD/FHDeX into FPU_chain commit 08bd4dc056cb30b18fcc4d9cb1cb5670d46068ae Author: Andy Nonaka Date: Mon Mar 2 13:42:55 2026 -0800 non-dimensionalize exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp commit 4323d04e227934be2a4d1341f538813d3cfe3ae1 Author: Andy Nonaka Date: Thu Feb 26 10:31:37 2026 -0800 simpler setup exec/FPU_FHD/inputs commit 231527a04f70c41d3ae21d9f57459e4c53fe1013 Author: Andy Nonaka Date: Thu Feb 26 10:04:30 2026 -0800 trailing whitespace exec/FPU_FHD/main.cpp commit 41167d7990e07da5da77572f7646b26b1933e230 Author: Andy Nonaka Date: Thu Feb 26 10:03:52 2026 -0800 codex cleanup exec/FPU_FHD/main.cpp commit 20457e560b16899e6225c4a69d31b3589a061f4a Author: Andy Nonaka Date: Thu Feb 26 09:54:28 2026 -0800 typos, fill all noise and scale correctly exec/FPU_FHD/main.cpp commit 0f8659641f0d3e5f383c0f7537c8099f06e0e7ad Author: Andy Nonaka Date: Tue Feb 24 15:41:13 2026 -0800 first cut at FHD version of anharmonic chain exec/FPU_FHD/GNUmakefile exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp commit 86a48e1b81588d70cd53ea4aa982319a781b14e7 Author: Andy Nonaka Date: Tue Feb 24 13:30:05 2026 -0800 remove exec/FPU_chain/plot_Salphaalpha.gp commit 12f8fe5464c6f6c3bdc7f8bd8698d87622917411 Merge: 5eabcc44 c2fa2701 Author: Andy Nonaka Date: Tue Feb 24 12:18:24 2026 -0800 Merge branch 'FPU_chain' of github.com:AMReX-FHD/FHDeX into FPU_chain commit 5eabcc44db41df0f430e8d53b180d13f522742c6 Author: Andy Nonaka Date: Tue Feb 24 12:16:49 2026 -0800 actual setup, 50k steps only, 64k samples exec/FPU_chain/inputs commit c2fa27013568800ff3c19ebbdb6e48675c342cfb Merge: 48e3cefd 19bf4c85 Author: Andy Nonaka Date: Tue Feb 24 10:18:27 2026 -0800 Merge branch 'FPU_chain' of github.com:AMReX-FHD/FHDeX into FPU_chain commit 48e3cefdba5851f0e1f3e4a9fa46d2e8879eb501 Author: Andy Nonaka Date: Tue Feb 24 10:17:55 2026 -0800 codex-spotted typos and comment errors exec/FPU_chain/main.cpp commit 19bf4c8563c19e7d81d155c8d67460875aefd409 Author: Andy Nonaka Date: Mon Feb 23 18:11:02 2026 -0800 timers exec/FPU_chain/main.cpp commit 367eef1a39441c9d30e3e108dde446a71e99070b Author: Andy Nonaka Date: Wed Feb 11 13:19:30 2026 -0800 trailing whitespace exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 5667592f26f0a63b084ceb2c7a7262cc648d07f7 Author: Andy Nonaka Date: Wed Feb 11 13:16:42 2026 -0800 shift C_alpha indices exec/FPU_chain/main.cpp commit ada67958ddfc1b55e5cc029aa0ba34d3b9ad5411 Author: Andy Nonaka Date: Wed Feb 11 13:04:36 2026 -0800 first cut at C_alphaalpha diags exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit 09a66828b4752b0eeb84d7446e1cf180332c9b2e Author: Andy Nonaka Date: Wed Feb 11 12:35:53 2026 -0800 adding analysis parameters exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit 805c4d37eea3cce992672a36eafc7059d2351fd3 Author: Andy Nonaka Date: Fri Feb 6 15:04:05 2026 -0800 EOL whitespace exec/FPU_FHD/main.cpp exec/FPU_chain/main.cpp commit d064d81b4c768448990054b6652e50d226e173f4 Author: Andy Nonaka Date: Fri Feb 6 15:03:27 2026 -0800 empty lines exec/FPU_FHD/main.cpp commit 758adf6b6e4b8f2edcf3bca2d979c98065989d0f Author: Andy Nonaka Date: Fri Feb 6 14:45:23 2026 -0800 shell code for linear FHD version of 1D chain exec/FPU_FHD/GNUmakefile exec/FPU_FHD/Make.package exec/FPU_FHD/inputs exec/FPU_FHD/main.cpp commit 44223848638c5311f8db260c097652ea217f705e Merge: 0a9fecdd d4366f7a Author: Andy Nonaka Date: Fri Feb 6 13:58:58 2026 -0800 Merge branch 'main' into FPU_chain commit d4366f7a12f8d3b735a36f2c6b6d3e98f0bdb04b Author: Andy Nonaka Date: Mon Jan 26 08:41:27 2026 -0800 fix comments exec/StochasticHeat/main.cpp commit 9a6bcb2871a89a9049da607d507ab5ac3898080c Merge: e6edeff4 ade6d95d Author: Andy Nonaka Date: Mon Jan 26 07:20:00 2026 -0800 Merge pull request #201 from AMReX-FHD/StochasticHeat AMReX Version of Alej's StochasticHeat commit ade6d95d96d9265084c7eba9753484caa14afed2 Author: Andy Nonaka Date: Sat Jan 24 12:42:09 2026 -0800 cleanup exec/StochasticHeat/main.cpp commit 24833d55a379e365bcfeb1c909a9963703f3b8da Author: Andy Nonaka Date: Sat Jan 24 12:36:06 2026 -0800 trailing whitespace exec/StochasticHeat/main.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp commit 741ddd961f481f5e04309f8d10c30808ce366ff8 Author: Andy Nonaka Date: Sat Jan 24 12:30:56 2026 -0800 structure factors working exec/StochasticHeat/GNUmakefile exec/StochasticHeat/main.cpp commit c820792dd5c4b7a7506f5461422f970ea6db631b Author: Andy Nonaka Date: Sat Jan 24 11:49:44 2026 -0800 tidy up code, fix small bug in correlation calculation exec/StochasticHeat/inputs exec/StochasticHeat/main.cpp commit 69ec6ab734db5c161ea1c83c0d1be6fdddb63fb3 Author: Andy Nonaka Date: Wed Jan 21 14:56:54 2026 -0800 correlations exec/StochasticHeat/main.cpp commit 31172672af90fae0d5ba775d53f4dc9117827c7b Author: Andy Nonaka Date: Wed Jan 21 14:52:41 2026 -0800 means and variances working exec/StochasticHeat/main.cpp commit 9d62601d88f687ab3740b3c01357dbb43007dfad Author: Andy Nonaka Date: Wed Jan 21 14:13:07 2026 -0800 fix scaling on stoch noise exec/StochasticHeat/main.cpp commit 4dbba54980ab98eefd0fdac7e0189367d09e2bd2 Author: Andy Nonaka Date: Wed Jan 21 13:54:52 2026 -0800 fix some bugs exec/StochasticHeat/inputs exec/StochasticHeat/main.cpp commit e169a60062fe11f8c3ef12740ee9832da9edcf0e Author: Andy Nonaka Date: Wed Jan 21 12:52:25 2026 -0800 more progress exec/StochasticHeat/inputs exec/StochasticHeat/main.cpp commit 580c08bc654a9d804650d5e76b76713caad34e19 Author: Andy Nonaka Date: Wed Jan 21 09:06:11 2026 -0800 add 1D support, build with random libraries exec/StochasticHeat/GNUmakefile exec/StochasticHeat/main.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp commit e6edeff437250037a6b31ea2a458d331ac0e2664 Author: Andy Nonaka Date: Wed Jan 21 08:26:08 2026 -0800 fix compilation issue src_MFsurfchem/MFsurfchem_functions.cpp commit 57f26476b427c8d088dc8d9b40e21cddec078bc6 Author: Andy Nonaka Date: Mon Jan 19 14:12:24 2026 -0800 WIP exec/StochasticHeat/main.cpp commit 2beb515960972ce29ecb38ed6abe55b0c41b6969 Author: Andy Nonaka Date: Mon Jan 19 13:49:31 2026 -0800 StochasticHeat in AMReX modified amrex tutorial for deterministc version as a starting point; runs in 1D/2D or 3D exec/StochasticHeat/GNUmakefile exec/StochasticHeat/Make.package exec/StochasticHeat/inputs exec/StochasticHeat/main.cpp commit 0a9fecdd6448a47e34cc5a203ae4f546030fe930 Author: Andy Nonaka Date: Wed Jan 14 14:10:09 2026 -0800 add beta back into initial momentum sample exec/FPU_chain/FPU.cpp exec/FPU_chain/plot_Salphaalpha.gp commit 7f1f1b5b2e090411add94b0dd45a33bd139baf16 Author: Andy Nonaka Date: Wed Jan 14 12:52:03 2026 -0800 comments and code cleanup exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 66ca6863e1a5baee815e0f167f4907ee851b5b77 Author: Andy Nonaka Date: Wed Jan 14 12:06:28 2026 -0800 fix normalization of stats exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit 4fda9fdfeb1824e7608d54a8c9cdc4197a25ab38 Author: Andy Nonaka Date: Wed Jan 7 20:11:01 2026 -0800 diagnostics indicating S_alphaalpha_avg file write exec/FPU_chain/main.cpp commit 421f7895b7cb908dcfbb30d8ab10f3779995679a Author: Andy Nonaka Date: Wed Jan 7 20:09:14 2026 -0800 print diagnostics for means file of S_alphaalpha exec/FPU_chain/FPU.cpp commit 77aa0949ae794712e10a5873f749414c47d98427 Author: Andy Nonaka Date: Wed Jan 7 18:03:20 2026 -0800 lower diag_inty exec/FPU_chain/inputs commit 248d2051ae6ecd6e6b3f1e8fbfd3d93a1220281b Author: Andy Nonaka Date: Wed Jan 7 17:46:40 2026 -0800 tabs and whitespace exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit c8f9e88f362bff544e828e8f5052a795dd0f20d3 Author: Andy Nonaka Date: Wed Jan 7 17:30:49 2026 -0800 writing means and S_alphaalpha to text files exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit d5670fb83b3aa702b39dc2bf1e7dcf0b2bec0bc0 Author: Andy Nonaka Date: Wed Jan 7 17:04:09 2026 -0800 working on S_alphaalpha diags exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit bf8a300116c0d51eab5b0fcf4eb1446de61d6db6 Author: Andy Nonaka Date: Wed Dec 17 13:23:37 2025 -0800 hard-code a "thin" of 1000- generalize it exec/FPU_chain/FPU.cpp commit 0307afbdb50abc9d15ddff3b61926dba9174d9ec Author: Andy Nonaka Date: Wed Dec 17 13:00:14 2025 -0800 progress toward structure factors exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 0a2433b4dc19435583c3cc09aae6039b686a3364 Author: Andy Nonaka Date: Wed Dec 17 12:43:11 2025 -0800 turn on MPI fix galphazero plotting issue exec/FPU_chain/GNUmakefile exec/FPU_chain/main.cpp commit 8645779a945ba8887df801aacb1d2dbad669d3db Author: Andy Nonaka Date: Tue Dec 16 17:53:03 2025 -0800 galpha exec/FPU_chain/main.cpp commit 4af93c7fde8d20fb341a3f29e98c19ee9a0ebd6c Author: Andy Nonaka Date: Tue Dec 16 17:20:58 2025 -0800 turn on managed memory for GPU init of r exec/FPU_chain/inputs commit a6a5690b5ee974e913f1343e19d622f5f43c3003 Author: Andy Nonaka Date: Tue Dec 16 17:09:05 2025 -0800 reference to multifab data exec/FPU_chain/FPU.cpp commit 78d461819a3e0e844c7327a1ca426f38f5eaca1d Author: Andy Nonaka Date: Mon Dec 15 12:35:56 2025 -0800 add energy to "state" exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 917abcb87c3daecc9de43f674ab8ac56abad8da5 Author: Andy Nonaka Date: Wed Dec 10 15:23:57 2025 -0800 mean energy computation exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 69f7d4efead771b3e0aa54aa7b6e68477e718843 Author: Andy Nonaka Date: Wed Dec 10 15:02:07 2025 -0800 typo in plotfile variable name exec/FPU_chain/main.cpp commit 3746c6e2034df89a666fbcda232794a9424b3326 Author: Andy Nonaka Date: Wed Dec 10 14:58:25 2025 -0800 first cut at RK4 time stepping with RHS exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit 1c541f5ce8a034a02a5f7dd1fbd6030c65f55699 Author: Andy Nonaka Date: Wed Dec 10 13:44:00 2025 -0800 RK structure exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 2964394d13915f0f51159aac28f4278e846b051b Author: Andy Nonaka Date: Wed Dec 10 13:23:55 2025 -0800 simplify data structures exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/main.cpp commit 351eb96014480882b87dea3eefe753eb112ecc54 Author: Andy Nonaka Date: Mon Dec 1 15:39:49 2025 -0800 comments exec/FPU_chain/FPU.cpp commit 364cb0abc2578ba11f17d68c5dd66e66071b0a99 Author: Andy Nonaka Date: Mon Dec 1 15:36:17 2025 -0800 initialization attempt complete exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit 2aaeed9cbe25cc93e13d353c8e539f81b6971e5f Author: Andy Nonaka Date: Mon Dec 1 11:50:19 2025 -0800 saving progress exec/FPU_chain/FPU.H exec/FPU_chain/FPU.cpp exec/FPU_chain/Make.package exec/FPU_chain/main.cpp commit 5f583c5ec659d7f70c4cd3612a45217b197a6f08 Author: Andy Nonaka Date: Thu Nov 20 16:52:19 2025 -0800 fix whitespace exec/FPU_chain/main.cpp commit 091da92a866eccd3fc5da033e3958d6dd019e3d3 Merge: 852c8956 f1b9cd7d Author: Andy Nonaka Date: Thu Nov 20 16:51:55 2025 -0800 Merge branch 'main' into FPU_chain commit f1b9cd7d2594303cfa9a675d7385caf283435226 Author: Andy Nonaka Date: Thu Nov 20 16:51:40 2025 -0800 fix trailing whitespace src_compressible_stag/main_driver.cpp commit 8505d38cccf3c1108974c5b8b7c704e47a2ea696 Author: isriva Date: Thu Nov 20 16:48:12 2025 -0800 options for Dirichlet boundaries in compressible stag src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible/transCoeffs.cpp src_compressible_stag/fluxStag.cpp commit 852c8956d6ab078e7da5b96aa7d1835a657ac82c Author: Andy Nonaka Date: Thu Nov 20 16:47:20 2025 -0800 shell of FPU chain code exec/FPU_chain/GNUmakefile exec/FPU_chain/Make.package exec/FPU_chain/inputs exec/FPU_chain/main.cpp commit e619503eb0c95ec68be72282768564ff96f08a7f Author: isriva Date: Tue Nov 18 16:21:08 2025 -0800 more edits for 4th order stats src_common/common_functions.cpp src_common/common_namespace.H commit 2ef5288d94846ddb7c38ec684adf4dafcd9f319d Author: isriva Date: Tue Nov 18 12:17:51 2025 -0800 4th moment computations in compressible staggered src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 619b8492271efac8e1c3b646a63b0007801a5007 Merge: cd48f1ce b250ce0a Author: Bhargav Sriram Siddani <45137944+siddanib@users.noreply.github.com> Date: Tue Oct 28 18:55:28 2025 -0700 Merge pull request #197 from siddanib/deankow_ensemble This MR creates a new folder that does NOT overlap with any existing code/folders. commit b250ce0acb2bf3aaf56485abe788a1d1254df13f Author: Bhargav Sriram Siddani Date: Sun Oct 26 13:55:18 2025 -0700 Particles on level=0 sample input file. exec/dean_kow/ensemble/inputs_particles src_deankow/ensemble/mykernel.H commit e0f5d13d0dc4c1816a941114e907dcad71a46ca3 Author: Bhargav Sriram Siddani Date: Fri Oct 24 16:48:38 2025 -0700 Another intermediate commit for Particles in ensemble mode. src_deankow/ensemble/AmrCoreAdv.cpp src_deankow/ensemble/ParticleData.H src_deankow/ensemble/StochasticPC.H src_deankow/ensemble/StochasticPC.cpp commit 8985313cc696108ac949443459b16e364fbfd042 Author: Bhargav Sriram Siddani Date: Fri Oct 24 14:55:17 2025 -0700 An intermediate commit during getting particles working in ensemble mode. src_deankow/ensemble/AmrCoreAdv.cpp src_deankow/ensemble/ParticleData.H src_deankow/ensemble/StochasticPC.H src_deankow/ensemble/StochasticPC.cpp src_deankow/ensemble/mykernel.H commit 915d1934f39660907cd0e646f2251c9d20fe03d5 Author: Bhargav Sriram Siddani Date: Thu Oct 23 17:08:16 2025 -0700 Another preliminary check exec/dean_kow/ensemble/inputs exec/dean_kow/ensemble/python_postprocess/check_ensemble_dir.py src_deankow/ensemble/mykernel.H commit 04518aa382a6c8dc04ed3e9c71703a93d6aecbc4 Author: Bhargav Sriram Siddani Date: Thu Oct 23 13:50:54 2025 -0700 An initial version of input file WITHOUT PARTICLES exec/dean_kow/ensemble/GNUmakefile exec/dean_kow/ensemble/inputs commit 0bcada047813c976db148b80efbbd8fbefa16c6d Author: Bhargav Sriram Siddani Date: Thu Oct 23 13:48:19 2025 -0700 Uniform initial condition in mykernel.H src_deankow/ensemble/mykernel.H commit d0162c721590cbfd9a3fadf02f90c572de3c9402 Author: Bhargav Sriram Siddani Date: Thu Oct 23 13:23:49 2025 -0700 Using max_level instead of finest_level exec/dean_kow/ensemble/inputs_bug1 exec/dean_kow/ensemble/inputs_bug2 src_deankow/ensemble/AmrCoreAdv.cpp commit 326c453f3996b52f170affe606dff1a01ddbe3cd Author: Bhargav Sriram Siddani Date: Thu Oct 23 12:59:07 2025 -0700 Ensure that you are reading the correct source directory exec/dean_kow/ensemble/Make.Adv src_deankow/ensemble/AdvancePhiAtLevel.cpp src_deankow/ensemble/AmrCoreAdv.H src_deankow/ensemble/AmrCoreAdv.cpp src_deankow/ensemble/myfunc.H src_deankow/ensemble/myfunc.cpp src_deankow/ensemble/mykernel.H commit 7d812d8f4858a12ffbefad31f11d6153832f75e1 Author: Bhargav Sriram Siddani Date: Thu Oct 23 10:36:52 2025 -0700 Copied exec/deankow/multiscale into exec/deankow/ensemble exec/dean_kow/ensemble/GNUmakefile exec/dean_kow/ensemble/Make.Adv exec/dean_kow/ensemble/Make.package exec/dean_kow/ensemble/amrvis.defaults exec/dean_kow/ensemble/inputs exec/dean_kow/ensemble/inputs_bug1 exec/dean_kow/ensemble/inputs_bug2 commit ade8516dee9f6cbf34c600cfc05e12b404f20923 Author: Bhargav Sriram Siddani Date: Thu Oct 23 10:34:00 2025 -0700 Copied multilevel folder contents into ensemble folder src_deankow/ensemble/AdvancePhiAtLevel.cpp src_deankow/ensemble/AmrCoreAdv.H src_deankow/ensemble/AmrCoreAdv.cpp src_deankow/ensemble/Kernels.H src_deankow/ensemble/Make.package src_deankow/ensemble/ParticleData.H src_deankow/ensemble/Src_K/Adv_K.H src_deankow/ensemble/Src_K/Make.package src_deankow/ensemble/Src_K/compute_flux_2D_K.H src_deankow/ensemble/Src_K/compute_flux_3D_K.H src_deankow/ensemble/Src_K/slope_K.H src_deankow/ensemble/StochasticPC.H src_deankow/ensemble/StochasticPC.cpp src_deankow/ensemble/Tagging.H src_deankow/ensemble/bc_fill.H src_deankow/ensemble/main.cpp src_deankow/ensemble/myfunc.H src_deankow/ensemble/myfunc.cpp src_deankow/ensemble/mykernel.H commit cd48f1cecc6463836c4fd5ebad3552b93fa1cf9a Author: HyuntaeJung Date: Fri Oct 10 05:21:02 2025 -0700 exec/compressible_stag/test_MFsurfchem_COAr_eq : README, inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_COAr_eq/README exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag commit 55070b68a778228faf968ccf1d93ee88d036418b Author: Andy Nonaka Date: Mon Sep 8 10:15:23 2025 -0700 whitespace and tabs exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/Init.cpp exec/multispec/main_driver.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MultiFabPhysBC_FH.cpp src_multispec/multispec_functions.H commit fc1934b6ad7c55801eb49fd38412d06dead1b845 Merge: 6a59f506 2a3cd758 Author: Andy Nonaka Date: Mon Sep 8 09:51:37 2025 -0700 Merge branch 'main' into flory_huggins_diag commit 2a3cd758c158cead21c4cde3e25c6c01cebb07f2 Merge: 5f037261 ebc7ed8e Author: Andy Nonaka Date: Mon Sep 8 09:46:46 2025 -0700 Merge pull request #195 from jmsexton03/fix_cuda_ci Update Cuda CI based on amrex and ERF commit ebc7ed8eca090142d87944655a9eb6b36af5c87a Author: Jean M. Sexton Date: Mon Sep 8 08:41:29 2025 -0700 Init fixes for z and AMREX_D_TERM exec/multispec/Init.cpp commit 5f74ec24306839393c1c31c55102bb65c7b75478 Author: Jean M. Sexton Date: Mon Sep 8 08:15:20 2025 -0700 Some more unused fixes and fix a typo exec/multispec/Init.cpp src_deankow/multilevel/ParticleData.H src_gmres/StagApplyOp.cpp src_hydro/StochMomFlux.cpp src_hydro/advance.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/FluidCharge.cpp src_multispec/InitialProjection.cpp src_multispec/MassFluxUtil.cpp commit dd89d3b7d157f2234ea8b36b125f7f9da089c2c4 Author: Jean M. Sexton Date: Fri Sep 5 14:52:33 2025 -0700 Unused parameters exec/immersedIons/Checkpoint.cpp exec/immersedIons/WritePlotFile.cpp src_geometry/paramplane_functions_K.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 8b83b0693833dcc7cdd32e8c253d503965354d34 Author: Jean M. Sexton Date: Fri Sep 5 14:45:55 2025 -0700 Add maybe_unused exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_analysis/TurbSpectra.cpp src_common/ComputeAverages.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_gmres/ApplyMatrix.cpp src_gmres/GMRES.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_hydro/advance.cpp src_hydro/hydro_functions.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 79bab376041163b713e4401124b6e77df944adc2 Author: Jean M. Sexton Date: Fri Sep 5 10:45:27 2025 -0700 Fix errors exec/reactDiff/GNUmakefile src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.cpp src_deankow/singlelevel/mykernel.H commit 54e818281086f028114b1799f18475f7f88d311b Author: Jean M. Sexton Date: Thu Sep 4 14:06:50 2025 -0700 Tweak dir .github/workflows/cuda.yml commit 61538156fb44c16dfc4c46c52478ec85451b6ed9 Author: Jean M. Sexton Date: Thu Sep 4 13:17:42 2025 -0700 Typo .github/workflows/cuda.yml commit 6242a14cfc30bd8403b29f8f675057df97b00689 Author: Jean M. Sexton Date: Thu Sep 4 13:15:38 2025 -0700 More artifact tweaks .github/workflows/cuda.yml commit 16a1adca6bbef22a00e1db78695e71a11357ce28 Author: Jean M. Sexton Date: Thu Sep 4 13:15:02 2025 -0700 Revert "One artifact with all errors and warnings per run" This reverts commit 495c7112ec7e9a15e0ccf0eb73fc37bc5117705c. .github/workflows/cuda.yml commit 495c7112ec7e9a15e0ccf0eb73fc37bc5117705c Author: Jean M. Sexton Date: Thu Sep 4 13:04:54 2025 -0700 One artifact with all errors and warnings per run .github/workflows/cuda.yml commit f0415d984d93bc3e50662480bdad67e98e9ba513 Author: Jean M. Sexton Date: Thu Sep 4 12:56:43 2025 -0700 Update names .github/workflows/cuda.yml commit 99c232c072404dbed4187741489f0db7deefca40 Author: Jean M. Sexton Date: Thu Sep 4 11:54:02 2025 -0700 Tweak upload name .github/workflows/cuda.yml commit 3e4fcac98dd34b3f7546a9c4aae78dea89fce338 Author: Jean M. Sexton Date: Thu Sep 4 11:43:12 2025 -0700 Add build reports as artifacts and links in the summary .github/workflows/cuda.yml commit 636fa571082bcf584891c01d15dee4ab8687eb4e Author: Jean M. Sexton Date: Thu Sep 4 11:26:03 2025 -0700 Tweak conditions for running ci steps .github/workflows/cuda.yml commit 61051ad49de9185da1484d8d3f1813adcac82581 Author: Jean M. Sexton Date: Thu Sep 4 10:00:42 2025 -0700 Don't make it overly complicated .github/workflows/cuda.yml commit c3a1e0a473bb62a8bc65c549c053b29c76b76007 Author: Jean M. Sexton Date: Thu Sep 4 09:53:30 2025 -0700 include more compiler lines in summary .github/workflows/cuda.yml commit 02f28bcbe0fe9f7bb64085adec371ebc7073b0a6 Author: Jean M. Sexton Date: Thu Sep 4 09:42:39 2025 -0700 More error catching .github/workflows/cuda.yml commit 24f1a957e685e5b259fcb0402de37585c15f4452 Author: Jean M. Sexton Date: Thu Sep 4 09:32:02 2025 -0700 Test continue for build .github/workflows/cuda.yml commit 540e1d42776b5ed549a819fc1a95160b354aa099 Author: Jean M. Sexton Date: Thu Sep 4 09:11:57 2025 -0700 Make error summary more useful .github/workflows/cuda.yml commit be58e37d60b4a370c7baa836b5d1bb50062f9fd7 Author: Jean M. Sexton Date: Thu Sep 4 09:01:13 2025 -0700 Don't exclude amrex from checking .github/workflows/cuda.yml commit a7a2de57eae0649bfc2535822dc0b3038aaa3dde Author: Jean M. Sexton Date: Thu Sep 4 08:31:16 2025 -0700 Forgot to add file .github/problem-matchers/gcc.json commit 792bfb9aa764b1634a9a9891446aa24d4893f4c2 Author: Jean M. Sexton Date: Thu Sep 4 08:28:56 2025 -0700 Make error summary more descriptive .github/workflows/cuda.yml commit c147f6dad0437af5c675ae6787968a5b52d4aa1d Author: Jean M. Sexton Date: Thu Sep 4 07:16:21 2025 -0700 Include more tests and turn off fail-fast .github/workflows/cuda.yml commit 5f037261c2827c378f4834a66cce14cec35716b6 Author: Andy Nonaka Date: Wed Sep 3 11:14:47 2025 -0700 USE_FFT=TRUE exec/reactDiff/GNUmakefile commit 6a59f506d940fd850c77a3b2f75565df3f8f9433 Merge: 4d817d21 c4e6b0bd Author: Andy Nonaka Date: Wed Sep 3 09:44:02 2025 -0700 Merge branch 'main' into flory_huggins_diag commit a4edf7da8d094356257528152d633bad4e87f864 Author: Jean M. Sexton Date: Wed Sep 3 08:23:43 2025 -0700 Add matrix for testing different exec directories .github/workflows/cuda.yml commit 4c3adceb2ede684904e50d1883661c07982ca124 Author: Jean M. Sexton Date: Wed Sep 3 05:28:41 2025 -0700 Slightly older ubuntu .github/workflows/cuda.yml commit 0b8081aa5a3725d4aa8e90ab5be8bedc42a10e87 Author: Jean M. Sexton Date: Wed Sep 3 05:24:32 2025 -0700 Update to newer cuda version .github/workflows/cuda.yml commit 3315c6cadee4cf64a19c7b9a146294372b079f93 Author: Jean M. Sexton Date: Wed Sep 3 05:16:34 2025 -0700 Add ccache and use amrex dependency scripts .github/workflows/cuda.yml commit 2028119a4d2114b06cb94767748b92abc9c1b522 Author: Jean M. Sexton Date: Wed Sep 3 04:47:56 2025 -0700 Try newer runner .github/workflows/cuda.yml commit c4e6b0bd26a41844e46504e11bfc23c3ad4072f1 Merge: 8838f9b1 be8f36fc Author: Ann Almgren Date: Tue Sep 2 19:26:33 2025 -0700 Merge pull request #194 from jmsexton03/fix_style_api Whitespace and Tabs Fixes commit 4d817d21585321a82c8c39e29caa73b30db7c384 Merge: 1d5e3df0 8838f9b1 Author: Andy Nonaka Date: Tue Sep 2 16:10:01 2025 -0700 Merge branch 'main' into flory_huggins_diag commit be8f36fc1ab4808aacbab80a0f3940bbd4309317 Author: Jean M. Sexton Date: Tue Sep 2 06:30:13 2025 -0700 Missed one exec/DSMC/Checkpoint.cpp commit 9c8220d5edbb1f019b29c8a2b3b617528d431003 Merge: 2110d9f6 8838f9b1 Author: Jean M. Sexton Date: Tue Sep 2 06:25:06 2025 -0700 Merge branch 'main' into fix_style_api commit 2110d9f6b788cfbaa66d71cefb05c1214b088551 Author: Jean M. Sexton Date: Tue Sep 2 06:20:39 2025 -0700 Try style workflow .github/workflows/style.yaml commit aa3f50ba178a004650c772ad759bc0c997b18784 Author: Jean M. Sexton Date: Tue Sep 2 06:19:36 2025 -0700 Manual fixes exec/DSMC/main_driver.cpp exec/DSMC/stats.cpp exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/stats.cpp exec/_1d_dk_hybrid/driver.f exec/_1d_staggered_comp/driver.f exec/cellbdytest_new/main_driver.cpp exec/cellbdytest_new/particleGen.cpp exec/compressible/chemistry_inputs_files/params_NO2_N2O4_thermochem.py exec/compressible/indexshift/index_shift.sh exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_stag/test_NO2_dimerization_eq/params_NO2_N2O4_thermochem.py exec/compressible_stag_mui/SPPARKS_MUI/app_diffusion.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_off_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_phasefield.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_sinter.cpp exec/compressible_stag_mui/SPPARKS_MUI/comm_off_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_cluster.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_density.cpp exec/compressible_stag_mui/SPPARKS_MUI/domain.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump_text.cpp exec/compressible_stag_mui/SPPARKS_MUI/image.cpp exec/compressible_stag_mui/SPPARKS_MUI/pair_lj_cut.cpp exec/compressible_stag_mui/SPPARKS_MUI/universe.cpp exec/compressible_stag_mui/SPPARKS_MUI/variable.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/main_driver.H exec/multispec/multispec_test_functions.H exec/phononDetector/particleGen.cpp exec/tutorials/ib_marker_basic/main_driver.cpp src_analysis/StructFact.cpp src_analysis/TurbSpectra.cpp src_compressible/flux.cpp src_compressible_stag/main_driver.cpp src_deankow/multilevel/mykernel.H src_deankow/singlelevel/main.cpp src_deankow/singlelevel/mykernel.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_hydro/BDS.cpp src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBParticleContainer.cpp src_mui/lib_dispatcher.h src_mui/lib_factory.h src_multispec/DiffusiveMassFluxdiv.cpp src_particles/FhdParticleContainer.cpp src_particles/FhdParticleContainer_WF.cpp unmaintained/_1d_staggered_comp/driver.f unmaintained/_GL_alt/timeStep.cpp unmaintained/_GL_alt_1D/timeStep.cpp unmaintained/src_chem/AmrCoreAdv.cpp commit 8838f9b16cb6c60dc8673c835101e219d7c1b9ef Merge: 1ed2ea33 ba5938e5 Author: Andy Nonaka Date: Fri Aug 29 10:20:12 2025 -0700 Merge pull request #193 from AMReX-FHD/surfchemtest Small fix in SF_surfcov_2D plot and mean_MFsurfchem commit ba5938e5ec523ed9a17ead96d8818566ff9f81e9 Author: Andy Nonaka Date: Fri Aug 29 09:25:07 2025 -0700 tabbing src_MFsurfchem/MFsurfchem_functions.cpp commit dc76cb5990d5374fd5d531403d856f49c72f88b1 Author: Andy Nonaka Date: Fri Aug 29 09:24:32 2025 -0700 more tabbing formatting src_MFsurfchem/MFsurfchem_functions.cpp commit 999bfac9e19a2ac3a7654a012b02662ed6f98639 Author: Andy Nonaka Date: Fri Aug 29 09:23:01 2025 -0700 fix indentation - github apparently doesn't like tabs and wants spaces for indentation src_MFsurfchem/MFsurfchem_functions.cpp commit 364e135cac55dc7265b09ba2c9a58c4352567d24 Author: HyuntaeJung Date: Fri Aug 29 04:44:48 2025 -0700 MFsurfchem_functions.cpp - small fix src_MFsurfchem/MFsurfchem_functions.cpp commit 35db69f03ad5cd8fa00e109926ddf99e24f55954 Author: HyuntaeJung Date: Fri Aug 29 04:07:37 2025 -0700 MFsurfchem - add mean_MFsurfchem to calculate adsorption and desorption rates with equilibrium values src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit 3ffd147706c8975f99e664649e2d1d1d9183a799 Author: HyuntaeJung Date: Fri Aug 29 03:59:39 2025 -0700 fix if condition for plt_SF_surfcov_2D plot src_compressible_stag/main_driver.cpp commit d40d73f0e837021d3770d60ba30fe17ccb342cfe Author: Jean M. Sexton Date: Thu Aug 28 11:33:32 2025 -0700 whitespace src_particles/DsmcParticleContainer.cpp commit f259a6e75f66d32335d0bd67ba146f120c95b8a3 Author: Jean M. Sexton Date: Thu Aug 28 11:32:10 2025 -0700 Manual fixes exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp exec/DSMC_granular/stats.cpp exec/_1d_dk_hybrid/_ensemble/stats.c exec/_1d_dk_hybrid/stats.c exec/_1d_staggered_comp/_reservoir/driver.f exec/_1d_staggered_comp/_reservoir/stats.c exec/_1d_staggered_comp/stats.c exec/cellbdytest_new/Checkpoint.cpp exec/cellbdytest_new/main_driver.cpp exec/compressible/chemistry_inputs_files/params_NO2_N2O4_thermochem.py exec/compressible/indexshift/index_shift.sh exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.cpp exec/compressible_stag/TURB_PDFS/main_multisteps.cpp exec/compressible_stag/test_NO2_dimerization_eq/params_NO2_N2O4_thermochem.py exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_sinter.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/comm_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/comm_off_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/create_sites.cpp exec/compressible_stag_mui/SPPARKS_MUI/image.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/cell_body/ib_md.cpp exec/multispec/Init.cpp exec/phononDSMC/stats.cpp src_analysis/StructFact.cpp src_compressible/compressible_functions.H src_compressible_stag/DeriveVelProp.cpp src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_geometry/paramplane_phonon_functions_K.H src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H src_mui/stream_unordered.h src_multispec/multispec_functions.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/FhdParticleContainer_WF.cpp unmaintained/_1d_staggered_comp/stats.c unmaintained/_GL_alt/timeStep.cpp unmaintained/src_chem/AmrCoreAdv.cpp unmaintained/src_low-density/compressible_functions_F.H commit 5b7422b9a6482abc558ef761680a79e08310465d Author: Jean M. Sexton Date: Wed Aug 27 16:08:45 2025 -0700 python api fix spaces exec/DSMC/Checkpoint.cpp exec/DSMC/DsmcCollide.cpp exec/DSMC/LocalFunctions.H exec/DSMC/ex_main_driver.cpp exec/DSMC/externalF.cpp exec/DSMC/globalVars.cpp exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp exec/DSMC/updateTimeStep.cpp exec/DSMC/writePlotFile.cpp exec/DSMC_granular/Checkpoint.H exec/DSMC_granular/Checkpoint.cpp exec/DSMC_granular/DsmcCollide.cpp exec/DSMC_granular/INS_functions.H exec/DSMC_granular/ex_main_driver.cpp exec/DSMC_granular/externalF.cpp exec/DSMC_granular/globalVars.cpp exec/DSMC_granular/main_DSMC_driver.cpp exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/particleGen.cpp exec/DSMC_granular/stats.cpp exec/DSMC_granular/updateTimeStep.cpp exec/DSMC_granular/writePlotFile.cpp exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/stats.c exec/_1d_dk_hybrid/stats.c exec/_1d_staggered_comp/_reservoir/driver.f exec/_1d_staggered_comp/_reservoir/stats.c exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/stats.c exec/cellbdytest_new/Checkpoint.cpp exec/cellbdytest_new/INS_functions.H exec/cellbdytest_new/WritePlotFileHydro.cpp exec/cellbdytest_new/main_driver.cpp exec/cellbdytest_new/particleGen.cpp exec/compressible/chemistry_inputs_files/params_NO2_N2O4_thermochem.py exec/compressible/indexshift/index_shift.sh exec/compressible_mui/pseudo_kmc/pseudo_kmc.cpp exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202106_before_summer/diag_surfchemtest.cpp exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.H 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commit 566c2370f60f88f57822ecf2e5ffaac537eef1b3 Author: Jean M. Sexton Date: Mon Aug 25 13:29:32 2025 -0700 Trailing whitespace replacement .github/workflows/cuda.yml exec/DSMC/Checkpoint.cpp exec/DSMC/DsmcCollide.cpp exec/DSMC/LocalFunctions.H exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp exec/DSMC/writePlotFile.cpp exec/DSMC_granular/Checkpoint.H exec/DSMC_granular/Checkpoint.cpp exec/DSMC_granular/INS_functions.H exec/DSMC_granular/particleGen.cpp exec/DSMC_granular/stats.cpp exec/Ek_calculator/main_driver.cpp exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/_1d_dk_hybrid/_ensemble/particles.f exec/_1d_dk_hybrid/_ensemble/stats.c exec/_1d_dk_hybrid/driver.f exec/_1d_dk_hybrid/flux.f exec/_1d_dk_hybrid/particles.f exec/_1d_dk_hybrid/stats.c exec/_1d_staggered_comp/_reservoir/driver.f exec/_1d_staggered_comp/_reservoir/flux.f exec/_1d_staggered_comp/_reservoir/flux_alt.f exec/_1d_staggered_comp/_reservoir/stats.c exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/flux.f 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15:05:49 2025 -0700 3d bds contact angle fix src_hydro/BDS.cpp commit 0648f2ddd3eb26602e3826c26909df963e95340b Author: Andy Nonaka Date: Mon Aug 18 12:03:22 2025 -0700 add SPEC_CONTACT_BC to BDS src_hydro/BDS.cpp commit 1ed2ea33339b369f525e113e4cfbfef1a085782c Merge: 73ba7435 429ecfce Author: isriva Date: Thu Aug 14 10:20:58 2025 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 73ba74353e523f628b49b8fe8a300d3c11aed561 Author: isriva Date: Thu Aug 14 10:20:13 2025 -0700 compute third moments in compressible staggered FHD src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 1449dd19c544322aaafbf0aad0264fa8738f7150 Merge: e9fa0bdc 429ecfce Author: Andy Nonaka Date: Mon Aug 4 13:19:40 2025 -0700 Merge branch 'main' into flory_huggins_diag commit e9fa0bdc287c13187d22aaa3652835fee00cf500 Author: John Bell Date: Mon Aug 4 13:17:18 2025 -0700 minor tweaks exec/multispec/Init.cpp src_multispec/MultiFabPhysBC_FH.cpp src_multispec/RhoUtil.cpp commit 429ecfce756afd63f39be4b0a57fc200ceccdce8 Author: Andy Nonaka Date: Mon Aug 4 11:31:28 2025 -0700 remove ASCII stuff exec/multispec/WritePlotFile.cpp commit dc0118862414b891538a9f3b5baaae659ea7185a Author: isriva Date: Wed Jun 18 21:22:10 2025 -0700 plot_vars and plot_covars requires plot_means src_compressible_stag/statsStag.cpp commit 78187e7fd40490ebcb9d6afabc0e47b5be5576a0 Merge: 8a7d96b6 fc0581d8 Author: Andy Nonaka Date: Tue Jun 17 08:53:20 2025 -0700 Merge pull request #191 from AMReX-FHD/tran_coef_1ghost 1 ghost cell for computing transport coefficients commit fc0581d8ec4c996fb1cda4fb36b84a33099859a9 Author: Andy Nonaka Date: Mon Jun 16 12:01:09 2025 -0700 fix for non do_1D case src_compressible/transCoeffs.cpp commit d292aec8dd357450dd540570e3efb6af0f7357ec Author: Andy Nonaka Date: Mon Jun 16 09:39:13 2025 -0700 1 ghost cell for computing transport coefficients src_compressible/transCoeffs.cpp commit 8a7d96b6d827ffb6898fc8a5fd74c18319d96a12 Merge: aa353e4f a2b44af3 Author: hjung <115668962+HyuntaeJung@users.noreply.github.com> Date: Thu May 1 13:57:36 2025 +0900 Merge pull request #190 from AMReX-FHD/sf_slice_do2D do_2d mode slice structure factor commit a2b44af3cbf680d6dbb62200a4d788aaeac9c27f Author: Andy Nonaka Date: Wed Apr 30 07:58:19 2025 -0700 fix logic for writing out first structure factor after n_steps_skip src_compressible_stag/main_driver.cpp commit 4181018e2dd161617c12d4793262089a8a90f2af Merge: 72b37fde aa353e4f Author: Andy Nonaka Date: Mon Apr 28 14:45:01 2025 -0700 Merge branch 'main' into sf_slice_do2D commit aa353e4f476c514946445cc7fdd9c96abb678eff Merge: cb9eaa98 5889d557 Author: Andy Nonaka Date: Mon Apr 28 14:44:49 2025 -0700 Merge pull request #189 from AMReX-FHD/fix_2d_surfcov_SF Fix errors in do_2D mode surface coverage structure factor commit 5889d55741b364fe3bbeb8c76b4ffd574adf4e58 Merge: 68174344 cb9eaa98 Author: Andy Nonaka Date: Mon Apr 28 14:40:33 2025 -0700 Merge branch 'main' into fix_2d_surfcov_SF commit 72b37fdeab9900a756491c5f7170f749ee171bed Merge: fda4205f cb9eaa98 Author: Andy Nonaka Date: Mon Apr 28 14:40:03 2025 -0700 Merge branch 'main' into sf_slice_do2D commit fda4205f6b47fbc430ea885835ce3c62297459a3 Author: Andy Nonaka Date: Mon Apr 28 14:38:25 2025 -0700 complete flattened do_2D mode structure factors src_compressible_stag/main_driver.cpp commit f8bcb359e868c292a8c1fbfddd7f2e24dc8d17da Author: Andy Nonaka Date: Mon Apr 28 14:18:44 2025 -0700 more cleanup src_compressible_stag/main_driver.cpp commit 9b2f315414ab4cc3722f1e289acd0c2423713018 Author: Andy Nonaka Date: Mon Apr 28 12:38:29 2025 -0700 cleanup src_compressible_stag/main_driver.cpp commit 2be87841a1e9c254047e172d1810a70a0716f027 Author: Andy Nonaka Date: Mon Apr 28 12:34:14 2025 -0700 prep for do_2D mode structure factors with slicepoint src_compressible_stag/main_driver.cpp commit 6817434496dbea47ae5aee37e8bcda8d1101e05f Author: Andy Nonaka Date: Mon Apr 28 09:27:46 2025 -0700 fix errors in do_2D mode surface coverage structure factor src_compressible_stag/main_driver.cpp commit cb9eaa98874038bf585b1fd2a10036e57a03b082 Merge: bbe7a355 183778f6 Author: Daniel Ladiges Date: Mon Mar 31 10:57:56 2025 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 183778f6d903e673e5bf6fffac67b4520679d56f Merge: 6f018539 938de373 Author: Andy Nonaka Date: Wed Mar 26 12:38:21 2025 -0700 Merge pull request #187 from AMReX-FHD/surfchemtest Small fixes - main_driver.cpp and MFsurfchem commit ab7100c9d47cfa4dd2a3165d5d7a80bbc902f6cd Author: John Bell Date: Sun Mar 16 17:14:03 2025 -0700 added code to support surfactants exec/multispec/Init.cpp exec/multispec/WritePlotFile.cpp exec/multispec/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_multispec/ComputeMixtureProperties.cpp src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 938de373e748d45f03b57cd1e5aa84d1e8a39617 Author: HyuntaeJung Date: Tue Mar 11 23:43:29 2025 -0700 fix GNUmakefile in exec/compressible_stag_mui exec/compressible_stag_mui/GNUmakefile commit 8ff61b686ee3a8a9e1e347b2f2c9d3b81f131f88 Author: HyuntaeJung Date: Tue Mar 11 23:42:31 2025 -0700 MFsurfchem - use ads_wall_dir for the calculation of Ntot src_MFsurfchem/MFsurfchem_functions.cpp commit d814f0ad7e4fa6cc89660aa68e2b287e0facd799 Author: HyuntaeJung Date: Tue Mar 11 23:39:24 2025 -0700 error message for do_1D src_compressible_stag/main_driver.cpp commit 6f0185390d1d075e54a840a80b03ea3dbc613e68 Merge: 0b782ada d8460bea Author: Andy Nonaka Date: Tue Mar 11 09:26:15 2025 -0700 Merge pull request #186 from AMReX-FHD/SF_do_2D_surfchem Support for ensemble of pencil structure factor multifabs for the surface chemistry in do_2D mode commit 0b782ada75d1e91fc14b70bf1e3dfa4dee8e3c50 Merge: 181246c8 14d303b1 Author: jbb Date: Sun Mar 2 17:51:17 2025 -0800 add potential commit 181246c8ac1733cfef7c01a61ce5c032a44fb7cd Author: jbb Date: Sun Mar 2 17:44:41 2025 -0800 added external potential to dk hybrid exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/_1d_dk_hybrid/_ensemble/particles.f exec/dean_kow/multilevel/inputs src_deankow/multilevel/AmrCoreAdv.H src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/mykernel.H commit 14d303b1ceca88beae6f569b44fc9640b98ddd88 Author: Ann Almgren Date: Mon Feb 24 11:59:25 2025 -0800 Add particle-coloring; particle-writing in plotfile; clean up white space .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh exec/dean_kow/multilevel/amrvis.defaults src_deankow/1d_stats/main.cpp src_deankow/1d_stats/myfunc.cpp src_deankow/1d_stats/mykernel.H src_deankow/multilevel/AmrCoreAdv.H src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/myfunc.cpp src_deankow/multilevel/mykernel.H src_deankow/singlelevel/main.cpp src_deankow/singlelevel/myfunc.cpp commit d8460bea7576b6374fed1413b1650e20ec08e430 Author: Andy Nonaka Date: Mon Feb 17 17:46:43 2025 -0800 comment src_compressible_stag/main_driver.cpp commit 59325aa28f4059b40b5f219c80c14740ec5a561f Author: Andy Nonaka Date: Mon Feb 17 17:40:01 2025 -0800 fix do_2D surfCov SF names src_compressible_stag/main_driver.cpp commit dd4503c52f9f0a3941dbd2dd03bb50f7bc54b747 Author: Andy Nonaka Date: Mon Feb 17 17:31:33 2025 -0800 enable ensemble of pencil structure factors for surface coverage in do_2D mode src_compressible_stag/main_driver.cpp commit c8249ef9597f9becb151d96e75d2128d5a13e2c5 Merge: 0fb95893 7bd05772 Author: Andy Nonaka Date: Mon Feb 17 14:44:50 2025 -0800 Merge pull request #185 from AMReX-FHD/cleanup_restart Cleanup restart commit 0fb958933de233b376b7c8f5471bbecb15fd885a Author: Ann Almgren Date: Sun Feb 16 18:29:33 2025 -0800 write the particles in the plotfile src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H commit c0a45abc241829e11462e1ac215db87c125c821b Author: Andy Nonaka Date: Fri Feb 14 10:37:03 2025 -0800 remove debugging statement src_compressible_stag/main_driver.cpp commit 7bd05772db0578ed0dfa35e592c464acc497b2ba Merge: 31507174 f0c127d9 Author: Andy Nonaka Date: Fri Feb 14 09:09:40 2025 -0800 Merge branch 'main' into cleanup_restart commit f0c127d994ea72e3381284ff5ffe284bd9554ab8 Author: Andy Nonaka Date: Fri Feb 14 08:20:58 2025 -0800 get compressible compiling again src_compressible/main_driver.cpp commit 3150717452c3a856b6b7249254e9196bdc13e63c Author: Andy Nonaka Date: Thu Feb 13 10:37:43 2025 -0800 fix restart for 2d case src_compressible_stag/Checkpoint.cpp src_compressible_stag/main_driver.cpp commit b890e2925b729c62e351f7581cceeec06ad0314c Author: Andy Nonaka Date: Thu Feb 13 10:22:00 2025 -0800 greatly cleanup restart code src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp commit 3aaf73316f682138ecdd124e1e87d75054807f5e Author: Andy Nonaka Date: Wed Feb 12 14:23:45 2025 -0800 cleanup only src_compressible_stag/Checkpoint.cpp commit 3ffa26ff055876b9460c6557e7e6983e5b29ea4c Merge: bdf6f516 771a1a3f Author: jbb Date: Wed Feb 12 09:18:40 2025 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit bdf6f5168865fb0db6c51f18fb05df1d0a5290a9 Author: jbb Date: Wed Feb 12 09:17:29 2025 -0800 fixed refluxing with periodic boundaries src_deankow/multilevel/AdvancePhiAtLevel.cpp src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/mykernel.H commit 771a1a3f9b59fe8e22b6c5f4e341b20862977efb Merge: ecd7eb28 1212ec08 Author: Andy Nonaka Date: Tue Feb 11 07:17:06 2025 -0800 Merge pull request #184 from AMReX-FHD/fix_do_2D_surfcov_restart do_2D mode with surface coverage restart fixes. commit 1212ec08d3e8c2a129d3234886eba5546398ee5a Author: Andy Nonaka Date: Tue Feb 11 07:16:41 2025 -0800 fix surfcov restart with random numbers src_compressible_stag/Checkpoint.cpp src_compressible_stag/main_driver.cpp commit 06bf2481033746c34d64e3a0cd42ca317eec0741 Author: Andy Nonaka Date: Tue Feb 11 06:59:22 2025 -0800 formatting src_compressible_stag/main_driver.cpp commit d917bf8f7023da23f72845052081fd558312a6a6 Author: Andy Nonaka Date: Tue Feb 11 06:55:02 2025 -0800 do_2D mode with surface coverage restart fixes. It runs but there is still an issue with the seed restart src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp commit ecd7eb285c7477989e799962b7910bb85be1751b Merge: a1a7552c 11d1551c Author: Andy Nonaka Date: Mon Feb 10 16:43:30 2025 -0800 Merge pull request #183 from AMReX-FHD/surfchemtest MFsurfchem - modification of desorption species commit 34b507a2d52c59644e1f529a121566934014b31a Author: jbb Date: Fri Feb 7 10:46:21 2025 -0800 updated average for stochastic flux. still some issue src_deankow/multilevel/mykernel.H commit 11d1551c9d051dcc322aa32db7d679941e18687a Author: HyuntaeJung Date: Wed Feb 5 21:10:50 2025 -0800 conversion_MFsurfchem to modify the species involved in the desorption process src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/main_driver.cpp commit a1a7552cfd4a8b26172acb65ac3eeda90e7fa50b Merge: 0b2c1149 3b09d018 Author: Andy Nonaka Date: Wed Feb 5 08:18:32 2025 -0800 Merge pull request #182 from AMReX-FHD/surfcov_fixes commit 3b09d018416178dd0af455786336c9851e1e604e Author: Andy Nonaka Date: Mon Feb 3 08:37:47 2025 -0800 proper error checking for surfcov cases src_compressible_stag/main_driver.cpp commit 182d86bb55cb5803a5f85f3898bdeb9c15e49a2e Author: Andy Nonaka Date: Mon Feb 3 08:30:52 2025 -0800 revert files exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag commit ce4789e0e9c745ee08b9e1e1e0e376179d7f3805 Author: Andy Nonaka Date: Mon Feb 3 08:30:30 2025 -0800 out of scope error exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag src_compressible_stag/main_driver.cpp commit 517cd1f69d718663bcd978f744426673429c58ea Author: Andy Nonaka Date: Mon Feb 3 08:18:12 2025 -0800 incorporate an ads_wall_dir for MFsurfchem surface direction better error checking to make sure there is more than 1 cell in the surface or else skip the structure factors src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/main_driver.cpp commit 0b2c11499cb100cbb6755e97f1deb5676339f4b0 Merge: 474d4ad1 bbf84972 Author: Andy Nonaka Date: Thu Jan 30 09:00:59 2025 -0800 Merge pull request #181 from AMReX-FHD/1D_SF_support 1D SF Support commit bbf849722772cc580162e4d72474453b332ce293 Author: Andy Nonaka Date: Thu Jan 30 09:00:35 2025 -0800 error checking for do_1D src_compressible_stag/main_driver.cpp commit cffcc5c15a387b98c035dd712b6de3a8e8bb29eb Author: Andy Nonaka Date: Wed Jan 29 18:43:00 2025 -0800 bugs in 1D SF src_compressible_stag/main_driver.cpp commit 00f1f9dec0fa7f06b22ab4a6773f7878afeb4108 Author: Andy Nonaka Date: Wed Jan 29 18:39:56 2025 -0800 toward 1D functionality src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit 8e4c171a04cd8c253ddfb8c8c4067a1e9be7b403 Merge: b8d18b41 474d4ad1 Author: Andy Nonaka Date: Wed Jan 29 18:24:01 2025 -0800 Merge branch 'main' into 1D_SF_support commit b8d18b410db491a48493fd933f991d715f6604bf Author: Andy Nonaka Date: Wed Jan 29 18:00:35 2025 -0800 created an x-pencil extraction routine src_common/ComputeAverages.cpp src_common/common_functions.H commit 474d4ad154273a177c04d399aa6d1350bd3ad9e9 Author: Andy Nonaka Date: Wed Jan 29 13:43:08 2025 -0800 cleanup of flattened SF data structures src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit 95a94eb2f0657fba564916c2e8aef1938e8aa9a3 Merge: 3a7d8a64 05e6a235 Author: Andy Nonaka Date: Wed Jan 29 12:57:59 2025 -0800 Merge pull request #180 from AMReX-FHD/structfact_fixes Structure Factor Fixes commit 05e6a2358f82d8a6a668aa181dea558bb6aae016 Author: Andy Nonaka Date: Mon Jan 27 16:35:35 2025 -0800 for uncoupled z-plane (do_2D) case, only write out structure factors of the average of each plane, not the vertical average src_compressible_stag/main_driver.cpp commit 3a7d8a64269c967e1d4d54dc862e04cb9be971e4 Merge: b6638d51 172cc777 Author: jbb Date: Mon Jan 27 14:05:29 2025 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b6638d513e607385d17147de1e27ddca10e00b13 Author: jbb Date: Mon Jan 27 14:04:58 2025 -0800 fixed bug in DK hybrid exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/_1d_dk_hybrid/_ensemble/particles.f src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/mykernel.H commit de2bff21158b674837727ca2bc13da00e122f941 Author: Andy Nonaka Date: Mon Jan 27 12:42:43 2025 -0800 do_2D mode structure factors at least runs now... src_compressible_stag/main_driver.cpp commit 17ddf089b8a1e2904587c337ed5624545cf3d782 Author: Andy Nonaka Date: Mon Jan 27 11:30:14 2025 -0800 comments src_compressible_stag/main_driver.cpp commit 11ce0f140b2960311e6ec36653e235fa5745227d Author: Andy Nonaka Date: Mon Jan 27 09:52:52 2025 -0800 style only src_compressible_stag/main_driver.cpp commit 6e3067409435d84372f0af1a1d328595554f5f31 Author: Andy Nonaka Date: Tue Jan 21 17:29:09 2025 -0800 require the use of project_dir for mfsurfchem simulations - it should work in any direction however if you run a 2D simulation in any context, the normal planes must be in the z direction - there is error checking for cases where there is only 1 plane to make sure the normal is in z src_MFsurfchem/MFsurfchem_functions.cpp src_compressible_stag/main_driver.cpp commit 38128cddbc078b2608bcf45383e06f1fb37e7a45 Merge: c99e143d 172cc777 Author: Andy Nonaka Date: Fri Jan 17 17:30:52 2025 -0800 Merge branch 'main' into structfact_fixes commit 172cc777ec6cb1e705317ddef637af1ffcf16b8a Merge: 0bd24f1b 8fb83a62 Author: Andy Nonaka Date: Fri Jan 17 17:21:38 2025 -0800 Merge pull request #179 from AMReX-FHD/average_cleanup Average cleanup commit c99e143d206455dd580967c2013864ec13fd9d7a Author: Andy Nonaka Date: Fri Jan 17 16:46:56 2025 -0800 don't do surfCov structure factor if nx=ny=1 - there would only be 1 cell src_compressible_stag/main_driver.cpp commit 104d909801b06d3ae40418b49af17dc1b10c4a62 Author: Andy Nonaka Date: Fri Jan 17 16:34:51 2025 -0800 fix do_2D geom issue src_compressible_stag/main_driver.cpp commit aa461ebe83366bcccdee04fbf619c3a4500300ef Author: Andy Nonaka Date: Fri Jan 17 14:47:15 2025 -0800 structure factors now report K space index in plotfile instead of physical location (which doesn't make sense) exec/DSMC/main_driver.cpp exec/DSMC_granular/main_driver.cpp exec/cellbdytest_new/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp src_reactDiff/main_driver.cpp commit 91786bb000361908e700eb3ee7e71e85aedb92dd Author: Andy Nonaka Date: Fri Jan 17 14:14:15 2025 -0800 work toward SF plotfiles having k space "physical locations" exec/hydro/main_driver.cpp src_compressible_stag/main_driver.cpp commit d9b2b162ec679ab50961fa20640a8f154b866f97 Author: Andy Nonaka Date: Fri Jan 17 13:46:05 2025 -0800 cleanup logic for when structure factors are permitted and computed based on do_1D, do_2D, project_dir, do_slab_sf src_compressible_stag/main_driver.cpp commit 8fb83a622c25a785a461cebf77f28ae2f67a0e3f Author: Andy Nonaka Date: Tue Jan 14 14:28:11 2025 -0800 updated gpu-safe computeverticalaverage that works for multi-components input multifabs src_common/ComputeAverages.cpp commit 7b72f52a34134b9cb4e4dcb0c361289ebc91534c Author: Andy Nonaka Date: Tue Jan 14 13:24:23 2025 -0800 gpu friendly ComputeVerticalAverage src_common/ComputeAverages.cpp commit 0bd24f1b0e802900c106acafb64972aa9d6c0555 Author: Andy Nonaka Date: Tue Jan 14 13:14:46 2025 -0800 fix compilation issue exec/structFactTest/main_driver.cpp commit a9bb05a0a8b2488d2619fa04b171092da995fb0e Author: Andy Nonaka Date: Mon Jan 13 14:42:41 2025 -0800 fix index bug for case where ComputeVerticalAverage is called with incomp>0 src_common/ComputeAverages.cpp commit 1ee25e1b7a4d4425a183ea9886cf8c115aa30aad Author: Andy Nonaka Date: Mon Jan 13 14:18:09 2025 -0800 cleanup ExtractSlice and ComputeVerticalAverage routines move toward modernizing ComputeVerticalAverage to leverage AMReX GPU calls exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/hydro/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp unmaintained/exercises/compressible/main_driver.cpp commit c13de1f6bc3d45cb25f3eb90c016569eea89bfe3 Merge: 65051476 48d14f39 Author: Andy Nonaka Date: Mon Jan 13 13:16:55 2025 -0800 Merge pull request #178 from AMReX-FHD/amrex_fft Structure Factors with amrex::FFT commit 48d14f398c07febb8b7f8d50fa271143bec8a5ad Author: Andy Nonaka Date: Mon Jan 6 08:08:58 2025 -0800 more structure factor cleanup exec/hydro/main_driver.cpp src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp commit c940ce777e4f1893bd3d316b8374e7ae1169affd Author: Andy Nonaka Date: Sat Jan 4 14:06:01 2025 -0800 fix the Nx=1 case and the (Nx=1 AND Ny=1) cases for unpacking the truncated FFT into a full multifab. In these cases the spectral box is from Ny/2+1 since there is only 1 cell in x, and analogous for the Nx=Ny=1 cases, the spectral box here is Nz/2+1 src_analysis/StructFact.cpp commit af2ac09af8ef770285346e7b109ad98112d12246 Author: Andy Nonaka Date: Fri Jan 3 20:07:53 2025 -0800 EOL whitespace src_analysis/StructFact.cpp commit 1d0fb7e398c8ee5fcb4720a2fc0db2cbc7ea8c6c Author: Andy Nonaka Date: Fri Jan 3 19:54:34 2025 -0800 more SF cleanup src_compressible_stag/main_driver.cpp commit f323cadad299b62b76a1fb352bf000b59e8a4692 Author: Andy Nonaka Date: Fri Jan 3 15:42:41 2025 -0800 renname variables src_common/common_functions.cpp src_compressible_stag/main_driver.cpp commit 68811a5b280c795127e8ec15f55c79408e82c9d2 Merge: 0542289f 65051476 Author: Andy Nonaka Date: Fri Jan 3 13:29:50 2025 -0800 Merge branch 'main' into amrex_fft commit 650514765a27a889cd43e756dea38d5a436058f6 Merge: de50cab0 19900023 Author: Andy Nonaka Date: Fri Jan 3 13:29:39 2025 -0800 Merge pull request #177 from AMReX-FHD/cleanup_turb_fft Retain only amrex::FFT for turbulence diagnostics commit 19900023c60619f613e927abdc24246bbb1b12ea Author: Andy Nonaka Date: Fri Jan 3 13:29:04 2025 -0800 cleanup makefile exec/compressible_stag/GNUmakefile commit 0542289fde51f6253008ae3ee1afae3059119989 Author: Andy Nonaka Date: Fri Jan 3 13:22:30 2025 -0800 fix surface coverage SF bugs src_compressible_stag/main_driver.cpp commit 45b79e362b8d3707b35b7422d364380e3536a69e Author: Andy Nonaka Date: Fri Jan 3 12:59:16 2025 -0800 cleanup flattened code, simplify a bit exec/hydro/main_driver.cpp src_common/Make.package src_common/RotateFlattenedMF.cpp src_common/common_functions.H src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp commit 927067d3c8394cbbade5b61f092e61b8b8a3225f Author: isriva Date: Fri Jan 3 12:34:52 2025 -0800 modified GNUMakefile to remove HEFFTE options exec/compressible_stag/GNUmakefile commit 8c94f931e9d85771878c3c8ccde26d8776c2b12f Author: Andy Nonaka Date: Fri Jan 3 12:14:57 2025 -0800 more cleanup exec/compressible_stag/GNUmakefile src_analysis/TurbSpectra.H commit be6c4cab82106bc5a8554e5a76189f2adc2ca69f Author: Andy Nonaka Date: Fri Jan 3 11:35:05 2025 -0800 more cleanup src_analysis/StructFact.H commit 3cbab64a97b609a63ce92bb8864e86e4aa6f3102 Author: Andy Nonaka Date: Fri Jan 3 11:24:19 2025 -0800 more removal of geometry dependence in SF code exec/DSMC/main_driver.cpp exec/DSMC_granular/main_driver.cpp exec/Ek_calculator/main_driver.cpp exec/cellbdytest_new/main_driver.cpp exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/cell_body/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/taylor_line/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp src_reactDiff/main_driver.cpp unmaintained/channel_soft/main_driver.cpp unmaintained/exercises/compressible/main_driver.cpp unmaintained/exercises/incompressible/main_driver.cpp commit 84a4be03c7cee79a95fb7a1175506f8de9da3b57 Author: Andy Nonaka Date: Fri Jan 3 11:11:06 2025 -0800 cleanup; remove dependence on geom in many functions exec/Ek_calculator/main_driver.cpp exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible/main_driver.cpp src_compressible_stag/main_driver.cpp commit aae027e6ea70a6bac7c2b8474446b10ae512b836 Author: Andy Nonaka Date: Fri Jan 3 09:48:27 2025 -0800 cleanup src_analysis/StructFact.H src_analysis/StructFact.cpp commit 30ff76475af7a7989992794aeadf886b4516be86 Author: Andy Nonaka Date: Fri Jan 3 09:20:21 2025 -0800 forward FFT now seems to work src_analysis/StructFact.cpp commit 740997f619216f40375b2345cb4cebbaeaee1430 Author: Andy Nonaka Date: Fri Jan 3 08:52:59 2025 -0800 beginnings of amrex::FFT - much work to do before it will even compile src_analysis/StructFact.H src_analysis/StructFact.cpp commit c28f5ae86baba3df58af9b85e2424340fd01809b Author: Andy Nonaka Date: Fri Jan 3 08:06:16 2025 -0800 remove the single and heffte versions of turbulence code - use only amrex::FFT now src_analysis/Make.package src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_analysis/TurbSpectra_distributed.H src_analysis/TurbSpectra_heffte.H src_analysis/TurbSpectra_heffte.cpp src_analysis/TurbSpectra_single.H src_analysis/TurbSpectra_single.cpp commit de50cab0f3410ed5d3940fa0fb023fc7272f563c Merge: af2bec36 dc29a33f Author: Andy Nonaka Date: Mon Dec 16 08:03:01 2024 -0800 Merge pull request #146 from AMReX-FHD/fhd_heffte HEFFTE support in compressible FHD + Advanced diagnostics for compressible turbulence commit dc29a33f85d9a9335b9b1dcfa0dc4475ebe0b131 Author: Andy Nonaka Date: Thu Dec 12 15:19:09 2024 -0800 get examples compiling exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/multispec/GNUmakefile exec/structFactTest/GNUmakefile src_compressible_stag/main_driver.cpp commit 7cc1c02441b991ec8b35adb14601c7e455a63823 Author: Andy Nonaka Date: Thu Dec 12 13:20:19 2024 -0800 remove blank file src_analysis/TurbSpectra.cpp commit fc4cec878a7ac88b217249c904cc7af4679b49b4 Author: Andy Nonaka Date: Thu Dec 12 11:55:13 2024 -0800 fix compilation USE_FFT=TRUE exec/multispec/GNUmakefile commit 9e883753cdc7acce8ea2c1016f12e580b0713082 Author: Andy Nonaka Date: Thu Dec 12 11:32:20 2024 -0800 get multispec compiling exec/multispec/GNUmakefile commit b83bb535ea828e1af5b0b650ba779812ae840d27 Author: Andy Nonaka Date: Thu Dec 12 09:18:37 2024 -0800 USE_FFT=TRUE in GNUmakefile exec/hydro/GNUmakefile commit b85480884fe02890f4e0f2f16a27ec191c2763f5 Author: Andy Nonaka Date: Thu Dec 12 09:11:46 2024 -0800 fix compilation of hydro with AMReX_FFT exec/hydro/GNUmakefile commit d16dd7e344ce4784d23c1b1235a5ea12c7362cb9 Author: Andy Nonaka Date: Tue Dec 10 09:44:43 2024 -0800 include Src/FFT exec/compressible_stag/GNUmakefile commit 7a816ca117ce2a20a00ada45915d6b185f75e2f6 Merge: f77ac6ee af2bec36 Author: Andy Nonaka Date: Tue Dec 10 09:43:03 2024 -0800 Merge branch 'main' into fhd_heffte commit af2bec369aaba90bc17aaee1f7fe6f6b71d7d099 Author: Andy Nonaka Date: Tue Dec 10 09:40:21 2024 -0800 bugfix; fix broken regression tests src_compressible_stag/writePlotFileStag.cpp commit f77ac6eed029d01678cd0a86c6daa987806a5043 Merge: 46d39832 5d41a5c9 Author: Andy Nonaka Date: Mon Dec 9 16:29:05 2024 -0800 Merge branch 'main' into fhd_heffte commit 5d41a5c952b64c57a0cccb6b43930e6d44748616 Merge: 96e467f7 8bbf830e Author: Andy Nonaka Date: Mon Dec 9 16:26:58 2024 -0800 Merge pull request #175 from AMReX-FHD/test_PR_for_CI test PR just to see how CI is working commit 8bbf830ec9bff04cba2e717e5fee37c305785a3d Author: Andy Nonaka Date: Mon Dec 9 16:03:25 2024 -0800 add libcusparse-dev-11-2 to the dependencies_nvc11.sh .github/workflows/dependencies/dependencies_nvcc11.sh commit b76887a7bd349e04fe5cbe6eef83566f3e526c6f Author: Andy Nonaka Date: Mon Dec 9 14:42:51 2024 -0800 test PR just to see how CI is working exec/hydro/main_driver.cpp commit 96e467f7e9376ccdd66110e8d3850b3d118e5363 Merge: d61978a0 9f1ccd2c Author: Andy Nonaka Date: Thu Dec 5 09:29:47 2024 -0800 Merge pull request #173 from AMReX-FHD/plotfile_deltaY add ability to write deltaY to plotfile in compressible_stag commit d61978a02d10e09e1b9925ea89d7a7ca532a0b0d Merge: 9cd3bd93 c3773dd4 Author: Andy Nonaka Date: Thu Dec 5 09:29:35 2024 -0800 Merge pull request #174 from AMReX-FHD/fix_giantflux_3d Fix inputs_giantfluct_3d to work by ensuring bc YK's sum to 1 commit 9f1ccd2cbfb4ed0f978a245541b33fbdf4d0c9ce Author: Andy Nonaka Date: Wed Dec 4 18:05:26 2024 -0800 use plot_deltaY_dir instead of project_dir src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/writePlotFileStag.cpp commit c3773dd490fde02525dd444480c9b480e9ff4e40 Author: Andy Nonaka Date: Wed Dec 4 17:21:52 2024 -0800 fix inputs_giantflux_3d to work by ensuring bc YK's sum to 1 add error checking for this condition in the compressible_stag code exec/compressible/inputs_giantfluct_3d src_compressible_stag/boundaryStag.cpp commit dd17133f446417d48966050abca99d0dad658e5a Author: Andy Nonaka Date: Wed Dec 4 15:29:27 2024 -0800 add ability to write deltaY to plotfile must specify plot_deltaY = 1 project_dir = (0, 1, or 2) src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/writePlotFileStag.cpp commit 9cd3bd93548b2849406058553399e9fc6837dcf9 Merge: 6041c07a 81ae8acc Author: Andy Nonaka Date: Mon Nov 25 17:04:19 2024 -0800 Merge pull request #172 from AMReX-FHD/slice_SF_compressible_stag Implement slice structure factor for compressible_stag commit 81ae8acc4f0aaf00ffac22f3b21d2fdd842e42d3 Author: Andy Nonaka Date: Thu Nov 21 14:32:39 2024 -0800 fix copy of slice MF components src_common/ComputeAverages.cpp commit 0cac562fdd31693f5110df4720fa2000566f10ea Author: Andy Nonaka Date: Tue Nov 19 19:21:28 2024 -0800 introduce code that forces the slice multifab to have index 0:0 in the dir direction, regardless of slicepoint the structure factor flattened code requires this src_common/ComputeAverages.cpp commit 0ff568fbe889b0a6b87f776c92378aa35cf165d2 Merge: 13f9d43e 6041c07a Author: Andy Nonaka Date: Tue Nov 19 18:12:10 2024 -0800 Merge branch 'main' into slice_SF_compressible_stag commit 067b8bebcf962956eededbc2766af14b53428a35 Merge: b2c27571 482b8e70 Author: John Bell Date: Mon Nov 18 12:12:20 2024 -0800 Merge branch 'flory_huggins_diag' of github.com:AMReX-FHD/FHDeX into flory_huggins_diag commit b2c275712b53d5827eb998c4658e92d562f8a43f Author: John Bell Date: Mon Nov 18 12:11:47 2024 -0800 tweaks to stuff exec/hydro/GNUmakefile exec/hydro/advance.cpp exec/multispec/Init.cpp exec/multispec/main_driver.cpp src_common/MultiFabPhysBC.cpp commit 482b8e70154167efb874c4f54b861ef8524de399 Merge: 4f13cd87 6041c07a Author: Andy Nonaka Date: Mon Nov 18 11:48:05 2024 -0800 Merge branch 'main' into flory_huggins_diag commit 6041c07a165cd28ea992c436347af05a286e4ad6 Author: Andy Nonaka Date: Mon Nov 18 11:47:47 2024 -0800 fix moving wall solver in delta form exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp commit 4f13cd872adfe403bc133fe79c241900665a4ca5 Merge: 90ce8403 c01b5831 Author: Andy Nonaka Date: Mon Nov 18 11:31:46 2024 -0800 Merge branch 'main' into flory_huggins_diag commit c01b5831d4d58e09eb721cf453cc52df9acad555 Author: Andy Nonaka Date: Mon Nov 18 11:31:25 2024 -0800 fix bug when hi-x wall moves in the y-direction src_common/MultiFabPhysBC.cpp commit 46d39832bd24c5faab3da9c81012873d43f76999 Merge: 21300afc f7d10c0f Author: Ishan Srivastava Date: Thu Nov 14 16:58:39 2024 -0500 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit f7d10c0ffc1ffd30cb5ca9d721872e09942a05bb Author: Weiqun Zhang Date: Thu Nov 14 14:21:39 2024 -0500 Fix an issue on Frontier Copy data to host first before calling MPI reduce. src_analysis/TurbSpectra_distributed.cpp commit bbe7a355a8b20ec012509f3487feb191d3bcaf14 Merge: ea31ff12 66ae99d6 Author: Daniel Ladiges Date: Tue Nov 5 14:14:41 2024 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 13f9d43e28564bd9a2efa4caa3c6d88229562775 Author: Andy Nonaka Date: Tue Nov 5 09:02:30 2024 -0800 Implement slice structure factor for compressible_stag To use, set project_dir (normal direction of plane) and slicepoint (coordinate in project_dir to slice) in the inputs file; e.g. if you care about the k=0 plane use project_dir=2 and slicepoint=0 If you do not specify slicepoint it will take the vertical average over project_dir over the entire dataset plt_SF_prim_Flattened plt_SF_cons_Flattened contains the result src_compressible_stag/main_driver.cpp commit 21300afc9f937564cf867860e068f6b8cc4636da Merge: 3abbea5b 08439dd9 Author: Ishan Srivastava Date: Fri Nov 1 17:06:33 2024 -0400 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit 3abbea5b5d5d0e8f5794971fc1f5456d37e80466 Merge: ce96feb6 66ae99d6 Author: Ishan Srivastava Date: Fri Nov 1 17:06:21 2024 -0400 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 08439dd9affc0c3f5375ff4976731fc914e137df Author: Weiqun Zhang Date: Fri Nov 1 17:01:28 2024 -0400 simplification of fft setup src_analysis/TurbSpectra_distributed.cpp commit ce96feb668f1d597f0d504655b0fd9666258fb00 Author: Ishan Srivastava Date: Fri Nov 1 13:25:38 2024 -0400 modified buld script for Frontier exec/compressible_stag/build_frontier_101324.sh commit 41d1da395ebdbb6ce28328b513385f1cd13e196c Merge: de7ad327 5dddc8d5 Author: Ishan Srivastava Date: Thu Oct 31 09:21:40 2024 -0700 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit de7ad327bfe07ff299f803db73c6d6819fac13b1 Author: Ishan Srivastava Date: Thu Oct 31 09:21:02 2024 -0700 small fixes to get amrex fft working src_analysis/TurbSpectra_distributed.cpp commit ca1e5045c9d014296a431bc93bd543fd0279572e Author: Ishan Srivastava Date: Thu Oct 31 09:20:40 2024 -0700 modified build script for Perlmutter exec/compressible_stag/build_perlmutter_101724.sh commit 66ae99d615baf33b2b8936347a7d8806ef84a5f0 Author: Changho Kim Date: Wed Oct 30 04:22:42 2024 -0700 exec/reactDiff/test_Schlogl_2d: Schlogl example added exec/reactDiff/test_Schlogl_2d/clean.sh exec/reactDiff/test_Schlogl_2d/inputs_Schlogl_2d exec/reactDiff/test_Schlogl_2d/job_script.sh exec/reactDiff/test_Schlogl_2d/submit_job.sh commit b14f0204faf2d4829216d69c05d1cf2e6d268da0 Author: Changho Kim Date: Mon Oct 28 01:29:20 2024 -0700 exec/compressible_stag/test_NO2_dimerization_neq_wall: entropy_check.py and zavg3.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/entropy_check.py exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg3.sh commit 5dddc8d5abe31fd63289cdd6ed405893defc138a Merge: 61be49aa 73705a75 Author: Ishan Srivastava Date: Fri Oct 25 19:40:47 2024 -0400 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit 61be49aa0f0398c90bf7f226ec065bc6834c986e Author: Ishan Srivastava Date: Fri Oct 25 19:36:40 2024 -0400 more build files for Frontier exec/compressible_stag/SPECTRAL_FILTER/build_frontier.sh exec/compressible_stag/TURB_PDFS/GNUmakefile exec/compressible_stag/TURB_PDFS/build_frontier.sh exec/compressible_stag/build_frontier_101324.sh commit 376abb100efd0139ba2f666334d2e697d59a5e41 Author: Ishan Srivastava Date: Fri Oct 25 19:35:24 2024 -0400 build on Frontier exec/compressible_stag/GNUmakefile commit 73705a750a856a12ec71189f5c6d986cdcac3efc Merge: ac3765c4 397dc361 Author: Ishan Srivastava Date: Fri Oct 25 15:37:28 2024 -0700 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit ac3765c446ce90e434f48652cf4d1f5a3734fa4e Author: Ishan Srivastava Date: Fri Oct 25 15:14:15 2024 -0700 modified Makefiles to build on Perlmutter exec/compressible_stag/GNUmakefile exec/compressible_stag/SPECTRAL_FILTER/GNUmakefile exec/compressible_stag/SPECTRAL_FILTER/build_perlmutter.sh exec/compressible_stag/TURB_PDFS/GNUmakefile exec/compressible_stag/TURB_PDFS/build_perlmutter.sh exec/compressible_stag/TURB_PDFS/main_multisteps.cpp exec/compressible_stag/build_perlmutter_101724.sh commit 529902b6e950df7552125a4570c6899a4289b82d Author: Ishan Srivastava Date: Fri Oct 25 15:13:29 2024 -0700 corrected spectral filter calculations exec/compressible_stag/SPECTRAL_FILTER/main_driver.cpp exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.H exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.cpp commit 8f8e12db29807a1f1284e305a8c9fba9c162f8ab Author: Ishan Srivastava Date: Fri Oct 25 12:58:11 2024 -0700 vorticity components written to plotfiles now src_compressible_stag/DeriveVelProp.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp commit 397dc361a2e090d299501f5bd12421495cf986b8 Merge: 6b605775 b9fd0e07 Author: isriva Date: Fri Oct 25 12:40:33 2024 -0700 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 6b6057759821b76990b3bc08066c67d3c9c35585 Author: isriva Date: Fri Oct 25 09:57:51 2024 -0700 setup APIs for AMREX_FFT exec/compressible_stag/GNUmakefile src_analysis/Make.package src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_analysis/TurbSpectra_distributed.H src_analysis/TurbSpectra_distributed.cpp src_analysis/TurbSpectra_heffte.H src_analysis/TurbSpectra_heffte.cpp src_analysis/TurbSpectra_single.H src_analysis/TurbSpectra_single.cpp src_compressible_stag/main_driver.cpp commit ea31ff12f80191a5de065e610d39f9bceba781c4 Merge: 76262cfe b9fd0e07 Author: Daniel Ladiges Date: Wed Oct 9 12:16:32 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 76262cfee1cac6570f028c0d7a9b746c6719eceb Author: Daniel Ladiges Date: Wed Oct 9 12:15:23 2024 -0700 Bugfix for DSMC/phonon modified BC detection src_geometry/paramPlane.cpp commit 6982e6179f2030986f3e624e4b2dbf54ec43c2b9 Author: Daniel Ladiges Date: Tue Oct 8 10:19:22 2024 -0700 Further updating of boundary collidion model for phonons/dsmc exec/phononDSMC/main_driver.cpp src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit b9fd0e07fccc848e066c77307c1e42de59c58c58 Merge: 0f6066a8 b3f3ae12 Author: Andy Nonaka Date: Thu Sep 26 11:41:35 2024 -0700 Merge pull request #171 from AMReX-FHD/surfchem_structure_factor surface chemistry structure factor commit b3f3ae12af8e70a43f4ff2d8a969445bbd75186d Author: Andy Nonaka Date: Thu Sep 26 11:39:30 2024 -0700 surface chemistry structure factor src_compressible_stag/main_driver.cpp commit 0f6066a80dcaada6d2dbf5ac2f71d5960c03a41d Author: Andy Nonaka Date: Thu Sep 26 10:21:58 2024 -0700 Paper setup SSA/2 + MN + SSA/2 exec/reactDiff/inputs_paper_BPM_2d commit 985bcd04f8abf9e49cbb6f4a52e9cbf014102dba Author: Andy Nonaka Date: Thu Sep 26 09:34:59 2024 -0700 more efficient brute force multinomial src_reactDiff/MultinomialDiffusion.cpp commit a0104d9fe673cc8f6ade45ccec6446637b719385 Author: Andy Nonaka Date: Thu Sep 26 09:00:48 2024 -0700 MN diffusion doesn't work on GPU (need sum reductions still) src_reactDiff/MultinomialDiffusion.cpp commit 0252d1039109ae7ec73b502751e41d4d76b7298b Author: Andy Nonaka Date: Thu Sep 26 08:49:03 2024 -0700 brute force binomial/multinomial (slow but seems to work) src_reactDiff/MultinomialDiffusion.cpp src_reactDiff/reactDiff_functions.H commit 14a6ed7d3563e2dca4b77318df17c17f66168076 Author: Andy Nonaka Date: Thu Sep 26 08:10:34 2024 -0700 more precision in n_avg diagnostic src_reactDiff/main_driver.cpp commit f1bfeaadeed391b2d122108afaff6bb0e54529a0 Merge: 156baafb 9e0bcf52 Author: hjung <115668962+HyuntaeJung@users.noreply.github.com> Date: Wed Sep 25 18:40:11 2024 +0900 Merge pull request #170 from AMReX-FHD/surfchemtest MFsurfchem - change number density to pressure commit 9e0bcf5293de26f605c44fa96c550723d0fcbfd6 Merge: bcaba8c2 156baafb Author: HyuntaeJung Date: Wed Sep 25 17:57:23 2024 +0900 Merge branch 'main' into surfchemtest commit 156baafb44da592225bbbba13aa85c10a7219e5d Merge: 8b15a8e7 c7ab993d Author: Daniel Ladiges Date: Tue Sep 24 06:52:49 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 8b15a8e7f1ca12814e491b26c33870feefdef82c Author: Daniel Ladiges Date: Tue Sep 24 06:52:05 2024 -0700 continued work on phonon BC code exec/phononDSMC/test_inputs/input_test src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit bcaba8c2dce769fff22e46ebb6bff3f6338aec5c Merge: 2149649b c7ab993d Author: HyuntaeJung Date: Tue Sep 24 16:15:56 2024 +0900 Merge branch 'main' into surfchemtest commit 2149649b90772160fcea4d3c50b91945ac012e33 Author: HyuntaeJung Date: Tue Sep 24 16:12:27 2024 +0900 dens to pres in Nads src_MFsurfchem/MFsurfchem_functions.cpp commit 8aa88c75aab22796acd8984ebad406b432c2872c Author: HyuntaeJung Date: Tue Sep 24 16:05:57 2024 +0900 renname dens to pres src_MFsurfchem/MFsurfchem_functions.cpp commit c7ab993de78a9adfd10dcfc87b6d4794086967eb Author: Andy Nonaka Date: Mon Sep 23 12:57:15 2024 -0700 scale noise appropriately in reactdiff diffusion module src_reactDiff/StochasticNFluxdiv.cpp commit bfe97969bdc1345268328238c52fff2a1987e45f Author: HyuntaeJung Date: Sun Sep 22 19:22:08 2024 -0700 MFsurfchem - change number density to pressure exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_COAr_eq/params_COAr_eq.py src_MFsurfchem/MFsurfchem_functions.cpp commit 9367bde2407501ac2fe2fb9af9211843ab17bdc0 Merge: d87d8aa0 c84bee98 Author: Matt Blomquist Date: Thu Sep 19 07:46:34 2024 -0700 Merge pull request #169 from AMReX-FHD/feature/avg_n_diagnostic Create diagnostic for printing average n. commit c84bee988e816a96df0324e517d5aae09d23b364 Author: Andy Nonaka Date: Thu Sep 19 07:15:35 2024 -0700 small tweaks to output format src_reactDiff/main_driver.cpp commit 318bbec541ca72297b8110a535a0a2dcce1ccede Author: Matthew Blomquist Date: Wed Sep 18 17:41:02 2024 -0700 Print avg_n to file averageDensity.txt src_reactDiff/main_driver.cpp commit d87d8aa0a5321a1618f37365748572a2cc380d77 Merge: 74af2ad6 2a80ae49 Author: Daniel Ladiges Date: Wed Sep 18 07:22:46 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 74af2ad6e5fae781dd758bb958c42fd28144abf4 Author: Daniel Ladiges Date: Wed Sep 18 07:22:01 2024 -0700 Initial code for including stochastic bounary interscetions in phonon code exec/phononDSMC/main_driver.cpp src_geometry/paramPlane.H src_geometry/paramPlane.cpp commit 2a80ae49caad5c1f0fb5b29884367151fd849784 Merge: a63a03a2 2645e22e Author: Andy Nonaka Date: Tue Sep 17 18:32:06 2024 -0700 Merge pull request #168 from AMReX-FHD/reactDiff Multinomial commit 2645e22e806f3b94efb41235bb5c5ec9178e673e Author: Andy Nonaka Date: Tue Sep 17 18:26:57 2024 -0700 multinomial unsplit case src_reactDiff/AdvanceReactionDiffusion.cpp commit 9e722e70664e96c3feaf97995553772e875c0cad Author: Andy Nonaka Date: Tue Sep 17 18:22:26 2024 -0700 multinomial diffusion fix src_reactDiff/MultinomialDiffusion.cpp commit dc9a4e16c0f9c32628f1d4b27eb786b7e1adc0a1 Author: Andy Nonaka Date: Tue Sep 17 18:10:02 2024 -0700 MN diffusion bug fixes turn off initial fluctuations if initial_variance_mass=0. src_reactDiff/InitN.cpp src_reactDiff/MultinomialDiffusion.cpp commit 9221dbc437f414b940af2f30ebba4f81d82d3aac Author: Andy Nonaka Date: Tue Sep 17 17:58:35 2024 -0700 multinomial WIP src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/MultinomialDiffusion.cpp src_reactDiff/reactDiff_functions.H commit 4e52116dc1adcb22f47f7cec5183ab9929f4c78c Author: Andy Nonaka Date: Tue Sep 17 17:09:02 2024 -0700 start of MN diffusion - WIP, host only src_reactDiff/Make.package src_reactDiff/MultinomialDiffusion.cpp src_reactDiff/reactDiff_functions.H commit c33c0d8f1aa2b748d47c044d71515d1bc7bb7dad Merge: e390e7da a63a03a2 Author: Daniel Ladiges Date: Tue Sep 17 13:42:43 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit e390e7dae4a7b5f67a79397edb643c02c5a4e14b Author: Daniel Ladiges Date: Tue Sep 17 13:41:19 2024 -0700 syncing exec/DSMC/DsmcCollide.cpp exec/DSMC/inputs_conc exec/DSMC/main_driver.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit a63a03a276527943713661f33e424c2af065b462 Merge: 5a2ef5c6 3098d67f Author: Andy Nonaka Date: Tue Sep 17 12:42:06 2024 -0700 Merge pull request #167 from AMReX-FHD/bugfix/temporal_integrator_check Correct typo in comparator for temporal integrator. commit 3098d67fd232a34856f661181de49ee98b1b4854 Author: Matthew Blomquist Date: Tue Sep 17 11:57:44 2024 -0700 Correct type in comparator for temporal integrator. src_reactDiff/AdvanceTimestep.cpp commit 06da69039f13756a27e19e85bdb0dccfa37834a6 Merge: 86839a52 5a2ef5c6 Author: Ishan Srivastava Date: Sun Sep 15 15:42:11 2024 -0700 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 9d29d03efe514daa3161ccb14d5390455a3f1032 Merge: 86839a52 5a2ef5c6 Author: Ishan Srivastava Date: Sat Sep 14 02:27:12 2024 -0400 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 86839a52db37efc1f56ca89fe3678a85364b3945 Merge: 6c601cea 19dfab0f Author: Andy Nonaka Date: Wed Sep 11 17:03:05 2024 -0700 Merge branch 'main' into fhd_heffte commit 5a2ef5c6a99949f22dc4d0a485f402551025be7f Merge: 19dfab0f f1d65bf2 Author: Andy Nonaka Date: Wed Sep 11 17:01:42 2024 -0700 Merge pull request #145 from AMReX-FHD/disjoining Add disjoining pressure commit f1d65bf2e946ba23c6ba65a76912b818e0687c57 Merge: 8d4d230f 19dfab0f Author: Andy Nonaka Date: Wed Sep 11 17:01:14 2024 -0700 Merge branch 'main' into disjoining commit 19dfab0f61bd6413f1ddfa9f1a6c11c9fb370c4e Author: Andy Nonaka Date: Wed Sep 11 14:53:40 2024 -0700 fix abort logic src_reactDiff/AdvanceTimestep.cpp commit 6893c2c64709764e8a56e988c006f3cc1d81f001 Merge: e711dccb ddcf0bf9 Author: Andy Nonaka Date: Mon Sep 9 17:11:05 2024 -0700 Merge pull request #165 from AMReX-FHD/reactDiff ReactDiff commit ddcf0bf93fc1157d9afa9a220da14edcd48b1bc7 Author: Andy Nonaka Date: Mon Sep 9 09:32:16 2024 -0700 structure factor implemented exec/reactDiff/inputs_paper_BPM_2d exec/reactDiff/inputs_paper_Lemarchand_3d src_reactDiff/main_driver.cpp commit e95745cdbfbb6a4e77fdce9bd014a19dd1c0167f Author: Andy Nonaka Date: Mon Sep 9 09:15:09 2024 -0700 unsplit SSA schemes src_reactDiff/AdvanceReactionDiffusion.cpp commit fb97cf363b5e53ff09b46b73989267a53fe03f60 Author: Andy Nonaka Date: Mon Sep 9 08:05:45 2024 -0700 ssa bugfix src_chemistry/chemistry_functions.cpp commit 32f6395d7abc55e69d1575307a0e0466ca090c41 Author: Andy Nonaka Date: Mon Sep 9 08:02:18 2024 -0700 SSA attempt src_chemistry/chemistry_functions.cpp commit b249fcc6d50fff30317445ca99189df0348e9d06 Author: Andy Nonaka Date: Fri Sep 6 20:47:12 2024 -0700 match paper exec/reactDiff/inputs_paper_Lemarchand_3d commit eb8b966101a69ee919b7321c55f6be3350d8684c Author: Andy Nonaka Date: Fri Sep 6 19:57:12 2024 -0700 implicit midpoint (non-SSA) unsplit implement volume scaling in 3d exec/reactDiff/inputs_paper_BPM_2d exec/reactDiff/inputs_paper_Lemarchand_3d src_chemistry/chemistry_functions.cpp src_reactDiff/AdvanceReactionDiffusion.cpp src_reactDiff/InitN.cpp src_reactDiff/StochasticNFluxdiv.cpp commit 8ae192da59cb9c999794e7ddb6e6af74b7f2a011 Author: Andy Nonaka Date: Fri Sep 6 16:51:34 2024 -0700 explicit midpoint (non-SSA) written src_reactDiff/AdvanceReactionDiffusion.cpp commit b13a58ed7da7cdfdf8758b66bcb699c82738a62b Author: Andy Nonaka Date: Fri Sep 6 16:12:51 2024 -0700 split out GenerateStochasticFluxdivCorrector for split and unsplit algorithms to use src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/reactDiff_functions.H commit 93bc0703504913d4d5f3d9410226d230ffeaaeee Author: Andy Nonaka Date: Fri Sep 6 16:06:28 2024 -0700 implement midpoint_stoch_flux_type for split integrators src_reactDiff/AdvanceDiffusion.cpp commit 5aad36003ed3ca8bd659be4a330c7a4aa40205ba Author: Andy Nonaka Date: Wed Sep 4 20:38:42 2024 -0700 CLE and tau leaping implemented exec/reactDiff/inputs_paper_BPM_2d src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 8b6539db8ca8806ee7fe3aeefae74dc26d143951 Author: Andy Nonaka Date: Wed Sep 4 16:57:46 2024 -0700 add integer populations option exec/reactDiff/inputs_paper_BPM_2d src_reactDiff/InitN.cpp commit 4468fb4ad0c422b40933ffa25ac910a3a4bf8468 Author: Andy Nonaka Date: Wed Sep 4 16:37:03 2024 -0700 implicit diffusion module, incorporated crank-nicolson strang option note this does NOT solve in delta formulation like the previous code this is because I am coding up generalized physical bc support, which the previous code didn't have (only periodic) src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/ImplicitDiffusion.cpp src_reactDiff/Make.package src_reactDiff/reactDiff_functions.H commit a018d364861b105ea37f93d6ee0066ccd3564440 Author: Andy Nonaka Date: Wed Sep 4 11:57:46 2024 -0700 fine tuning of 3d setup. still needs work for larger time steps (implicit options) exec/reactDiff/inputs_paper_Lemarchand_3d src_reactDiff/main_driver.cpp commit c9076f3dff01fa49825cb0389841f742bc1afa89 Author: Andy Nonaka Date: Wed Sep 4 11:27:59 2024 -0700 paper setups exec/reactDiff/inputs_paper_BPM_2d exec/reactDiff/inputs_paper_Lemarchand_3d commit 67ea8d51e1a082ef8d2eaea096cbf3f5d97f4999 Author: Andy Nonaka Date: Thu Aug 29 09:54:30 2024 -0700 paper setup exec/reactDiff/inputs_paper_Lemarchand_3d commit ce9414bbf8023f3cd93282f26bb04e194785570b Author: Andy Nonaka Date: Thu Aug 29 09:41:37 2024 -0700 diffusive noise exec/reactDiff/inputs_paper_BPM_2d src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/InitN.cpp src_reactDiff/StochasticNFluxdiv.cpp commit 1c46839d828c28640fa2c649d3d61892ddf0b9c5 Author: Andy Nonaka Date: Wed Aug 28 19:30:13 2024 -0700 fix first order unsplit integrator src_reactDiff/AdvanceTimestep.cpp commit 1193194ed8de45a49ef3d14e87df584e2c8852ae Author: Andy Nonaka Date: Wed Aug 28 19:21:03 2024 -0700 unsplit integrator shell src_reactDiff/AdvanceReactionDiffusion.cpp src_reactDiff/AdvanceTimestep.cpp src_reactDiff/Make.package src_reactDiff/reactDiff_functions.H commit 17be21cf80c1628ca7f5c96bd84de0b06f32b541 Author: Andy Nonaka Date: Wed Aug 28 17:52:02 2024 -0700 stochastic diffusion work src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/DiffusiveNFluxdiv.cpp src_reactDiff/Make.package src_reactDiff/StochasticNFluxdiv.cpp src_reactDiff/reactDiff_functions.H commit efcd0816abc48ece89beb02aee1d29e75a18cb5a Author: Andy Nonaka Date: Wed Aug 28 15:14:44 2024 -0700 incorporate include_discrete_LMA_correction option src_chemistry/chemistry_functions.cpp src_reactDiff/main_driver.cpp commit 828da13e6cdaa0be0892b4e22d50ef5608a68b38 Author: Andy Nonaka Date: Wed Aug 28 12:54:54 2024 -0700 implemented both strang splitting schemes src_reactDiff/AdvanceTimestep.cpp commit 0b86555b514945a4722fb7e80eaa86354779e243 Author: Andy Nonaka Date: Wed Aug 28 12:26:06 2024 -0700 second-order split scheme chemistry src_chemistry/chemistry_functions.cpp src_reactDiff/AdvanceReaction.cpp commit 020e76e64dcd973004f7787dc3c3af8c7bd454c9 Author: Andy Nonaka Date: Wed Aug 28 11:48:40 2024 -0700 cleanup, added several reactDiff_diffusion_types exec/reactDiff/inputs_paper_BPM_2d src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/reactDiff_functions.H commit 09f563cd2dae30da61101fe79160ad0093633304 Author: Andy Nonaka Date: Tue Aug 27 16:54:04 2024 -0700 sign fix src_reactDiff/AdvanceReaction.cpp commit 786028eb0080a2a820247a66c5d39e79d5a2c730 Author: Andy Nonaka Date: Tue Aug 27 16:52:31 2024 -0700 chemistry loop bugfix src_chemistry/chemistry_functions.cpp commit a3d7bb2dd4023c18c61cd664cb58ee8a967014ff Author: Andy Nonaka Date: Tue Aug 27 08:49:25 2024 -0700 bugfix src_reactDiff/main_driver.cpp commit 5dcd786121a87d1ca902706431dbbd27d20a2e22 Author: Andy Nonaka Date: Tue Aug 27 08:22:26 2024 -0700 more debugging src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_reactDiff/AdvanceReaction.cpp commit 01194aaefd3f5b35b649825b9541711c1408086f Author: Andy Nonaka Date: Tue Aug 27 08:10:58 2024 -0700 starting the testing/debugging exec/reactDiff/inputs_paper_BPM_2d src_reactDiff/AdvanceDiffusion.cpp commit 1e9b93d43878c991aa0c7b162c0bfd91b56b5135 Author: Andy Nonaka Date: Mon Aug 26 20:45:17 2024 -0700 more chemistry routines src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 62f6d3dfe328eadc585b180c9fd1f6cec299b0c5 Author: Andy Nonaka Date: Mon Aug 26 20:43:58 2024 -0700 more chemistry routines src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 9c3c7fe4528ab49013fc105313389a6a05f654d6 Author: Andy Nonaka Date: Mon Aug 26 16:43:29 2024 -0700 outline for reactions exec/reactDiff/inputs_paper_BPM_2d src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/AdvanceReaction.cpp src_reactDiff/AdvanceTimestep.cpp src_reactDiff/Make.package src_reactDiff/reactDiff_functions.H commit ff6d8e15deec5fc43a918cb0e3b41161e2fe7bfb Author: Andy Nonaka Date: Mon Aug 26 09:57:32 2024 -0700 lots of more work exec/reactDiff/GNUmakefile exec/reactDiff/inputs_2d exec/reactDiff/inputs_3d exec/reactDiff/inputs_paper_BPM_2d exec/reactDiff/inputs_paper_Lemarchand_3d src_reactDiff/InitN.cpp commit 99f5b28d61bd97093511670de159d68be1eaecd2 Merge: 497c984b e711dccb Author: Andy Nonaka Date: Mon Aug 26 09:31:03 2024 -0700 Merge branch 'main' into reactDiff commit e711dccbc4c4500430be89c3ec5b616e4355bde7 Merge: cdda2e7b 99b752ff Author: Andy Nonaka Date: Mon Aug 26 09:30:49 2024 -0700 Merge pull request #166 from AMReX-FHD/remove_spec_bc_comp remove bc_spec_lo/hi commit 99b752ff37730be0b06e0caf9a1cf82affc83d2b Author: Andy Nonaka Date: Mon Aug 26 09:29:52 2024 -0700 remove bc_spec_lo/hi - not being used (bc_mass_lo/hi is implemented) exec/DSMC/inputs_conc exec/DSMC/inputs_conc_gpu src_common/common_functions.cpp src_common/common_namespace.H commit 497c984b50a313be1ead013fcca0fbc42e7f0f8d Author: Andy Nonaka Date: Mon Aug 26 09:28:18 2024 -0700 more work exec/reactDiff/inputs_2d exec/reactDiff/inputs_3d src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/InitN.cpp src_reactDiff/Make.package src_reactDiff/main_driver.cpp src_reactDiff/reactDiff_functions.H commit fcbe57b64e665d3b082b5fb28b7220f30b327586 Author: Andy Nonaka Date: Mon Aug 26 09:28:00 2024 -0700 more work src_reactDiff/InitN.cpp src_reactDiff/main_driver.cpp commit 80fd7e145b9abc6a28f451a845bea72431584c25 Author: John Bell Date: Mon Aug 26 09:01:18 2024 -0700 small tweaks for specific problems exec/multispec/Init.cpp exec/multispec/main_driver.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/ComputeMixtureProperties.cpp commit 3f4d752c0ef28cb22f2efa2ff3240c7b1836faeb Author: Andy Nonaka Date: Fri Aug 23 17:47:50 2024 -0700 build diffusion operator for explicit src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/reactDiff_functions.H src_reactDiff/reactDiff_namespace.H commit 9bf6d2c8a2fee122883639c8bd1c5136654a6253 Author: Andy Nonaka Date: Fri Aug 23 13:46:49 2024 -0700 diffusion outline exec/reactDiff/main_driver.cpp src_reactDiff/AdvanceDiffusion.cpp src_reactDiff/AdvanceTimestep.cpp src_reactDiff/Make.package src_reactDiff/reactDiff_functions.H commit 9576543ea7143033ad382c9c87ea33e6998e67fa Author: Andy Nonaka Date: Fri Aug 23 12:34:17 2024 -0700 setup preliminaries exec/reactDiff/inputs_2d exec/reactDiff/inputs_3d exec/reactDiff/main_driver.cpp src_reactDiff/Make.package src_reactDiff/WritePlotFile.cpp src_reactDiff/reactDiff_functions.H src_reactDiff/reactDiff_functions.cpp src_reactDiff/reactDiff_namespace.H commit cdda2e7b8e37de268f4387ca7811b9d9b9e23175 Merge: 0ad0292e b7a9ce4a Author: jbb Date: Thu Aug 22 15:54:10 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 0ad0292e68932916938eff0500f4b228db97c421 Author: jbb Date: Thu Aug 22 15:53:43 2024 -0700 added ensemble stuff exec/_1d_dk_hybrid/_ensemble/driver.f exec/_1d_dk_hybrid/_ensemble/flux.f exec/_1d_dk_hybrid/_ensemble/particles.f exec/_1d_dk_hybrid/_ensemble/stats.c commit b381c607df07fe8fc452955c87c1c067500dda09 Author: jbb Date: Thu Aug 22 15:51:04 2024 -0700 added plot of level 1 src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/mykernel.H commit 1e2cc296e9b7e185181a397bb62624f8d8e2072d Author: Andy Nonaka Date: Thu Aug 22 13:14:56 2024 -0700 reactDiff namespace src_reactDiff/reactDiff_functions.cpp src_reactDiff/reactDiff_namespace.H commit 92cad719e5d9671a373c7fdc04810d47f4c6c88e Author: Andy Nonaka Date: Thu Aug 22 10:43:47 2024 -0700 namelist exec/reactDiff/GNUmakefile src_reactDiff/Make.package src_reactDiff/reactDiff_functions.H src_reactDiff/reactDiff_functions.cpp src_reactDiff/reactDiff_namespace.H commit 4e59a7a3b1219316f648c44498ca6a85165b1ba9 Author: Andy Nonaka Date: Wed Aug 21 20:20:32 2024 -0700 chemistry functions src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit c8befe2eaf452b0a7eb8d59c364edbda25560e5f Author: Andy Nonaka Date: Wed Aug 21 15:58:50 2024 -0700 build chemistry namespace src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H commit 1533f0fa29bc17591b9d36266cc8d3ae752218f8 Merge: fba95df4 b7a9ce4a Author: Andy Nonaka Date: Wed Aug 21 15:46:08 2024 -0700 Merge branch 'main' into reactDiff commit b7a9ce4addad6876751f69671d8dcf1ab61e2de8 Merge: 13cf36c4 fca4acdc Author: Andy Nonaka Date: Wed Aug 21 15:45:51 2024 -0700 Merge pull request #164 from AMReX-FHD/cleanup_chemistry Prep Chemistry for new LM and reactDiff routines commit fca4acdcaaf86e7b3a66ffc4e68bab9a18e66f65 Author: Andy Nonaka Date: Wed Aug 21 15:41:08 2024 -0700 prep code for rewrite of new chemistry routines for the low Mach and reactDiff codes exec/chemistry_testing/chemistry_testing_functions.H exec/chemistry_testing/chemistry_testing_functions.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_compressible/timeStep.cpp src_compressible_stag/timeStepStag.cpp commit 13cf36c4fef5010f767e055ff1e203b30821fb05 Merge: 5e11529e bdbae1a8 Author: Andy Nonaka Date: Wed Aug 21 14:43:06 2024 -0700 Merge pull request #163 from AMReX-FHD/cleanup_chemistry More Chemistry Cleanup commit bdbae1a8beba8084a88100a3ef8a9f62edb75c5e Author: Andy Nonaka Date: Wed Aug 21 14:21:35 2024 -0700 spacing exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile exec/compressible_stag_mui/GNUmakefile commit f2433ed6c74fbdd3be9070cf437523520ee34900 Author: Andy Nonaka Date: Wed Aug 21 14:19:14 2024 -0700 make MAX_REAC a compile-time option in the GNUmakefile instead of hard-coded in chemistry_namespace error checking to make sure MAX_REAC and MAX_SPEC are larger than nreaction and nspecies exec/chemistry_testing/GNUmakefile exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile exec/compressible_stag_mui/GNUmakefile src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H src_common/common_functions.cpp commit 5e11529e838c2eaba320ac809f0d8ef6b6a02a8f Merge: 6e7fd538 d802798d Author: Andy Nonaka Date: Wed Aug 21 13:50:05 2024 -0700 Merge pull request #162 from AMReX-FHD/cleanup_chemistry Cleanup src_chemistry commit d802798da1bf2812c27bfc0787ee7814fc812a66 Author: Andy Nonaka Date: Wed Aug 21 12:54:09 2024 -0700 clean up src_chemistry by moving chemistry-testing(only) specific code into chemistry_testing exec/chemistry_testing/Make.package exec/chemistry_testing/chemistry_testing_functions.H exec/chemistry_testing/chemistry_testing_functions.cpp exec/chemistry_testing/main.cpp exec/chemistry_testing/myfunc.H src_chemistry/CLE_EM.cpp src_chemistry/CLE_RK3.cpp src_chemistry/Make.package src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit fba95df4861669b45dbe6cf1066b0bb09bb72d5c Author: Andy Nonaka Date: Wed Aug 21 12:12:08 2024 -0700 reactDiff shell exec/reactDiff/GNUmakefile exec/reactDiff/main_driver.cpp commit 6e7fd538c82096b148aa70c0643c0ae7464d0ec1 Merge: 39a93b30 16d8018b Author: Andy Nonaka Date: Mon Aug 19 16:04:18 2024 -0700 Merge pull request #161 from AMReX-FHD/avogadro Avogadro Number commit 16d8018be285ae5ef182d8feab0dec0183a2db94 Author: Andy Nonaka Date: Mon Aug 19 16:01:39 2024 -0700 address a long-standing issue where sometimes its preferable to specify the avogadro number instead of Runiv. If avogadro is supplied, then Runiv is set to avogadro * k_b Default behavior is preserved as all codes presently set Runiv The code will abort if you try to specify both. exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.cpp src_common/common_functions.cpp src_common/common_namespace.H src_compressible/compressible_functions.cpp src_compressible/main_driver.cpp src_compressible_stag/reservoirStag.cpp commit 8ea6df2d41eff69d9b96c83e4b306e5f8e2833a6 Merge: d85bf697 39a93b30 Author: jbb Date: Thu Aug 15 14:24:37 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 31e6022168058f9f2c888d536ea2a078af39c619 Author: jbb Date: Thu Aug 15 14:00:01 2024 -0700 better meniscus initialization exec/multispec/Init.cpp commit 39a93b30fb4c4265b492b1606619ef2d3bc4aadf Author: Andy Nonaka Date: Wed Aug 14 12:37:32 2024 -0700 simplify struct fact class restart exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 17ed8fab8fff0e998df939d447dc62f28733aece Merge: a09bf827 a1129a5b Author: Andy Nonaka Date: Tue Aug 13 08:53:02 2024 -0700 Merge pull request #160 from AMReX-FHD/SF_restart Structure factor restart commit a1129a5bd33e01d92838be8e041ef85d64def28b Author: Andy Nonaka Date: Tue Aug 13 08:35:15 2024 -0700 fix selected pair option for structure factor restart exec/hydro/main_driver.cpp commit 66015ecc3094365798fb9f9307bdcdcf73dd80ab Author: Andy Nonaka Date: Tue Aug 13 08:18:19 2024 -0700 structure factor restart - seems to be working; further testing... exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 29b052088cbda188b63ea959c7ada8859abe3af6 Author: Andy Nonaka Date: Mon Aug 12 17:38:14 2024 -0700 read checkpoint WIP src_analysis/StructFact.H src_analysis/StructFact.cpp commit 4e16e62c44e049ab17b777de80aa51117806f1be Author: Andy Nonaka Date: Mon Aug 12 17:27:34 2024 -0700 checkpoint write src_analysis/StructFact.H src_analysis/StructFact.cpp commit 61abbe05a3a039556660aea196a3f4aff27f7572 Author: Andy Nonaka Date: Mon Aug 12 17:04:13 2024 -0700 begin work on structure factor restart exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit a09bf8279e78575ff645ccc10859da444a694840 Merge: 2d19e101 31d16725 Author: Andy Nonaka Date: Mon Aug 12 11:37:41 2024 -0700 Merge pull request #159 from AMReX-FHD/flux_index_bug Flux Index Bugs commit 2d19e10183c448e1fd3b935127c4004f5862de79 Author: Changho Kim Date: Mon Aug 12 04:57:01 2024 -0700 exec/compressible_stag/test_NO2_dimerization_neq_wall: routines for checking the entropy flux / production balance added to the noneq steady-state NO2 dimerization example exec/compressible_stag/test_NO2_dimerization_neq_wall/diff.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/entropy_check.py exec/compressible_stag/test_NO2_dimerization_neq_wall/entropy_check_funcs.py exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg3.sh commit 31d16725673b4e6af5468fc915deeba53dfdb5a1 Author: Andy Nonaka Date: Thu Aug 8 16:21:28 2024 -0700 Update src_compressible_stag/fluxStag.cpp src_compressible_stag/fluxStag.cpp commit e74cb4c4690eac013a1f7e0a0c8af776f83c2ef9 Author: Andy Nonaka Date: Thu Aug 8 08:17:59 2024 -0700 fixed a bug in the z ChiX stencil fixed an error in the z heat flux indexing which doesn't ultimately affect the simulation since it's summed into the same location in memory in the end anyway regression tests will likely change when this is merged src_compressible_stag/fluxStag.cpp commit 2c51354f8be355d343dbfcf04158fa29f0f837b8 Merge: 47ca675a 375ecb6b Author: Andy Nonaka Date: Wed Aug 7 15:28:16 2024 -0700 Merge pull request #158 from AMReX-FHD/surfchemtest Strang splitting scheme implementation commit 47ca675a2e8961c8e23e9234821d0c82b0e948b2 Author: quinton Date: Wed Aug 7 08:31:55 2024 -0700 particle_viewer displays plot and distance between specified points exec/immersed_boundary/cell_body/Particle_viewer.ipynb commit 375ecb6b81d9c3483ff4f597a8e36d2cb4dc9a67 Merge: 9869e9ff 542ae0ea Author: HyuntaeJung Date: Fri Aug 2 16:01:25 2024 +0900 Merge branch 'surfchemtest' of https://github.com/AMReX-FHD/FHDeX into surfchemtest commit 9869e9ff36381315090797223bbb43f22f2f16ea Author: HyuntaeJung Date: Fri Aug 2 16:01:07 2024 +0900 revised; replaced accessor function with splitting_MFsurfchem src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible_stag/main_driver.cpp commit 542ae0eaac1bd425bb7eb31b6781a142d0b6d111 Author: Andy Nonaka Date: Thu Aug 1 19:42:41 2024 -0700 since splitting_MFsurfchem is in the MFsurfchem namespace there is no need to use an accessor function; just reference splitting_MFsurfchem directly in other parts of the code src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible_stag/main_driver.cpp commit 8c22dff945e8f356647c752ed7f00ab0c961a290 Merge: 23b9ba4e 5992e423 Author: Andy Nonaka Date: Thu Aug 1 19:37:31 2024 -0700 Merge branch 'main' into surfchemtest commit 5992e423a944d9173a7430c7dc7087cd2b030625 Author: Gang Xu Date: Thu Aug 1 13:41:26 2024 -0700 updated all related inputs for bigger domain exec/cellbdytest_new/sphere_python/bonds.csv exec/cellbdytest_new/sphere_python/particles.dat exec/immersed_boundary/cell_body/inputs_coupling commit 5e219bdb2aa9f2ce16d43027f11d96e353ce33ff Merge: dcbafbb6 bfb1cf58 Author: Gang Xu Date: Tue Jul 30 16:12:39 2024 -0700 change to smaller 8um cell body Merge branch 'main' of github.com:AMReX-FHD/FHDeX commit dcbafbb6c896a7f65dfe9d4191d638c6d99f34d5 Author: Gang Xu Date: Tue Jul 30 16:11:40 2024 -0700 smaller 8um cell body exec/cellbdytest_new/sphere_python/chlamy_gen.py exec/immersed_boundary/cell_body/bonds.csv exec/immersed_boundary/cell_body/inputs_coupling exec/immersed_boundary/cell_body/particles.dat commit bfb1cf588f97e0acd837cd8c34363d2c900a59d6 Author: Johannes Blaschke Date: Tue Jul 30 11:01:22 2024 -0700 wip gpu-ize ibmarkers exec/immersed_boundary/cell_body/GNUmakefile exec/immersed_boundary/cell_body/Make.package src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 23b9ba4eadd215205154eae1f0f9c6ddedae4084 Merge: 2f201e8e 3c653450 Author: HyuntaeJung Date: Tue Jul 30 11:14:04 2024 +0900 Merge branch 'main' into surfchemtest commit 3c653450de3a1ffe709a0fc1b791aab93a9f62a7 Author: quinton Date: Wed Jul 24 20:33:04 2024 -0700 Taylor_video displays pressure,vectors,and particles exec/immersed_boundary/taylor_line/Taylor_video.ipynb commit b55d5a9e92c8473daafea941c3af4ddddd926086 Author: Gang Xu Date: Tue Jul 23 16:18:54 2024 -0700 corrected how to update the flagellar orientation exec/immersed_boundary/cell_body/ib_md.cpp commit 904e96007c429c00beabcd103b16b02253458cb8 Author: quinton Date: Mon Jul 22 10:46:50 2024 -0700 added vectors and colorbar exec/immersed_boundary/taylor_line/PresRend_vid.ipynb commit 2f201e8ea4a89325d10a7c7b4b0363f56eeb87fb Merge: ee20f273 277e0685 Author: HyuntaeJung Date: Mon Jul 22 21:09:08 2024 +0900 Merge branch 'main' into surfchemtest commit 277e06859b8c004d8cde21198a72501e3d412a5e Author: Gang Xu Date: Fri Jul 19 15:14:57 2024 -0700 minor update in ib_md exec/immersed_boundary/cell_body/ib_md.cpp commit fdd634a2b1cf36e518aaac6a024f094f539e68a2 Author: Gang Xu Date: Fri Jul 19 14:03:00 2024 -0700 adjusted cell body particle and bonds data exec/cellbdytest_new/Checkpoint.cpp exec/cellbdytest_new/GNUmakefile exec/cellbdytest_new/INS_functions.H exec/cellbdytest_new/Make.package exec/cellbdytest_new/Make_debug.package exec/cellbdytest_new/WritePlotFile.cpp exec/cellbdytest_new/WritePlotFileHydro.cpp exec/cellbdytest_new/defaultinputs/bonds.csv exec/cellbdytest_new/defaultinputs/inputs_membrane_kuhn exec/cellbdytest_new/defaultinputs/particles.dat exec/cellbdytest_new/delPlots exec/cellbdytest_new/logruns exec/cellbdytest_new/main_driver.cpp exec/cellbdytest_new/particleGen.cpp exec/cellbdytest_new/sphere_python/.chlamy_gen.py.swp exec/cellbdytest_new/sphere_python/chlamy_gen.py exec/cellbdytest_new/sphere_python/point_map.ipynb exec/cellbdytest_new/sphere_python/tutorial_chlamy_gen exec/cellbdytest_new/testinputs/inputs_body exec/cellbdytest_new/testinputs/readme exec/cellbdytest_new/wetRad_KernelES/wetRad_w3.dat exec/cellbdytest_new/wetRad_KernelES/wetRad_w4.dat exec/cellbdytest_new/wetRad_KernelES/wetRad_w5.dat exec/cellbdytest_new/wetRad_KernelES/wetRad_w6.dat exec/cellbdytest_new/wetRad_KernelES/wetRad_w7.dat exec/immersed_boundary/cell_body/bonds.csv exec/immersed_boundary/cell_body/particles.dat commit a4ecdf461c4e33d07a4f94bcafe85e0439683f23 Author: Gang Xu Date: Fri Jul 19 13:29:33 2024 -0700 updated euqil_pos function to allow flagellum rotation exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/inputs_coupling exec/immersed_boundary/cell_body/main_driver.H exec/immersed_boundary/cell_body/main_driver.cpp commit 89a565e34fae66675c4aa054e3e51d8d8169cca4 Author: Gang Xu Date: Thu Jul 18 16:32:08 2024 -0700 added coupling of anchor markers on flagellum with cell body exec/immersed_boundary/cell_body/advance_stokes.cpp exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/main_driver.H commit 5879319f79390083aa094d3d59516c82b47d0f0e Merge: 6152f671 3cbc7260 Author: Gang Xu Date: Thu Jul 18 15:02:04 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX commit 6152f671e69258ed1335fa30a1c7c01f80ea741b Author: Gang Xu Date: Thu Jul 18 11:22:39 2024 -0700 minor update to show bond pairs during force calculations exec/immersed_boundary/cell_body/ib_md.cpp commit 3cbc7260ca8cee7191895eb7cee936bba5b26bd5 Merge: f295a2ae 084fadf4 Author: quinton Date: Wed Jul 17 15:20:06 2024 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX commit f295a2ae1d2ab82e9732959eea04539a46810f49 Author: quinton Date: Wed Jul 17 14:51:32 2024 -0700 notebook for generating a video from plts exec/immersed_boundary/taylor_line/PresRend_vid.ipynb commit 084fadf4d6af37df6c6e4e098d03178ce8d18621 Author: Gang Xu Date: Wed Jul 17 14:44:49 2024 -0700 minor changes. running. exec/immersed_boundary/cell_body/inputs_coupling exec/immersed_boundary/cell_body/main_driver.cpp commit f2a514aacffd6293febde8a850e7ef235a0adc74 Author: Gang Xu Date: Wed Jul 17 13:51:56 2024 -0700 correct some minor errors exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/inputs_coupling commit 803dd097a22542782ae1089d642d15d5f1cb1cd6 Author: Gang Xu Date: Wed Jul 17 13:25:15 2024 -0700 passing bond maps is working exec/immersed_boundary/cell_body/advance_stokes.cpp exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/main_driver.H exec/immersed_boundary/cell_body/main_driver.cpp commit 66eeaca59a836bf2f27a403e5288aee5b9e0ce76 Author: Gang Xu Date: Tue Jul 16 17:07:56 2024 -0700 correct body particle force calculations exec/immersed_boundary/cell_body/ib_md.cpp commit 98bb710fd76d9c6d1b9eeb98159ecf6530581dd7 Author: Gang Xu Date: Tue Jul 16 14:22:08 2024 -0700 added codes for updating forces among cell body particles exec/immersed_boundary/cell_body/advance_stokes.cpp exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/inputs_coupling exec/immersed_boundary/cell_body/main_driver.H exec/immersed_boundary/cell_body/main_driver.cpp commit 45399d74b67a148f03695c0746e14c15a81ef45a Author: Johannes Blaschke Date: Mon Jul 15 15:57:19 2024 -0700 wip bonds forces exec/immersed_boundary/cell_body/main_driver.cpp exec/immersed_boundary/flagellum/ib_md.cpp commit d0b65cc91e1a678320ebc60b71ea23f374d840e6 Author: Johannes Blaschke Date: Mon Jul 15 14:28:03 2024 -0700 wip work on reading particle data exec/immersed_boundary/cell_body/bonds.csv exec/immersed_boundary/cell_body/main_driver.cpp exec/immersed_boundary/cell_body/particles.dat commit f2ccb63a6bc71919f1bdb0593ef7320e4d5a0c4e Author: Johannes Blaschke Date: Mon Jul 15 13:51:01 2024 -0700 start work on cell body exec/immersed_boundary/cell_body/Explore Data MP.ipynb exec/immersed_boundary/cell_body/Explore Data.ipynb exec/immersed_boundary/cell_body/GNUmakefile exec/immersed_boundary/cell_body/Make.package exec/immersed_boundary/cell_body/Render Frames.ipynb exec/immersed_boundary/cell_body/WritePlotFile.cpp exec/immersed_boundary/cell_body/advance_CN.cpp exec/immersed_boundary/cell_body/advance_midpoint.cpp exec/immersed_boundary/cell_body/advance_stokes.cpp exec/immersed_boundary/cell_body/compute_convfact_2.sh exec/immersed_boundary/cell_body/ib_md.cpp exec/immersed_boundary/cell_body/init_funcs.F90 exec/immersed_boundary/cell_body/init_s_funcs.F90 exec/immersed_boundary/cell_body/inputs_2d exec/immersed_boundary/cell_body/inputs_3d exec/immersed_boundary/cell_body/inputs_3d_test exec/immersed_boundary/cell_body/inputs_3d_test.scaled exec/immersed_boundary/cell_body/inputs_3d_test.scaled.highres exec/immersed_boundary/cell_body/inputs_chlamy exec/immersed_boundary/cell_body/inputs_chlamy.buddy exec/immersed_boundary/cell_body/inputs_chlamy.cori exec/immersed_boundary/cell_body/inputs_chlamy.highres exec/immersed_boundary/cell_body/inputs_chlamy.highres-thin exec/immersed_boundary/cell_body/inputs_chlamy.large exec/immersed_boundary/cell_body/inputs_chlamy.large-thin exec/immersed_boundary/cell_body/inputs_chlamy_data exec/immersed_boundary/cell_body/inputs_incomp_equil_fluct_2d exec/immersed_boundary/cell_body/inputs_incomp_equil_fluct_3d exec/immersed_boundary/cell_body/inputs_regression_chlamy exec/immersed_boundary/cell_body/inputs_taylor exec/immersed_boundary/cell_body/lazycsv.H exec/immersed_boundary/cell_body/main_driver.H exec/immersed_boundary/cell_body/main_driver.cpp exec/immersed_boundary/cell_body/main_driver_F.H exec/immersed_boundary/cell_body/run_conv_tests_2.sh commit ebe031e0d1972d6bee3be8ece9dbfd82ddf952f6 Author: Johannes Blaschke Date: Mon Jul 15 13:47:54 2024 -0700 remove spurious import exec/immersed_boundary/flagellum/main_driver.cpp commit a2ee3af7e816bdfb5fa9db5b201c6ef62de4addd Author: Johannes Blaschke Date: Mon Jul 15 13:46:22 2024 -0700 cleanup exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit ee20f273f30f61927101b2966f35af02d5b0b53b Author: HyuntaeJung Date: Wed Jul 10 15:12:48 2024 +0900 Strang splitting for MFsurfchem (if n_ads_spec>0) src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/main_driver.cpp commit bcbd53198eff3df57da7de22067b00d404b54f8c Author: HyuntaeJung Date: Wed Jul 10 14:52:19 2024 +0900 test_MFsurfchem_COAr_eq: modified equilibrium example exec/compressible_stag/test_MFsurfchem_COAr_eq/README exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.py exec/compressible_stag/test_MFsurfchem_COAr_eq/diff.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_COAr_eq/job_script.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/mass_cons.py exec/compressible_stag/test_MFsurfchem_COAr_eq/params_COAr_eq.py exec/compressible_stag/test_MFsurfchem_COAr_eq/params_CO_Ar_thermochem.py exec/compressible_stag/test_MFsurfchem_COAr_eq/run.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/surfcoVar.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/surfcoVar.py exec/compressible_stag/test_MFsurfchem_COAr_eq/surfcoVar.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/theta_eq.py exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg_rhoY1mean.plt commit ba3ac0e5071f4042d67bbddd25d31bcd043068b8 Author: Changho Kim Date: Tue Jun 18 11:20:52 2024 -0700 src_compressible_stag/statsStag.cpp: for Tmean now using the actual time averaging rather than GetTemperature() src_compressible_stag/statsStag.cpp commit 87b1ce9194a409e3080d707ed2f35b223f875bb6 Author: Changho Kim Date: Tue Jun 11 05:19:45 2024 -0700 src_chemistry/chemistry_functions.cpp: reaction_type=0 (deterministic chemistry) is allowed for compute_chemistry_source_CLE src_chemistry/chemistry_functions.cpp commit 09284b94c3d24cfadabb6bf9abb64a6327f50532 Author: Changho Kim Date: Tue Jun 11 03:52:59 2024 -0700 test_NO2_dimerization_neq_wall: new steady-state example setup exec/compressible_stag/test_NO2_dimerization_neq_wall/README exec/compressible_stag/test_NO2_dimerization_neq_wall/clean.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/diff.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/inputs_NO2_dimerization_neq_wall exec/compressible_stag/test_NO2_dimerization_neq_wall/job_script.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/submit_job.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg.plt exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg.sh exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg2.plt exec/compressible_stag/test_NO2_dimerization_neq_wall/zavg2.sh commit a6a633ae133ae2dfcedde23a25b308c034f6bc4d Author: Changho Kim Date: Mon Jun 10 05:52:41 2024 -0700 test_NO2_dimerization_neq_bulk: clean-up exec/compressible_stag/test_NO2_dimerization_neq/diff.sh exec/compressible_stag/test_NO2_dimerization_neq_bulk/README exec/compressible_stag/test_NO2_dimerization_neq_bulk/avg.sh exec/compressible_stag/test_NO2_dimerization_neq_bulk/clean.sh exec/compressible_stag/test_NO2_dimerization_neq_bulk/diff.sh exec/compressible_stag/test_NO2_dimerization_neq_bulk/inputs_NO2_dimerization_neq_bulk0 exec/compressible_stag/test_NO2_dimerization_neq_bulk/inputs_NO2_dimerization_neq_bulk1 exec/compressible_stag/test_NO2_dimerization_neq_bulk/job_script.sh exec/compressible_stag/test_NO2_dimerization_neq_bulk/submit_job.sh commit 4aa299282ddaacaaf26b81b0c41825eeba130d7d Author: Changho Kim Date: Mon Jun 10 03:40:26 2024 -0700 test_NO2_dimerization_neq: clean-up exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq0 exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq1 exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq exec/compressible_stag/test_NO2_updated_input_files/inputs_NO2_N2O4_eq_SF commit 9d44597906149996603924f56ad06c1c5d191fad Merge: b134b60c 79e16dff Author: Daniel Ladiges Date: Thu Jun 6 15:09:06 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b134b60c6f7a4f28b847b899957e8b12f0309e7d Author: Daniel Ladiges Date: Thu Jun 6 15:08:37 2024 -0700 added in phonon detector subdir exec/phononDSMC/GNUmakefile exec/phononDetector/Checkpoint.H exec/phononDetector/Checkpoint.cpp exec/phononDetector/DsmcCollide.cpp exec/phononDetector/GNUmakefile exec/phononDetector/LocalFunctions.H exec/phononDetector/Make.package exec/phononDetector/delPlots exec/phononDetector/ex_main_driver.cpp exec/phononDetector/externalF.cpp exec/phononDetector/globalVars.cpp exec/phononDetector/main_driver.cpp exec/phononDetector/paramPlane_array_aligned_sideSink.ipynb exec/phononDetector/paramplanes.dat exec/phononDetector/particleGen.cpp exec/phononDetector/py/paramPlane.ipynb exec/phononDetector/py/paramPlane.nb exec/phononDetector/stats.cpp exec/phononDetector/test_inputs/input_detector exec/phononDetector/test_inputs/input_test exec/phononDetector/test_inputs/input_test.save exec/phononDetector/totalparts exec/phononDetector/updateTimeStep.cpp exec/phononDetector/writePlotFile.cpp src_common/common_functions.cpp src_common/common_namespace.H src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.H commit 79e16dffde56f8b0d2fc89ba512f1e1e0af966d6 Merge: 82c4e647 9dcceed0 Author: hjung <115668962+HyuntaeJung@users.noreply.github.com> Date: Fri May 31 09:59:50 2024 +0900 Merge pull request #157 from AMReX-FHD/surfchemtest MFsurfchem parameter and plot surface covariances commit 9dcceed00722312309f5c23b0de9b2c90f8bc415 Merge: 32e404d8 82c4e647 Author: Andy Nonaka Date: Wed May 29 16:25:59 2024 -0700 Merge branch 'main' into surfchemtest commit 82c4e647ddae57086fc7de414d3e57046f26bcba Author: Andy Nonaka Date: Wed May 29 11:21:59 2024 -0700 2d compilation fix src_common/InterpCoarsen.cpp commit 32e404d891dc7f13a819b46c35f176a236766dd4 Merge: a6ac210e c8102fa8 Author: HyuntaeJung Date: Wed May 29 15:06:21 2024 +0900 Merge branch 'main' into surfchemtest commit c8102fa848b60edb33f66bdb425c035f9abe343e Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Tue May 28 17:42:17 2024 -0700 Kinetic parameters (#156) * added alpha_param and beta_param in input files * FHDeX/src_chemistry/chemistry_functions.cpp added queryarr routine to get alpha_param and beta_param from input files * src_chemistry: updating formula for reaction rates with alpha_param and beta_param * updated inputs file to include values of alpha_param and beta_param and new rate constants * updated input files for non equilibrium case for NO2 dimerization * fixed value of rate constants * fixed values of rate constants and updated comments in input files for non-equilibrium case * Now src_chemistry/chemistry_functions.cpp is consistent with the formulation in the paper. More specifically, 1. rate constants are now based on molar concentrations. (previously, partial pressure based) 2. reaction rates are now (molar concentration)/(time). (previously, number of reactions/time) * test_NO2_dimerization_neq: simple noneq simulation example directory updated * exec/compressible_stag/test_NO2_dimerization_eq: equilibrium simulation parameters updated, variance analysis along z added --------- Co-authored-by: Matteo Polimeno Co-authored-by: Matteo Polimeno Co-authored-by: Changho Kim Co-authored-by: Andy Nonaka exec/compressible_stag/test_NO2_dimerization_eq/README exec/compressible_stag/test_NO2_dimerization_eq/clean.sh exec/compressible_stag/test_NO2_dimerization_eq/diff.sh exec/compressible_stag/test_NO2_dimerization_eq/inputs_NO2_dimerization_eq exec/compressible_stag/test_NO2_dimerization_eq/job_script.sh exec/compressible_stag/test_NO2_dimerization_eq/params_NO2_dimerization_eq.py exec/compressible_stag/test_NO2_dimerization_eq/zavg.plt exec/compressible_stag/test_NO2_dimerization_eq/zavg.sh exec/compressible_stag/test_NO2_dimerization_neq/README exec/compressible_stag/test_NO2_dimerization_neq/diff.sh exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq0 exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq1 exec/compressible_stag/test_NO2_dimerization_neq/job_script.sh exec/compressible_stag/test_NO2_dimerization_neq/params_NO2_dimerization_rate_const.py exec/compressible_stag/test_NO2_dimerization_neq_kinetic_params/inputs_NO2_dimerization_neq exec/compressible_stag/test_NO2_updated_input_files/inputs_NO2_N2O4_eq_SF src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H commit 64d10fae3aa978b74833893a52d1ca9ed0ab107b Author: Andy Nonaka Date: Tue May 28 17:25:01 2024 -0700 remove #include src_common/common_functions.H commit b866cdc0975e84794c04fd84086f55d0ba05b861 Author: Daniel Ladiges Date: Tue May 28 16:44:22 2024 -0700 Fixed missing file src_common/InterpCoarsen.cpp commit d85bf697295c7a550c6853cf172e9c2396d77384 Author: jbb Date: Tue May 28 11:55:09 2024 -0700 removed reference to nonexistent interpolation routine src_common/Make.package commit 72f1204205465763e3e8633668060a13d59a298f Merge: a618f7ed 7986cf9f Author: Daniel Ladiges Date: Tue May 28 06:42:05 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit a618f7edfa618379423a11bcdcb03058277c1ac2 Author: Daniel Ladiges Date: Tue May 28 06:40:56 2024 -0700 Brining files for phonon black hole detector into main exec/DSMC/inputs_conc exec/DSMC/main_driver.cpp exec/multispec/GNUmakefile exec/multispec/Init.cpp exec/multispec/WritePlotFile.cpp exec/multispec/inputs_droplet_3d_mod src_common/Debug.cpp src_common/Make.package src_common/common_functions.H src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit a6ac210ed5ee516e6eee96979544bebae6036788 Author: HyuntaeJung Date: Mon May 27 17:42:04 2024 +0900 MFsurfchem - k_beta (temperature dependency) and e_beta (energy update) compressible_stag_mui - plot for surface covariance src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 9ef88362600195c8e9be5e90680a90491a19d31c Merge: 09cada4e 7986cf9f Author: HyuntaeJung Date: Mon May 27 16:45:42 2024 +0900 Merge branch 'main' into surfchemtest commit 09cada4e692d694b808cc0b4ed4e5678e3907b5a Author: HyuntaeJung Date: Mon May 27 16:04:13 2024 +0900 Revert "MFsurfchem - k_beta (temperature dependency) and e_beta (energy update)" This reverts commit 80c6025b4737f3ab7b684cd77f6ff97a57a82ed9. src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 7986cf9fd94da0ea7a26d1c27e602096d21e6696 Author: Ann Almgren Date: Sun May 26 12:51:36 2024 -0700 fix to regridding src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/myfunc.cpp commit bc70d383d3589a88f11cb3fcfb2e714d0d7e0bd8 Author: jbb Date: Thu May 23 11:56:47 2024 -0700 tryign to average down after reflux exec/dean_kow/multilevel/inputs_bug1 src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/mykernel.H commit 0382c06c701ef17cb1b8a49b3dc395379ccc8efd Merge: 5c8cf2a8 dd4d5432 Author: jbb Date: Wed May 22 10:17:45 2024 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 80c6025b4737f3ab7b684cd77f6ff97a57a82ed9 Author: HyuntaeJung Date: Wed May 22 14:31:20 2024 +0900 MFsurfchem - k_beta (temperature dependency) and e_beta (energy update) compressible_stag_mui - plot for surface covariance src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit dd4d5432876a45aeb1e311ed01ae260e8f6a5b1c Author: Andrew Myers Date: Tue May 21 13:33:53 2024 -0700 Some fixes for regridding and refluxing particles src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.cpp commit 90ce8403c3916759cd225b8f21ca673c69054b55 Author: John Bell Date: Tue May 21 12:38:23 2024 -0700 modified contact angle boundary condition src_multispec/MultiFabPhysBC_FH.cpp src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 91a46eb410de44193ad9ad9b256e195d759511ff Merge: df9bc6da df5feca8 Author: Andy Nonaka Date: Tue Apr 9 15:52:49 2024 -0700 Merge pull request #155 from WeiqunZhang/flory_huggins_diag Update reduction in John's diagnostics commit df5feca851f9b2a9beb78ef9dab0f54d7feb064e Author: Weiqun Zhang Date: Tue Apr 9 15:46:50 2024 -0700 update reduction exec/multispec/main_driver.cpp commit df9bc6da846dd7561b0e917e5cfe81bb6806d179 Author: Andy Nonaka Date: Tue Apr 9 14:09:44 2024 -0700 some fixes, still not working exec/multispec/main_driver.cpp commit 63f3037489f91a7dd9f8330f9a9fec978c182f11 Author: jbb Date: Tue Apr 9 13:49:59 2024 -0700 added new inputs exec/multispec/inputs_bubble_90 commit 58ec8d469a35621e904443e58e488249b9406855 Author: jbb Date: Tue Apr 9 13:22:47 2024 -0700 put in diagnostic that doesn't work on GPU exec/multispec/Init.cpp exec/multispec/main_driver.cpp commit 48975da297f38cb1454a639b20925edc1ee42b84 Merge: a89cf770 9eb8dc1f Author: jbb Date: Tue Apr 9 13:20:18 2024 -0700 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit a89cf770aeccb720341583bd758183ed4011312a Author: jbb Date: Tue Apr 9 11:51:34 2024 -0700 test exec/multispec/GNUmakefile commit 9eb8dc1ffd27e29df759914374cc8265c993e162 Merge: fa397c74 0e147ef5 Author: Andy Nonaka Date: Wed Apr 3 09:51:18 2024 -0700 Merge branch 'main' into flory_huggins commit fa397c746cbfd41e7ac2f95b717e1c7bf6ac7448 Author: Andy Nonaka Date: Tue Apr 2 10:55:58 2024 -0700 avoiding merge conflicts src_common/BCPhysToMath.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp src_hydro/BDS.cpp commit 95903b5fea682a0ced1b56d02021c186bd96352f Author: Andy Nonaka Date: Tue Apr 2 10:53:40 2024 -0700 compilation fixes src_common/BCPhysToMath.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp src_hydro/BDS.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/RhoUtil.cpp commit 97b1b2135ea1b80acded5508880197e24ffa8837 Author: jbb Date: Wed Mar 27 17:03:24 2024 -0700 set up hemisphere initial data exec/multispec/Init.cpp commit 5c8cf2a8e8da42ebc263f9b8bc2001bbb5a1f796 Merge: 501dd3ac 0e147ef5 Author: jbb Date: Fri Feb 16 09:45:36 2024 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 0e147ef57a646b6f2fe0d66803f8abffb7c0998c Author: Andrew Myers Date: Thu Feb 15 16:34:07 2024 -0800 fix handling of particle creation outside of domain boundaries src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/StochasticPC.cpp commit 2bd05e1598b893429680911166d0533b4db4c298 Author: jbb Date: Thu Feb 15 14:28:55 2024 -0800 tweaked input exec/multispec/Init.cpp commit 97cec1094e8c41d5d7d3edc3e5283a8eba1fc741 Author: Andrew Myers Date: Thu Feb 15 11:06:18 2024 -0800 particleData should not be static src_deankow/multilevel/AmrCoreAdv.H src_deankow/multilevel/AmrCoreAdv.cpp commit bee8d61a6cac1e7a280e936b82cb93d16cdf3a36 Author: Andrew Myers Date: Thu Feb 15 11:06:05 2024 -0800 ParticleData::Checkpoint should be const src_deankow/multilevel/ParticleData.H commit 501dd3ac07d5281a37d7da2b1cc40a571ee47619 Author: jbb Date: Wed Feb 7 15:51:56 2024 -0800 minor tweaks to dk code exec/_1d_dk_hybrid/driver.f exec/_1d_dk_hybrid/flux.f exec/_1d_dk_hybrid/inputs_fv commit bc8297cb6295a3dcda523f2a628793a74d267784 Merge: c5c17e31 16f671d6 Author: jbb Date: Tue Feb 6 12:09:11 2024 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit c5c17e31e86bebe7ffaada7a4ac924863c1d84f7 Author: jbb Date: Tue Feb 6 12:08:20 2024 -0800 inputs files that show bugs exec/dean_kow/multilevel/inputs_bug1 exec/dean_kow/multilevel/inputs_bug2 commit 905bc01c1b0067d54b6a030456267d6b44e7b8fc Author: jbb Date: Fri Feb 2 12:50:09 2024 -0800 adjust range in contact anglre bc to use ce to 1-ce src_multispec/MultiFabPhysBC_FH.cpp commit 6c601cea53f8deb9a1546847f61132dcc7ebf10b Merge: fd7dddc5 bb869553 Author: Ishan Srivastava Date: Wed Jan 31 12:28:16 2024 -0500 Merge remote-tracking branch 'origin/fhd_heffte' into fhd_heffte commit fd7dddc5361dd756abf4c164de0c75d139cfda6b Author: Ishan Srivastava Date: Wed Jan 31 12:23:21 2024 -0500 build script for frontier exec/compressible_stag/TURB_PDFS/build_frontier.sh commit bb8695531a51f081dbe0269e52548d6d7bacf7fd Author: Ishan Srivastava Date: Wed Jan 31 09:11:47 2024 -0800 fixed spectral filter calculations exec/compressible_stag/SPECTRAL_FILTER/main_driver.cpp exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.H exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.cpp commit b819acf9cdf2208ab1240824395c3fb546c684e6 Author: Ishan Srivastava Date: Wed Jan 31 09:11:26 2024 -0800 fix spectra calculations src_analysis/TurbSpectra.cpp commit 34230dbe1bb083df4e4cee7636df1045060d8f80 Author: jbb Date: Fri Jan 26 15:16:08 2024 -0800 fix disjoining pressure bug exec/multispec/AdvanceTimestepBousq.cpp commit 19dcda3d1f8893e6055c7185a3ab8436674a2103 Author: jbb Date: Fri Jan 26 14:26:28 2024 -0800 added disjoining pressure and fixed contact angle BC exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/GNUmakefile exec/multispec/Init.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MultiFabPhysBC_FH.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 07d17443ce51ee0eefa2cebe2ef2c4b0e1f7b47a Merge: f6715493 16f671d6 Author: Ishan Srivastava Date: Fri Jan 26 14:20:49 2024 -0800 Merge remote-tracking branch 'origin/main' into fhd_heffte commit f67154937f457369a5ce9006f72a5ad9ef7e1b89 Author: Ishan Srivastava Date: Fri Jan 26 14:19:42 2024 -0800 spectral calculations for turbulence outupt exec/compressible_stag/SPECTRAL_FILTER/GNUmakefile exec/compressible_stag/SPECTRAL_FILTER/Make.package exec/compressible_stag/SPECTRAL_FILTER/build_perlmutter.sh exec/compressible_stag/SPECTRAL_FILTER/main.cpp exec/compressible_stag/SPECTRAL_FILTER/main_driver.cpp exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.H exec/compressible_stag/SPECTRAL_FILTER/spectral_functions.cpp exec/compressible_stag/build_perlmutter.sh commit ef07931517e75034e389742b12622c62e72a6422 Author: Ishan Srivastava Date: Fri Jan 26 14:19:12 2024 -0800 get heffte to compile on perlmutter and more PDF diagnostics exec/compressible_stag/TURB_PDFS/GNUmakefile exec/compressible_stag/TURB_PDFS/main_decomp.cpp src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/main_driver.cpp commit b0e5e75bece2da85b69cc41f4e2a48b38b59509b Author: jbb Date: Wed Jan 24 10:03:18 2024 -0800 tweaks to DK stuff exec/dean_kow/multilevel/GNUmakefile exec/dean_kow/multilevel/inputs exec/dean_kow/singlelevel/GNUmakefile exec/dean_kow/singlelevel/inputs src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/mykernel.H src_deankow/singlelevel/main.cpp src_deankow/singlelevel/mykernel.H commit 16f671d6d7985fd6d821f9ad8b9c0a77b6cb15d9 Merge: 180b53bd 87ff1fe0 Author: Weiqun Zhang Date: Mon Jan 22 14:32:15 2024 -0800 Merge pull request #147 from WeiqunZhang/amrex_prefix Prepare for amrex changes commit 87ff1fe0032dee3e37580859714c322cd5353161 Author: Weiqun Zhang Date: Mon Jan 22 14:23:25 2024 -0800 Prepare for amrex changes exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/taylor_line/main_driver.cpp src_common/BCPhysToMath.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp src_deankow/multilevel/AmrCoreAdv.cpp src_hydro/BDS.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/RhoUtil.cpp src_particles/DsmcParticleContainer.cpp src_particles/DsmcParticleContainer.cpp.old src_particles/FhdParticleContainer.cpp src_particles/FhdParticleContainer_WF.cpp src_particles/particle_mobility.cpp unmaintained/src_chem/AmrCoreAdv.cpp commit 5272e0592d7f478cdccec21e315c66415eb5da69 Author: jbb Date: Thu Jan 11 14:25:35 2024 -0800 fixed bug in contact angle boundary conditions exec/multispec/AdvanceTimestepBousq.cpp src_common/BCPhysToMath.cpp src_common/MultiFabPhysBC.cpp src_multispec/MultiFabPhysBC_FH.cpp src_multispec/RhoUtil.cpp src_multispec/StochMassFlux.cpp commit 1cdac6ecee7c68fb9416d7d0798f6521a1832816 Author: jbb Date: Thu Jan 4 16:15:20 2024 -0800 fixed up 1d stats version of DK src_deankow/1d_stats/main.cpp src_deankow/1d_stats/myfunc.H src_deankow/1d_stats/myfunc.cpp src_deankow/1d_stats/mykernel.H src_multispec/StochMassFlux.cpp commit 3779b933da8ee4bfe03838ecb86172135a934df1 Author: jbb Date: Wed Dec 20 11:15:27 2023 -0800 added code to do an ensemble of 1d simulations for basic statistics src_deankow/1d_stats/Make.package src_deankow/1d_stats/main.cpp src_deankow/1d_stats/myfunc.H src_deankow/1d_stats/myfunc.cpp src_deankow/1d_stats/mykernel.H commit 180b53bd41cb71e0d7f8ad0a1ac6f3df9faa0c1b Author: Ann Almgren Date: Fri Dec 15 15:37:04 2023 -0800 Fix with atomicAdd src_deankow/multilevel/StochasticPC.cpp commit 9f83e46d0c85bf2199cbbe4bfb284ac0744a9a42 Author: Andrew Myers Date: Thu Dec 14 14:10:52 2023 -0800 update refluxing functions src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp commit 281b30db80061261480ae9310289fb93b4a525e6 Author: Andrew Myers Date: Mon Dec 11 13:17:59 2023 -0800 implement InitParticles in terms of AddParticles src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp commit 0c7bfdbe38c8f27aedd2d71bc8c283cd72d2d298 Author: Andrew Myers Date: Mon Dec 11 12:57:23 2023 -0800 fix implicit *this capture src_deankow/multilevel/AmrCoreAdv.cpp commit 5b05a1e3fc3a9ef1a145b991e1c2da9c4ac71f3b Author: Andrew Myers Date: Mon Dec 11 12:57:06 2023 -0800 port InitParticles for GPU src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp commit af68571df19d3da024eead34517bda19d6dc501f Author: isriva Date: Sun Dec 10 17:08:35 2023 -0800 enable cross-platform compilation exec/compressible_stag/GNUmakefile src_analysis/TurbSpectra.cpp commit fada4dfe10f6716a0504d2389bb038746e48d751 Author: isriva Date: Fri Dec 8 16:09:00 2023 -0800 include FFTW libraries for heffte fftw backend exec/compressible_stag/GNUmakefile commit d863f843575ffea026012dbecded9b5c0a649aa8 Author: isriva Date: Thu Dec 7 22:39:27 2023 -0800 compute individual vorticity components and their PDFs exec/compressible_stag/TURB_PDFS/main_decomp.cpp commit 27a019e22f864046ec9b171d67c252afbde91314 Author: isriva Date: Thu Dec 7 09:47:27 2023 -0800 PDFs of decomposed velocities exec/compressible_stag/TURB_PDFS/GNUmakefile exec/compressible_stag/TURB_PDFS/Make.package exec/compressible_stag/TURB_PDFS/main_decomp.cpp commit b50e410947a6ba82d4843b740de28de9b04cebfe Author: isriva Date: Wed Dec 6 18:01:42 2023 -0800 minor change to PDF calculation exec/compressible_stag/TURB_PDFS/main.cpp commit fd59c064e524760f01dca02c27bfe1a3bc81e4f0 Merge: 71549d8c d7a2b375 Author: isriva Date: Wed Dec 6 10:30:21 2023 -0800 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 71549d8cd2b87cf5cb287e089316f16eb1691aa3 Author: isriva Date: Wed Dec 6 10:29:41 2023 -0800 PDFs for turbulence fields: velocity, pressure, density, temperature exec/compressible_stag/TURB_PDFS/GNUmakefile exec/compressible_stag/TURB_PDFS/Make.package exec/compressible_stag/TURB_PDFS/main.cpp commit d7a2b375a6667d07420a077fe000f6a0a5a36a82 Author: jbb Date: Tue Dec 5 10:51:21 2023 -0800 minor fixed for 3d src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/mykernel.H commit 5c690ceeb6f054b3bd93504bbce2a336e117fcdd Merge: d33f844c 636b476e Author: jbb Date: Tue Dec 5 09:49:19 2023 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit d33f844cc1464ea89b78ec6e706d75d9d2b077ae Author: jbb Date: Tue Dec 5 09:47:51 2023 -0800 changed initial condition src_deankow/multilevel/mykernel.H commit 636b476e8bb56ecc61bd3debc8d43c287c9d99d0 Author: Ann Almgren Date: Mon Dec 4 17:33:12 2023 -0800 This version is conservative even when the fine region touches the periodic boundary src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/ParticleData.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/mykernel.H commit ee8c3f832f93ea97d0ba2cc45a665dca306e0ab7 Author: Andrew Myers Date: Mon Dec 4 11:18:13 2023 -0800 add commented-out version of GPU initialization src_deankow/multilevel/StochasticPC.cpp commit 683d6587bdc483fffadc1ce9e3ca93cfa5e9e42a Author: Ann Almgren Date: Sun Dec 3 16:38:26 2023 -0800 add inputs for multilevel deankow exec/dean_kow/multilevel/inputs commit e18b9cf1c6f8c5e8468cf4fdd701b9e255982751 Author: Ann Almgren Date: Sun Dec 3 16:37:35 2023 -0800 Add multilevel capability exec/dean_kow/GNUmakefile exec/dean_kow/multilevel/GNUmakefile exec/dean_kow/multilevel/Make.Adv exec/dean_kow/multilevel/Make.package exec/dean_kow/multilevel/inputs exec/dean_kow/singlelevel/GNUmakefile exec/dean_kow/singlelevel/inputs src_deankow/multilevel/AdvancePhiAtLevel.cpp src_deankow/multilevel/AmrCoreAdv.H src_deankow/multilevel/AmrCoreAdv.cpp src_deankow/multilevel/Kernels.H src_deankow/multilevel/Make.package src_deankow/multilevel/ParticleData.H src_deankow/multilevel/Src_K/Adv_K.H src_deankow/multilevel/Src_K/Make.package src_deankow/multilevel/Src_K/compute_flux_2D_K.H src_deankow/multilevel/Src_K/compute_flux_3D_K.H src_deankow/multilevel/Src_K/slope_K.H src_deankow/multilevel/StochasticPC.H src_deankow/multilevel/StochasticPC.cpp src_deankow/multilevel/Tagging.H src_deankow/multilevel/bc_fill.H src_deankow/multilevel/main.cpp src_deankow/multilevel/myfunc.H src_deankow/multilevel/myfunc.cpp src_deankow/multilevel/mykernel.H src_deankow/singlelevel/Make.package src_deankow/singlelevel/main.cpp src_deankow/singlelevel/myfunc.H src_deankow/singlelevel/myfunc.cpp src_deankow/singlelevel/mykernel.H commit 442ce97b3d8d000928fb2cec6a353682b969290a Author: jbb Date: Fri Dec 1 17:31:23 2023 -0800 fixed switch between regular and Gaussian model exec/dean_kow/inputs src_deankow/mykernel.H commit dd332e2a5b98abfb4deeeccb696849530dce5b70 Author: jbb Date: Fri Dec 1 10:50:19 2023 -0800 added support for contact angle boundary conditions for flory huggins model -- still a wip exec/multispec/Init.cpp src_common/BCPhysToMath.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_common/common_namespace.H src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/Make.package src_multispec/MultiFabPhysBC_FH.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 7f7ddfbbb2f80ec31edf828d78b72ae2a76c2ba2 Merge: 63e79046 fcdbf991 Author: Ishan Srivastava Date: Wed Nov 29 10:26:54 2023 -0800 Merge remote-tracking branch 'origin/main' into fhd_heffte commit 63e790467646c4ef5f6e6a1bb6111b4bdbf875f8 Author: Ishan Srivastava Date: Wed Nov 29 10:26:27 2023 -0800 use bulk viscosity in bulk dissipation src_compressible_stag/DeriveVelProp.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp commit 379d721806380f5e1fa8a9751f427f73c80edcbe Merge: 7bebd683 fcdbf991 Author: jbb Date: Mon Nov 13 10:46:43 2023 -0800 Merge branch 'main' into flory_huggins commit fcdbf991761d1d60907d4580a6e2653a760f378c Merge: 8f2d12f7 aca47b4b Author: jbb Date: Mon Nov 13 10:45:05 2023 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7bebd6835bb06ab5c61d0cc3a7e2c561a6bb5c85 Merge: 481f5bd6 46f74a3e Author: jbb Date: Mon Nov 13 10:43:45 2023 -0800 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit aca47b4bbd50438eb51bb25f1a25e48080e5fccf Author: Andy Nonaka Date: Fri Nov 10 08:13:03 2023 -0800 fix structure factor and checkpointing for USE_MPI=FALSE case exec/hydro/Checkpoint.cpp src_analysis/StructFact.H commit 5fff523c880d02a582ef2914cbe2f27691301b73 Merge: a7d90048 d39f83ca Author: Ishan Srivastava Date: Thu Nov 9 15:12:55 2023 -0800 Merge remote-tracking branch 'origin/main' into fhd_heffte commit d39f83ca613c4e42f8d896f2850614e457cae685 Merge: e22b57d6 1deab085 Author: Ishan Srivastava Date: Thu Nov 9 15:21:23 2023 -0700 Merge pull request #144 from AMReX-FHD/bulk_visc Added support for bulk viscosity in staggered compressible FHD commit 8d4d230f2e83e2443b2276bc75c3a67c31cf41c4 Author: jbb Date: Thu Nov 9 13:56:08 2023 -0800 fixed bug in disjoining pressure exec/thinFilm/main_driver.cpp commit 1deab085b64a12fd23311ddc400ba5a361c9ed3e Merge: 9271cbfb e22b57d6 Author: Ishan Srivastava Date: Thu Nov 9 13:47:23 2023 -0800 Merge remote-tracking branch 'origin/main' into bulk_visc commit e22b57d64230a9c881d22dee0fca88a12258e488 Author: Andy Nonaka Date: Wed Nov 8 14:01:02 2023 -0800 remove algorithm_type=2 from inputs_incomp_equil_fluct_2d; that shouldn't be there exec/hydro/inputs_incomp_equil_fluct_2d commit 8f2d12f70f73426d39ea637b40a4efb9daaa726b Author: jbb Date: Wed Nov 8 13:44:44 2023 -0800 DK for mean field version and variable viscosity mods exec/multispec/Init.cpp src_deankow/main.cpp src_deankow/myfunc.H src_deankow/myfunc.cpp src_deankow/mykernel.H src_multispec/ComputeMixtureProperties.cpp commit 9cfa60320dc0d3c73de667dc63ac259cf1ae1a1a Author: Andy Nonaka Date: Mon Nov 6 17:16:25 2023 -0800 final cleanup - some testing now required exec/thinFilm/main_driver.cpp commit f7bc077ac88102a790cc602d9606dd6d0a79c9e2 Author: Andy Nonaka Date: Mon Nov 6 17:15:17 2023 -0800 more readability exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp commit 9dff1494157e7dade625d33cf5b5e4fa7a0d05de Author: Andy Nonaka Date: Mon Nov 6 17:13:44 2023 -0800 readability exec/thinFilm/main_driver.cpp commit 2a39ddb9f125bcddf71bc9c9d6f1dcba039fa298 Author: Andy Nonaka Date: Mon Nov 6 17:10:39 2023 -0800 disjoining pressure exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp exec/thinFilm/thinfilm_namespace.H commit a7d900485ff0b0b85051a2d5a590bbc977dd147e Author: Ishan Srivastava Date: Sun Nov 5 12:45:24 2023 -0800 do reductions on MFab and not BaseFab src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp commit 37bd3c3adc6cdbbc1979600426de3a246a0e60f3 Author: Ishan Srivastava Date: Fri Nov 3 16:54:55 2023 -0400 recompute transport coeff. when restarting for turbulent FFTs src_compressible_stag/main_driver.cpp commit 124e761d974f7fd67bd49f3253da54011f429e16 Author: Ishan Srivastava Date: Thu Nov 2 18:16:34 2023 -0400 fix typo src_compressible_stag/DeriveVelProp.cpp commit 0abe9cd69db30b61f5f91d4b9199827a94c8fbd1 Author: Ishan Srivastava Date: Thu Nov 2 18:05:15 2023 -0400 reading checkpoint does not require old box array src_compressible_stag/Checkpoint.cpp commit ddf50e995cb0abc09ed5e395f5ac02771992a42a Author: Ishan Srivastava Date: Thu Nov 2 18:04:42 2023 -0400 use native amrex functions for MFab reduction src_compressible_stag/DeriveVelProp.cpp commit 9d4c66aed156e201a74b6c885d71f78e6e79e7aa Author: Ishan Srivastava Date: Thu Nov 2 18:04:16 2023 -0400 GPU-aware MPI compilation on Frontier -- ongoing tests exec/compressible_stag/build_frontier.sh commit f682b7a3b44e19bfee6467130c61bb45359f9a2f Author: Ishan Srivastava Date: Sat Oct 28 18:23:38 2023 -0400 get heffte and k-space integration working on frontier src_analysis/TurbSpectra.cpp commit c6e97baa99f42aed59d6989891769ca80395e268 Author: Ishan Srivastava Date: Thu Oct 26 21:27:28 2023 -0700 heffte seems to be working now src_analysis/TurbSpectra.cpp commit 5b7ad925256dd606e8c296343f8e75fe1de0cf00 Author: Ishan Srivastava Date: Thu Oct 12 13:16:06 2023 -0700 more changes src_analysis/TurbSpectra.cpp commit d2e0f807ade3e351c851725dae9882e9b28b2e94 Author: Ishan Srivastava Date: Thu Oct 12 11:23:22 2023 -0700 minor change src_analysis/TurbSpectra.cpp commit b625dc4538b1222825a0a5e6005028a206680656 Author: Ishan Srivastava Date: Wed Oct 11 19:17:40 2023 -0400 more compilation mods to get heffte working on frontier exec/compressible_stag/GNUmakefile exec/compressible_stag/build_frontier.sh src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/main_driver.cpp commit 48bca93f3f454e4522f794ff21832fa4a38c413d Author: Ishan Srivastava Date: Mon Oct 9 09:41:28 2023 -0700 flag to restart without advancing time. also more changes to heffte src_analysis/TurbSpectra.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/main_driver.cpp commit 40a635d0abab73c208f2fd1c859d748afc21b211 Author: isriva Date: Thu Oct 5 11:10:59 2023 -0700 heffte works well. needs tests on multiple cuda and amd gpus src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/DeriveVelProp.cpp commit 965d88967ffa2f3de627ddc80cfe48ee0d671114 Author: isriva Date: Thu Sep 28 18:39:18 2023 -0700 heffte compiles and runs fine, needs longer run testing exec/compressible_stag/GNUmakefile src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/DeriveVelProp.cpp src_compressible_stag/main_driver.cpp commit 4d6a4b2c13fa468a0a68e459c5ff22780c21a613 Author: isriva Date: Wed Sep 27 08:07:59 2023 -0700 heffte compiles fine both on host and cuda device exec/compressible_stag/GNUmakefile src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/main_driver.cpp commit 9271cbfbd811073a077b4eb9b3d5382a874ef01e Merge: 1fd3499f 46f74a3e Author: isriva Date: Fri Sep 22 12:40:29 2023 -0700 Merge remote-tracking branch 'origin/main' into bulk_visc commit 40fd5748d96ef8f72829889449844b654263bac8 Author: isriva Date: Fri Sep 22 11:18:05 2023 -0700 added code for heffte usage in fhdex; needs testing src_analysis/Make.package src_analysis/TurbSpectra.H src_analysis/TurbSpectra.cpp src_compressible_stag/main_driver.cpp commit 1fd3499f9e32267cc286a8fea9915de906657d2f Author: isriva Date: Wed Sep 20 23:28:28 2023 -0700 output bulk viscosity in plotfiles src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit b2f345093f4b26445c7cc8f06761d4dd3162d0c9 Author: isriva Date: Wed Sep 20 13:15:29 2023 -0700 initial commits for bulk viscosity in compressible FHD src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible/transCoeffs.cpp commit 46f74a3e9f40ff20b631239a8b4a453d5060e527 Author: Andy Nonaka Date: Wed Sep 20 13:13:52 2023 -0700 write height data to ascii text on plot_int exec/thinFilm/main_driver.cpp commit 3d34e8a0fe7d78b0b67d7586336294daf83dde9d Author: Andy Nonaka Date: Wed Sep 20 13:04:47 2023 -0700 get this properly compiling/running again exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp commit c39702feab8e4f470958c48666a91dee9e8992f8 Merge: 9528ecc5 3b40fb78 Author: Ishan Srivastava Date: Wed Sep 20 11:20:23 2023 -0600 Merge pull request #143 from AMReX-FHD/reservoir_compress Reservoirs in the Compressible Staggered FHD commit 3b40fb781a0101d8fe411f38824acce99a68388f Author: isriva Date: Wed Sep 20 10:13:22 2023 -0700 minor changes to boundary stochastic shear stress flux src_compressible_stag/boundaryStag.cpp commit 32cf520ce68371b8b2fa32b6a11f92f7479bd10d Author: isriva Date: Tue Sep 19 12:31:50 2023 -0700 fix some more benign bugs src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit 9fdc9586649c87a397d66544bc6440c040d54986 Author: isriva Date: Tue Sep 19 11:07:57 2023 -0700 fix a small bug src_compressible_stag/reservoirStag.cpp commit 36ad1047d7a0707921e7bcc8c128c17136d8a53b Author: isriva Date: Tue Sep 19 11:04:05 2023 -0700 reservoir now works in x, y, and z dirs src_compressible_stag/main_driver.cpp src_compressible_stag/reservoirStag.cpp src_compressible_stag/timeStepStag.cpp commit 750cd5c59ecb9f82f829f74afe5978aeda02fb57 Merge: 572fcbe9 9528ecc5 Author: isriva Date: Tue Sep 19 08:09:30 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 9528ecc529d9077bb20d3c037caa442e703ec917 Merge: 87a29bcd 1cc9bc67 Author: Andy Nonaka Date: Mon Sep 18 17:20:47 2023 -0700 Merge pull request #142 from AMReX-FHD/turb_SF Enhanced Structure Factor Calculations for Turbulence commit 87a29bcd320a8ed656f0b034e64938b3251b082f Merge: 7ed8ece9 71f5c87d Author: jbb Date: Mon Sep 18 13:46:36 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7ed8ece9c0e77ac83e0b672e45fb383420e6d35e Author: jbb Date: Mon Sep 18 13:42:19 2023 -0700 fixed bug and added option to put in perturbation to initial profile exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp exec/thinFilm/thinfilm_namespace.H commit 572fcbe948a502dc706d74ca502d64ac3604b7e4 Merge: 86738ee4 71f5c87d Author: isriva Date: Sat Sep 16 17:08:55 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 1cc9bc670c4215b8ea1a01de990bcd6cfd24aec4 Merge: 778af207 036995f6 Author: Ishan Srivastava Date: Sat Sep 16 11:56:26 2023 -0700 Merge remote-tracking branch 'origin/turb_SF' into turb_SF commit 778af2076c313e8be99028570a1308f155867f7e Author: Ishan Srivastava Date: Sat Sep 16 11:06:29 2023 -0700 fixed a small bug src_compressible_stag/DeriveVelProp.cpp commit 036995f64fbbab82ce15c95898e8b1f18ff32048 Author: Ishan Srivastava Date: Fri Sep 15 19:04:26 2023 -0400 change default build parameters for OLCF exec/compressible_stag/build_frontier.sh commit 1d4cba917b12a17bb78f0f57164d54398a2bdd92 Author: isriva Date: Fri Sep 15 16:02:39 2023 -0700 minor changes to turbulence analysis src_compressible_stag/DeriveVelProp.cpp commit 871b3d47bf92d0ce885c98a29f29db4dce09ac88 Merge: 24a5353f 71f5c87d Author: isriva Date: Wed Sep 13 18:55:18 2023 -0700 Merge remote-tracking branch 'origin/main' into turb_SF commit 24a5353f58e9cbfc787b3ad8b1d2e87ba88f9f36 Merge: 2b679da7 aafdd1bd Author: isriva Date: Wed Sep 13 18:54:01 2023 -0700 Merge branch 'turb_SF' of github.com:AMReX-FHD/FHDeX into turb_SF commit 2b679da7542c4adcf533c24d36daf6a72ffea261 Author: isriva Date: Wed Sep 13 18:53:06 2023 -0700 decompose velocity and output several velocity gradient properties src_analysis/StructFact.H src_analysis/StructFact.cpp src_common/NormInnerProduct.cpp src_common/common_functions.H src_compressible_stag/DeriveVelProp.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit 71f5c87dd6e91cc26086ff64f7d4b5ac8c07bdb5 Author: isriva Date: Wed Sep 13 18:51:49 2023 -0700 fix npts in IntegrateKShell to prevent out of memory access src_analysis/StructFact.cpp commit 04213e6706f72dfce27ff2a24d548e27585d2ce1 Merge: d865e260 3cc8fdf1 Author: Andy Nonaka Date: Wed Sep 13 12:13:29 2023 -0700 Merge pull request #129 from AMReX-FHD/thinfilm Thinfilm commit aafdd1bd54d6d23bfc722299def81fffdf2348f4 Author: Andy Nonaka Date: Wed Sep 13 11:09:34 2023 -0700 move file exec/compressible_stag/inputs_SF_decomp_test commit d13ce7f4c278579b0e0869329470049f0fdd870b Author: isriva Date: Tue Sep 12 21:32:41 2023 -0700 minor notational change src_analysis/StructFact.cpp commit 71236d0cc4db051296c7c61f9c75c635fda99058 Author: isriva Date: Tue Sep 12 16:24:51 2023 -0700 test inputs file for turb structure factor inputs_SF_decomp_test commit 9d9b204d088e2616eccd8d89966af16f989f6920 Author: isriva Date: Tue Sep 12 16:23:10 2023 -0700 velocity decomposition in Fourier space implemented pending testing src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible_stag/main_driver.cpp commit ce81d297f40fbdabc255099679e85400a9ad1e14 Author: isriva Date: Tue Sep 12 15:09:38 2023 -0700 remove more unecessary random number creations src_compressible_stag/timeStepStag.cpp commit af1683be2b99d66cd3ec933440412197df3f3da9 Author: isriva Date: Thu Sep 7 23:50:16 2023 -0700 added capability for k-space velocity decomposition into solenoidal and dilatational parts. works for staggered velocities. also inverse FFT back to real space exec/tests/FourierDecompVel/GNUmakefile exec/tests/FourierDecompVel/Make.package exec/tests/FourierDecompVel/inputs exec/tests/FourierDecompVel/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 86738ee47f0d2cfebf303ef0f8932083b3b530e9 Merge: d7377a8f d865e260 Author: isriva Date: Fri Sep 1 13:09:02 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit d865e260049c1d5fb2d0d7a391ac0cee9176cfb7 Merge: fd0d51a2 1349cc28 Author: Ishan Srivastava Date: Mon Aug 28 14:56:48 2023 -0600 Merge pull request #140 from AMReX-FHD/max_element Max element commit 1349cc286e96a9a022257978f387985323db4157 Author: Andy Nonaka Date: Mon Aug 28 13:00:00 2023 -0700 logic fix src_multispec/multispec_functions.cpp commit 7ec96f4fbcb2d87f439ab9e8819e0c42f2a41790 Author: Andy Nonaka Date: Mon Aug 28 12:49:22 2023 -0700 add max_element to makefile instead of hard-coding exec/multispec/GNUmakefile src_common/common_namespace.H src_multispec/multispec_functions.cpp commit fd0d51a261910615ab40d5abc457a408aa487eac Merge: 32d82218 2305a779 Author: Andy Nonaka Date: Mon Aug 28 12:42:45 2023 -0700 Merge pull request #139 from AMReX-FHD/max_species Max species commit 2305a7799f6af557f2e7f1695e10efaada343240 Author: isriva Date: Mon Aug 28 12:26:23 2023 -0700 include MAX_SPEC parameter to one more Makefile exec/immersedIons/GNUmakefile commit 44f36dfac080189d3b2dff5667d3c5fee7b93264 Author: isriva Date: Mon Aug 28 12:16:04 2023 -0700 now define MAX_SPEC as a compile-time parameter instead of hard-coded. Default value is 8 exec/DSMC/GNUmakefile exec/DSMC_granular/GNUmakefile exec/Ek_calculator/GNUmakefile exec/chemistry_testing/GNUmakefile exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile exec/compressible_stag_mui/GNUmakefile exec/dean_kow/GNUmakefile exec/hydro/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/immersed_boundary/taylor_line/GNUmakefile exec/multispec/GNUmakefile exec/structFactTest/GNUmakefile exec/tests/RFDanalysis/GNUmakefile exec/thinFilm/GNUmakefile exec/tutorials/amrex_mpi_basic/GNUmakefile exec/tutorials/ib_marker_basic/GNUmakefile src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/main_driver.cpp commit 32d82218d357a23585828665fccf0c280492259f Merge: 20487439 fae33e9b Author: Andy Nonaka Date: Mon Aug 28 10:16:51 2023 -0700 Merge pull request #137 from AMReX-FHD/compress_turb forced isotropic turbulence in compressible FHD commit fae33e9badcb75fcf8f0e9897ed0c0fe03c844c3 Author: Andy Nonaka Date: Mon Aug 28 09:57:03 2023 -0700 Update src_common/common_namespace.H src_common/common_namespace.H commit d7377a8feac589619ccc6bee19bbd99fd1cbe803 Author: isriva Date: Fri Aug 25 16:55:48 2023 -0700 reservoir coded for 2D and 3D (pending testing) src_compressible_stag/compressible_functions_stag.H src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit abb73fbf0913dcd47e407aa096e83a50f4ee9afa Merge: 4b79a4cd 20487439 Author: Ishan Srivastava Date: Fri Aug 25 14:32:20 2023 -0400 Merge remote-tracking branch 'origin/main' into compress_turb commit da5fb03ab8d1861f2c7d1eb061de256c9b926603 Merge: 58a11baa 20487439 Author: isriva Date: Fri Aug 25 11:27:10 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 204874391c83a3e0c14cb1530d8c48bb2739ef39 Merge: 3550fc19 7f05beba Author: Ishan Srivastava Date: Fri Aug 25 12:13:47 2023 -0600 Merge pull request #138 from AMReX-FHD/rocFFT HIP rocFFT for structure factor commit 7f05bebac3b3d7d3649c7d2398ccf0ebd42f5ba0 Author: Andy Nonaka Date: Fri Aug 25 10:52:09 2023 -0700 style/cleanup only exec/compressible_stag/GNUmakefile src_analysis/StructFact.cpp commit 4b79a4cd4b8c1abbd3c13add4d8b69534188520d Author: Ishan Srivastava Date: Fri Aug 25 01:35:31 2023 -0400 build script for Frontier exec/compressible_stag/build_frontier.sh commit 2c45b9bd841fb5cee99dbe539523f5b9c38b31aa Author: Ishan Srivastava Date: Fri Aug 25 01:34:29 2023 -0400 profiling functions in turbulent forcing src_compressible_stag/TurbForcingComp.cpp commit 4806f56011082983f413618d3ba88fba25e90a8e Merge: 8ea3d6f2 38c4f217 Author: Ishan Srivastava Date: Fri Aug 25 00:40:25 2023 -0400 Merge remote-tracking branch 'origin/rocFFT' into compress_turb commit 38c4f217d9a24ce597277277b6c889cb8694f2d7 Author: Ishan Srivastava Date: Fri Aug 25 00:22:09 2023 -0400 rocFFT now works on Frontier src_analysis/StructFact.H src_analysis/StructFact.cpp commit 46b2d0eb733910224694790ec171d4208b16b81e Author: Ishan Srivastava Date: Fri Aug 25 00:21:35 2023 -0400 printf does not work on device src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit 294f6d40528d745844b6cd5f0d3b2e295a1e30ca Author: isriva Date: Thu Aug 24 17:44:17 2023 -0700 add support for HIP rocFFT for structure factor on Frontier exec/compressible_stag/GNUmakefile src_analysis/StructFact.H src_analysis/StructFact.cpp commit 58a11baa02a8d96805eca57641e99e4891eec201 Author: isriva Date: Tue Aug 22 12:16:59 2023 -0700 remove unecessary MFabs for reservoir src_compressible_stag/timeStepStag.cpp commit e67bab3466cdba18449b40d5d74d912d710faffd Merge: 1b2146d6 3550fc19 Author: isriva Date: Mon Aug 21 22:07:47 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 1b2146d69fecf96583aefa4a2d4d453b5a2ce356 Author: isriva Date: Mon Aug 21 22:07:10 2023 -0700 1/N correction to fluxes at reservoir-FHD interface src_compressible_stag/reservoirStag.cpp commit 8ea3d6f29028dc2e45dcd369367ecf26888ac3c2 Author: isriva Date: Mon Aug 21 21:59:13 2023 -0700 getting ready to merge turbulence code into main exec/compressible_stag/GNUmakefile src_compressible_stag/Checkpoint.cpp src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit eabb622930d79bfeca14c33d57e62657f9d0d0d1 Merge: 768aa33d 3550fc19 Author: isriva Date: Mon Aug 21 16:20:46 2023 -0700 Merge remote-tracking branch 'origin/main' into compress_turb commit 3550fc19ecbb1d9393ca4116590458dc160d769d Merge: a61da752 7f868367 Author: Ishan Srivastava Date: Mon Aug 21 17:14:43 2023 -0600 Merge pull request #136 from AMReX-FHD/fillrandom_test use new FillRandom routines in staggered compressible FHD commit 7f868367855cd4136c1ddd1906eb11d761aede22 Author: isriva Date: Mon Aug 21 15:54:44 2023 -0700 cleaned up functions for MultiFabFillRandomNormal and MultiFabFillRandomUniform src_compressible_stag/timeStepStag.cpp src_rng/MultiFabFillRandom.cpp src_rng/rng_functions.H commit e6c6e8018e3449dbace5c07c766bcafad5094c30 Author: isriva Date: Sun Aug 20 21:43:16 2023 -0700 cleanup comments src_compressible_stag/timeStepStag.cpp commit a07486330bbd9f30bd43a9a3c1fc08dc2241bc78 Author: isriva Date: Sun Aug 20 21:38:04 2023 -0700 use new FillRandom routines in staggered compressible FHD src_compressible_stag/timeStepStag.cpp commit a61da752457eff141234ddfd8b0fddf7ec63350a Author: Andy Nonaka Date: Fri Aug 18 16:38:57 2023 -0700 turn off fft diagnostics by default (slow) exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp commit 6b1b35a07537c6997262fb2322316af0bc398e80 Author: Andy Nonaka Date: Thu Aug 17 17:06:02 2023 -0700 add hooks to compile/run on gpu exec/thinFilm/thinfilm_functions.H exec/thinFilm/thinfilm_functions.cpp commit 4a3f65540e1c308997d2af1b25a0b4b1b190332a Author: Andy Nonaka Date: Thu Aug 17 16:43:17 2023 -0700 power spectrum exec/thinFilm/main_driver.cpp commit 9dbfb7f9eef030c3743141ac9fc72b6dc9c4cbd9 Author: Andy Nonaka Date: Thu Aug 17 13:47:57 2023 -0700 fix bugs in fft routines exec/thinFilm/main_driver.cpp commit 689d2e62a574ac1cdc16534d27b44018ffd4b2ad Author: Andy Nonaka Date: Thu Aug 17 09:58:36 2023 -0700 bugfix in fft for thinfilm exec/thinFilm/main_driver.cpp commit 13ec2423e10b9680ec8b1eab6352c25a3055912b Author: Andy Nonaka Date: Wed Aug 16 16:01:36 2023 -0700 flag to control fft diag exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp exec/thinFilm/thinfilm_namespace.H commit 00c26ee970ed6c8b9106bddf6ec0d219a5dfb58b Author: Andy Nonaka Date: Wed Aug 16 15:56:30 2023 -0700 fft diagnostic exec/thinFilm/GNUmakefile exec/thinFilm/main_driver.cpp commit 7290a13f02fbb53a3fe145f017efb566a75a7fa8 Author: Andy Nonaka Date: Wed Aug 16 15:33:13 2023 -0700 structure of FFT calls laid out exec/thinFilm/main_driver.cpp commit 768aa33d6fbd65d791b8357b4ea5b6c57f17d59e Merge: 8ca118bd 923d6053 Author: isriva Date: Wed Aug 16 09:55:59 2023 -0700 Merge remote-tracking branch 'origin/main' into compress_turb commit 923d6053c99a3966c0b0131b58d6261be91cb719 Author: Andy Nonaka Date: Tue Aug 15 12:27:51 2023 -0700 force 1d setup to use pencils exec/thinFilm/inputs_1d exec/thinFilm/main_driver.cpp commit d68103509ef6003fce424ade69d3468402d56bd2 Merge: 3d63e693 286e75b0 Author: isriva Date: Mon Aug 14 11:37:58 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 286e75b0824dc7047daf9e296dc5e1e10d1442d8 Author: Andy Nonaka Date: Fri Aug 11 16:51:30 2023 -0700 cfl works for 2d with unequal dx/dy now exec/thinFilm/main_driver.cpp commit 8ca118bdfb403a0e0a4e5ffe16c081de3d5ba370 Author: isriva Date: Thu Aug 10 23:15:11 2023 -0700 resolve race conditions src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp commit 56250ab36a1f389b18cf8b515041ada467df4d4c Author: isriva Date: Thu Aug 10 23:11:11 2023 -0700 very small changes to race conditions src_compressible_stag/timeStepStag.cpp commit 7f2e38daf7c61a97c768794bc11addb6a950ccfc Author: isriva Date: Thu Aug 10 22:55:54 2023 -0700 resolve race conditions in MFIter with tiling src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp commit 0e791cc59ad28c9c15de0ec5b9c987599e3e679c Author: Andy Nonaka Date: Wed Aug 9 15:00:31 2023 -0700 implement cfl exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp commit 3f2e6567e620c7c9c79799a1c13b15b11355085b Author: Andy Nonaka Date: Wed Aug 9 12:11:40 2023 -0700 diagnostics bug exec/thinFilm/thinfilm_functions.cpp commit 3d63e69334e9ee1a7e0e469157d33012ad86ab70 Merge: af236b7e 8cca1d83 Author: isriva Date: Wed Aug 9 11:14:37 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit af236b7edf2917f221984fda2230763ac8f26d40 Author: isriva Date: Wed Aug 9 10:09:04 2023 -0700 some more changes to the reservoir code src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit 70cfda80f43832dadfc0243cd2a405ad75f5000f Author: isriva Date: Tue Aug 8 13:15:29 2023 -0700 fixed some more bugs in thermostat, temp. seems better behaved in initial tests src_compressible_stag/timeStepStag.cpp commit f6920afdc711e1d0f453b3064cdac5a202e8f723 Author: isriva Date: Mon Aug 7 20:57:46 2023 -0700 fixed a bug, but temp still rises in forced turbulence src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit f3f6ceba56761b046e01255048e4f642b826ae38 Merge: 3638c012 8cca1d83 Author: isriva Date: Fri Aug 4 15:42:02 2023 -0700 Merge remote-tracking branch 'origin/main' into compress_turb commit 8cca1d836a44cd98aa5cc114227861d1bfc247c3 Author: isriva Date: Fri Aug 4 15:38:06 2023 -0700 remove unecessary setVals to make code faster src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit a2aa77e52413b545156aeb838657d82f314ecafd Author: Andy Nonaka Date: Thu Aug 3 10:06:23 2023 -0700 more time steps exec/thinFilm/main_driver.cpp commit 3638c012bee6c3391c6fa4ebad77b96b263a2cc4 Author: isriva Date: Thu Aug 3 07:43:07 2023 -0700 move turbulent forcing calculation to host from device src_compressible_stag/TurbForcingComp.H src_compressible_stag/TurbForcingComp.cpp commit 6b0e50401e9ab4e173bee97ee817b4257732b2bd Author: isriva Date: Wed Aug 2 14:57:20 2023 -0700 mamnged memory issue solved in IntegratekShellsMisc function of structure factor src_analysis/StructFact.cpp commit ad689ffcbb25c0e8339e8734b653aa44100af3bf Merge: d114b838 bb26113d Author: ilimarrujo Date: Wed Aug 2 13:08:54 2023 -0700 Merge remote-tracking branch 'origin/main' into compress_turb commit bb26113d3de975b9553c95b51af8ac01479d7c8b Author: Andy Nonaka Date: Wed Aug 2 11:52:44 2023 -0700 fix managed memory issue src_analysis/StructFact.cpp commit d114b8388e9c2e47dd497deee58b820e33d80c53 Merge: b30d8894 bd7064db Author: Iliana Marrujo Date: Wed Aug 2 13:29:20 2023 -0400 Merge branch 'compress_turb' of https://github.com/AMReX-FHD/FHDeX into compress_turb commit b30d889429dcc905c88809c1f850fbe60bf9e63c Author: Iliana Marrujo Date: Wed Aug 2 13:22:05 2023 -0400 abort when mass is negitive or greater than unity mass fraction src_compressible/transCoeffs.cpp commit 7b4aee27ec830a9ade827c617f6ddb4440082ec4 Author: Iliana Marrujo Date: Wed Aug 2 12:44:46 2023 -0400 remove print statements that Frontier doesnt like src_compressible/compressible_functions.H commit bd7064db0b9fdc580748122e2a4645ffb627c53a Author: Iliana Marrujo Date: Wed Aug 2 12:44:46 2023 -0400 abort when mass is negitive or greater than unity mass fraction src_compressible/compressible_functions.H commit 2b60aa6c97ad734c3027164ed8e0d66c3649a463 Author: isriva Date: Tue Aug 1 16:00:39 2023 -0700 fix managed memory issues in staggered compressible turbulence src_compressible_stag/TurbForcingComp.cpp commit acd0c7202904ede37af2836b518ef5f0e5fbdc17 Merge: b8a9e375 b16d44dc Author: Andy Nonaka Date: Tue Aug 1 13:11:04 2023 -0700 Merge pull request #135 from AMReX-FHD/fix_managed_memory fix managed memory commit b16d44dc9d0c9d23760d1295a131d0a0ec613997 Author: Andy Nonaka Date: Tue Aug 1 13:04:47 2023 -0700 stencil bugfix src_gmres/StagApplyOp.cpp commit 0e2c2c3f4c94a442df1cb368ea5d26e84af3d547 Author: Andy Nonaka Date: Tue Aug 1 12:12:12 2023 -0700 fix managed memory src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit b8a9e3755382f6cf3ad6aa6061d9926c9743129e Author: Andy Nonaka Date: Mon Jul 31 16:43:35 2023 -0700 fix managed memory issue src_analysis/StructFact.cpp commit 996f3769a63414273d2bad6287bb917d03086bc1 Author: Andy Nonaka Date: Mon Jul 31 07:57:08 2023 -0700 fix comments in fft unpacking and shifting routines src_analysis/StructFact.cpp commit 82299776408935554ad8fa8ef0412d9f994093d6 Author: isriva Date: Fri Jul 28 13:28:10 2023 -0700 fixed bugs; rewritten turbulent forcing class src_compressible_stag/Checkpoint.cpp src_compressible_stag/TurbForcingComp.H src_compressible_stag/TurbForcingComp.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit 9e054f5378be535a1a25c66d374f8677be9fa806 Author: isriva Date: Wed Jul 26 12:02:08 2023 -0700 output local velocity gradients to a plotfile src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit d2a6dae0ed05545a54d51eac69d72ea33edefb3d Author: isriva Date: Tue Jul 25 15:41:33 2023 -0700 save temporary progress -- not working src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit 97b2723ef9f01eca9db6cb4a5d583824c07ad1be Author: isriva Date: Mon Jul 24 11:34:01 2023 -0700 some more debugging outputs src_compressible_stag/main_driver.cpp src_compressible_stag/reservoirStag.cpp commit 14f827744ab069ae920ba72784171d0317218473 Merge: b842b92f 22fcd554 Author: Andy Nonaka Date: Mon Jul 24 10:12:27 2023 -0700 Merge pull request #134 from AMReX-FHD/thinfilm_2d Stochastic Thinfilm 2D commit dd74586a40b07a15cf83c6b1296467621b193746 Author: isriva Date: Mon Jul 24 08:55:46 2023 -0700 fixed minor bugs src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit 22fcd554830b191bfcd448fbafee69b618dfaa5f Author: Andy Nonaka Date: Mon Jul 24 08:53:06 2023 -0700 correlations for 1d case exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp commit 2d6ff7366d9f07c01bc020c97895bdfc893fba8e Author: Andy Nonaka Date: Mon Jul 24 08:33:54 2023 -0700 2d correlations2d correlations exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.cpp commit a5a532de3f936950cfe6c20722b55634a4921951 Merge: 8613c2d7 b842b92f Author: Andy Nonaka Date: Mon Jul 24 08:06:33 2023 -0700 Merge branch 'main' into thinfilm_1d commit 4c5b4a1554df94e5b909a3ef21f6416c88f9bbe8 Author: isriva Date: Fri Jul 21 16:35:33 2023 -0700 more outputs src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 98f06543e2b867b7e5cf5964f6707ad4df3a0847 Author: isriva Date: Fri Jul 21 16:04:57 2023 -0700 added refluxing; reservoirs almost working src_compressible_stag/compressible_functions_stag.H src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit b842b92fc0c8e793c86345860e512b10eea95e9e Author: Matthew Huber Date: Fri Jul 21 13:51:21 2023 -0700 add taylor line stuff exec/immersed_boundary/taylor_line/Explore Data MP.ipynb exec/immersed_boundary/taylor_line/Explore Data.ipynb exec/immersed_boundary/taylor_line/GNUmakefile exec/immersed_boundary/taylor_line/Make.package exec/immersed_boundary/taylor_line/Render Frames.ipynb exec/immersed_boundary/taylor_line/Taylor Line.ipynb exec/immersed_boundary/taylor_line/Untitled.ipynb exec/immersed_boundary/taylor_line/WritePlotFile.cpp exec/immersed_boundary/taylor_line/advance_CN.cpp exec/immersed_boundary/taylor_line/advance_midpoint.cpp exec/immersed_boundary/taylor_line/advance_stokes.cpp exec/immersed_boundary/taylor_line/compute_convfact_2.sh exec/immersed_boundary/taylor_line/ib_md.cpp exec/immersed_boundary/taylor_line/init_funcs.F90 exec/immersed_boundary/taylor_line/init_s_funcs.F90 exec/immersed_boundary/taylor_line/inputs_2d exec/immersed_boundary/taylor_line/inputs_3d exec/immersed_boundary/taylor_line/inputs_3d_test exec/immersed_boundary/taylor_line/inputs_3d_test.scaled exec/immersed_boundary/taylor_line/inputs_3d_test.scaled.highres exec/immersed_boundary/taylor_line/inputs_chlamy exec/immersed_boundary/taylor_line/inputs_chlamy.buddy exec/immersed_boundary/taylor_line/inputs_chlamy.cori exec/immersed_boundary/taylor_line/inputs_chlamy.highres exec/immersed_boundary/taylor_line/inputs_chlamy.highres-thin exec/immersed_boundary/taylor_line/inputs_chlamy.large exec/immersed_boundary/taylor_line/inputs_chlamy.large-thin exec/immersed_boundary/taylor_line/inputs_chlamy_data exec/immersed_boundary/taylor_line/inputs_incomp_equil_fluct_2d exec/immersed_boundary/taylor_line/inputs_incomp_equil_fluct_3d exec/immersed_boundary/taylor_line/inputs_regression_chlamy exec/immersed_boundary/taylor_line/inputs_taylor exec/immersed_boundary/taylor_line/main_driver.H exec/immersed_boundary/taylor_line/main_driver.cpp exec/immersed_boundary/taylor_line/main_driver_F.H exec/immersed_boundary/taylor_line/run_conv_tests_2.sh commit eb3e2113e4e752e76e43133d23760167c87966e9 Author: isriva Date: Thu Jul 20 17:11:26 2023 -0700 particle-based reservoir now works with compressible staggered code. needs extensive physics testing src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible_stag/Make.package src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/reservoirStag.cpp src_compressible_stag/reservoirStag_K.H src_compressible_stag/timeStepStag.cpp commit ea61f89cc43d8901591b733f616511d545d86f9e Merge: 0ab86cc5 58889446 Author: isriva Date: Tue Jul 18 13:53:19 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 8196b9344de5ef72daa1e591212f290837e02811 Author: Ishan Srivastava Date: Fri Jul 14 14:52:08 2023 -0700 restart functionality for random forced compressible turbulence src_compressible_stag/Checkpoint.cpp src_compressible_stag/TurbForcingComp.H src_compressible_stag/TurbForcingComp.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp commit 8613c2d74be23d68ff72a587e3f7de4fe5f7e4ef Author: Andy Nonaka Date: Wed Jul 12 18:13:09 2023 -0700 correlation points exec/thinFilm/thinfilm_functions.cpp exec/thinFilm/thinfilm_namespace.H commit 2868606f7262726214af8fb6d1cd179f919b1058 Author: Andy Nonaka Date: Wed Jul 12 17:40:54 2023 -0700 separate thinfile namespace exec/thinFilm/GNUmakefile exec/thinFilm/Make.package exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp exec/thinFilm/thinfilm_functions.H exec/thinFilm/thinfilm_functions.cpp exec/thinFilm/thinfilm_namespace.H commit 4d58fca06ca6f250f2b5353b763146ad6a99efe9 Author: Andy Nonaka Date: Wed Jul 12 17:05:05 2023 -0700 revert exec/multispec/inputs_droplet_3d_mod commit 4516c8f77130d497a03400e8884123e57a0daed5 Merge: 37aaa7ee 58889446 Author: Andy Nonaka Date: Wed Jul 12 17:03:19 2023 -0700 Merge branch 'main' into thinfilm_2d commit 90331902dcda84e792a85f23160b04553dd618c5 Author: isriva Date: Tue Jul 11 23:07:56 2023 -0700 fix uninitialized memory src_compressible_stag/timeStepStag.cpp commit 0478f26864ae49ae397268d56e58dec177399c8a Author: isriva Date: Tue Jul 11 16:06:26 2023 -0700 added thermostat for turbulence by reomving the average added energy src_compressible_stag/timeStepStag.cpp commit 3e4c37c332d694cd018cd07cc1e75b1303092506 Author: isriva Date: Tue Jul 11 16:05:58 2023 -0700 fix turbulence structure factor src_compressible_stag/main_driver.cpp commit 822ba44a4da9c1c067147b96f162b925e28ccc25 Author: isriva Date: Tue Jul 11 16:04:35 2023 -0700 make turbulence GPU kernels for efficient by passing pointers src_compressible_stag/TurbForcingComp.H src_compressible_stag/TurbForcingComp.cpp commit 37aaa7ee4db9ad6f34eb17d68420b69ae39ef8a2 Author: Andy Nonaka Date: Tue Jul 11 11:26:13 2023 -0700 cleanup exec/thinFilm/main_driver.cpp commit 71159b38fb99512e4acbaf7365f0e667bf5388da Author: Andy Nonaka Date: Tue Jul 11 11:21:20 2023 -0700 cleanup exec/thinFilm/main_driver.cpp commit 03cb37adf93deb7310d4151f4c9bd9cd01d3a578 Author: Andy Nonaka Date: Mon Jul 10 16:56:41 2023 -0700 y box index bug exec/thinFilm/main_driver.cpp commit 620be835d1eeef6dc192a5c26d1de77819e79b0c Author: Andy Nonaka Date: Mon Jul 10 16:32:36 2023 -0700 3 supported bc types exec/thinFilm/main_driver.cpp commit f7629189bc3a55e2a013d835cb2f701ac6e1eef4 Author: Andy Nonaka Date: Mon Jul 10 15:39:06 2023 -0700 bc hooks exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp commit b576723b30d82711a57b4ab73e72c80390afc606 Author: Ishan Srivastava Date: Mon Jul 10 13:09:07 2023 -0700 set turbForcing flags correctly src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit ae486d734e9e24fe824bc7235b799d08a4bc9d13 Author: Andy Nonaka Date: Mon Jul 10 11:36:06 2023 -0700 plotfile name exec/thinFilm/main_driver.cpp commit 7d6275a6c423b018e45f1a29a1e6eae1fc6774c8 Author: Andy Nonaka Date: Mon Jul 10 10:45:06 2023 -0700 1D mode in y exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d exec/thinFilm/main_driver.cpp commit 599fff74c695165c113f4919c9c52dd46fda62af Author: Andy Nonaka Date: Mon Jul 10 08:35:15 2023 -0700 more time steps exec/thinFilm/inputs_1d exec/thinFilm/inputs_2d commit 88b5560051e22a5c71d1a708831f9083ddc0b5be Author: isriva Date: Fri Jul 7 13:50:52 2023 -0700 added forced turbulence in compressible staggered. needs testing src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/Make.package src_compressible_stag/TurbForcingComp.H src_compressible_stag/TurbForcingComp.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit 5888944661168810678bb898d9eb0e7cfceb766f Merge: 92e157f7 150e2a79 Author: jbb Date: Fri Jul 7 10:04:30 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 92e157f77d99330d7edca8a2365adede948ab991 Author: jbb Date: Fri Jul 7 10:03:22 2023 -0700 added inputs to run PNAS paper results exec/multispec/_PNAS_inputs/README exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_3.0 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_3.25 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_3.5 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_3.75 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_4.0 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_4.25 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_4.5 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_4.75 exec/multispec/_PNAS_inputs/_laplace_pressure/inputs_bubble_chi_5.0 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_3.0 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_3.25 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_3.5 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_3.75 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_4.0 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_4.25 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_4.5 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_4.75 exec/multispec/_PNAS_inputs/_thickness/inputs_slab_chi_5.0 exec/multispec/_PNAS_inputs/inputs_RayleighPlateau exec/multispec/_PNAS_inputs/inputs_high_schmidt exec/multispec/_PNAS_inputs/inputs_spectrum exec/multispec/_PNAS_inputs/inputs_torus commit be6c7f1b374c9eb11bc589954af11c225b15595c Author: Andy Nonaka Date: Fri Jul 7 08:15:38 2023 -0700 stats work exec/thinFilm/inputs exec/thinFilm/inputs_1d exec/thinFilm/main_driver.cpp commit 28981cd8939b9352fb872711742bf81526974024 Author: isriva Date: Wed Jul 5 14:11:51 2023 -0700 also output other spectra (rho, press, temp) src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible_stag/main_driver.cpp commit 3b52e055129118cb1a64aa9f5f7b95ec798b58da Author: isriva Date: Wed Jul 5 12:57:58 2023 -0700 fixed taylor-green inputs file exec/compressible_stag/inputs_taylor_green_turbulence commit fcb81ec164176dd405cf70fc96ee8e1a94bd20d0 Merge: a9501472 150e2a79 Author: isriva Date: Wed Jul 5 12:57:39 2023 -0700 Merge remote-tracking branch 'origin/main' into compressible_tgv commit 150e2a79f7d16283fda782cc6f75d28eeea0cdcd Author: jgalenwang Date: Wed Jun 28 16:29:29 2023 -0700 defined MAX_BONDS src_common/common_namespace.H commit f959b0f33c62707ec0fe74161895126aa8070984 Author: jgalenwang Date: Wed Jun 28 15:54:32 2023 -0700 fixed RFD; added loadBonds function src_common/common_functions.cpp src_common/common_namespace.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit deb5d317afd6ba44b8ab82238c3fad1a099391c8 Author: Andy Nonaka Date: Wed Jun 28 10:29:52 2023 -0700 1d option exec/thinFilm/inputs_1d commit da2e3086c773940a949ffc386cd565c7053cb658 Author: Andy Nonaka Date: Wed Jun 28 10:14:32 2023 -0700 1d option; algorithm_type=1 makes each row an independent trial exec/thinFilm/main_driver.cpp commit aa12202a64b71bae21fc6aafb7c915b48e933504 Author: Andy Nonaka Date: Wed Jun 28 10:00:45 2023 -0700 update time exec/thinFilm/main_driver.cpp commit 12164279f1e90608930d0e4cacc923f37de3ca85 Author: Andy Nonaka Date: Wed Jun 28 09:59:53 2023 -0700 fill h ghost cells after update exec/thinFilm/main_driver.cpp commit 2ac3f4a69837c739496c0c43f55a7fd8fcfa6e60 Author: Andy Nonaka Date: Wed Jun 28 09:56:40 2023 -0700 typo exec/thinFilm/main_driver.cpp commit f8aa5a5103cc31d6714f8eac3776e2b9c922be8e Author: Andy Nonaka Date: Wed Jun 28 09:52:09 2023 -0700 first cut at thin film 2d exec/multispec/inputs_droplet_3d_mod exec/thinFilm/inputs exec/thinFilm/main_driver.cpp commit 30a02c95b5f93c3b1bb06d3dc38f5db5b7fb6af9 Author: Andy Nonaka Date: Tue Jun 27 18:12:13 2023 -0700 2d thin film starting point exec/thinFilm/GNUmakefile exec/thinFilm/inputs exec/thinFilm/main_driver.cpp commit a950147232d2789c7d792da3e575771bb71be90a Author: isriva Date: Wed Jun 21 13:11:07 2023 -0700 added TG vortex inputs file exec/compressible_stag/inputs_taylor_green_turbulence commit 716d1529925ebee0cf219bcc428f97af6889fb1f Merge: 6c4a46a6 41e52452 Author: Andy Nonaka Date: Mon Jun 12 11:46:57 2023 -0700 Merge pull request #133 from AMReX-FHD/add_bds_proj Add BDS Edge State Projection commit 41e5245235804992078b6106cd8a545c3dcc73ff Author: Andy Nonaka Date: Mon Jun 12 10:40:08 2023 -0700 bds edge state projection work exec/multispec/inputs_2_bubbles_3d src_hydro/hydro_functions.H commit 5b288ce69411841012417f8170b9f70d56672e89 Author: Andy Nonaka Date: Mon Jun 12 10:36:11 2023 -0700 EOS edge state projection for boussinesq with bds exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 6bda398db53de03e1e5bf2e60ca35864bd0dcf16 Author: Andy Nonaka Date: Fri Jun 9 18:13:33 2023 -0700 adding bds edge state projection - WIP src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 6c4a46a699aac45c0ecf04e95cee83c00ddc2549 Merge: de7fe6af a8885381 Author: Andy Nonaka Date: Fri Jun 9 11:37:17 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit de7fe6af8a3abf88a2859b6a7cef3a55439a717a Author: Andy Nonaka Date: Fri Jun 9 11:35:51 2023 -0700 fix rng sequence preserving for boussinesq exec/multispec/AdvanceTimestepBousq.cpp src_multispec/InitialProjection.cpp commit a888538152db3d791135bef2c0d4debaf2213b28 Author: jbb Date: Fri Jun 9 10:56:27 2023 -0700 tweaked smoothing exec/multispec/Init.cpp commit 03a4e4f6865d269c44c0605374900ce5d5a2a42c Merge: 40cd9a3c 15c0c84d Author: jbb Date: Fri Jun 9 09:12:46 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 40cd9a3c3fb63f82239ac88eb946e4316af3cb6e Author: jbb Date: Fri Jun 9 09:12:01 2023 -0700 added smoothed interface model exec/multispec/Init.cpp commit 15c0c84ddcc244212f540d21dba660f0103b1c36 Author: Andy Nonaka Date: Fri Jun 9 09:07:11 2023 -0700 fix RNG consistency in bousinesq alg upon initialization exec/multispec/AdvanceTimestepBousq.cpp src_multispec/InitialProjection.cpp commit 25127484ae3a2973723a17e78decce8ba4d92613 Author: Andy Nonaka Date: Thu Jun 8 18:15:50 2023 -0700 turn on initial projection for boussinesq algorithm exec/multispec/main_driver.cpp src_multispec/InitialProjection.cpp commit 8310e61d86b7c5c868dc502393dc5642fd1da40a Author: Andy Nonaka Date: Thu Jun 8 14:57:12 2023 -0700 use limited bds instead of unlimited exec/multispec/inputs_droplet_3d exec/multispec/inputs_droplet_3d_mod commit 3cc8fdf1992caa938f7ebf20b14c9abb3cd67d6e Merge: ab1ad5f0 b0328651 Author: Andy Nonaka Date: Thu Jun 8 14:51:54 2023 -0700 Merge branch 'main' into thinfilm commit b0328651e1cea219cf3a0e09f283a0f35005e0bc Merge: 8aa1f951 bc5b4f49 Author: Andy Nonaka Date: Thu Jun 8 14:51:12 2023 -0700 Merge pull request #132 from AMReX-FHD/more_bds BDS Advection for Boussinesq commit ab1ad5f043d8eb0e32add9299c2722d8090ad956 Merge: 8bba7d25 8aa1f951 Author: Andy Nonaka Date: Thu Jun 8 14:30:56 2023 -0700 Merge branch 'main' into thinfilm commit bc5b4f49f7d54ca739facb7aa45737edc96ccec9 Author: Andy Nonaka Date: Thu Jun 8 14:29:01 2023 -0700 bds for boussinesq working exec/multispec/AdvanceTimestepBousq.cpp commit 8aa1f9510d67c1eb71fdcda664c5919ac9d1636f Author: Matteo Polimeno Date: Thu Jun 8 14:02:11 2023 -0700 exec/compressible_stag/test_NO2_dimerization_neq: updated input files and clean.sh to include restart routine exec/compressible_stag/test_NO2_dimerization_neq/clean.sh exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq commit 148dc4a5a21bba85281548ab6ce53cde6adc0d10 Author: Andy Nonaka Date: Wed Jun 7 18:39:54 2023 -0700 more BDS updates - still WIP exec/multispec/AdvanceTimestepBousq.cpp commit 0844ab5aaa3ad89736015ded33ca7ffc8f6e5395 Author: Andy Nonaka Date: Wed Jun 7 14:52:23 2023 -0700 WIP - implement BDS in the boussinesq algorithm Also the ghost cell treatment in the inertial algorithm needs work (extrapolation ghost filler needed) exec/multispec/AdvanceTimestepBousq.cpp commit a9ef8de1e5b494dc22f024c5a4ea6fec43ea7939 Author: Daniel Ladiges Date: Wed Jun 7 13:05:08 2023 -0700 added some input files for diagnostics exec/multispec/inputs_droplet_3d exec/multispec/inputs_droplet_3d_mod commit 77c7ebbaa101eb2424c0aa7765adbc57711ae0cb Merge: 2c56f631 27ce544c Author: jbbel Date: Tue Jun 6 13:26:30 2023 -0700 Merge pull request #131 from AMReX-FHD/flory_huggins Flory huggins commit 27ce544cb9dcb95ed008c5ee63ccac63bdfde877 Merge: ed8baafd 37f703f0 Author: John Bell Date: Tue Jun 6 12:57:10 2023 -0700 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit ed8baafd0a11a0c568bd2aaaede5f5bb7740ec62 Author: John Bell Date: Tue Jun 6 10:10:12 2023 -0700 minor tweaks exec/hydro/GNUmakefile exec/multispec/GNUmakefile exec/multispec/Init.cpp src_multispec/ComputeMassFluxdiv.cpp commit 2c56f6314d18fb4a22b773e6b3691fbfbe0edc9e Merge: 7369c276 331d5eb2 Author: jbb Date: Fri Jun 2 11:17:02 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7369c276b6555b7a8e8e8ac0543e9e3ee2c0e8e4 Author: jbb Date: Fri Jun 2 11:15:46 2023 -0700 added 1d hybrid exec/_1d_dk_hybrid/Makefile exec/_1d_dk_hybrid/driver.f exec/_1d_dk_hybrid/flux.f exec/_1d_dk_hybrid/inputs_fv exec/_1d_dk_hybrid/inputs_hybrid exec/_1d_dk_hybrid/inputs_pure exec/_1d_dk_hybrid/particles.f exec/_1d_dk_hybrid/stats.c commit 8bba7d25fdff685314cb45dede1160c7053aeaa7 Merge: 0edb8f2e 331d5eb2 Author: Andy Nonaka Date: Thu May 11 14:12:48 2023 -0700 Merge branch 'main' into thinfilm commit 331d5eb2bfafbcea77c82fa376906fb512ff6631 Author: Andy Nonaka Date: Thu May 11 14:11:48 2023 -0700 properly implement gravity in corrector step of low mach inertial alg exec/multispec/AdvanceTimestepInertial.cpp commit f08b26bd5282ef971c698fb97bbd2df263cbf6aa Merge: 40cfe5d0 b931e447 Author: Andy Nonaka Date: Thu May 11 14:02:41 2023 -0700 Merge pull request #130 from AMReX-FHD/stag_chemistry FHDeX/src_compressible_stag: adding chemistry source commit b931e44724ed451a3bf9e485491ed20eb4d87bfc Author: Changho Kim Date: Thu May 11 00:57:03 2023 -0700 exec/compressible_stag: test_NO2_dimerization_eq, test_NO2_dimerization_neq exec/compressible_stag/test_NO2_dimerization_eq/README exec/compressible_stag/test_NO2_dimerization_eq/clean.sh exec/compressible_stag/test_NO2_dimerization_eq/diff.sh exec/compressible_stag/test_NO2_dimerization_eq/inputs_NO2_dimerization_eq exec/compressible_stag/test_NO2_dimerization_eq/job_script.sh exec/compressible_stag/test_NO2_dimerization_eq/params_NO2_N2O4_thermochem.py exec/compressible_stag/test_NO2_dimerization_eq/params_NO2_dimerization_eq.py exec/compressible_stag/test_NO2_dimerization_eq/submit_job.sh exec/compressible_stag/test_NO2_dimerization_neq/README exec/compressible_stag/test_NO2_dimerization_neq/avg.sh exec/compressible_stag/test_NO2_dimerization_neq/clean.sh exec/compressible_stag/test_NO2_dimerization_neq/diff.sh exec/compressible_stag/test_NO2_dimerization_neq/inputs_NO2_dimerization_neq exec/compressible_stag/test_NO2_dimerization_neq/job_script.sh exec/compressible_stag/test_NO2_dimerization_neq/params_NO2_dimerization_rate_const.py exec/compressible_stag/test_NO2_dimerization_neq/submit_job.sh commit 40cfe5d04f3922124375473e0940b57ad8980219 Author: Daniel Ladiges Date: Tue May 9 11:05:40 2023 -0700 Removed accidental change to timestep causing regression fails exec/immersedIons/main_driver.cpp commit d1859315b4bf9e48be33e30645d3d169969c2274 Author: isriva Date: Thu May 4 10:59:06 2023 -0700 elaborate stats routine for compressible turbulence src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/main_driver.cpp commit 6567adac4e4dbb60e53d691c6766782e5e5873c6 Author: Matteo Polimeno Date: Tue May 2 12:50:34 2023 -0700 FHDeX/src_compressible_stag: adding chemistry source src_compressible_stag/compressible_functions_stag.H src_compressible_stag/main_driver.cpp src_compressible_stag/timeStepStag.cpp commit 55d550aabddbdc9eee724fd7784e01d646babb2f Author: isriva Date: Fri Apr 28 08:01:12 2023 -0700 add energy spectrum calculation src_compressible_stag/main_driver.cpp commit a4dc5272ecb53b70165776dbc64fb10cda953140 Author: isriva Date: Wed Apr 26 10:24:52 2023 -0700 contant rho, varying p and rho TGV src_compressible/compressible_functions.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/main_driver.cpp commit 544a425d67be03fd734a48383e041ca83ef214e5 Author: isriva Date: Mon Apr 24 15:59:15 2023 -0700 setup Taylor-Green Vortex in compressible code src_common/common_functions.cpp src_common/common_namespace.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/main_driver.cpp commit 262e79fff8a75933559a615d31a95acd97551baf Author: Andy Nonaka Date: Fri Apr 21 09:52:27 2023 -0700 fix compilation issue for multispecies exec/multispec/AdvanceTimestepInertial.cpp commit 345f38fbca1b008abe48ddd66bf371a2b3def960 Merge: 790ac25a 606147fe Author: Daniel Ladiges Date: Wed Apr 19 12:01:02 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 790ac25ad9a344321a8cf06b03c03210036dc05d Author: Daniel Ladiges Date: Wed Apr 19 11:57:30 2023 -0700 Saving some changes to droplet collisions, phonons, and DSMC before branch switch exec/DSMC/inputs_conc exec/DSMC/main_driver.cpp exec/DSMC/stats.cpp exec/DSMC/writePlotFile.cpp exec/immersedIons/delPlots exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/Init.cpp exec/multispec/inputs_2_bubbles_3d exec/multispec/main_driver.cpp src_analysis/StructFact.cpp src_geometry/paramPlane.H src_geometry/paramplane_functions_K.H src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp src_particles/DsmcParticleContainer.cpp commit 0ab86cc547fe54bcf1197d018390c9b328a85bb9 Merge: 9626a8b7 606147fe Author: isriva Date: Wed Apr 12 15:19:34 2023 -0700 Merge remote-tracking branch 'origin/main' into reservoir_compress commit 606147fee1fc874c5dac424f92e815ebd89b7d98 Author: jbb Date: Tue Apr 4 17:01:53 2023 -0700 remove debugging src_deankow/mykernel.H commit ba2b869dce24a8c72e0cdb359a14f802a079c877 Author: jbb Date: Fri Mar 31 14:52:29 2023 -0700 changed to work with number density and added diagnostics src_deankow/main.cpp src_deankow/myfunc.H src_deankow/myfunc.cpp src_deankow/mykernel.H commit 298247e2b2cf4c21faeb64b4d7cbda17a48f7831 Merge: 6807dc7e 29a48eb2 Author: jbb Date: Fri Mar 31 12:48:41 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 29a48eb2bd08097b89f7688abc8ee18f01eda3d9 Author: Changho Kim Date: Wed Mar 29 17:56:37 2023 -0700 exec/compressible_stag_mui/test_O2Ar_eq_slurm exec/compressible_stag_mui/test_O2Ar_eq_slurm/README exec/compressible_stag_mui/test_O2Ar_eq_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/diff.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/params_O2Ar.py exec/compressible_stag_mui/test_O2Ar_eq_slurm/zavg.plt exec/compressible_stag_mui/test_O2Ar_eq_slurm/zavg_rhoY1mean.plt exec/compressible_stag_mui/test_O2Ar_eq_slurm/zavg_rhoY1mean.sh commit 0edb8f2e5b8a925f49ff329e9b498b5e9027aa91 Author: Andy Nonaka Date: Mon Mar 27 11:21:40 2023 -0700 fix error message logic exec/multispec/main_driver.cpp commit 0bcb970aac6a126f75eff54f44547c26e2a2dd0a Author: Changho Kim Date: Mon Mar 27 01:53:30 2023 -0700 exec/compressible_stag_mui/test_O2Ar_eq_slurm: correct setup and scripts exec/compressible_stag/test_MFsurfchem_COAr_eq/README exec/compressible_stag/test_MFsurfchem_COAr_eq/diff.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/README exec/compressible_stag_mui/test_O2Ar_eq_slurm/ads.plt exec/compressible_stag_mui/test_O2Ar_eq_slurm/ads.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/amrex_mpmd.conf exec/compressible_stag_mui/test_O2Ar_eq_slurm/diff.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_O2Ar_eq_slurm/params_O2Ar.py exec/compressible_stag_mui/test_O2Ar_eq_slurm/zavg.plt exec/compressible_stag_mui/test_O2Ar_eq_slurm/zavg.sh commit 26665434c383419b504ce6b93aa1010ac93eca15 Merge: 9061cd56 b63169d0 Author: Andy Nonaka Date: Wed Mar 22 14:36:51 2023 -0700 Merge branch 'main' into thinfilm commit b63169d00a78e1e0f91efb74dcb7d476ddd76105 Merge: 5c16a4c8 37f703f0 Author: Andy Nonaka Date: Wed Mar 22 14:36:40 2023 -0700 Merge pull request #92 from AMReX-FHD/flory_huggins bulk of functionality to do general flory huggins still a WIP commit 9061cd562a76dcc291e839cc07b0d7acf6d29185 Author: Andy Nonaka Date: Tue Mar 21 11:27:56 2023 -0700 compute eta correctly for both inertial algorithms add error checking exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp commit 6e29fc7c5d3d6d80688cdba8528f790353868c9e Author: Andy Nonaka Date: Mon Mar 20 12:48:31 2023 -0700 fix variable viscosity exec/multispec/inputs.slab exec/multispec/inputs.slab_2d commit c7bd26642cd7b2481d05050adcf3d9a02c8a38f7 Merge: 13014f7a 37f703f0 Author: Andy Nonaka Date: Mon Mar 20 12:43:32 2023 -0700 Merge branch 'flory_huggins' into thinfilm commit 37f703f0ff8bcb0ef575b278580ebc14a73d9e30 Merge: 3866e421 5c16a4c8 Author: Andy Nonaka Date: Mon Mar 20 12:43:08 2023 -0700 Merge branch 'main' into flory_huggins commit 5c16a4c8bcb16c50980c2767f9fcb78be2383b26 Author: Daniel Ladiges Date: Mon Mar 20 09:06:46 2023 -0700 REverted number of ghost cells in MFCopy in stochmflux src_hydro/StochMomFlux.cpp commit e907b0f2003675f7a7882fcfaea54a8bdf859b3b Author: Daniel Ladiges Date: Fri Mar 17 17:45:42 2023 -0700 Changed number of ghost cells on noise MF to fix reg test src_hydro/StochMomFlux.cpp commit 13014f7a8604d23ebf44522cb973a611a0da4128 Author: Andy Nonaka Date: Thu Mar 16 16:30:31 2023 -0700 thinfilm branching off flory_huggins - WIP to make parallel work without bugs exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/inputs.slab_2d exec/multispec/main_driver.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/multispec_functions.H commit 5640ce73ee6c59c26b622179e32144ef672cc1de Merge: bbbd9038 515877da Author: Daniel Ladiges Date: Thu Mar 16 16:00:27 2023 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit bbbd903868f40f6cd777188257169be7fe4f14df Author: Daniel Ladiges Date: Thu Mar 16 15:59:14 2023 -0700 Added third order stochastic divergence function to test FDT Added extra layer of ghost cells to multifab holding noise terms src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 3866e4213d4e7a601e204916b99e3e24307c8ff1 Author: John Bell Date: Wed Mar 15 14:00:07 2023 -0700 fix bug in film thickness thing exec/multispec/Init.cpp commit 676a0bf812ac73c989d5b3170659d47c895c6715 Author: John Bell Date: Wed Mar 15 13:40:51 2023 -0700 added inputs for slab geometry exec/multispec/inputs.slab commit 0ca087308120054b0fb07b287b1a4b3c4c120eed Author: John Bell Date: Wed Mar 15 13:39:58 2023 -0700 add torus and slab configurations for Flory Huggins exec/multispec/Init.cpp src_common/common_functions.cpp src_common/common_namespace.H commit 56ef828f89f1144e84f2ff0616c1f4f079f7b2f2 Author: John Bell Date: Wed Mar 15 12:47:36 2023 -0700 fix trace species for more than 3 species src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H commit 515877daa04ba9b160c6939251d5d235df759715 Merge: 7394fac7 efcc6db8 Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Wed Mar 15 00:39:57 2023 -0700 Merge pull request #128 from AMReX-FHD/surfchemtest Surfchemtest commit efcc6db8380817f29d50fb740dd71c5f3d6ceb98 Author: HyuntaeJung Date: Mon Mar 13 18:09:58 2023 -0700 compressible_stag_mui nspec_mui=3 test exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/ads.py exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/ads.sh exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/amrex_mpmd.conf exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/clean.sh exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/create_site_file.py exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/event_rate_FHD.py exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/in.kmc_amrex exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COO2CO2Ar_reaction_slurm/submit_job.sh commit 26b574fc5fd835cd476d59191132d1eecea9d4c2 Author: HyuntaeJung Date: Mon Mar 13 18:08:47 2023 -0700 nspec_mui=3 case (FHD), reaction event & TOF (KMC) exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_stag_mui/SPPARKS_MUI/diag_surfchemtest.cpp src_surfchem_amrex/surfchem_mui_functions.cpp commit 7394fac76a7d19865b242c0f7e11d5149c638dab Merge: d6135e1b 2491d26e Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Mon Mar 13 16:07:43 2023 -0700 Merge pull request #127 from AMReX-FHD/surfchemtest New branch first commit commit d6135e1b58a154098c6c859d63b1fa6d93d44b28 Author: Changho Kim Date: Mon Mar 13 04:06:37 2023 -0700 exec/compressible_stag/test_MFsurfchem_COAr_eq: README exec/compressible_stag/test_MFsurfchem_COAr_eq/README exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.py exec/compressible_stag/test_MFsurfchem_COAr_eq/diff.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/job_script.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/mass_cons.py exec/compressible_stag/test_MFsurfchem_COAr_eq/submit_job.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/theta_eq.py commit 6807dc7e375a39d276513537304ddb9c77df60e9 Merge: 8767c6ff b057831a Author: jbb Date: Tue Jan 17 17:04:00 2023 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 2491d26e2e9b7efbb97e49bc43e3265be09a487e Author: HyuntaeJung Date: Thu Dec 15 19:03:00 2022 -0800 compressible_stag_mui tests exec/compressible_stag_mui/test_COO2Ar_eq_slurm/ads.py exec/compressible_stag_mui/test_COO2Ar_eq_slurm/ads.sh exec/compressible_stag_mui/test_COO2Ar_eq_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_COO2Ar_eq_slurm/amrex_mpmd.conf exec/compressible_stag_mui/test_COO2Ar_eq_slurm/clean.sh exec/compressible_stag_mui/test_COO2Ar_eq_slurm/create_site_file.py exec/compressible_stag_mui/test_COO2Ar_eq_slurm/data.strips exec/compressible_stag_mui/test_COO2Ar_eq_slurm/in.kmc_amrex exec/compressible_stag_mui/test_COO2Ar_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COO2Ar_eq_slurm/params_COO2Ar_eq.py exec/compressible_stag_mui/test_COO2Ar_eq_slurm/submit_job.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/ads.py exec/compressible_stag_mui/test_O2Ar_eq_slurm/ads.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/amrex_mpmd.conf exec/compressible_stag_mui/test_O2Ar_eq_slurm/clean.sh exec/compressible_stag_mui/test_O2Ar_eq_slurm/data.strips exec/compressible_stag_mui/test_O2Ar_eq_slurm/in.kmc_amrex exec/compressible_stag_mui/test_O2Ar_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_O2Ar_eq_slurm/params_O2Ar.py exec/compressible_stag_mui/test_O2Ar_eq_slurm/submit_job.sh commit 24778cc987d1f6a53cabdaf21cb7ceb0f2970047 Author: Hyuntae Jung Date: Thu Dec 15 18:06:30 2022 -0800 nspec_mui 2 code exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h src_surfchem_amrex/surfchem_mui_functions.cpp commit b057831a7909b0afc5d2a445427b3b1569c8a2a7 Author: Daniel Ladiges Date: Tue Nov 1 10:35:29 2022 -0700 modified some flagellum related code so the DISCOS compiles for GPU. Have to test pushup/pulldown functions on GPU still src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp commit 14a7f4c469ab1f3034d27a6c361c169142248532 Author: Daniel Ladiges Date: Wed Oct 26 15:16:52 2022 -0700 reverted previous commit src_immersed-boundary/IBMarkerContainerBaseI.H commit c9c74c9aeb0097eb66f0fe960968f9b08aeca4d7 Author: Daniel Ladiges Date: Wed Oct 26 14:55:19 2022 -0700 Temporary comment out of UpdatePIDMap (flagellum related) to figure out CUDA compilation in main branch src_immersed-boundary/IBMarkerContainerBaseI.H commit e2e34af1690fac498b3d3ed33f6ed2a6d3b30658 Author: Daniel Ladiges Date: Wed Oct 26 13:58:45 2022 -0700 Mods to DISCOS for flows with body force exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp commit f4f68ce53665b6b5fb33a5a52fdbc9d0243c1ef1 Author: Daniel Ladiges Date: Tue Oct 25 16:45:00 2022 -0700 Added body force variable to common namespace exec/immersedIons/inputs_template src_common/common_functions.cpp src_common/common_namespace.H commit d1bdb99c8db7e2452b46680b2d89e5b525755540 Merge: d196883c e860cd25 Author: Daniel Ladiges Date: Mon Oct 24 11:50:09 2022 -0700 Merge pull request #125 from jackieyao0114/main fixed totalparts writing error commit e860cd2502446e7dd9da9df8e84a5d263553af1a Author: Zhi (Jackie) Yao <58234082+jackieyao0114@users.noreply.github.com> Date: Mon Oct 24 11:48:48 2022 -0700 Delete paramplanes.dat exec/phononDSMC/paper_aligned/paramplanes.dat commit c461f68c600f271d48e83f16a69efe6dfbcff77c Author: jackieyao0114 Date: Mon Oct 24 11:41:28 2022 -0700 fixed totalparts writing error exec/phononDSMC/paper_aligned/paramplanes.dat src_particles/DsmcParticleContainer.cpp commit d196883cda2a18b23006c6ff7af3da22edc56c5e Merge: 6fb02a02 abbf3d38 Author: Daniel Ladiges Date: Wed Oct 19 11:36:41 2022 -0700 Merge pull request #124 from jackieyao0114/main Added functionality of writing out "totalparts" file commit 8767c6ff4fee8d1e361da1f2d45f9abcb8da01d7 Merge: 58cd0573 6fb02a02 Author: jbb Date: Wed Oct 19 09:44:51 2022 -0700 M rge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 481f5bd6ad1e7ca7a65a8f19d7aba7bad2fdc6bb Author: jbb Date: Wed Oct 19 09:44:05 2022 -0700 tweaks to initial conditions exec/multispec/GNUmakefile exec/multispec/Init.cpp src_multispec/ComputeMassFluxdiv.cpp commit abbf3d384b24db4e23f8825869683477b6fc082c Author: Zhi (Jackie) Yao <58234082+jackieyao0114@users.noreply.github.com> Date: Tue Oct 18 17:25:00 2022 -0700 Update GNUmakefile exec/DSMC/GNUmakefile commit 11cef0d3c6dda23081e60df703c893ceb4136157 Merge: 941987b2 6183b9ea Author: jackieyao0114 Date: Tue Oct 18 17:21:02 2022 -0700 Merge branch 'main' of https://github.com/jackieyao0114/FHDeX into main commit 941987b2890d1c37cccbdd055f38ef50827c6bf2 Author: jackieyao0114 Date: Tue Oct 18 17:20:47 2022 -0700 output totalparts file src_particles/DsmcParticleContainer.cpp commit 6183b9ea66e3c12072add31ad4de3a1efb5c6fe6 Merge: 66a34c58 fcb92f9d Author: jackieyao0114 Date: Tue Oct 18 15:28:26 2022 -0700 Merge branch 'main' of https://github.com/jackieyao0114/FHDeX into main commit 66a34c58c8169cf288c4025198ede6d2486a4778 Author: jackieyao0114 Date: Tue Oct 18 15:28:19 2022 -0700 synced with upstream/main exec/phononDSMC/GNUmakefile exec/phononDSMC/GNUmakefile commit fcb92f9d35965609345554c6822dc83d8872edc3 Merge: 63b455d4 6fb02a02 Author: jackieyao0114 Date: Tue Oct 18 14:07:10 2022 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 6fb02a0207cc0b151e2c2b5af366a238bbc37cf8 Merge: 5cbad13a b2a9fc06 Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Sun Oct 16 01:38:10 2022 -0700 Merge pull request #123 from AMReX-FHD/branch_surfchemtest New branch first commit commit e1992594201f814931ec1ddf04f7121ff01db0ae Author: John Bell Date: Fri Oct 14 12:06:06 2022 -0700 changes to some initial conditions exec/multispec/Init.cpp commit 53b0c55cf42202b94b2e71cf3d031f0b815a615e Author: John Bell Date: Fri Oct 14 12:04:10 2022 -0700 added additional inputs file exec/multispec/inputs_fh_3d_cyl_hi commit 5cbad13af974b5b93677dd9e9431f3db1cdf2dc2 Author: Daniel Ladiges Date: Thu Oct 13 15:26:01 2022 -0700 Fixed output bug in phonon code src_common/common_namespace.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit b2a9fc069772b191ac8693d58f12b21441600deb Author: HyuntaeJung Date: Thu Oct 13 08:34:27 2022 +0900 New branch first commit exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit bbc24b0504b0bdcae1e9b24ad8506d7131e899d5 Author: Daniel Ladiges Date: Tue Oct 11 16:22:12 2022 -0700 Forgot to add some files... src_geometry/MakeDSMC.package src_geometry/paramplane_phonon_functions_K.H commit e250897d3cf90ba6a1516495a6fd197c0cbc42a5 Merge: 740e6fbb 8887b4f2 Author: Daniel Ladiges Date: Tue Oct 11 15:50:10 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 740e6fbb18be2efe9ca6aad5f096633227708ca5 Author: Daniel Ladiges Date: Tue Oct 11 15:49:30 2022 -0700 Further GPU optimization for phononDSMC exec/phononDSMC/GNUmakefile exec/phononDSMC/main_driver.cpp src_common/common_namespace.H src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit 8887b4f2f3050c6c1f3cdea31016cc4fefeef813 Merge: 8a8dde60 808d4f21 Author: Andy Nonaka Date: Tue Oct 11 13:43:09 2022 -0700 Merge pull request #121 from AMReX-FHD/BDS BDS commit 8a8dde60d91913269d2a7dd41404a3d23adc4cb6 Author: Daniel Ladiges Date: Tue Oct 11 11:48:17 2022 -0700 Fixed DISCOS compliation bug (trying to compile a phonon function) src_common/common_namespace.H src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 05cab0fc7b0791c4e091bc3ed523a66f752494c3 Author: Daniel Ladiges Date: Wed Oct 5 17:55:17 2022 -0700 Phonon DSMC now running on GPU. Have to optimize file writing and stats recording exec/phononDSMC/delPlots exec/phononDSMC/main_driver.cpp exec/phononDSMC/particleGen.cpp exec/phononDSMC/py/paramPlane.ipynb src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 79f9c6cb55165efe9288101259a48b2ba1f113e0 Author: Daniel Ladiges Date: Mon Oct 3 16:42:11 2022 -0700 Finishing phonon GPU conversion. Code now compiles but doesn't run exec/DSMC/inputs_conc exec/DSMC/main_driver.cpp exec/phononDSMC/GNUmakefile exec/phononDSMC/Make.package exec/phononDSMC/stats.cpp exec/phononDSMC/test_inputs/input_test src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 3c50505fa1b9f6a76aa8ebfaa81a9590fd937aec Author: jbb Date: Thu Sep 22 09:58:53 2022 -0700 fixed test in higher-order term src_deankow/mykernel.H src_multispec/DiffusiveMassFluxdiv.cpp commit 14eabdff0d233d1e689afbae4e7fec2461f5d7d3 Author: jbb Date: Tue Sep 20 13:49:55 2022 -0700 fix test for dx == dy == dz src_multispec/DiffusiveMassFluxdiv.cpp commit 808d4f21e2099b8286605bc1d3410093b9b38836 Author: Andy Nonaka Date: Wed Aug 31 18:13:02 2022 -0700 index bugfix src_hydro/BDS.cpp commit c79715a2cb63c0dbccb488cbf3f12e880afa7720 Author: Andy Nonaka Date: Wed Aug 31 17:45:54 2022 -0700 time center velocity in corrector exec/multispec/AdvanceTimestepInertial.cpp commit ae6624884dbd56d7bbaf4085fe7426f9206b9dcb Author: Andy Nonaka Date: Wed Aug 31 17:44:22 2022 -0700 first cut at inertial BDS - WIP exec/multispec/AdvanceTimestepInertial.cpp src_hydro/hydro_functions.H commit 8ee254395361558116400e92eb2536e7847ba199 Author: Andy Nonaka Date: Wed Aug 31 17:05:02 2022 -0700 add advection_type hook add option for limiting in BDS exec/multispec/AdvanceTimestepInertial.cpp src_common/common_functions.cpp src_common/common_namespace.H src_hydro/BDS.cpp commit d7b7124b86fa1f5ddf2c908ebf131e3f1d0ccc04 Author: Andy Nonaka Date: Wed Aug 31 15:38:22 2022 -0700 boundary condition support src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 69945ab37cf3042fb5fe974b58b5bc3f39680032 Author: Andy Nonaka Date: Wed Aug 31 15:20:34 2022 -0700 toward working BDS src_hydro/BDS.cpp src_hydro/hydro_functions.H commit af7ad22423390951f1f18ad8019b72f470e8e3d6 Author: Andy Nonaka Date: Tue Aug 30 17:50:17 2022 -0700 more cleanup src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 93d493f1b288d2ae6b857c1a563b123cf9b7807e Author: Andy Nonaka Date: Tue Aug 30 17:06:20 2022 -0700 remove more unneeded options src_hydro/BDS.cpp commit 9043baff74ad273358769106a7ed97c4e6fc79b3 Author: Andy Nonaka Date: Tue Aug 30 16:58:21 2022 -0700 get rid of velocity-advection specific flags src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 8d40cbff2c4b6f670d0a9ad5404a6f6125a640d0 Author: Andy Nonaka Date: Tue Aug 30 16:47:25 2022 -0700 remove non-conservative discretization src_hydro/BDS.cpp src_hydro/hydro_functions.H commit 94281b6a24d693f1481dc841017762ce4b777e10 Author: Andy Nonaka Date: Tue Aug 30 16:16:39 2022 -0700 BDS port begins src_hydro/BDS.cpp src_hydro/Make.package src_hydro/hydro_functions.H commit b22055d836c968e13d18efb89f9ff30fdb3940aa Merge: 63b455d4 296a85cd Author: jackieyao0114 Date: Mon Aug 22 15:33:52 2022 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 61eb3c5835190146d4d548e80314e054265d075f Merge: 2f0dbbdb 4a52b6b8 Author: John Bell Date: Fri Aug 19 16:35:20 2022 -0700 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit 2f0dbbdb9db2bc943be587febe558a294429973e Author: John Bell Date: Fri Aug 19 16:33:08 2022 -0700 added dean kowasaki code exec/dean_kow/GNUmakefile exec/dean_kow/inputs exec/multispec/Init.cpp src_deankow/Make.package src_deankow/main.cpp src_deankow/myfunc.H src_deankow/myfunc.cpp src_deankow/mykernel.H commit 296a85cd3c1a5dad30e1b2392f2be17dcce00599 Merge: 17793b9a bf9680b4 Author: Daniel Ladiges Date: Tue Aug 16 15:33:23 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 17793b9a461c2c138c945440ef534ac374090e34 Author: Daniel Ladiges Date: Tue Aug 16 15:32:43 2022 -0700 Various updates for dsmc and phonon gpu exec/DSMC/DsmcCollide.cpp exec/DSMC/GNUmakefile exec/DSMC/inputs_conc exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp exec/DSMC/writePlotFile.cpp exec/immersedIons/inputs_template exec/phononDSMC/stats.cpp src_common/common_namespace.H src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit bf9680b42e9ac1927f6cee734f259e573907807b Merge: 8a0a02ef b6e30c72 Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Mon Aug 15 14:59:40 2022 -0700 Merge pull request #120 from WeiqunZhang/amrex_kmc_domain Second attempt to fix the domain decomposition bug when there are a lot of KMC processes commit b6e30c7201b624349176c2fbef3ac46c38755dcf Author: Weiqun Zhang Date: Mon Aug 15 14:20:36 2022 -0700 Second attempt to fix the domain decomposition bug when there are a lot of KMC processes. exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 8a0a02ef2d02856bf991ea84cd56c8dc4f75b6b8 Merge: 075536e4 26ba1a46 Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Thu Aug 11 14:17:01 2022 -0700 Merge pull request #119 from WeiqunZhang/amrex_kmc_domain Fix a bug when using amrex::MPMD commit 26ba1a4691491114da169d4024b18e85749c0406 Author: Weiqun Zhang Date: Thu Aug 11 13:49:59 2022 -0700 Fix a bug when using amrex::MPMD The domain decomposition on the KMC side might split an FHD cell between two different MPI processes. This commit fixes a bug that did not take this into account. exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit 075536e4fa0b66c832f8de7d986481cee1e2eb6d Merge: 53b4cbaa b7584ff4 Author: Ishan Srivastava Date: Tue Aug 9 23:00:18 2022 -0600 Merge pull request #118 from AMReX-FHD/stag_interp_prim New advection schemes in staggered compressible code commit b7584ff431cce49d24935d4cc7e44b61c266cf6d Author: isriva Date: Tue Aug 9 16:02:24 2022 -0700 added advection_type=negative resulting in no advection src_compressible_stag/fluxStag.cpp commit c6cfd07d1a6a246b3cbb3261265470882e739429 Author: isriva Date: Tue Aug 9 15:45:26 2022 -0700 swap advection scheme switches src_compressible_stag/fluxStag.cpp commit 6f440eacf03179b83ccec86b4a0137f5b10f61ce Merge: 85d1d09f 53b4cbaa Author: isriva Date: Thu Aug 4 15:04:28 2022 -0700 Merge remote-tracking branch 'origin/main' into stag_interp_prim commit 53b4cbaaae06959dc361a19a84120493a511319e Author: isriva Date: Thu Aug 4 15:02:33 2022 -0700 added a new prob_type for checkerboard setup in compressible and compressible_stag src_compressible/compressible_functions.cpp src_compressible_stag/compressible_functions_stag.cpp commit 85d1d09fc6ce344f813d1cef3fa18b23580c52a2 Author: isriva Date: Thu Aug 4 14:19:15 2022 -0700 compiles on GPU now src_common/common_functions.cpp src_common/common_namespace.H commit 04b5f60ea248bd836eb51526c1674a493254ff84 Merge: ad6493b3 24ab3111 Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Wed Aug 3 14:54:36 2022 -0700 Merge pull request #117 from WeiqunZhang/mpmd_csm Using AMReX instead of MUI to glue together FHD and KMC. commit 24ab311144501a46642ba3171aa7656d436d582f Author: Weiqun Zhang Date: Fri Jul 29 12:52:08 2022 -0700 Using AMReX instead of MUI to glue together FHD and KMC. FHD and SPPARKS are compiled with `make USE_AMREX_MPMD=TRUE USE_MUI=FALSE` and `make USE_AMREX_MPMD=TRUE USE_MUI=FALSE spk`, respectively. exec/compressible_stag_mui/GNUmakefile exec/compressible_stag_mui/SPPARKS_MUI/Make.package exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_stag_mui/SPPARKS_MUI/input.cpp exec/compressible_stag_mui/SPPARKS_MUI/main.cpp exec/compressible_stag_mui/SPPARKS_MUI/spparks.cpp exec/compressible_stag_mui/main.cpp exec/compressible_stag_mui/test_COAr_eq/in.kmc_amrex exec/compressible_stag_mui/test_COAr_eq/inputs_fhd_stag_amrex exec/compressible_stag_mui/test_COAr_eq/run_amrex.sh exec/compressible_stag_mui/test_COAr_eq_slurm/amrex_job_script.sh exec/compressible_stag_mui/test_COAr_eq_slurm/amrex_mpmd.conf exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc_amrex src_MFsurfchem/MFsurfchem_functions.cpp src_analysis/StructFact.cpp src_chemistry/chemistry_functions.cpp src_common/ComputeAverages.cpp src_common/ConvertStag.cpp src_common/InhomogeneousBCVal.H src_compressible/boundary.cpp src_compressible/checkpoint.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/flux.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp src_rng/bl_random_c.cpp src_surfchem_amrex/Make.package src_surfchem_amrex/surfchem_mui_functions.H src_surfchem_amrex/surfchem_mui_functions.cpp commit afdd62a05794f1d6f488727e2aadb5fe9a1d7c30 Author: isriva Date: Tue Aug 2 14:50:43 2022 -0700 another new advection method; advection_type = 0 (does energy flux differently -- see comments in fluxStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/main_driver.cpp commit 3f48dca618e537230efb3045bc34352ff5baf41c Merge: 7f3d04f9 ad6493b3 Author: isriva Date: Tue Aug 2 13:03:14 2022 -0700 Merge remote-tracking branch 'origin/main' into stag_interp_prim commit ad6493b3f868bc841f0fba9cad68df3d68539e97 Author: Changho Kim Date: Tue Aug 2 02:07:45 2022 -0700 compressible_stag_mui: depletion example scripts updated exec/compressible_stag_mui/test_COAr_depletion/mass_cons.py exec/compressible_stag_mui/test_COAr_depletion/zavg.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/in.kmc exec/compressible_stag_mui/test_COAr_depletion_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_depletion_slurm/mass_cons.py exec/compressible_stag_mui/test_COAr_depletion_slurm/zavg.sh commit 9f9d0eba1c9b232b9aff8532837dec470e772057 Author: Changho Kim Date: Sun Jul 31 21:10:30 2022 -0700 exec/compressible_stag_mui/test_COAr_depletion_slurm: depletion for slurm mui exec/compressible_stag_mui/test_COAr_depletion/diff.sh exec/compressible_stag_mui/test_COAr_depletion/init_rho.py exec/compressible_stag_mui/test_COAr_depletion/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_depletion/mass_cons.py exec/compressible_stag_mui/test_COAr_depletion/theta_eq.py exec/compressible_stag_mui/test_COAr_depletion/theta_eq.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/ads.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/clean.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/diff.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/in.kmc exec/compressible_stag_mui/test_COAr_depletion_slurm/init_rho.py exec/compressible_stag_mui/test_COAr_depletion_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_depletion_slurm/job_script.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/mass_cons.py exec/compressible_stag_mui/test_COAr_depletion_slurm/mass_cons.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/mpmd.conf exec/compressible_stag_mui/test_COAr_depletion_slurm/submit_job.sh exec/compressible_stag_mui/test_COAr_depletion_slurm/zavg.sh commit bc8a2eacd7aa99ad7241a360e867b4b696d219e8 Author: Changho Kim Date: Sun Jul 31 16:43:50 2022 -0700 exec/compressible_stag_mui/test_COAr_depletion: depletion setup for compressible_stag_mui exec/compressible_stag_mui/test_COAr_depletion/ads.sh exec/compressible_stag_mui/test_COAr_depletion/clean.sh exec/compressible_stag_mui/test_COAr_depletion/diff.sh exec/compressible_stag_mui/test_COAr_depletion/in.kmc exec/compressible_stag_mui/test_COAr_depletion/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_depletion/mass_cons.py exec/compressible_stag_mui/test_COAr_depletion/mass_cons.sh exec/compressible_stag_mui/test_COAr_depletion/run.sh exec/compressible_stag_mui/test_COAr_depletion/theta_eq.py exec/compressible_stag_mui/test_COAr_depletion/theta_eq.sh exec/compressible_stag_mui/test_COAr_depletion/zavg.sh commit 6738a15c4914bb711cd545bfc6f9b5276f0fd912 Author: Changho Kim Date: Sun Jul 31 15:16:32 2022 -0700 exec/compressible_stag_mui/test_COAr_eq_slurm: setup updated exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc exec/compressible_stag_mui/test_COAr_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_eq_slurm/job_script.sh exec/compressible_stag_mui/test_COAr_eq_slurm/mpmd.conf commit 849fe1cad4efa2aa6a0bffda9e6537d9ebfd7d82 Author: isriva Date: Sat Jul 30 22:24:36 2022 -0700 fixed a few minor bugs pointed by Weiqun, and some more. not pernicious, but might break regtests src_compressible_stag/boundaryStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/statsStag.cpp commit e473c999bb155fab4c9155b69f71de38b844a153 Merge: 32599c57 4d2cb8de Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Fri Jul 29 16:33:42 2022 -0700 Merge pull request #116 from AMReX-FHD/compressible_stag_mui Compressible stag mui commit 4d2cb8de235c98f1da7034fb8f67b2e6152ab7f7 Author: Changho Kim Date: Thu Jul 28 13:49:54 2022 -0700 exec/compressible_stag_mui/test_COAr_eq: unnecessary jump labels in the SPPARKS script in.kmc deleted exec/compressible_stag_mui/test_COAr_eq/in.kmc exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc commit 98ec40034ae8f1f18079472262a9363dd71dce66 Author: Changho Kim Date: Thu Jul 28 13:47:19 2022 -0700 compressible_stag_mui: debug codes (which were already commented) deleted exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.cpp commit 7f3d04f98cee98c424b427e11549b2741774ca5a Author: isriva Date: Thu Jul 28 11:56:08 2022 -0700 completed implementation of new advective fluxes based on face momenta src_compressible_stag/fluxStag.cpp commit 184bff6c46b7c45fbd542271fc2d49f99b9e4f2b Author: isriva Date: Wed Jul 27 22:31:07 2022 -0700 started interpolation primitive for momentum based flux evaluation at the faces. WIP src_compressible_stag/fluxStag.cpp commit b78ba63b59c94403068207887d78247bb6bf77cc Author: Changho Kim Date: Wed Jul 27 19:39:56 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI: setup2() to recompute propensities exec/compressible_stag_mui/SPPARKS_MUI/app.cpp exec/compressible_stag_mui/SPPARKS_MUI/app.h exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.h commit 01e73b125ec7bd76fe4e70d0f7428ebc44f65b71 Merge: 5a7e2f15 32599c57 Author: Changho Kim Date: Wed Jul 27 10:17:46 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 5a7e2f158f72db1dc13378962f9f26f968d68503 Author: Changho Kim Date: Tue Jul 26 17:17:46 2022 -0700 exec/compressible_stag_mui/README: instructions are added exec/compressible_stag_mui/README commit f68b5c4b380d834a360e125327a8a55c60300dba Author: Changho Kim Date: Tue Jul 26 17:16:59 2022 -0700 exec/compressible_stag_mui/test_COAr_eq: analysis script updated exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg.plt exec/compressible_stag_mui/test_COAr_eq/diff.sh exec/compressible_stag_mui/test_COAr_eq/theta_eq.py exec/compressible_stag_mui/test_COAr_eq/zavg_rhoY1mean.plt exec/compressible_stag_mui/test_COAr_eq/zavg_rhoY1mean.sh commit 32599c573ca6613c4077652dc77c14fc57f10cc3 Author: Daniel Ladiges Date: Tue Jul 26 11:12:23 2022 -0700 debug input exec/DSMC/inputs_conc_gpu commit cc8d2c691e66b3e6a22b61335ef587acf29e4c8c Author: Daniel Ladiges Date: Tue Jul 26 10:55:16 2022 -0700 added input file for debugging exec/DSMC/inputs_conc commit 6388da82425f1fac7b2c306ac4daca339914ea0b Author: Changho Kim Date: Tue Jul 26 10:08:09 2022 -0700 exec/compressible_stag/test_MFsurfchem_COAr_eq: additional analysis scripts exec/compressible_stag/test_MFsurfchem_COAr_eq/diff.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/theta_eq.py exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg_rhoY1mean.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg_rhoY1mean.sh commit 41df01d0367cfd512b48a6d446a2fabfb9506675 Merge: 1cd38079 bf79c92b Author: Daniel Ladiges Date: Mon Jul 25 23:59:32 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 1cd38079d32d0efc1923e689b4a58f39506afc09 Author: Daniel Ladiges Date: Mon Jul 25 23:58:19 2022 -0700 DSMC now compiles and 'runs' with USE_CUDA=TRUE. Some weird behavior with Redistribute() to check with Andrew... exec/DSMC/DsmcCollide.cpp exec/DSMC/GNUmakefile exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit bf79c92b2a2564e8320279c14378ffdb49940ed7 Author: Andy Nonaka Date: Mon Jul 25 15:45:44 2022 -0700 clean up some structure factor code; lots of redundant code in the restart logic when restart isn't even properly implemented src_compressible_stag/main_driver.cpp commit 340190014226221f52079380fa2a420d360ba8d5 Author: Changho Kim Date: Fri Jul 22 16:56:10 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI: start to add modules that validate SPPARKS KMC setup exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit f959ab0ceef1b264764e90f55eff9d3d5ad8cd90 Author: Changho Kim Date: Fri Jul 22 14:28:56 2022 -0700 compressible_stag_mui: functionality to confirm mui communication is correct exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit 18e39b15ad291567833af8ee3382954382229de2 Author: Changho Kim Date: Thu Jul 21 15:25:20 2022 -0700 compressible_stag_mui/SPPARKS_MUI: more log for validation in mui_init_agg exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp src_MFsurfchem/MFsurfchem_functions.cpp src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.cpp commit d7d022c0742332062c8acdf9ba4d62cec175f460 Merge: 3265656d c7d2d20f Author: Changho Kim Date: Thu Jul 21 11:12:45 2022 -0700 Merge branch 'main' into compressible_stag_mui commit c7d2d20fa9a2a0ff15a3d7e60049b5030570d452 Merge: 30fa5ab1 8d0079f8 Author: Daniel Ladiges Date: Wed Jul 20 12:05:00 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 30fa5ab143946a6315a395fb929c2c4f98af6815 Author: Daniel Ladiges Date: Wed Jul 20 12:04:20 2022 -0700 Final? structure factor code for DSMC and started last bits of CUDA conversion exec/DSMC/main_driver.cpp src_common/Debug.cpp src_common/common_functions.H commit 8d0079f80362eab9287d5029cc9a7120affda41c Merge: 72bad6e0 1e36da95 Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Tue Jul 19 18:55:30 2022 -0700 Merge pull request #115 from AMReX-FHD/MFsurfchem FHDeX/src_MFsurfchem: flag to turn on/off sampling for initial surfac… commit 3265656d2e587a7f40b71b98e5e273d1416cfdd6 Author: Changho Kim Date: Tue Jul 19 15:29:50 2022 -0700 compressible_stag_mui/SPPARKS_MUI//MAKE/Makefile.nonmui: updated exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.nonmui commit 4a52b6b84af6ad4402eb44595001587e142ce3f6 Author: jbb Date: Mon Jul 18 14:08:23 2022 -0700 fixed issue in higher-order flux for more than one monomer per molecule src_multispec/DiffusiveMassFluxdiv.cpp commit f96e583bab94c6f9521b520687a3e0f6aa6e2333 Merge: fcade35a 932d6b99 Author: jbb Date: Mon Jul 18 12:26:05 2022 -0700 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit 1e36da95a506b68b14bc1fa9c334d11675d9bc33 Merge: a35934c7 72bad6e0 Author: Andy Nonaka Date: Mon Jul 18 11:06:21 2022 -0700 Merge branch 'main' into MFsurfchem commit a35934c74a9637eac470cb67f5eec6b8cf879b0d Author: Andy Nonaka Date: Mon Jul 18 11:05:40 2022 -0700 Update src_MFsurfchem/MFsurfchem_namespace.H src_MFsurfchem/MFsurfchem_namespace.H commit b6aad9da5b1541601379d7f79148c3397ec26c89 Author: Andy Nonaka Date: Mon Jul 18 11:04:47 2022 -0700 Update src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_functions.cpp commit 2ecd6dcd2dbc7d9d1a942126ced5f719fa242c24 Author: Andy Nonaka Date: Mon Jul 18 11:04:28 2022 -0700 Update src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_functions.cpp commit 40f6d96647b630c12f67d67b16a5fe39cf083641 Author: Matteo Polimeno Date: Thu Jul 14 22:34:21 2022 -0700 FHDeX/src_MFsurfchem: flag to turn on/off sampling for initial surface coverage and small changes src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit c2bd8836a8487482050054460df5d5f7e412ed58 Author: Changho Kim Date: Thu Jul 14 02:19:56 2022 -0700 exec/compressible_stag_mui/test_COAr_eq: python scripts updated (print for python3) exec/compressible_stag_mui/test_COAr_eq/ads.py exec/compressible_stag_mui/test_COAr_eq/mass_cons.py exec/compressible_stag_mui/test_COAr_eq/theta_eq.py commit 4860fdb150abbf3cde263bb404718faed6655391 Merge: afe4f030 72bad6e0 Author: Changho Kim Date: Thu Jul 14 01:48:34 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 72bad6e0ca99e2374fc0067c275ecd74a8dbd2dc Author: Johannes Blaschke Date: Tue Jul 12 09:51:58 2022 -0700 change sorted_map to use triplet exec/immersed_boundary/flagellum/ib_md.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 2b4c6f6a59c55a2de7b48f8d36db50ec27bb17db Author: Johannes Blaschke Date: Tue Jul 12 09:49:02 2022 -0700 don't use NextID to check max id -- instead use the_next_id src_immersed-boundary/IBMarkerContainerBase.H commit afe4f030dec83e69b2b333b2b690a5b46da846bd Author: Changho Kim Date: Sat Jul 9 10:03:14 2022 -0700 exec/compressible_stag_mui/test_COAr_eq_slurm: updated exec/compressible_stag_mui/test_COAr_eq/run.sh exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc exec/compressible_stag_mui/test_COAr_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_eq_slurm/job_script.sh exec/compressible_stag_mui/test_COAr_eq_slurm/mpmd.conf commit f79756d61bf8a64cf66c99b9887549bf10a20182 Author: Changho Kim Date: Sat Jul 9 08:45:51 2022 -0700 exec/compressible_stag_mui/test_COAr_eq/params_COAr_eq.py: python3 print exec/compressible_stag_mui/test_COAr_eq/params_COAr_eq.py commit b161f237e0a9c4cf914ab0dfceda8b05f3e51c77 Author: Changho Kim Date: Sat Jul 9 06:52:13 2022 -0700 compressible_stag_mui: slurm and non-slurm implementation and test cases exec/compressible_stag_mui/GNUmakefile exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.mui exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.mui_cori exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.mui_slurm exec/compressible_stag_mui/SPPARKS_MUI/main.cpp exec/compressible_stag_mui/main.cpp exec/compressible_stag_mui/test_COAr_eq/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_eq_slurm/clean.sh exec/compressible_stag_mui/test_COAr_eq_slurm/diff.sh exec/compressible_stag_mui/test_COAr_eq_slurm/in.kmc exec/compressible_stag_mui/test_COAr_eq_slurm/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_eq_slurm/job_script.sh exec/compressible_stag_mui/test_COAr_eq_slurm/mpmd.conf exec/compressible_stag_mui/test_COAr_eq_slurm/submit_job.sh src_mui/lib_mpi_split.h commit 313fa9aec0dc5b2a14e36755946f6ec27b8d979a Author: Changho Kim Date: Fri Jul 8 09:50:57 2022 -0700 exec/compressible_stag_mui/appnum: simple example for appnum (mpmd) exec/compressible_stag_mui/appnum/compile.sh exec/compressible_stag_mui/appnum/job_script.sh exec/compressible_stag_mui/appnum/main.cpp exec/compressible_stag_mui/appnum/mpmd.conf exec/compressible_stag_mui/appnum/run.sh exec/compressible_stag_mui/appnum/submit.sh commit b9317b44945067c6c0dc366cc8c620daf876416d Author: Changho Kim Date: Fri Jul 8 09:40:08 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI/style_app.h: this file should not be included (auto generated) exec/compressible_stag_mui/SPPARKS_MUI/style_app.h commit 6a8c9fe1e8a24012d97db698604b938ab42d35e8 Merge: 4290f884 83352337 Author: Changho Kim Date: Fri Jul 8 09:34:43 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 83352337010405e99283e377d1a4da044fad205c Merge: f6c10c81 ace98a75 Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Thu Jul 7 13:40:57 2022 -0700 Merge pull request #114 from AMReX-FHD/MFsurfchem MFsurfchem commit ace98a75cea1cf4e4d5c5e15f1b787a344c89abf Merge: 2614ebca f6c10c81 Author: Matteo Polimeno Date: Thu Jul 7 13:16:40 2022 -0700 Merge branch 'main' into MFsurfchem commit f6c10c8147952c4610f1597266f1798d8200b3bf Merge: 9ef9809f 5d5ffcdf Author: Gang Xu Date: Wed Jul 6 10:20:17 2022 -0700 Implmented PullDown marker positions in force calculations. Merge branch 'gx/new_force' into main commit 2614ebcafbd790761a487555c35dc036e319fa30 Author: Matteo Polimeno Date: Wed Jul 6 08:31:48 2022 -0700 src_MFsurfchem/: small changes src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp commit 5d5ffcdf3f715f0d250e476759be67e0296bac15 Author: Gang Xu Date: Wed Jul 6 07:56:39 2022 -0700 minor updates exec/immersed_boundary/flagellum/main_driver.cpp src_common/main.cpp commit c2677aa43ba4b490076ca756b0f00e82cefc5be1 Author: Matteo Polimeno Date: Tue Jul 5 15:46:31 2022 -0700 src_compressible_stag/ updated driver src_compressible_stag/main_driver.cpp commit 19b152e30e1f672ab2f5859a5df5b4af7d3fdd58 Author: Matteo Polimeno Date: Tue Jul 5 15:45:20 2022 -0700 src_compressible/ updated driver src_compressible/main_driver.cpp commit 881203d04435f8f9d859e10338de6dbf92f58e74 Author: Matteo Polimeno Date: Tue Jul 5 15:41:42 2022 -0700 src_MFsurfchem/: fix GPU issue updates src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp commit 9a9d31f7f656c9f8c1bba0f2f1213c40ecfc2786 Merge: ac8cfc6a 9ef9809f Author: Matteo Polimeno Date: Tue Jul 5 12:08:17 2022 -0700 Merge branch 'main' into MFsurfchem commit 9ef9809f9ef49f81cf0403710508157ee579b609 Author: isriva Date: Tue Jul 5 10:56:16 2022 -0700 set the correct flags for interpolation for advective fluxes exec/compressible_stag/inputs_RT_thermal exec/compressible_stag/inputs_RT_thermal_block exec/compressible_stag/inputs_RT_thermal_slab exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_regression_concentration_3D exec/compressible_stag/inputs_regression_periodic_3D exec/compressible_stag/inputs_regression_reservoir_1D exec/compressible_stag/inputs_regression_reservoir_3D exec/compressible_stag/inputs_regression_slip_adiabatic_3D exec/compressible_stag/inputs_regression_tempgrad_1D exec/compressible_stag/inputs_regression_tempgrad_3D exec/compressible_stag/inputs_reservoir_equil exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag_det src_compressible_stag/fluxStag.cpp src_compressible_stag/main_driver.cpp commit 4290f8844112e7616656cbfd3576b566f28509b5 Merge: d3ba613b d03393a4 Author: Changho Kim Date: Tue Jul 5 10:16:02 2022 -0700 Merge branch 'main' into compressible_stag_mui commit d3ba613b460ff4f73123c1cab90945d38835102d Merge: 4598d993 c46ff47b Author: Changho Kim Date: Tue Jul 5 10:14:39 2022 -0700 Merge branch 'compressible_stag_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_stag_mui commit ac8cfc6adb3d063bfc6fb7aba1228322ce967bae Author: Andy Nonaka Date: Tue Jul 5 09:22:11 2022 -0700 fix GPU issue src_MFsurfchem/MFsurfchem_functions.cpp commit d03393a4e5dca81fff8dc090c374fe43287d22d3 Author: Changho Kim Date: Fri Jul 1 15:31:13 2022 -0700 exec/compressible_stag_mui/test_COAr_eq: test case updated so that direct comparison with MFsurfchem can be done exec/compressible_stag_mui/test_COAr_eq/ads.plt exec/compressible_stag_mui/test_COAr_eq/ads.py exec/compressible_stag_mui/test_COAr_eq/ads.sh exec/compressible_stag_mui/test_COAr_eq/clean.sh exec/compressible_stag_mui/test_COAr_eq/diff.sh exec/compressible_stag_mui/test_COAr_eq/in.kmc exec/compressible_stag_mui/test_COAr_eq/inputs_fhd_stag exec/compressible_stag_mui/test_COAr_eq/mass_cons.py exec/compressible_stag_mui/test_COAr_eq/mass_cons.sh exec/compressible_stag_mui/test_COAr_eq/params_COAr_eq.py exec/compressible_stag_mui/test_COAr_eq/run.sh exec/compressible_stag_mui/test_COAr_eq/theta_eq.py exec/compressible_stag_mui/test_COAr_eq/theta_eq.sh exec/compressible_stag_mui/test_COAr_eq/zavg.plt exec/compressible_stag_mui/test_COAr_eq/zavg.sh exec/compressible_stag_mui/test_COadsPt/ads.py exec/compressible_stag_mui/test_COadsPt/diff.sh exec/compressible_stag_mui/test_COadsPt/zavg.plt commit 6bf696089000262d39d64e84c03961eb657a1ae9 Author: Changho Kim Date: Fri Jul 1 11:44:22 2022 -0700 exec/compressible_stag/test_MFsurfchem_COAr_eq: test case updated significantly exec/compressible_stag/test_MFsurfchem/ads.py exec/compressible_stag/test_MFsurfchem/clean.sh exec/compressible_stag/test_MFsurfchem/diff.sh exec/compressible_stag/test_MFsurfchem/params_CO_Ar_eq_SF.py exec/compressible_stag/test_MFsurfchem/run.sh exec/compressible_stag/test_MFsurfchem/zavg.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.py exec/compressible_stag/test_MFsurfchem_COAr_eq/ads.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/clean.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/diff.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_COAr_eq/mass_cons.py exec/compressible_stag/test_MFsurfchem_COAr_eq/mass_cons.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/params_COAr_eq.py exec/compressible_stag/test_MFsurfchem_COAr_eq/run.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/theta_eq.py exec/compressible_stag/test_MFsurfchem_COAr_eq/theta_eq.sh exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg.plt exec/compressible_stag/test_MFsurfchem_COAr_eq/zavg.sh commit 8686bf3c6b24be89cba9ad1c953c7d9cc806223f Merge: 68cfebb5 c46ff47b Author: ckim103 <54189867+ckim103@users.noreply.github.com> Date: Fri Jul 1 10:54:16 2022 -0700 Merge pull request #113 from AMReX-FHD/compressible_stag_mui Compressible stag mui commit 68cfebb518728ee406b063beb519965bfe0f1dd6 Merge: ca486c4f 51fc8d48 Author: Daniel Ladiges Date: Thu Jun 30 14:59:32 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit ca486c4f640574c60ab554810194e214439c9429 Author: Daniel Ladiges Date: Thu Jun 30 14:58:50 2022 -0700 Added structure factor to DSMC. Still need to test exec/DSMC/delPlots exec/DSMC/main_driver.cpp exec/DSMC/stats.cpp exec/DSMC/writePlotFile.cpp commit c46ff47bd662a29e20e8ce9a8aeb0b0c318c7c58 Merge: c17893e7 51fc8d48 Author: Changho Kim Date: Thu Jun 30 13:12:11 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 51fc8d48bf70e6a57c9a29756cc12e3cd8532ba5 Merge: 8ebfff70 e780f58c Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Thu Jun 30 12:10:30 2022 -0700 Merge pull request #112 from AMReX-FHD/MFsurfchem MFsurfchem commit e780f58c084d1b03e1211fecfad3bc2ba43420fa Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Thu Jun 30 11:53:14 2022 -0700 Update src_MFsurfchem/MFsurfchem_functions.cpp Co-authored-by: Andy Nonaka src_MFsurfchem/MFsurfchem_functions.cpp commit 6a45b7f8b2cf3296d38b6c84846264426d25bd3f Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Thu Jun 30 11:53:01 2022 -0700 Update src_MFsurfchem/MFsurfchem_functions.cpp Co-authored-by: Andy Nonaka src_MFsurfchem/MFsurfchem_functions.cpp commit c17893e7d75336660e065d3a3962810c5112e865 Merge: 1a0c0eec 8ebfff70 Author: Changho Kim Date: Wed Jun 29 16:34:15 2022 -0700 Merge branch 'main' into compressible_stag_mui commit ce9015baee3ddc1b8443a6a6e310d673e21646bc Author: Changho Kim Date: Wed Jun 29 16:29:59 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: small changes in init_surfcov src_MFsurfchem/MFsurfchem_functions.cpp commit 19be4765d1ed3ad29eb3546b297f2900183148d0 Merge: 4ad6d40d 8ebfff70 Author: Changho Kim Date: Wed Jun 29 11:51:36 2022 -0700 Merge branch 'main' into MFsurfchem commit 4ad6d40d0118dc33d44faabb46724d4331fad83d Author: Matteo Polimeno Date: Wed Jun 29 10:54:31 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: update src_MFsurfchem/MFsurfchem_functions.cpp commit 4598d993278a15dc399245dfe7a5c9292751187d Merge: 1a0c0eec 8ebfff70 Author: Changho Kim Date: Tue Jun 28 18:10:19 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 5206cb93acda9690d586a44e1719ad61c42fd961 Author: Gang Xu Date: Tue Jun 28 17:23:50 2022 -0700 fixed index related bugs exec/immersed_boundary/flagellum/ib_md.cpp commit d4b5181c36de95516ba37031516cdb6f48ebb53f Author: Matteo Polimeno Date: Tue Jun 28 15:11:06 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: updates src_MFsurfchem/MFsurfchem_functions.cpp commit c9e761eed53191e2f6d886c7ce4ef92811e37790 Author: Changho Kim Date: Tue Jun 28 02:20:25 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: corrections src_MFsurfchem/MFsurfchem_functions.cpp commit 1a0c0eec450473ce68b0eee50195b0b7f960eca8 Author: Changho Kim Date: Tue Jun 28 01:37:50 2022 -0700 compressible_stag_mui: muitifab Ntot implemented exec/compressible_stag_mui/test_COadsPt/in.kmc src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit ac81e12717a65461b049afbb4a8946a2f4f9182a Author: Matteo Polimeno Date: Mon Jun 27 19:00:13 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: sample initial surfcov for one species src_MFsurfchem/MFsurfchem_functions.cpp commit 8ebfff708bb54e346772dd521f8172857e5fdaa7 Author: Changho Kim Date: Mon Jun 27 17:17:32 2022 -0700 compressible_stag / compressible_stag_mui: test cases updated exec/compressible_stag/test_MFsurfchem/clean.sh exec/compressible_stag/test_MFsurfchem/zavg.plt exec/compressible_stag/test_MFsurfchem_RB/zavg.plt exec/compressible_stag_mui/test_COadsPt/ads.plt exec/compressible_stag_mui/test_COadsPt/ads.py exec/compressible_stag_mui/test_COadsPt/ads.sh exec/compressible_stag_mui/test_COadsPt/clean.sh exec/compressible_stag_mui/test_COadsPt/diff.sh exec/compressible_stag_mui/test_COadsPt/in.kmc exec/compressible_stag_mui/test_COadsPt/inputs_fhd_stag exec/compressible_stag_mui/test_COadsPt/run.sh exec/compressible_stag_mui/test_COadsPt/zavg.plt exec/compressible_stag_mui/test_COadsPt/zavg.sh commit 8db0d6b55f4f093756d22e4e37dffac0f6db0b52 Merge: bbc23bd5 536ae779 Author: emercado9 <68758761+emercado9@users.noreply.github.com> Date: Mon Jun 27 14:57:52 2022 -0700 Merge pull request #110 from AMReX-FHD/compressible_stag_mui MUI: surfcov, nspec_surfcov, mui_commit, mui_forget, mui push occ1-5, mui push one commit 295ab88e35e5ab078bfc26d6522994dbd0d8bcc3 Author: Gang Xu Date: Mon Jun 27 14:25:39 2022 -0700 minor bugs fixed exec/immersed_boundary/flagellum/ib_md.cpp commit 2032aa039b8cfd5de090cf43e8623c7459f47aae Author: Gang Xu Date: Mon Jun 27 14:12:46 2022 -0700 adding reduced map exec/immersed_boundary/flagellum/ib_md.cpp exec/tutorials/ib_marker_basic/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 536ae779c7ecb9ca37c14f0eb79f442a643b2b71 Author: Changho Kim Date: Mon Jun 27 10:54:20 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp: mui_fetch_surfcov (on fhd side) now works with mui_push_agg (on spparks side) exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/test_COadsPt/in.kmc commit dfbc9c9e4d723a6b33adc80e265779f053eefbb2 Author: Changho Kim Date: Sun Jun 26 00:40:22 2022 -0700 compressible_stag_mui: on spparks side, mui_push occ1-5 and one implemented to implement mui_fetch_surfcov on fhd side exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/test_COadsPt/in.kmc src_surfchem_mui/surfchem_mui_functions.cpp commit 143d99e5628901f5f1d92c19ec2c3c531877190f Author: Changho Kim Date: Fri Jun 24 17:47:29 2022 -0700 compressible_stag_mui: both mui_commit and mui_forget have been seperated from mui_push or mui_fetch (or mui_fetch_surfcov) in fhd and kmc exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_stag_mui/test_COadsPt/clean.sh exec/compressible_stag_mui/test_COadsPt/diff.sh exec/compressible_stag_mui/test_COadsPt/in.kmc exec/compressible_stag_mui/test_COadsPt/inputs_fhd src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit bbc23bd556489b15b17831325ceb8972d0456990 Merge: 3348a643 6862c029 Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Fri Jun 24 17:19:17 2022 -0700 Merge pull request #111 from AMReX-FHD/MFsurfchem MFsurfchem commit 1632f31a2fe8397d97a45193a7ede50ddd7a2e40 Merge: 2ca711aa 3348a643 Author: Changho Kim Date: Fri Jun 24 17:06:56 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 87c870f0603840ef4576f89a7e97a01712e29361 Author: Gang Xu Date: Fri Jun 24 16:53:30 2022 -0700 wip on new forcing exec/immersed_boundary/flagellum/ib_md.cpp commit 3348a643037f0400bf1d370cbc6d64f55ebf24da Author: Gang Xu Date: Fri Jun 24 16:51:14 2022 -0700 add feature: map to sort pulldown pushup exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H commit 6862c0296878b8302a5a18c7e3cf5cccfd7dda14 Merge: abe4d971 f1deb312 Author: Matteo Polimeno Date: Fri Jun 24 16:42:44 2022 -0700 Merge branch 'main' into MFsurfchem commit 2ca711aac897af6e1594d30a2d22ca1d581a0fdf Author: Enrique Mercado Date: Fri Jun 24 16:25:21 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI/: created mui_commit function; src_surfchem_mui/surfchem_mui_functions.cpp disabled uniface forget exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_stag_mui/test_COadsPt/in.kmc src_surfchem_mui/surfchem_mui_functions.cpp commit 06769913ae8bf7d1539f4c653b36e6821723b291 Merge: 326bccc9 f1deb312 Author: Gang Xu Date: Fri Jun 24 13:42:55 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit f1deb312e9f0ac8947dbc463b43371c4812d01dc Author: Gang Xu Date: Fri Jun 24 13:42:22 2022 -0700 add placeholder for sorted marker list src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit abe4d971d09d93038888d2093b0416a0a1599da2 Author: Matteo Polimeno Date: Fri Jun 24 13:23:17 2022 -0700 /FHDeX/exec/compressible_stag/test_MFsurfchem/inputs_fhd_stag: updated inputs file exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag commit 264147fe6bb775d57a83fe953b6ffb8416be8dbf Author: Matteo Polimeno Date: Fri Jun 24 11:10:50 2022 -0700 /test_MFsurfchem_depletion/: deterministic input files exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag_det commit 41c9515ee7e123b7c771e549ea845eb9fbcc75f9 Author: Changho Kim Date: Fri Jun 24 10:03:07 2022 -0700 src_MFsurfchem: small changes src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit b6abcb2293218f3f21872896158822f0a2b57db0 Author: Changho Kim Date: Thu Jun 23 13:35:47 2022 -0700 exec/compressible_stag_mui/test_COadsPt: test case updated accordingly exec/compressible_stag_mui/test_COadsPt/in.kmc exec/compressible_stag_mui/test_COadsPt/inputs_fhd commit 552608d5d3e1f4dafdbefe5e42d2e9a3665231f2 Author: Matteo Polimeno Date: Thu Jun 23 13:32:28 2022 -0700 /src_MFsurfchem/: added stoch_MFsurfchem flag src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit 1310fa226d5d1de6d7792070bd5d695dc4cdbf0d Author: Changho Kim Date: Thu Jun 23 13:26:00 2022 -0700 compressible_stag / compressible_stag_mui : implementation of nspec_surfcov src_compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 87e2e0d99e29c0b8d4f49873330fc8491f3e5e47 Author: Changho Kim Date: Wed Jun 22 18:04:51 2022 -0700 WIP: implementing surfcov to compressible_stag_mui exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible_stag/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit f31928382ad361c69bfc421d0c38239d7876fe1b Author: emercado9 Date: Wed Jun 22 15:16:17 2022 -0700 exec/compressible_stag_mui/SPPARKS_MUI/MAKE updated Makefile.mui to include correct src_mui directory exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.mui commit 3157bcb089ee7b0b6d64c8c5379312fd45d7fd7d Merge: 19b0c54b 311e11be Author: emercado9 <68758761+emercado9@users.noreply.github.com> Date: Wed Jun 22 11:35:36 2022 -0700 Merge pull request #109 from AMReX-FHD/compressible_stag_mui Compressible stag mui commit 311e11be1cebddc052305e99bda597a7657bc3bd Author: Enrique Mercado Date: Tue Jun 21 15:56:45 2022 -0700 created src_mui directory for common MUI source files, removed MUI directories from exec/compressible_mui and exec/compressible_stag_mui exec/compressible_mui/GNUmakefile 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exec/compressible_stag_mui/MUI/exception.h exec/compressible_stag_mui/MUI/geometry.h exec/compressible_stag_mui/MUI/lib_dispatcher.h exec/compressible_stag_mui/MUI/lib_factory.h exec/compressible_stag_mui/MUI/lib_mpi_hepler.h exec/compressible_stag_mui/MUI/lib_mpi_multidomain.h exec/compressible_stag_mui/MUI/lib_mpi_split.h exec/compressible_stag_mui/MUI/lib_singleton.h exec/compressible_stag_mui/MUI/lib_uri.h exec/compressible_stag_mui/MUI/message.h exec/compressible_stag_mui/MUI/mui.h exec/compressible_stag_mui/MUI/point.h exec/compressible_stag_mui/MUI/reader.h exec/compressible_stag_mui/MUI/reader_variable.h exec/compressible_stag_mui/MUI/sampler.h exec/compressible_stag_mui/MUI/sampler_exact.h exec/compressible_stag_mui/MUI/sampler_gauss.h exec/compressible_stag_mui/MUI/sampler_kmc_fhd.h exec/compressible_stag_mui/MUI/sampler_mov_avg.h exec/compressible_stag_mui/MUI/sampler_nn.h exec/compressible_stag_mui/MUI/sampler_null.h exec/compressible_stag_mui/MUI/sampler_pseudo_n2_linear.h exec/compressible_stag_mui/MUI/sampler_pseudo_nn.h exec/compressible_stag_mui/MUI/sampler_shepard_quintic.h exec/compressible_stag_mui/MUI/sampler_sph_quintic.h exec/compressible_stag_mui/MUI/sampler_sum_quintic.h exec/compressible_stag_mui/MUI/span.h exec/compressible_stag_mui/MUI/spatial_storage.h exec/compressible_stag_mui/MUI/stream.h exec/compressible_stag_mui/MUI/stream_ordered.h exec/compressible_stag_mui/MUI/stream_string.h exec/compressible_stag_mui/MUI/stream_tuple.h exec/compressible_stag_mui/MUI/stream_unordered.h exec/compressible_stag_mui/MUI/stream_vector.h exec/compressible_stag_mui/MUI/uniface.h exec/compressible_stag_mui/MUI/util.h exec/compressible_stag_mui/MUI/virtual_container.h exec/compressible_stag_mui/MUI/wrapper_c/Makefile exec/compressible_stag_mui/MUI/wrapper_c/mui_3d.cpp exec/compressible_stag_mui/MUI/wrapper_c/mui_3d.h exec/compressible_stag_mui/MUI/wrapper_c/unit_test.c exec/compressible_stag_mui/MUI/wrapper_f/Makefile 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src_mui/sampler_kmc_fhd.h src_mui/sampler_mov_avg.h src_mui/sampler_nn.h src_mui/sampler_null.h src_mui/sampler_pseudo_n2_linear.h src_mui/sampler_pseudo_nn.h src_mui/sampler_shepard_quintic.h src_mui/sampler_sph_quintic.h src_mui/sampler_sum_quintic.h src_mui/span.h src_mui/spatial_storage.h src_mui/stream.h src_mui/stream_ordered.h src_mui/stream_string.h src_mui/stream_tuple.h src_mui/stream_unordered.h src_mui/stream_vector.h src_mui/uniface.h src_mui/util.h src_mui/virtual_container.h src_mui/wrapper_c/Makefile src_mui/wrapper_c/mui_3d.cpp src_mui/wrapper_c/mui_3d.h src_mui/wrapper_c/unit_test.c src_mui/wrapper_f/Makefile src_mui/wrapper_f/TODO src_mui/wrapper_f/mui.F90 src_mui/wrapper_f/mui_3df.cpp src_mui/wrapper_f/unit_test.f90 commit e7eb03a92f31da9677b35c6af0e44dd66aa476af Merge: 0976ed05 19b0c54b Author: Enrique Mercado Date: Tue Jun 21 08:19:29 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 326bccc9e4c0391907f19271c19f9031451823e5 Author: Gang Xu Date: Mon Jun 20 14:25:10 2022 -0700 implementing PullDown for calculating forces exec/immersed_boundary/flagellum/ib_md.cpp commit 19b0c54b425c22d7a3372e47eddbd2ad88444bd3 Author: Changho Kim Date: Fri Jun 17 11:12:20 2022 -0700 exec/compressible_stag/test_MFsurfchem_depletion: updated exec/compressible_stag/test_MFsurfchem_depletion/ads.sh exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_depletion/zavg.sh commit 190913cb7c8bf2bfba5c5086f353d5017b7e1e44 Author: Changho Kim Date: Thu Jun 16 21:59:06 2022 -0700 exec/compressible_stag/test_MFsurfchem_depletion exec/compressible_stag/test_MFsurfchem_depletion/ads.sh exec/compressible_stag/test_MFsurfchem_depletion/clean.sh exec/compressible_stag/test_MFsurfchem_depletion/diff.sh exec/compressible_stag/test_MFsurfchem_depletion/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_depletion/run.sh exec/compressible_stag/test_MFsurfchem_depletion/zavg.sh commit 0976ed0534f806eb5e27a3079b1d215640c63991 Author: emercado9 Date: Thu Jun 16 14:22:10 2022 -0700 src_surfchem_mui/: energy update (mui fetch) src_surfchem_mui/surfchem_mui_functions.cpp commit 4fea0adc0889bf4fed60f54b317ee3c860792072 Author: Changho Kim Date: Thu Jun 16 13:59:35 2022 -0700 exec/compressible_stag_mui: minor corrections exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/test_COadsPt/in.kmc commit 5cf0a9a50ff004309e67fda50018232460f9c695 Author: emercado9 Date: Thu Jun 16 13:38:32 2022 -0700 /exec/compressible_stag_mui/SPPARKS_MUI/: include correct surfchemtest files exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit a8b9853341383655ba156b22e58a69319f09a892 Author: emercado9 Date: Thu Jun 16 13:24:17 2022 -0700 exec/compressible_stag_mui/: implemented ads_beta exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h commit a8e78a9ce75b845b66ac66925231116d5d1f80cf Merge: afd46102 8b688ab5 Author: emercado9 Date: Thu Jun 16 13:19:44 2022 -0700 Merge branch 'compressible_stag_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_stag_mui commit 8b688ab56603b2a25150b6bd44ab24c04afac264 Author: Changho Kim Date: Thu Jun 16 13:17:08 2022 -0700 SPPARKS_MUI moved from exec/compressible_mui to exec/compressible_stag/mui exec/compressible_mui/SPPARKS_MUI/.gitignore exec/compressible_mui/SPPARKS_MUI/README exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.blackrose exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.chama exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.cygwin exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.flamer.gnu exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.g++ exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.linux exec/compressible_stag_mui/SPPARKS_MUI/MAKE/Makefile.mac 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exec/compressible_stag_mui/SPPARKS_MUI/app.cpp exec/compressible_stag_mui/SPPARKS_MUI/app.h exec/compressible_stag_mui/SPPARKS_MUI/app_chemistry.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_chemistry.h exec/compressible_stag_mui/SPPARKS_MUI/app_diffusion.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_diffusion.h exec/compressible_stag_mui/SPPARKS_MUI/app_erbium.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_erbium.h exec/compressible_stag_mui/SPPARKS_MUI/app_ising.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_ising.h exec/compressible_stag_mui/SPPARKS_MUI/app_ising_single.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_ising_single.h exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_lattice.h exec/compressible_stag_mui/SPPARKS_MUI/app_membrane.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_membrane.h exec/compressible_stag_mui/SPPARKS_MUI/app_off_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_off_lattice.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_additive.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_additive.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_grad.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_grad.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_neigh.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_neigh.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_neighonly.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_neighonly.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_phasefield.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_phasefield.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_pin.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_pin.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_strain.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_strain.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_strain_pin.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_strain_pin.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_weld.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_weld.h exec/compressible_stag_mui/SPPARKS_MUI/app_potts_weld_jom.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_potts_weld_jom.h exec/compressible_stag_mui/SPPARKS_MUI/app_relax.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_relax.h exec/compressible_stag_mui/SPPARKS_MUI/app_sinter.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_sinter.h exec/compressible_stag_mui/SPPARKS_MUI/app_sos.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_sos.h exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_stag_mui/SPPARKS_MUI/app_test_group.cpp exec/compressible_stag_mui/SPPARKS_MUI/app_test_group.h exec/compressible_stag_mui/SPPARKS_MUI/cluster.cpp exec/compressible_stag_mui/SPPARKS_MUI/cluster.h exec/compressible_stag_mui/SPPARKS_MUI/comm_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/comm_lattice.h exec/compressible_stag_mui/SPPARKS_MUI/comm_off_lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/comm_off_lattice.h exec/compressible_stag_mui/SPPARKS_MUI/create_box.cpp exec/compressible_stag_mui/SPPARKS_MUI/create_box.h exec/compressible_stag_mui/SPPARKS_MUI/create_sites.cpp exec/compressible_stag_mui/SPPARKS_MUI/create_sites.h exec/compressible_stag_mui/SPPARKS_MUI/diag.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag.h exec/compressible_stag_mui/SPPARKS_MUI/diag_array.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_array.h exec/compressible_stag_mui/SPPARKS_MUI/diag_cluster.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_cluster.h exec/compressible_stag_mui/SPPARKS_MUI/diag_diffusion.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_diffusion.h exec/compressible_stag_mui/SPPARKS_MUI/diag_energy.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_energy.h exec/compressible_stag_mui/SPPARKS_MUI/diag_erbium.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_erbium.h exec/compressible_stag_mui/SPPARKS_MUI/diag_propensity.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_propensity.h exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_density.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_density.h exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_free_energy.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_free_energy.h exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_free_energy_pore.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_sinter_free_energy_pore.h exec/compressible_stag_mui/SPPARKS_MUI/diag_surfchemtest.cpp exec/compressible_stag_mui/SPPARKS_MUI/diag_surfchemtest.h exec/compressible_stag_mui/SPPARKS_MUI/domain.cpp exec/compressible_stag_mui/SPPARKS_MUI/domain.h exec/compressible_stag_mui/SPPARKS_MUI/dump.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump.h exec/compressible_stag_mui/SPPARKS_MUI/dump_image.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump_image.h exec/compressible_stag_mui/SPPARKS_MUI/dump_sites.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump_sites.h exec/compressible_stag_mui/SPPARKS_MUI/dump_text.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump_text.h exec/compressible_stag_mui/SPPARKS_MUI/dump_vtk.cpp exec/compressible_stag_mui/SPPARKS_MUI/dump_vtk.h exec/compressible_stag_mui/SPPARKS_MUI/error.cpp exec/compressible_stag_mui/SPPARKS_MUI/error.h exec/compressible_stag_mui/SPPARKS_MUI/finish.cpp exec/compressible_stag_mui/SPPARKS_MUI/finish.h exec/compressible_stag_mui/SPPARKS_MUI/groups.cpp exec/compressible_stag_mui/SPPARKS_MUI/groups.h exec/compressible_stag_mui/SPPARKS_MUI/image.cpp exec/compressible_stag_mui/SPPARKS_MUI/image.h exec/compressible_stag_mui/SPPARKS_MUI/input.cpp exec/compressible_stag_mui/SPPARKS_MUI/input.h exec/compressible_stag_mui/SPPARKS_MUI/irregular.cpp exec/compressible_stag_mui/SPPARKS_MUI/irregular.h exec/compressible_stag_mui/SPPARKS_MUI/lattice.cpp exec/compressible_stag_mui/SPPARKS_MUI/lattice.h exec/compressible_stag_mui/SPPARKS_MUI/lattice.py exec/compressible_stag_mui/SPPARKS_MUI/library.cpp exec/compressible_stag_mui/SPPARKS_MUI/library.h exec/compressible_stag_mui/SPPARKS_MUI/main.cpp exec/compressible_stag_mui/SPPARKS_MUI/main.kmc_only exec/compressible_stag_mui/SPPARKS_MUI/math_const.h exec/compressible_stag_mui/SPPARKS_MUI/math_extra.cpp exec/compressible_stag_mui/SPPARKS_MUI/math_extra.h exec/compressible_stag_mui/SPPARKS_MUI/memory.cpp exec/compressible_stag_mui/SPPARKS_MUI/memory.h exec/compressible_stag_mui/SPPARKS_MUI/output.cpp exec/compressible_stag_mui/SPPARKS_MUI/output.h exec/compressible_stag_mui/SPPARKS_MUI/pair.cpp exec/compressible_stag_mui/SPPARKS_MUI/pair.h exec/compressible_stag_mui/SPPARKS_MUI/pair_lj_cut.cpp exec/compressible_stag_mui/SPPARKS_MUI/pair_lj_cut.h exec/compressible_stag_mui/SPPARKS_MUI/pointers.h exec/compressible_stag_mui/SPPARKS_MUI/pool_shape.h exec/compressible_stag_mui/SPPARKS_MUI/potential.cpp exec/compressible_stag_mui/SPPARKS_MUI/potential.h exec/compressible_stag_mui/SPPARKS_MUI/random_mars.cpp exec/compressible_stag_mui/SPPARKS_MUI/random_mars.h exec/compressible_stag_mui/SPPARKS_MUI/random_park.cpp exec/compressible_stag_mui/SPPARKS_MUI/random_park.h exec/compressible_stag_mui/SPPARKS_MUI/read_sites.cpp exec/compressible_stag_mui/SPPARKS_MUI/read_sites.h exec/compressible_stag_mui/SPPARKS_MUI/region.cpp exec/compressible_stag_mui/SPPARKS_MUI/region.h exec/compressible_stag_mui/SPPARKS_MUI/region_block.cpp exec/compressible_stag_mui/SPPARKS_MUI/region_block.h exec/compressible_stag_mui/SPPARKS_MUI/region_cylinder.cpp exec/compressible_stag_mui/SPPARKS_MUI/region_cylinder.h exec/compressible_stag_mui/SPPARKS_MUI/region_intersect.cpp exec/compressible_stag_mui/SPPARKS_MUI/region_intersect.h exec/compressible_stag_mui/SPPARKS_MUI/region_sphere.cpp exec/compressible_stag_mui/SPPARKS_MUI/region_sphere.h exec/compressible_stag_mui/SPPARKS_MUI/region_union.cpp exec/compressible_stag_mui/SPPARKS_MUI/region_union.h exec/compressible_stag_mui/SPPARKS_MUI/set.cpp exec/compressible_stag_mui/SPPARKS_MUI/set.h exec/compressible_stag_mui/SPPARKS_MUI/shell.cpp exec/compressible_stag_mui/SPPARKS_MUI/shell.h exec/compressible_stag_mui/SPPARKS_MUI/solve.cpp exec/compressible_stag_mui/SPPARKS_MUI/solve.h exec/compressible_stag_mui/SPPARKS_MUI/solve_group.cpp exec/compressible_stag_mui/SPPARKS_MUI/solve_group.h exec/compressible_stag_mui/SPPARKS_MUI/solve_linear.cpp exec/compressible_stag_mui/SPPARKS_MUI/solve_linear.h exec/compressible_stag_mui/SPPARKS_MUI/solve_tree.cpp exec/compressible_stag_mui/SPPARKS_MUI/solve_tree.h exec/compressible_stag_mui/SPPARKS_MUI/spktype.h exec/compressible_stag_mui/SPPARKS_MUI/spparks.cpp exec/compressible_stag_mui/SPPARKS_MUI/spparks.h exec/compressible_stag_mui/SPPARKS_MUI/style_app.h exec/compressible_stag_mui/SPPARKS_MUI/style_command.h exec/compressible_stag_mui/SPPARKS_MUI/style_diag.h exec/compressible_stag_mui/SPPARKS_MUI/style_dump.h exec/compressible_stag_mui/SPPARKS_MUI/style_pair.h exec/compressible_stag_mui/SPPARKS_MUI/style_region.h exec/compressible_stag_mui/SPPARKS_MUI/style_solve.h exec/compressible_stag_mui/SPPARKS_MUI/teardrop.h exec/compressible_stag_mui/SPPARKS_MUI/timer.cpp exec/compressible_stag_mui/SPPARKS_MUI/timer.h exec/compressible_stag_mui/SPPARKS_MUI/universe.cpp exec/compressible_stag_mui/SPPARKS_MUI/universe.h exec/compressible_stag_mui/SPPARKS_MUI/variable.cpp exec/compressible_stag_mui/SPPARKS_MUI/variable.h exec/compressible_stag_mui/SPPARKS_MUI/version.h exec/compressible_stag_mui/SPPARKS_MUI/viz.py exec/compressible_stag_mui/SPPARKS_MUI/weld_geometry.h commit afd461026ad993e7bc392c64473b1f5f182d1dd9 Merge: 3791a35c 5fd16fb4 Author: emercado9 Date: Thu Jun 16 12:47:14 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 3791a35cf552f061fa974786b7749ea32288ef52 Author: emercado9 Date: Thu Jun 16 11:59:09 2022 -0700 exec/compressible_mui/SPPARKS_MUI/: updated ads_beta default value implementation exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 29f9ce4dbd24afd24ac62e71d5d0e0915b579e20 Author: emercado9 Date: Wed Jun 15 17:33:16 2022 -0700 added mui_push temp to src_surfchem_mui/surfchem_mui_functions.cpp; implemented temperature correction using ads_beta array in exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h src_surfchem_mui/surfchem_mui_functions.cpp commit 5fd16fb4693af945adeaccaa92b5b0e8be5cd99f Author: Matteo Polimeno Date: Wed Jun 15 12:27:47 2022 -0700 /FHDeX/exec/compressible_stag/test_MFsurfchem_RB: added python script to get e0 and cv for CO exec/compressible_stag/test_MFsurfchem_RB/params_COrb_thermochem.py commit 247c2486296ae58594f619646b97751d6d1e31bb Merge: fd20a578 1423290d Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Wed Jun 15 11:29:39 2022 -0700 Merge pull request #108 from AMReX-FHD/MFsurfchem MFsurfchem commit 47c1e5768a80f94ae0ec561e87b987f88b057d05 Merge: 89173531 cc7a13fc Author: emercado9 Date: Wed Jun 15 10:58:20 2022 -0700 Merge branch 'compressible_stag_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_stag_mui commit cc7a13fc25447d907425a74e67c09b6bb8ac8ac0 Author: Changho Kim Date: Wed Jun 15 01:18:39 2022 -0700 exec/compressible_stag_mui/test_COadsPt: test case exec/compressible_stag_mui/test_COadsPt/clean.sh exec/compressible_stag_mui/test_COadsPt/in.kmc exec/compressible_stag_mui/test_COadsPt/inputs_fhd exec/compressible_stag_mui/test_COadsPt/run.sh commit c485b7a9c6f34776fe398c92d6d5f743f1071480 Author: Changho Kim Date: Wed Jun 15 01:15:42 2022 -0700 exec/compressible_stag_mui/main.cpp: need for mpi_split (MUI) exec/compressible_stag_mui/main.cpp commit 721ca2d96d5a7df03d32b55b1513922b7b541bdb Author: Changho Kim Date: Tue Jun 14 21:52:39 2022 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF: obsolete options deleted exec/compressible_mui/RUN_COadsPt111_eq_SF/clean.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/inputs_fhd commit fd20a578c880655fccf8402f62f541cd567e0a70 Merge: 3e644e4b b9581aef Author: Daniel Ladiges Date: Tue Jun 14 17:24:41 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 3e644e4b3096b351115a0cf9a092cd9413b91537 Author: Daniel Ladiges Date: Tue Jun 14 17:24:03 2022 -0700 Some modifications for Avery's project exec/DSMC/main_driver.cpp exec/immersedIons/inputs_template exec/immersedIons/main_driver.cpp exec/phononDSMC/delPlots exec/phononDSMC/py/paramPlane.ipynb exec/phononDSMC/writePlotFile.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 8917353128f0e97fbb5bf8315c42e99fc85200b6 Merge: 165e744d 2a73c121 Author: emercado9 Date: Tue Jun 14 16:51:05 2022 -0700 Merge branch 'compressible_stag_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_stag_mui commit 2a73c121695e722fdcf94b703c7236315d9f1efb Author: Changho Kim Date: Tue Jun 14 16:33:53 2022 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF: prob size reduced so that it can be run with 5 cpus. confirmed that it runs. exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py exec/compressible_mui/RUN_COadsPt111_eq_SF/run.sh commit 51c9b9b09f3d79e054da9dd54e11b571831dc32f Author: Changho Kim Date: Tue Jun 14 16:24:33 2022 -0700 exec/compressible_stag_mui/MUI/spatial_storage.h somehow this file was not included exec/compressible_stag_mui/MUI/spatial_storage.h commit 6c77b1021d9a5273199ea471741e50e885c777bc Merge: 0750ea48 b9581aef Author: Changho Kim Date: Tue Jun 14 15:17:36 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 165e744d1301948a45a70e815b0cc13cd6f20277 Merge: 0750ea48 b9581aef Author: emercado9 Date: Tue Jun 14 14:03:55 2022 -0700 Merge branch 'main' into compressible_stag_mui commit 1423290d5d11b9973efce83d4ba7c81e7923d970 Author: Matteo Polimeno Date: Mon Jun 13 16:57:06 2022 -0700 /FHDeX/src_compressible_stag/main_driver.cpp: updated driver src_compressible_stag/main_driver.cpp commit 5aabaa8680ca741b2bb6cda65840c7d517f15153 Author: Matteo Polimeno Date: Mon Jun 13 16:55:40 2022 -0700 /FHDeX/src_compressible/main_driver.cpp: updated driver src_compressible/main_driver.cpp commit 8727c0ca09f5effcc2debc7ac5de853cc711e256 Author: Matteo Polimeno Date: Mon Jun 13 16:52:58 2022 -0700 /FHDeX/src_MFsurfchem/: prim implementation src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp commit 0750ea48b9d08bf9cdd6d0e28536c4a19a57f007 Author: emercado9 Date: Mon Jun 13 16:22:11 2022 -0700 src_compressible_stag/: added setBCStag procedure after mui fetch command src_compressible_stag/main_driver.cpp commit a5ffbc15b472008c7e0f9c63e992faff4463f4ee Merge: 83ca48b0 a18169d3 Author: emercado9 Date: Mon Jun 13 11:53:00 2022 -0700 Merge branch 'main' into compressible_stag_mui commit b9581aeff56f17634c877e20c19de092ce176ed7 Merge: 080716fa 862bf39b Author: Johannes Blaschke Date: Mon Jun 13 10:49:39 2022 -0700 Merge branch 'jpb/new-pushpull' commit 862bf39b226c9764509626d897d6e11466509ee5 Author: Johannes Blaschke Date: Sun Jun 12 17:26:48 2022 -0700 new versions of pulldown exec/tutorials/ib_marker_basic/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 92bf0a97b25fc09f3701b2becdb8f5bb6aebef3d Author: Gang Xu Date: Sun Jun 12 14:50:46 2022 -0700 changes related to querying/setting do_tiling values src_common/main.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp commit 080716fa19d457e76599a9ee26afdcbaa6c3c006 Author: Changho Kim Date: Fri Jun 10 23:45:27 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: correct temperature correction and energy update src_MFsurfchem/MFsurfchem_functions.cpp commit 83ca48b07f5914ce18711bd592884249909e9d21 Author: emercado9 Date: Fri Jun 10 13:49:46 2022 -0700 implemented MUI into src_compressible_stag/main_driver.cpp, created exec/compressible_stag_mui directory exec/compressible_stag_mui/GNUmakefile exec/compressible_stag_mui/MUI/Doxyfile exec/compressible_stag_mui/MUI/LICENSE-Apache-v2 exec/compressible_stag_mui/MUI/LICENSE-GPL-v3 exec/compressible_stag_mui/MUI/README.md exec/compressible_stag_mui/MUI/bin.h exec/compressible_stag_mui/MUI/chrono_sampler_exact.h exec/compressible_stag_mui/MUI/chrono_sampler_gauss.h exec/compressible_stag_mui/MUI/chrono_sampler_mean.h exec/compressible_stag_mui/MUI/chrono_sampler_null.h exec/compressible_stag_mui/MUI/chrono_sampler_sum.h exec/compressible_stag_mui/MUI/comm.h exec/compressible_stag_mui/MUI/comm_factory.h exec/compressible_stag_mui/MUI/comm_mpi.h exec/compressible_stag_mui/MUI/comm_mpi_nxn.h exec/compressible_stag_mui/MUI/comm_mpi_smart.h exec/compressible_stag_mui/MUI/comm_tcp.h exec/compressible_stag_mui/MUI/config.h exec/compressible_stag_mui/MUI/dim.h exec/compressible_stag_mui/MUI/dynstorage.h exec/compressible_stag_mui/MUI/exception.h exec/compressible_stag_mui/MUI/geometry.h exec/compressible_stag_mui/MUI/lib_dispatcher.h exec/compressible_stag_mui/MUI/lib_factory.h exec/compressible_stag_mui/MUI/lib_mpi_hepler.h exec/compressible_stag_mui/MUI/lib_mpi_multidomain.h exec/compressible_stag_mui/MUI/lib_mpi_split.h exec/compressible_stag_mui/MUI/lib_singleton.h exec/compressible_stag_mui/MUI/lib_uri.h exec/compressible_stag_mui/MUI/message.h exec/compressible_stag_mui/MUI/mui.h exec/compressible_stag_mui/MUI/point.h exec/compressible_stag_mui/MUI/reader.h exec/compressible_stag_mui/MUI/reader_variable.h exec/compressible_stag_mui/MUI/sampler.h exec/compressible_stag_mui/MUI/sampler_exact.h exec/compressible_stag_mui/MUI/sampler_gauss.h exec/compressible_stag_mui/MUI/sampler_kmc_fhd.h exec/compressible_stag_mui/MUI/sampler_mov_avg.h exec/compressible_stag_mui/MUI/sampler_nn.h exec/compressible_stag_mui/MUI/sampler_null.h exec/compressible_stag_mui/MUI/sampler_pseudo_n2_linear.h exec/compressible_stag_mui/MUI/sampler_pseudo_nn.h exec/compressible_stag_mui/MUI/sampler_shepard_quintic.h exec/compressible_stag_mui/MUI/sampler_sph_quintic.h exec/compressible_stag_mui/MUI/sampler_sum_quintic.h exec/compressible_stag_mui/MUI/span.h exec/compressible_stag_mui/MUI/stream.h exec/compressible_stag_mui/MUI/stream_ordered.h exec/compressible_stag_mui/MUI/stream_string.h exec/compressible_stag_mui/MUI/stream_tuple.h exec/compressible_stag_mui/MUI/stream_unordered.h exec/compressible_stag_mui/MUI/stream_vector.h exec/compressible_stag_mui/MUI/uniface.h exec/compressible_stag_mui/MUI/util.h exec/compressible_stag_mui/MUI/virtual_container.h exec/compressible_stag_mui/MUI/wrapper_c/Makefile exec/compressible_stag_mui/MUI/wrapper_c/mui_3d.cpp exec/compressible_stag_mui/MUI/wrapper_c/mui_3d.h exec/compressible_stag_mui/MUI/wrapper_c/unit_test.c exec/compressible_stag_mui/MUI/wrapper_f/Makefile exec/compressible_stag_mui/MUI/wrapper_f/TODO exec/compressible_stag_mui/MUI/wrapper_f/mui.F90 exec/compressible_stag_mui/MUI/wrapper_f/mui_3df.cpp exec/compressible_stag_mui/MUI/wrapper_f/unit_test.f90 src_compressible_stag/main_driver.cpp commit a18169d3ee504e4d59a178e57cb16f4178d62f37 Merge: 27863ada dfca5fab Author: emercado9 <68758761+emercado9@users.noreply.github.com> Date: Thu Jun 9 16:55:53 2022 -0700 Merge pull request #107 from AMReX-FHD/compressible_stag_mui moved main_driver.cpp from exec/compressible_stag to src_compressible… commit dfca5fab7624e5fbbc585f3f513a4af5fecd81ff Author: emercado9 Date: Thu Jun 9 16:30:50 2022 -0700 moved main_driver.cpp from exec/compressible_stag to src_compressible_stag/ src_compressible_stag/main_driver.cpp commit 27863ada179a3f14830f24a66329505be43631fc Merge: 6114a9b4 8b188fa3 Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Thu Jun 9 11:43:56 2022 -0700 Merge pull request #106 from AMReX-FHD/MFsurfchem MFsurfchem commit 8b188fa310141a65af3105a0fa71626d9d587fc0 Merge: e449a8dc 6114a9b4 Author: Andy Nonaka Date: Thu Jun 9 11:27:58 2022 -0700 Merge branch 'main' into MFsurfchem commit e449a8dcb9dd25bf9dc93b337271e815d8952e8d Author: Matteo Polimeno Date: Thu Jun 9 10:09:08 2022 -0700 FHDeX/src_MFsurfchem/MFsurfchem_functions.cpp: pp.getarr() -> pp.queryarr() src_MFsurfchem/MFsurfchem_functions.cpp commit 50e89287475fc85349c9fd47229cd6515b787dd3 Author: Changho Kim Date: Thu Jun 9 01:09:54 2022 -0700 MFsurfchem: small changes exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit e68d79bb473721d0b138abf00e7012bd1b263adf Author: Matteo Polimeno Date: Wed Jun 8 17:48:15 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: introduced ParmParse.getarr() to extract arrays from input files and updated functions accordingly src_MFsurfchem/MFsurfchem_functions.cpp commit 4df78f46252fb643b11cb3843ad7b8124ef453c9 Author: Matteo Polimeno Date: Wed Jun 8 17:43:36 2022 -0700 src_MFsurfchem/MFsurfchem_namespace.H: declared surfcov0, ads_rate_const and des_rate as GpuArrays src_MFsurfchem/MFsurfchem_namespace.H commit c90b7c6563e271bafa3d6d0ad59ccae6988da363 Author: Matteo Polimeno Date: Wed Jun 8 17:34:48 2022 -0700 exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag: updated inputs file exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag commit 6523482e6c90087fbdbc2cd0ed2fc2238bd752a9 Merge: 3bc664cc 6114a9b4 Author: Johannes Blaschke Date: Wed Jun 8 17:34:21 2022 -0700 Merge branch 'main' into jpb/new-pushpull commit 6114a9b4708aaf940c025b06d98fc3b2378d8094 Author: Johannes Blaschke Date: Wed Jun 8 17:34:00 2022 -0700 fix dumbells exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/Make.package exec/immersed_boundary/channel_dumbbell/init_funcs.F90 exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver_F.H exec/immersed_boundary/flagellum/main_driver_F.H commit 2016decf7d14a4cf7a1bc7118dec261f87159e0a Author: Johannes Blaschke Date: Wed Jun 8 16:57:52 2022 -0700 add &end back in exec/immersed_boundary/flagellum/inputs_taylor commit afdc1634668f754053bdb16129a831f7810aa554 Author: Matteo Polimeno Date: Wed Jun 8 16:33:34 2022 -0700 /exec/compressible_stag/test_MFsurfchem: pushing new branch exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag commit 3bc664cc2502d689e764269f875b6272c85a48ee Author: Johannes Blaschke Date: Wed Jun 8 13:28:06 2022 -0700 compute cpu offsets for push down/pull up exec/tutorials/ib_marker_basic/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 91f00c0be71124adb6e40d132cfe8d2e0d375f76 Author: Changho Kim Date: Sat Jun 4 04:55:49 2022 -0700 src_MFsurfchem/MFsurfchem_functions.cpp: temperature correction src_MFsurfchem/MFsurfchem_functions.cpp commit 4278733244a9479cad44df7eb23ab9521890b44d Author: Changho Kim Date: Sat Jun 4 04:54:57 2022 -0700 exec/compressible_stag/test_MFsurfchem: script updated exec/compressible_stag/test_MFsurfchem/ads.plt exec/compressible_stag/test_MFsurfchem/ads.py exec/compressible_stag/test_MFsurfchem/ads.sh exec/compressible_stag/test_MFsurfchem/ads_var.plt exec/compressible_stag/test_MFsurfchem/diff.sh commit 222a1bfd597dcb13061d05a763e53ca0785d005c Author: Changho Kim Date: Wed Jun 1 04:55:21 2022 -0700 exec/compressible_stag/test_MFsurfchem_RB: test plot scripts updated exec/compressible_stag/test_MFsurfchem_RB/ads.plt exec/compressible_stag/test_MFsurfchem_RB/ads.sh exec/compressible_stag/test_MFsurfchem_RB/ads_var.plt exec/compressible_stag/test_MFsurfchem_RB/diff.sh commit 262a105d19016bb741bd5ed9da4e595aa6974f3b Author: Changho Kim Date: Mon May 30 16:12:31 2022 -0700 exec/compressible_stag: test_MFsurfchem and test_MFsurfchem_RB updated exec/compressible_stag/test_MFsurfchem/ads.py exec/compressible_stag/test_MFsurfchem/ads.sh exec/compressible_stag/test_MFsurfchem/ads_var.plt exec/compressible_stag/test_MFsurfchem/diff.sh exec/compressible_stag/test_MFsurfchem/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem/params_CO_Ar_eq_SF.py exec/compressible_stag/test_MFsurfchem_RB/diff.sh exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag commit 9e70f270956f05bd2f1269140c9fd52af5cb35de Author: Changho Kim Date: Mon May 30 16:09:08 2022 -0700 MFsurfchem: typo in updateupdate_MFsurfchem(), also dt removed from input argument list exec/compressible_stag/main_driver.cpp src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible/main_driver.cpp commit 1d85879f23b1711e5a79c055c15880150e61f2e4 Author: Changho Kim Date: Sun May 29 19:20:46 2022 -0700 exec/compressible_stag/test_MFsurfchem_RB: forgot to add a script exec/compressible_stag/test_MFsurfchem_RB/ads_var.plt commit b400247671e9ad486c622d01d76cb674afc78ddb Author: Changho Kim Date: Sun May 29 19:19:19 2022 -0700 exec/compressible_stag/test_MFsurfchem_RB: analysis scripts corrected and updated exec/compressible_stag/test_MFsurfchem_RB/ads.py exec/compressible_stag/test_MFsurfchem_RB/ads.sh exec/compressible_stag/test_MFsurfchem_RB/clean.sh exec/compressible_stag/test_MFsurfchem_RB/params_COrb_eq_SF.py commit b187ef8e4fe4d49992af371940ef5683dcc56904 Author: Changho Kim Date: Sun May 29 05:51:55 2022 -0700 exec/compressible_stag/test_MFsurfchem_RB: red/blue test case exec/compressible_stag/test_MFsurfchem_RB/ads.py exec/compressible_stag/test_MFsurfchem_RB/ads.sh exec/compressible_stag/test_MFsurfchem_RB/clean.sh exec/compressible_stag/test_MFsurfchem_RB/diff.sh exec/compressible_stag/test_MFsurfchem_RB/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem_RB/params_COrb_eq_SF.py exec/compressible_stag/test_MFsurfchem_RB/run.sh exec/compressible_stag/test_MFsurfchem_RB/zavg.plt exec/compressible_stag/test_MFsurfchem_RB/zavg.sh commit 765a154f2c09c77c5d451109960ae1c9501d7a72 Author: Changho Kim Date: Fri May 27 10:00:25 2022 -0700 compressible_stag: surfcov, surfcovMeans, surfcovVars included to plotfile if n_ads_spec>0 exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 308f32259fccff5185a4e76a3c6466421d1c403d Author: Johannes Blaschke Date: Thu May 26 10:09:40 2022 -0700 wip on new pulldown exec/tutorials/ib_marker_basic/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit d234efa36e6d58cb1ac85f0e4b9c94918c902acf Author: Andy Nonaka Date: Thu May 26 09:23:25 2022 -0700 parallel for with RNG syntax - compiles on GPU again src_MFsurfchem/MFsurfchem_functions.cpp commit 932d6b99518a4fd34f12837692985059c63d2f06 Merge: 8744c6b1 31dfaae8 Author: John Bell Date: Tue May 24 15:43:24 2022 -0700 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit 8744c6b11cc4335c1ded72c5e171babc2b050849 Author: John Bell Date: Tue May 24 15:40:05 2022 -0700 added inputs for rayleigh plateau exec/multispec/Init.cpp exec/multispec/inputs_fh_3d_cyl exec/multispec/main_driver.cpp commit 5fbb68c93c8c34529320954303a03fd46ba7fb30 Merge: 9a2ba071 ab6dc601 Author: isriva Date: Tue May 24 12:58:07 2022 -0700 Merge remote-tracking branch 'origin/main' into main commit 9a2ba0716162eee5b28f4a957508cafe3e2e9d1e Author: isriva Date: Tue May 24 12:57:05 2022 -0700 added screen output exec/compressible_stag/main_driver.cpp commit ab6dc601e05b407f93d60c36e8a703a6f38d4722 Merge: 18946ca8 72600ef6 Author: Daniel Ladiges Date: Mon May 23 14:21:11 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 18946ca893eb8c347971ae47fa54fdc4cc89d7e1 Author: Daniel Ladiges Date: Mon May 23 10:40:00 2022 -0700 Real 'volume generating' reservoir in DSMC - not currently working exec/DSMC/main_driver.cpp exec/DSMC/writePlotFile.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 72600ef68d3ce67c7c505b0aeb6fbf56d0acfb73 Author: Changho Kim Date: Sat May 21 23:06:32 2022 -0700 exec/compressible_MFsurfchem deleted and the test directory moved under exec/compressible exec/compressible/test_MFsurfchem/clean.sh exec/compressible/test_MFsurfchem/diff.sh exec/compressible/test_MFsurfchem/inputs_fhd exec/compressible/test_MFsurfchem/params_CO_Ar_eq_SF.py exec/compressible/test_MFsurfchem/run.sh exec/compressible/test_MFsurfchem/zavg.plt exec/compressible/test_MFsurfchem/zavg.sh exec/compressible_MFsurfchem/GNUmakefile commit df52eb22b16941745f83a658b4db850cff68d586 Author: Changho Kim Date: Sat May 21 22:49:18 2022 -0700 MFsurfchem: multiple ads-des spec via n_ads_spec (previously, 1 spec defined by ads_spec) exec/compressible_MFsurfchem/RUN0/inputs_fhd exec/compressible_stag/main_driver.cpp exec/compressible_stag/test_MFsurfchem/inputs_fhd_stag src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible/main_driver.cpp src_compressible_stag/Checkpoint.cpp commit 31dfaae8b8d521b4bbec2025b00d4ffe03fdb1db Author: Andy Nonaka Date: Thu May 19 13:16:59 2022 -0700 sync with main exec/multispec/AdvanceTimestepBousq.cpp commit ba12dce9eb1b22ab47c35116d0ef8e6952234cbb Author: Andy Nonaka Date: Thu May 19 13:11:39 2022 -0700 DIM=2 exec/multispec/GNUmakefile commit 7d35699330a5e2e3faea3067ed83238a3e412e35 Author: Andy Nonaka Date: Thu May 19 10:19:56 2022 -0700 turn noise back on exec/multispec/inputs_fh_2d commit 15075cab1bd902f292f559c5acc49b1567c7e5cf Author: Johannes Blaschke Date: Wed May 18 21:25:36 2022 -0700 pass through IBMarkerContainer::NextID exec/tutorials/ib_marker_basic/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit a276633112cce0d7f8f039fe282b96d2f4eb9fb2 Merge: 6bff5d80 4aeaea22 Author: isriva Date: Wed May 18 16:20:32 2022 -0700 Merge remote-tracking branch 'origin/main' into main commit 6bff5d805c63618c9cd9466565ebdee9aacdf9e4 Author: isriva Date: Wed May 18 16:19:48 2022 -0700 fix small compile bug exec/compressible_stag/main_driver.cpp commit 9f1f82d720f488e6033cb0358d6429565db8b509 Author: isriva Date: Wed May 18 16:17:34 2022 -0700 right conservedtoprimitive and setBCStag for chemistry stuff in staggered code exec/compressible_stag/main_driver.cpp commit 4aeaea22aedb26bb71a094f90511f89154f3bb33 Merge: 34f9fcd5 bf57f8f7 Author: Daniel Ladiges Date: Wed May 18 12:26:43 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 34f9fcd5fe7973c8ac9198e3cbc59710ff868742 Author: Daniel Ladiges Date: Wed May 18 12:25:40 2022 -0700 fixed duplicate field in plotfile. Implemented volume generating reservior but still debugging exec/DSMC/writePlotFile.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit c30c3517d735d915ea1f1f8464cb4634f3215a9d Merge: 26e6a13a bf57f8f7 Author: Andy Nonaka Date: Tue May 17 15:57:48 2022 -0700 Merge branch 'main' into flory_huggins commit bf57f8f7b30b9920b7cc2689d0de4bb8f866d451 Author: Andy Nonaka Date: Tue May 17 15:49:28 2022 -0700 pass reference to geometry object instead of making a local copy src_compressible/boundary.cpp src_compressible/checkpoint.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/flux.cpp src_compressible/membrane.cpp src_compressible/timeStep.cpp src_compressible/writePlotFile.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 0495db7ff56abb0ebdb7ee2e5c097edf030572cd Author: Andy Nonaka Date: Tue May 17 15:33:18 2022 -0700 fill ghost cells for cuMeans/Vars and primMeans/Vars - this is needed for restarting properly for copying data from one grid layout to possibly another We need at least one ghost cell for rho treatment at boundary exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit 26e6a13ab9bb5b592c8cafacb813dfc8a8698448 Merge: 9493bd6e d06a9c30 Author: Andy Nonaka Date: Mon May 16 18:07:38 2022 -0700 Merge branch 'main' into flory_huggins commit d06a9c30dda713a568d5d383ff97344b42ce5f1d Merge: 11237968 7e640e15 Author: Andy Nonaka Date: Mon May 16 18:07:18 2022 -0700 Merge pull request #102 from AMReX-FHD/wallspeed_fix Wallspeed fix commit 7e640e15654ed70f41268ba99befe0aa1503d95e Author: Andy Nonaka Date: Mon May 16 16:41:10 2022 -0700 whitespace src_gmres/ApplyMatrix.cpp commit 9493bd6e66549be6ea7acd72eda420792cd8e355 Merge: a249ce94 9aa64778 Author: Andy Nonaka Date: Mon May 16 16:39:35 2022 -0700 Merge branch 'main' into flory_huggins commit 11237968f55514c383cd0a13a147fab2e412b3a2 Merge: 1f8941a5 7260cd6f Author: Andy Nonaka Date: Mon May 16 16:38:02 2022 -0700 Merge pull request #103 from etpalmer63/ci_speedup CI: Download only needed CUDA modules commit 0f1ec80dfba0397f32d70d52194a2690a9f9be02 Author: Andy Nonaka Date: Mon May 16 16:37:25 2022 -0700 complete shear walls for all examples exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/advance_midpoint.cpp exec/immersed_boundary/flagellum/advance_stokes.cpp exec/lib_hydro/demo/main_driver.cpp src_gmres/GMRES.cpp commit 1f8941a5cf617aa72cfc97ccac6bf7ff85346cef Author: Changho Kim Date: Mon May 16 02:42:59 2022 -0700 src_MFsurfchem: init_surfcov, sample_MFsurfchem --> RandomPoisson exec/compressible_stag/main_driver.cpp src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible/main_driver.cpp commit c7a8d5ce056c95787c70415df61ff18a76b99ad1 Author: Changho Kim Date: Mon May 16 02:40:30 2022 -0700 exec/compressible_stag//test_MFsurfchem/zavg.sh: TVar --> TVarDirect exec/compressible_stag/test_MFsurfchem/zavg.sh commit d9e63c0a025d14bd2ebf5d5e6249d14f49eddffb Author: Daniel Ladiges Date: Sun May 15 19:20:13 2022 -0700 Fixed bug in calculation in DSMC. Fixed error in mass conserving reservoir option exec/DSMC/stats.cpp src_particles/DsmcParticleContainer.cpp commit 7260cd6f2ab1b535222aa0a14e3e12e1c612fbd9 Author: Erik Palmer Date: Fri May 13 17:03:08 2022 -0400 CI--CUDA: Download specific CUDA packages instead of full toolkit. .github/workflows/dependencies/dependencies_nvcc11.sh commit 240f59eec287230a0599c8d9b9654753d386e725 Merge: 09824fe1 9aa64778 Author: Andy Nonaka Date: Fri May 13 13:47:02 2022 -0700 Merge branch 'main' into wallspeed_fix commit 9aa6477853f6fbc2710e13f6137e0527ca5f28f3 Merge: 8ab0130f 10ae3a0b Author: Erik Date: Fri May 13 16:44:13 2022 -0400 Merge pull request #101 from etpalmer63/ci_key_fix Ci key fix commit 09824fe133042baa6ef31d87ff01b897059f0af9 Author: Andy Nonaka Date: Fri May 13 13:40:37 2022 -0700 ApplyMatrix in inhomogeneous fix needs inhomogeneous bcs src_gmres/ApplyMatrix.cpp src_gmres/GMRES.cpp src_gmres/gmres_functions.H commit 291cfe825a53f6220666317290aff9b1e00c4407 Merge: 6c5ec4bc 8ab0130f Author: Andy Nonaka Date: Thu May 12 14:45:24 2022 -0700 Merge branch 'main' into wallspeed_fix commit 8ab0130f1c0396421ecc00997c22ba34e1004e96 Author: Daniel Ladiges Date: Thu May 12 14:41:17 2022 -0700 Fixed call to app_bc_gpu in DISCOS after changes made for DSMC src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 6c5ec4bc090e9515b3cf629dafdf70c0a515acfb Author: Andy Nonaka Date: Thu May 12 14:34:19 2022 -0700 more shear wall updates exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp src_hydro/advance.cpp commit b5b2450a94942889ee2b6c764ce78cb6a62f723f Author: Andy Nonaka Date: Thu May 12 13:55:21 2022 -0700 more boundary filling. still WIP exec/hydro/advance.cpp src_hydro/MacProj_hydro.cpp commit 7122070e7cebf76bcc05a53878159fcc76824d0f Author: Andy Nonaka Date: Thu May 12 10:11:17 2022 -0700 warning message src_common/common_functions.cpp commit 6e203b75f3656b134379274358b3fcce9b57e552 Author: Andy Nonaka Date: Wed May 11 15:56:43 2022 -0700 more wall fixes src_hydro/AddMFluctuations.cpp src_hydro/MacProj_hydro.cpp src_hydro/advance.cpp commit 3f51841bd252af3718dc19388ed1edbac25c8cbf Author: Andy Nonaka Date: Wed May 11 15:40:41 2022 -0700 wall WIP exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/main_driver.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_gmres/GMRES.cpp src_multispec/InitialProjection.cpp commit c8e5589180f78645875a976ec3976873df40ea3e Merge: 45873b48 730d4d26 Author: Daniel Ladiges Date: Wed May 11 00:58:40 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 45873b4843b4110f162e408bfbc3da8704058305 Author: Daniel Ladiges Date: Wed May 11 00:56:21 2022 -0700 Mass conserving reservoir implemented exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 730d4d26733f8863ad2cc167911db8db224d0fc0 Author: Andy Nonaka Date: Tue May 10 16:23:18 2022 -0700 rewrite MFsurfchem_functions to work on GPU src_MFsurfchem/MFsurfchem_functions.cpp commit f886727ece1908cac5b7ec59097e779ed96f8e00 Author: Andy Nonaka Date: Tue May 10 16:12:55 2022 -0700 implement MFsurfchem checkpoint/restart also set the number of ghost cells in surfcov and dNadsdes to zero (tested); they are not necessary exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H commit 10ae3a0b87b6ddc61fe595af1d08b022a82cd14a Author: Erik Palmer Date: Tue May 10 13:35:21 2022 -0400 update cuda package signing key .github/workflows/dependencies/dependencies_nvcc11.sh commit 7795da5321a0896ae8b369fead4c705147cc5bc6 Merge: 36834b27 ec7c27f6 Author: Changho Kim Date: Mon May 9 15:53:42 2022 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 36834b277e8d60254b9053cb9bf55a9b173b3501 Author: Changho Kim Date: Mon May 9 15:51:52 2022 -0700 exec/compressible_stag/test_MFsurfchem: test run directory added exec/compressible_stag/test_MFsurfchem/clean.sh exec/compressible_stag/test_MFsurfchem/diff.sh exec/compressible_stag/test_MFsurfchem/inputs_fhd_stag exec/compressible_stag/test_MFsurfchem/params_CO_Ar_eq_SF.py exec/compressible_stag/test_MFsurfchem/run.sh exec/compressible_stag/test_MFsurfchem/zavg.plt exec/compressible_stag/test_MFsurfchem/zavg.sh commit ec7c27f698807a41c400864e757d7d58d18e285b Author: isriva Date: Mon May 9 15:36:16 2022 -0700 added direct and indirect (Garcia formula) for temperature variance src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit d9bd8efcc1f7182a3d9c890093298019b20b4c59 Author: Changho Kim Date: Mon May 9 11:41:03 2022 -0700 forgot to add GNUmakefile exec/compressible_stag/GNUmakefile commit 5195716be0133c19fa90cb26f4d1b0dbe3f0f450 Author: Changho Kim Date: Mon May 9 11:37:15 2022 -0700 exec/compressible_stag: MFsurfchem added. need to abort if restart with ads_spec exec/compressible_stag/main_driver.cpp commit 1f2b8ac2b9ae035d83e3f66423fdfc2abc31bdc4 Author: Changho Kim Date: Sat May 7 16:32:59 2022 -0700 src_MFsurfchem: function sample_MFsurfchem takes prim as an input src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible/main_driver.cpp commit ec48e8d15945913ea48559acc2f8d82b83337ea2 Author: Galen Wang Date: Thu May 5 16:16:53 2022 -0700 Update esc kernel wetRad table. Allow spread to work on refined grid exec/immersedIons/wetRad_KernelES/wetRad_w4.dat exec/immersedIons/wetRad_KernelES/wetRad_w5.dat exec/immersedIons/wetRad_KernelES/wetRad_w6.dat exec/immersedIons/wetRad_KernelES/wetRad_w7.dat src_particles/FhdParticleContainer.cpp commit fc108a73fda0705d20a5bbdf1c903fecea6e61b8 Author: Daniel Ladiges Date: Thu May 5 16:01:22 2022 -0700 Fixed wrong cell size being passed to new spreading function exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp commit 83ff13eec3efac683b97f69acd16ea509c776f97 Author: Johannes Blaschke Date: Thu May 5 10:52:19 2022 -0700 add marker basics exec/tutorials/ib_marker_basic/GNUmakefile exec/tutorials/ib_marker_basic/Make.package exec/tutorials/ib_marker_basic/inputs exec/tutorials/ib_marker_basic/main_driver.cpp commit ec2e584a9ade19823a2db9089d0b272726e4426b Author: Johannes Blaschke Date: Thu May 5 10:50:47 2022 -0700 clean up includes exec/tutorials/amrex_mpi_basic/main_driver.cpp commit a8fe5ffdb15a081f0b7fdf22198978ea801967e2 Author: Johannes Blaschke Date: Thu May 5 09:04:54 2022 -0700 expand example exec/tutorials/amrex_mpi_basic/main_driver.cpp commit bfe8c808212bf202f4bb9a63e0b3aba64c16d529 Author: Johannes Blaschke Date: Wed May 4 18:43:00 2022 -0700 add basic amrex-style mpi tutorial exec/tutorials/amrex_mpi_basic/GNUmakefile exec/tutorials/amrex_mpi_basic/Make.package exec/tutorials/amrex_mpi_basic/main_driver.cpp commit 2aa902eb7dcd57d5dcb98f5003d3f050671bbe42 Merge: 759c7938 fa46fc26 Author: Daniel Ladiges Date: Wed May 4 14:57:26 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 759c7938c04e589bfefff7c4d7ec72ce5d3d0c4b Author: Daniel Ladiges Date: Wed May 4 14:56:59 2022 -0700 re-enabled 'reflecting species wall' in DSMC src_geometry/paramplane_functions_K.H commit fa46fc26169b2a9411027affc42661bd6e8b7a17 Author: jgalenwang Date: Tue May 3 11:16:31 2022 -0700 turn back on the check for negative diffusion exec/immersedIons/main_driver.cpp commit f36d7be73fbdcc606fd82368eaf7763ec2888bf5 Author: Galen Wang Date: Tue May 3 10:23:50 2022 -0700 bugfix for spread exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 3ee7e4411fde21123793b223835e65236e4ca0f4 Author: Andy Nonaka Date: Fri Apr 29 14:07:19 2022 -0700 fixed typo - compiles again src_geometry/paramplane_functions_K.H commit 7b99f751278dac609d165a8b9396fc674d644e5c Merge: 7f63b4be d3547da8 Author: Andy Nonaka Date: Thu Apr 28 08:25:57 2022 -0700 Merge pull request #100 from AMReX-FHD/shear_wall Shear wall commit d3547da809d9ab3e516c4ba9b5dcb512bf98f507 Author: Andy Nonaka Date: Thu Apr 28 08:01:42 2022 -0700 robustify inhomogeneous solver src_gmres/GMRES.H src_gmres/GMRES.cpp commit 743394174887610c767f812c1f5ffa6853a9f6dc Author: Andy Nonaka Date: Thu Apr 28 07:51:54 2022 -0700 whitespace exec/hydro/advance.cpp commit 69b2be5e69029a85c6dc2e520273f90d9aba59ef Author: Andy Nonaka Date: Thu Apr 28 07:51:14 2022 -0700 more wall work exec/hydro/advance.cpp exec/hydro/inputs_shearwall_2d exec/hydro/inputs_shearwall_3d src_gmres/GMRES.cpp commit 7be99bb8db75f9301e23ca7bb93022b69e68e3ac Author: Andy Nonaka Date: Wed Apr 27 16:07:20 2022 -0700 shear wall example in 2d exec/hydro/advance.cpp exec/hydro/inputs_shearwall_2d src_common/common_functions.cpp commit 9626a8b72400505c9e6862660362ed579729aac8 Author: isriva Date: Wed Apr 27 16:00:41 2022 -0700 added capability to separately set diffusive and stochastic momentum flux to zero in the reservoirs src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp commit 19f329840caef3c6ba2d06e7fa0d14e2b960938e Author: Andy Nonaka Date: Wed Apr 27 15:36:01 2022 -0700 implement transverse macvel moving walls support src_common/MultiFabPhysBC.cpp src_common/common_functions.cpp src_common/common_namespace.H commit c3273cec3d1b7b1c46108dc41c20fde51811bbef Author: Andy Nonaka Date: Wed Apr 27 15:12:55 2022 -0700 starting shear wall branch src_common/MultiFabPhysBC.cpp commit 7f63b4be187875561cce4fb540e677542c128bd8 Merge: 1b54fe08 45027a0a Author: drladiges Date: Tue Apr 26 16:24:53 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 1b54fe08661f2e15d8f9b2707bba0e0ba9fcd303 Author: drladiges Date: Tue Apr 26 16:24:20 2022 -0700 Trying uniform dist instead of Lambert for phonons src_geometry/paramplane_functions_K.H commit 45027a0a00a3758f76b3cbbef46362e5cd081a78 Author: Changho Kim Date: Mon Apr 25 04:30:17 2022 -0700 exec/compressible_MFsurfchem: test run directory (CO+Ar,eq,ads/des) exec/compressible_MFsurfchem/RUN0/clean.sh exec/compressible_MFsurfchem/RUN0/diff.sh exec/compressible_MFsurfchem/RUN0/inputs_fhd exec/compressible_MFsurfchem/RUN0/params_CO_Ar_eq_SF.py exec/compressible_MFsurfchem/RUN0/run.sh exec/compressible_MFsurfchem/RUN0/zavg.plt exec/compressible_MFsurfchem/RUN0/zavg.sh commit 58cd057301ab001c3acc02b893f831d6c87d0ca3 Merge: eae308e5 bb7cda35 Author: jbb Date: Thu Apr 21 10:01:56 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit fcade35a2135ad52fbc4e6e92bbc657bc3946dd3 Author: jbb Date: Thu Apr 21 09:58:54 2022 -0700 added new problem type and enable changing timestep with fixed dt exec/multispec/Init.cpp exec/multispec/main_driver.cpp commit bb7cda35f50e18c9be22c193e59a84fc8de1add3 Merge: 4787377c 2727e232 Author: Andy Nonaka Date: Wed Apr 20 12:35:11 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 4787377c32ccac4be23d42460215abb8c4091b82 Author: Andy Nonaka Date: Wed Apr 20 12:34:58 2022 -0700 fix reservoir implementation on y and z faces src_compressible/boundary.cpp commit 2727e2326b9fd14bbfc927fcb249056d933ecc82 Author: Changho Kim Date: Sun Apr 17 18:15:01 2022 -0700 compressible_MFsurfchem: mean-field surface chemistry for one-spec one-site adsorption/desorption implemented src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_compressible/main_driver.cpp commit 77ce3ea82620db630da5a7d7daa9dc7ab0631534 Author: Daniel Ladiges Date: Mon Apr 11 14:40:19 2022 -0700 Changed a minus sign in electrostatic defs, requires update to input files with Neumann BCs exec/immersedIons/regression_inputs/inputs_regression_eo commit 3442ab5b685f40f39b922f4ecbbd406bf29578f0 Author: Daniel Ladiges Date: Mon Apr 11 13:45:16 2022 -0700 trying to fix bug that's stopping EO regression from working src_geometry/paramplane_functions_K.H commit 0e9db395ff32b6df0e4acf3dacef74b5d8ba0647 Merge: 4bc30c64 c567fabe Author: drladiges Date: Mon Apr 11 13:06:43 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 4bc30c64f17c05f7cb57bafc09404f2c33aeb592 Author: drladiges Date: Mon Apr 11 13:06:21 2022 -0700 removed notebook dir from FHDeX. Has its own repo now tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/NeumannCond.nb tools/notebooks/channel_mob.ipynb tools/notebooks/channel_mobility.nb tools/notebooks/chargeAnalysis.nb tools/notebooks/debyemath.nb tools/notebooks/densityAnalysis.nb tools/notebooks/dsmcPlotting.ipynb tools/notebooks/energyAnalysis.nb tools/notebooks/eo_analysis.nb tools/notebooks/mobility_calc.nb tools/notebooks/phononPlotting.ipynb tools/notebooks/plank.nb tools/notebooks/plotting.ipynb tools/notebooks/plotting_dsmc.ipynb tools/notebooks/poissonChannel.nb tools/notebooks/positionGenerator.nb tools/notebooks/potentialAnalysis.nb tools/notebooks/units.nb tools/notebooks/velAnalysis.nb tools/notebooks/velAnalysisX.nb tools/notebooks/velAnalysisY.nb tools/notebooks/wall_repulsion.nb commit bf13ae4986429873cb6f4bc68111e7b9562c83aa Author: drladiges Date: Mon Apr 11 13:05:53 2022 -0700 commiting notebook dir so I can delete it tools/notebooks/plotting.ipynb commit c567fabecc14f10aac002601eacc30a919958ecf Author: Changho Kim Date: Mon Apr 11 04:33:24 2022 -0700 compressible_MFsurfchem: surfcov, dNadsdes, init_surfcov, surf_site_num_dens src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_compressible/main_driver.cpp commit c4ae54958ffa5f0d1caa1f28a271bb01d70b3b56 Author: Changho Kim Date: Sun Apr 10 18:30:20 2022 -0700 src_MFsurfchem: surfcov0 added src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H commit f07e72c60374d179024d6a781ce13c78d33c9a8e Author: Changho Kim Date: Sun Apr 10 18:29:18 2022 -0700 exec/compressible_mui: simple update (no additional momentum and energy update due to adsorption/desorption) exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h src_surfchem_mui/surfchem_mui_functions.cpp src_surfchem_mui/surfchem_mui_namespace.H commit 4ba2b88aefb049a87ed81199bc7ffc96431f20f5 Author: Changho Kim Date: Sun Apr 10 17:49:27 2022 -0700 forgot to update GNUmakefile (adding src_MFsurfchem) for compressible and compressible_mui exec/compressible/GNUmakefile exec/compressible_mui/GNUmakefile src_compressible/main_driver.cpp commit 63df6930a420c38f6f435dd381318ef230932c1e Author: Changho Kim Date: Sun Apr 10 16:54:04 2022 -0700 exec/compressible_MFsurfchem: setup exec/compressible_MFsurfchem/GNUmakefile src_MFsurfchem/MFsurfchem_functions.H src_MFsurfchem/MFsurfchem_functions.cpp src_MFsurfchem/MFsurfchem_namespace.H src_MFsurfchem/Make.package src_compressible/main_driver.cpp commit bb4be6315cac27464408464be03239ac593ed2ba Author: Daniel Ladiges Date: Thu Apr 7 12:30:54 2022 -0700 Yet another fix to the regression tests src_particles/FhdParticleContainer.H commit 20fbc7686e981e82dc7f4fc2f6bdbdf31992f994 Author: drladiges Date: Thu Mar 31 16:02:04 2022 -0700 Removed some debugging code from DSMC src_particles/DsmcParticleContainer.cpp commit b25eca4d4e2ee3898714d9e5b1a3a5954db7ef6d Author: drladiges Date: Thu Mar 31 11:05:56 2022 -0700 Fixed DISCOS bugs breaking reg test exec/immersedIons/main_driver.cpp commit 4c1c6324fedd1f5df1cd724a40c652cb6f5aee6f Merge: 7641c8c3 12ba5609 Author: drladiges Date: Thu Mar 31 09:49:09 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7641c8c3618d09a6f9d61a2212735256327ba410 Author: drladiges Date: Thu Mar 31 09:48:50 2022 -0700 notebook update tools/notebooks/dsmcPlotting.ipynb commit 12ba56097847ee789e80a28a5091cacd76d3c48b Author: Andy Nonaka Date: Wed Mar 30 14:14:12 2022 -0700 fix weighting at boundary src_compressible/flux.cpp commit f388f40962ef8004b1133acd024195dfdfafb75b Author: Daniel Ladiges Date: Wed Mar 30 11:49:44 2022 -0700 DSMC FIXED exec/DSMC/DsmcCollide.cpp exec/DSMC/GNUmakefile exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H commit a249ce94d3586a90424f39e1600d714d2abf2bd5 Author: jbb Date: Tue Mar 29 19:33:48 2022 -0700 changed Laplacian to try to improve behavior at vanishing mass frac exec/multispec/inputs_fh_3d_cyl src_multispec/DiffusiveMassFluxdiv.cpp commit ff44d99ded3d22ef82d28a87a45bdd36e2fd474a Author: John Bell Date: Tue Mar 29 13:01:42 2022 -0700 setup for nanocylinder exec/multispec/Init.cpp exec/multispec/inputs_fh_3d_jet src_common/common_functions.cpp src_common/common_namespace.H commit 26c9a7bf19e9179dd7446466658f2b46bf2253ec Merge: c68edea7 4fc58c72 Author: Daniel Ladiges Date: Tue Mar 29 09:40:49 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit c68edea7c355464ba01d826076cc26bdc3ab7e8e Author: Daniel Ladiges Date: Tue Mar 29 09:39:31 2022 -0700 Added member to FHDparticle struct that we use for DSMC to allow compilation. We need to seperate DISCOS and DSMC src_particles/FhdParticleContainer.H commit 4fc58c72f6b14d97fe49442dca08ee965be34a2e Author: drladiges Date: Tue Mar 29 09:27:21 2022 -0700 more post processing notebooks tools/notebooks/dsmcPlotting.ipynb tools/notebooks/poissonChannel.nb commit 766c0a49827d987bd19ae59499717b8a47fee9ca Merge: f6f09dcf 99839ff2 Author: drladiges Date: Tue Mar 29 09:26:38 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit f6f09dcf42417dd95a88399f45e64d6d417222b7 Author: drladiges Date: Tue Mar 29 09:21:40 2022 -0700 update postprocessing notebooks tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/plotting.ipynb tools/notebooks/wall_repulsion.nb commit 99839ff2a666ca69add9822a1e4cba2732e27fcb Author: Andy Nonaka Date: Fri Mar 25 16:25:51 2022 -0700 fix boundary stencil at hi-z src_compressible/flux.cpp commit 436dd358c44bd7adde15f02e6484de81b5091e88 Merge: d69c7785 24a994db Author: Daniel Ladiges Date: Wed Mar 23 12:26:40 2022 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit d69c778539423b42a4d66a0a82bc6e6301746aa8 Author: Daniel Ladiges Date: Wed Mar 23 12:26:18 2022 -0700 Various DSMC fixes exec/DSMC/stats.cpp exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_electrostatic/electrostatic.cpp src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 24a994db913a1a2e7adc6289b5363c877d0a9e40 Author: isriva Date: Fri Mar 11 13:46:54 2022 -0800 fixed a small bug in staggered -- this should fix reg tests src_compressible_stag/fluxStag.cpp commit f04034cbdca1c58d8f50ea8808a1190d3d0dccbd Merge: 6bccf3dc 8f69a5fe Author: jbb Date: Fri Mar 11 10:49:35 2022 -0800 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit 6bccf3dc6cf73bd4d48dafd539dc684207c74fce Author: jbb Date: Fri Mar 11 10:48:57 2022 -0800 adding test input files for flory huggins exec/multispec/inputs_fh_2d exec/multispec/inputs_fh_3d commit 6147c88f4330bccb9c35f0919e7a95fb7c964efe Author: Andy Nonaka Date: Tue Mar 8 11:53:07 2022 -0800 bugfix in stencil near boundary for hyperbolic flux src_compressible/flux.cpp commit 8f69a5fe2af37f21c4b11848a813f6bb82343d74 Merge: 7933d286 db2daab3 Author: Andy Nonaka Date: Mon Feb 28 15:53:48 2022 -0800 Merge branch 'main' into flory_huggins commit db2daab32887a1e452c69b2098fc465a62d11c48 Merge: c3f6e497 fe2ab264 Author: Ishan Srivastava Date: Thu Feb 24 14:41:42 2022 -0700 Merge pull request #99 from AMReX-FHD/compressibleStagBC Dirichlet BC for compressible staggered code commit c3f6e49796b91a736b8d4e709c36065c10948043 Merge: 73471d77 60e28510 Author: Johannes Blaschke Date: Wed Feb 23 19:38:24 2022 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 73471d77d5c2fa08b7fa64f8bdd6e79ca3b87294 Author: Johannes Blaschke Date: Wed Feb 23 19:38:17 2022 -0800 update parameters and analysis scripts exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres exec/immersed_boundary/src_analysis/data_model.py commit fe2ab2645b6af827478dce494fcfe95539f17710 Author: isriva Date: Wed Feb 23 12:59:02 2022 -0800 fix minor compile errors src_compressible_stag/fluxStag.cpp commit 112a7d5311107eb8ac5acaa6d23b7dbd91044adf Author: isriva Date: Wed Feb 23 12:28:26 2022 -0800 Dirichlet BC for compressible staggered code src_compressible_stag/boundaryStag.cpp src_compressible_stag/fluxStag.cpp commit 60e285101704196db24afe8b2461283753526fc5 Merge: 4d95c706 653c0b68 Author: Ishan Srivastava Date: Tue Feb 22 10:27:56 2022 -0700 Merge pull request #98 from AMReX-FHD/compressibleBC Dirichlet boundary conditions for the cell-centered compressible code: Dirichlet values are copied into ghost cells rather than extrapolated. commit 653c0b68a67ba4e3c981bb01c3a978edbcbf7590 Merge: 0345203c 4d95c706 Author: isriva Date: Wed Feb 16 15:37:21 2022 -0800 Merge remote-tracking branch 'origin/main' into compressibleBC commit 0345203c951dfd83e17723d5c600d3972f9f6359 Merge: 3da1a4a2 19176980 Author: isriva Date: Wed Feb 16 15:36:56 2022 -0800 Merge remote-tracking branch 'origin/compressibleBC' into compressibleBC commit 3da1a4a2dc2c1e6552af0c964afbcd9d6767ceee Author: isriva Date: Wed Feb 16 15:36:24 2022 -0800 print every 100 steps src_compressible/main_driver.cpp commit 191769805ba4126149f109272ffc703e3ab57f40 Author: Andy Nonaka Date: Thu Feb 10 14:19:28 2022 -0800 implemented stencil for 4 point average to faces one cell in from mass boundary src_compressible/flux.cpp commit 629c9d284e67bd53b502e0beaa20f70a93e3d78a Author: Andy Nonaka Date: Thu Feb 10 13:44:43 2022 -0800 cleanup src_compressible/flux.cpp commit 4d95c706b0a7e9242dbc70567450d331776f286d Author: Galen Wang Date: Wed Feb 9 11:08:18 2022 -0800 minor bug fix of timestep ramp-up after restart exec/immersedIons/main_driver.cpp commit 7933d2860262eeeab110295bd154e8f58cffdbfe Merge: 566a7c9d f5d87f2b Author: Andy Nonaka Date: Wed Feb 9 10:44:33 2022 -0800 Merge branch 'main' into flory_huggins commit bb832b664737290b1e0b3b32dc50e4c9a4246034 Author: Andy Nonaka Date: Tue Feb 8 13:41:30 2022 -0800 comment src_common/common_namespace.H commit bd82a99712a1a60cea96150e162b293996b8bfb8 Author: isriva Date: Fri Feb 4 22:20:47 2022 -0800 added a comment regarding reservoir boundary condition in inputs files (bc_mass=3), seprate from concentration boundaries (bc_mass=2) exec/compressible/chemistry_inputs_files/inputs_CO_Ar_eq_SF exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF exec/compressible/inputs_RT_3d exec/compressible/inputs_SFtest exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d_mem exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_profiling_gpu exec/compressible/inputs_regression_RT_3d exec/compressible/inputs_regression_equil_3d exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic exec/compressible/inputs_regression_temp_grad exec/compressible/inputs_temp_grad exec/compressible/inputs_test_3d exec/compressible/inputs_test_deterministic exec/compressible/inputs_tg exec/compressible_stag/inputs_RT_thermal exec/compressible_stag/inputs_RT_thermal_block exec/compressible_stag/inputs_RT_thermal_slab exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_regression_concentration_3D exec/compressible_stag/inputs_regression_periodic_3D exec/compressible_stag/inputs_regression_slip_adiabatic_3D exec/compressible_stag/inputs_regression_tempgrad_1D exec/compressible_stag/inputs_regression_tempgrad_3D exec/compressible_stag/inputs_reservoir_equil exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify commit 52e1ba5e46f14c98b194b3c81aa2b2594d0b1a49 Author: isriva Date: Fri Feb 4 21:49:25 2022 -0800 small changes and fix compilation errors src_compressible/flux.cpp commit 3c0189b6987a961a38c78c05ace1d0ada29457d8 Author: isriva Date: Fri Feb 4 15:52:48 2022 -0800 corrected stochastic flux for Dirichlet BC src_compressible/flux.cpp commit c830edef77caf5d2aa6d5589c51000b2f256488a Author: isriva Date: Fri Feb 4 10:58:48 2022 -0800 fixed diffusive fluxes at Dirichlet boundaries stochastic fluxes remaining src_compressible/flux.cpp commit 0dbdd26892fe42253251c5412dfd9841d3c60fe4 Merge: 6e470306 f5d87f2b Author: isriva Date: Thu Feb 3 23:20:14 2022 -0800 Merge remote-tracking branch 'origin/main' into compressibleBC commit 6e4703063af672eb4afb659897078e6968444cb0 Author: isriva Date: Thu Feb 3 23:11:49 2022 -0800 saving progress: modified boundary fluxes for Dirichlet BC to be done: diffusive fluxes for y,z dirs and stochastic fluxes for x,y,z dirs src_compressible/flux.cpp commit eeaf0465fc68683a645d2ef26341bf29dd4c7fb8 Author: isriva Date: Thu Feb 3 23:11:24 2022 -0800 set boundary values in ghost cells for Dirichlet BC src_compressible/boundary.cpp commit f5d87f2bcce2f450177be39414f611bc94c0056e Author: isriva Date: Sun Jan 30 15:38:25 2022 -0800 unbiased mean T and P -- Garcia 2007 src_compressible_stag/statsStag.cpp commit a049fa98239e6f35e2b5ccdc7e1076525362a6c9 Merge: f2405d73 2a9998a0 Author: isriva Date: Sun Jan 30 10:12:46 2022 -0800 Merge remote-tracking branch 'origin/main' into main commit f2405d73f0f2a905b996ae7cb4d6566546b2ee9d Author: isriva Date: Sun Jan 30 10:11:31 2022 -0800 option to specify a linearly varying initial state for conc. gradient src_compressible_stag/compressible_functions_stag.cpp commit 2a9998a08a438ca02c38bd5f8c1cb884e54bbf47 Merge: dd1514c8 ce509bf3 Author: Andy Nonaka Date: Fri Jan 28 17:53:38 2022 -0800 Merge pull request #97 from AMReX-FHD/cleanup_increment Cleanup Increment Options commit ce509bf35bd68153dd9ceadf0ea22a51c226ac8b Author: Andy Nonaka Date: Fri Jan 28 17:32:51 2022 -0800 bugfix in increment src_hydro/MkAdvSFluxdiv.cpp commit 5285b3c1dde7532e61f7b602977535005b49e8ad Author: Andy Nonaka Date: Fri Jan 28 17:11:31 2022 -0800 cleanup indentation only src_hydro/StochMomFlux.cpp commit 6d8d5a83913703175eaa5c7a2b562c19b27bba68 Author: Andy Nonaka Date: Fri Jan 28 17:10:10 2022 -0800 fix increment src_hydro/MkAdvSFluxdiv.cpp commit ddf5fc93335f322cec7a4b6d8728b165407dbb91 Author: Andy Nonaka Date: Fri Jan 28 17:07:44 2022 -0800 attempt to at increment cleanup src_common/ComputeDivAndGrad.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.cpp commit c5f53a3f9ce7ce79969f8bd2efa052b4be36533d Merge: 1bf1bac6 dd1514c8 Author: Andy Nonaka Date: Fri Jan 28 16:55:46 2022 -0800 Merge branch 'main' into cleanup_increment commit dd1514c8148b4221e344f90590f3ba65305d20a7 Merge: 20420770 accb78b1 Author: Andy Nonaka Date: Fri Jan 28 16:53:10 2022 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 20420770c93a84cd1a3e886231184d540d6d8531 Author: Andy Nonaka Date: Fri Jan 28 16:52:18 2022 -0800 fix potential bug with gradient increment function at physical boundaries src_common/ComputeDivAndGrad.cpp commit 1bf1bac68b2ac205c4ade0ee1edce2bb06a73401 Author: Andy Nonaka Date: Fri Jan 28 15:53:56 2022 -0800 all of the "increment" branching statements have been combined this affects many routines and eliminates a lot of of redudant code. for example, ComputeGrad: if (increment == 1) grad += ... else grad = ... now is simply grad = increment*grad + ... src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.cpp src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit eae308e5185517c0dd1f475180f31e2d55117d7f Author: jbb Date: Tue Jan 25 11:52:31 2022 -0800 minor tweak exec/_1d_staggered_comp/flux.f commit accb78b1962bc3fcab5e71e5f7d705111d677dd7 Author: isriva Date: Fri Jan 21 23:14:29 2022 -0800 fix compile errors src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H commit 535ead7bb669ba6e3924d180f13e6f82b9e38399 Author: isriva Date: Fri Jan 21 17:46:28 2022 -0800 set diffusive and stochastic momentum flux to zero in reservoirs src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp commit e0b95c879153f100af48ac5674d633a06b9e4a5a Author: isriva Date: Fri Jan 21 14:54:00 2022 -0800 set zero velocity in the reservoir -- zero out momentum advection src_compressible_stag/boundaryStag.cpp commit 1638b4b9bc193efdc90c04d7a9544cc9fc0dccda Author: isriva Date: Fri Jan 21 13:59:14 2022 -0800 direct computation of mean T and P src_compressible_stag/statsStag.cpp commit e2d4207ba424d1c91544b4be0eacd6c3f05827c6 Author: Daniel Ladiges Date: Fri Jan 7 14:09:20 2022 -0800 Changed allocation of paramplane list exec/phononDSMC/main_driver.cpp src_particles/DsmcParticleContainer.cpp commit aba690d00ad8eaf339b5a8700ae23eb15908577d Merge: c873b8c7 8216234a Author: Daniel Ladiges Date: Fri Jan 7 08:51:47 2022 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit c873b8c71382dd3c35248d7bbba983f15c798d84 Author: Daniel Ladiges Date: Fri Jan 7 08:51:28 2022 -0800 bug finding code for dsmc exec/immersedIons/particles.dat src_particles/DsmcParticleContainer.cpp commit 8216234a9da8294496b7de0f5b56c0763a92e0a2 Author: jbb Date: Thu Jan 6 16:27:10 2022 -0800 added 1d model with reservoir bc exec/_1d_staggered_comp/_reservoir/Makefile exec/_1d_staggered_comp/_reservoir/driver.f exec/_1d_staggered_comp/_reservoir/flux.f exec/_1d_staggered_comp/_reservoir/flux_alt.f exec/_1d_staggered_comp/_reservoir/stats.c commit ae0c06479236026c65479c539ca4b1cd1498a1ad Merge: a36b623f 830c0136 Author: Daniel Ladiges Date: Tue Jan 4 14:40:58 2022 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit a36b623f8b2f292abe5aed4bf953b50c661202e3 Author: Daniel Ladiges Date: Tue Jan 4 14:39:51 2022 -0800 Not sure, I think I deleted some whitespace exec/DSMC/main_driver.cpp src_particles/DsmcParticleContainer.cpp tools/notebooks/EO_Rezaei_parameters.nb commit 830c01369c8e8049ab8be60a7f1bd188d8972fea Author: Andy Nonaka Date: Fri Dec 17 09:57:58 2021 -0800 plot out FFTs in structFactTest exec/structFactTest/main_driver.cpp commit 566a7c9df665d898d6a61a7ea8f52ab0be113411 Merge: e2b607fb 9bd8a4c4 Author: Andy Nonaka Date: Fri Dec 17 07:31:14 2021 -0800 Merge branch 'main' into flory_huggins commit 9bd8a4c453dac3c1e007063d4c9d4903136a01ea Author: John Bell Date: Tue Dec 14 14:55:32 2021 -0800 modified pdf thing to compile on nersc and added version that does all derivatives with one read exec/hydro/PDF/GNUmakefile exec/hydro/PDF/Make.package exec/hydro/PDF/PDF_all.cpp commit e2b607fb006c766afc9991f6f35dc780d0f30bf0 Merge: 6906bda6 588a0185 Author: Andy Nonaka Date: Tue Dec 14 12:42:06 2021 -0800 Merge branch 'main' into flory_huggins commit 6906bda632d42f6f5392346220ca77cceac032be Author: Andy Nonaka Date: Tue Dec 14 12:24:41 2021 -0800 Apply suggestions from code review exec/multispec/AdvanceTimestepBousq.cpp commit 60b28517f7edbbaff5f5ce1ad3f2c9152ea31e2c Author: Andy Nonaka Date: Tue Dec 14 12:23:49 2021 -0800 Apply suggestions from code review exec/multispec/AdvanceTimestepBousq.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp commit f880709d686868b6c4accbdd596e15aa8be4bd43 Author: Andy Nonaka Date: Tue Dec 14 11:43:22 2021 -0800 cleanup only src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H commit 87fe342a846c68fb20ae39c84eb17ed1609525fb Author: Andy Nonaka Date: Tue Dec 14 11:39:20 2021 -0800 cleanup exec/multispec/main_driver.cpp commit f5a44840dab8fa2f427bd2b3d8412c0332cf972c Author: Andy Nonaka Date: Tue Dec 14 11:30:48 2021 -0800 fix gpu compilation src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 861d001a287a48b1a4176ae8ca14387a96425983 Author: jbb Date: Tue Dec 14 11:17:00 2021 -0800 tweak gamma for unequal species to get right ordering for matvecmul src_multispec/MassFluxUtil.cpp commit eab55fc04f74c8832f4f07129a3bf0051440723a Author: jbb Date: Mon Dec 13 19:10:40 2021 -0800 fixed picky thing for FH src_multispec/ComputeDivReversibleStress.cpp commit 101fb596b13e2480c282d92955e098535024689b Author: jbb Date: Mon Dec 13 18:59:08 2021 -0800 3d input files for flory huggins run using old rtil and new fh exec/multispec/inputs_fh_3d exec/multispec/inputs_rtil_fh_3d commit bc0106132467cade66f230c55262822c6981bea4 Author: jbb Date: Mon Dec 13 18:57:12 2021 -0800 more files exec/multispec/AdvanceTimestepBousq.cpp src_multispec/ComputeDivReversibleStress.cpp commit 46473c6364886bf013136eee98ed0126da035895 Author: jbb Date: Mon Dec 13 18:56:03 2021 -0800 flory huggins works on cpu exec/multispec/GNUmakefile exec/multispec/main_driver.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.cpp commit f972860839dc4eec07d9db20f12407abe81a1936 Author: jbb Date: Mon Dec 13 12:00:02 2021 -0800 add test files exec/multispec/inputs_fh_2d exec/multispec/inputs_rtil_fh_2d commit a9ac1548b494834626c56a998537e22470a9bdfa Author: jbb Date: Mon Dec 13 11:44:56 2021 -0800 debugging progress still wip exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/main_driver.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.cpp commit 76e9215420dca53c5d35e4812d4a767164f3f5dd Merge: 38620cf3 588a0185 Author: drladiges Date: Mon Dec 13 14:24:20 2021 +1100 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 38620cf3cf5e38fc9f766ac39e8dc9d0bbddc346 Author: drladiges Date: Mon Dec 13 14:23:53 2021 +1100 updated notebooks tools/notebooks/channel_mob.ipynb tools/notebooks/plotting.ipynb commit 6891a5260712ae8881410e8be8f4790acb41c02a Author: jbb Date: Fri Dec 10 15:07:13 2021 -0800 fixed bug so now old rtil regression works src_multispec/DiffusiveMassFluxdiv.cpp commit 326ebc03821ace2d98b5d614e81c7a6484a1d165 Author: jbb Date: Thu Dec 9 13:15:30 2021 -0800 additional steps for flory huggins wip exec/multispec/AdvanceTimestepBousq.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/multispec_functions.H commit b6aaba36025096a6145e8020499c2599c82c1c2c Merge: 0f15ad21 588a0185 Author: John Bell Date: Thu Dec 9 12:14:01 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3ba53d4f477759d51f465ae1b06212fbef0bac18 Author: jbb Date: Wed Dec 1 13:13:48 2021 -0800 another FH file src_common/common_functions.cpp commit 5c3e75b77ff8f783b88e5e4613e91240ef3a28cc Author: jbb Date: Wed Dec 1 13:04:13 2021 -0800 added more stuff for flory huggins src_multispec/ComputeDivReversibleStress.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 588a0185f76752cbdeb2e28ec06bea2da7b4c294 Author: Andy Nonaka Date: Mon Nov 29 15:06:55 2021 -0800 gpu bugfix for computing E(k)... need atomic adds src_analysis/StructFact.cpp commit 0f15ad21a742a80531386d4f29c74a38637db054 Merge: be615225 a7f617e3 Author: John Bell Date: Tue Nov 23 13:59:00 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit be6152257eefea69bb36453cd60084011116cbb7 Author: John Bell Date: Tue Nov 23 13:57:56 2021 -0800 make pdf for -laplacian to the n exec/hydro/PDF/PDF.cpp commit a7f617e3941a4e147557e83e01c1217c407fd68d Author: Andy Nonaka Date: Tue Nov 23 11:49:58 2021 -0800 comment exec/Ek_calculator/inputs_3d commit 7498165fc214ce448296478470bfe73324ed163d Author: Andy Nonaka Date: Tue Nov 23 11:42:21 2021 -0800 program to compute E(k) given an input plotfile exec/Ek_calculator/GNUmakefile exec/Ek_calculator/inputs_3d exec/Ek_calculator/main_driver.cpp exec/hydro/inputs_force commit f928a1f395dbadd70239e187f9085520ed62b386 Merge: 6d03f5b8 a6e43b9c Author: jbb Date: Mon Nov 22 13:31:32 2021 -0800 Merge branch 'flory_huggins' of github.com:AMReX-FHD/FHDeX into flory_huggins commit ed156b389d945117c8a2f507ddcfdcef2a99ba56 Author: Andy Nonaka Date: Mon Nov 22 08:11:47 2021 -0800 automatically detect and perform error checking on refinement ratio for restart-from-(possibly coarser)-plotfile option exec/hydro/Init.cpp commit ca9caaafa8a9aac3ad975c8ac4332958fbe3c488 Merge: 76ec9979 3d1eddee Author: drladiges Date: Sat Nov 20 10:37:56 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 76ec99792b1c061381ca59720563cc7a1980937f Author: drladiges Date: Sat Nov 20 10:37:36 2021 -0800 plotting update tools/notebooks/channel_mob.ipynb tools/notebooks/plotting.ipynb commit 3d1eddee03d6722f658acba4ecb9213d73e6234d Author: Andy Nonaka Date: Fri Nov 19 21:55:37 2021 -0800 fix comments exec/hydro/Init.cpp commit b10ed421b670f1805d954c449d029389ac04e005 Author: Andy Nonaka Date: Fri Nov 19 21:51:11 2021 -0800 cleanup plotfile init exec/hydro/Init.cpp commit 74874926d391fe5f633cd9b0f388dbdc5a67eb21 Author: Andy Nonaka Date: Fri Nov 19 21:41:26 2021 -0800 option to start a new simulation from a coarser plotfile exec/hydro/Init.cpp src_common/common_functions.cpp src_common/common_namespace.H commit 8ea052e2f9d939d7a6c52c2bd7bf6038861652d6 Author: Andy Nonaka Date: Fri Nov 19 19:04:18 2021 -0800 wrote ShiftCCToFace_onegrid to shift cell-centered data to faces (and do the domain edge copy as well) src_common/ConvertStag.cpp src_common/common_functions.H commit 8cb7f2de51ed8ac133a8079c8ae03fcc2fc93f13 Author: Andy Nonaka Date: Fri Nov 19 16:43:07 2021 -0800 test commit exec/compressible/inputs_equil_3d commit b37f09d06f2469fcf9022e69000ed887ba3806f3 Author: Andy Nonaka Date: Thu Nov 18 10:51:46 2021 -0800 comments src_analysis/StructFact.H src_analysis/StructFact.cpp commit 26be69accdcfd77614198d927673937c2ed87fe2 Author: Andy Nonaka Date: Wed Nov 17 15:53:52 2021 -0800 eliminate more redundant code src_analysis/StructFact.H src_analysis/StructFact.cpp commit 9f96fcebddea855b43f82dbeece8d21a1c64f71d Author: Andy Nonaka Date: Wed Nov 17 15:40:50 2021 -0800 remove redudant SF code (the constructors now call define) src_analysis/StructFact.cpp commit 1a012fba55037d0db204a761563689d72b4e163a Merge: 6a2028f6 fc65526e Author: jbb Date: Wed Nov 17 11:24:39 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 6a2028f6d37c556fc802e4f542186a5199728d2b Author: jbb Date: Wed Nov 17 11:24:03 2021 -0800 RT input files exec/compressible_stag/inputs_RT_thermal_block exec/compressible_stag/inputs_RT_thermal_slab commit a6e43b9ce64722e00f90e54a200be4add5f08412 Merge: 19ae76d3 fc65526e Author: Andy Nonaka Date: Wed Nov 17 09:23:02 2021 -0800 Merge branch 'main' into flory_huggins commit fc65526ee7b1545669df5370d8b4590d0c9d30fc Author: Andy Nonaka Date: Tue Nov 16 11:01:39 2021 -0800 remove unused variables src_analysis/StructFact.cpp commit 3a0368185b4208bc4d879f453a6f5d86935c95e5 Author: Andy Nonaka Date: Tue Nov 16 10:59:19 2021 -0800 fix bug in code where plotfiles for SF weren't written out if turbForcing==1 exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_compressible/main_driver.cpp commit 717b8c6a2ba1bb3b3b7c69f88095a31dabf7b6b4 Author: Andy Nonaka Date: Mon Nov 15 15:47:31 2021 -0800 typo in inputs file exec/compressible/inputs_tg src_compressible/main_driver.cpp commit 82c9d858a67c4166a892074d99a7c4f5aea9a8c7 Merge: d79ae055 98ccb10e Author: Daniel Ladiges Date: Sun Nov 14 15:42:18 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit d79ae055b6e699188a4e2f0711450aca4460ca44 Author: Daniel Ladiges Date: Sun Nov 14 15:41:54 2021 -0800 added some more options for EO partially dry running exec/immersedIons/main_driver.cpp src_particles/particle_functions_K.H commit 98ccb10e6cd61755b766d2c00b59be37ccaf377b Author: Changho Kim Date: Sun Nov 14 06:08:56 2021 -0800 src_surfchem_mui/surfchem_mui_functions.cpp: maxwellian inflow velocity sampling, mui_push Vz to KMC exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc src_surfchem_mui/surfchem_mui_functions.cpp commit 6ce65c9de7698934d5ac76504af9234e13290fe8 Author: Changho Kim Date: Sun Nov 14 06:02:23 2021 -0800 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp: Vz-dependent adsorption rate exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 0102b9f21f865f70460b7f89b96d242d7e6935cb Author: Changho Kim Date: Sun Nov 14 05:14:59 2021 -0800 exec/compressible_mui/SPPARKS_MUI: add Vz for mui_fetch exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h commit 43e82d5e453b02eb5459fcbdc9d7b5af67c07c8f Author: Changho Kim Date: Sun Nov 14 04:54:32 2021 -0800 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp: comments exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 43d585d65bedb5b7867553444b144052f322bff3 Author: Changho Kim Date: Sun Nov 14 04:19:04 2021 -0800 exec/compressible_mui/GNUmakefile exec/compressible_mui/GNUmakefile commit ef7a2f357fe4f5e2fe43dc5eab1056cb9f4920b2 Merge: 12a3dfa7 4a25e05d Author: Daniel Ladiges Date: Sat Nov 13 14:55:55 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 12a3dfa74208186efeb80f7d9b55f864efc7c8ff Author: Daniel Ladiges Date: Sat Nov 13 14:55:36 2021 -0800 a few more changes to dry mobility... exec/immersedIons/main_driver.cpp src_particles/particle_functions_K.H commit 4a25e05df3387a0e8d3021b298d73a8168a49404 Author: jbb Date: Fri Nov 12 17:56:17 2021 -0800 added prob_type 3 for 2 bubbles colliding exec/multispec/Init.cpp exec/multispec/inputs_2_bubbles_3d commit 6d03f5b86332e0da7ebc55b5f37cb0666097c880 Author: jbb Date: Fri Nov 12 09:11:39 2021 -0800 minor tweak to diffusion src_multispec/DiffusiveMassFluxdiv.cpp commit 5f7aba787e1bc4c0614002c035f0568d08431726 Merge: c06fc09b 4384ee8e Author: Daniel Ladiges Date: Fri Nov 12 01:02:13 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit c06fc09b954b0730e3f7db9a69476acb49899345 Author: Daniel Ladiges Date: Fri Nov 12 01:01:48 2021 -0800 fixed bug in dry mobility calculation for EO problem exec/immersedIons/main_driver.cpp src_particles/particle_functions_K.H tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/channel_mob.ipynb tools/notebooks/plotting.ipynb commit 19ae76d36f0409a9540bad3f0ac0307e31aef253 Author: jbb Date: Thu Nov 11 13:21:05 2021 -0800 bulk of functionality to do general flory huggins still a WIP src_common/common_functions.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H commit 4384ee8ef4718ec389f890748f72e78766af4f2b Author: Andy Nonaka Date: Mon Nov 8 11:35:58 2021 -0800 make stuff src_compressible/main_driver.cpp commit 953e970aa225a1e8e9080b5b39bbc36d3e834e80 Merge: edda275e 4fc516eb Author: Andy Nonaka Date: Fri Nov 5 18:49:08 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit edda275e4c3dbe5771263350e3ab4b5e068f3259 Author: Andy Nonaka Date: Fri Nov 5 18:48:24 2021 -0700 implement variance_coef_ener for energy give cc compressible code option to control variance_coef_mass/mom/ener normal RNGs are scaled by variance^2 src_common/common_functions.cpp src_common/common_namespace.H src_compressible/timeStep.cpp commit 4fc516eb9170d065e76b52b2852e09193b2d2f48 Merge: 4d228ade f3c7ace5 Author: Daniel Ladiges Date: Fri Nov 5 16:59:23 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 4d228ade72095607a940d4605bc4d4a2eeced14d Author: Daniel Ladiges Date: Fri Nov 5 16:59:05 2021 -0700 Another analysis notebook... tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/debyemath.nb tools/notebooks/plotting.ipynb commit f3c7ace50695127b65ddaf09bbb4cd50ac9c343c Author: Andy Nonaka Date: Fri Nov 5 12:34:49 2021 -0700 stats_int and timer exec/compressible/inputs_tg exec/compressible/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H commit 049b318cbaa59ea987243cd6b1041755cd9ed4ed Author: Andy Nonaka Date: Thu Nov 4 17:38:48 2021 -0700 unify main drivers for compressible and compressible_mui using #ifdef MUI's exec/compressible/main_driver.cpp exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp commit 79207fbdc2aae5a14e97d3fec665b7ab2393ce50 Merge: b9130364 a96ca49d Author: Andy Nonaka Date: Thu Nov 4 17:03:57 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit b91303647b8c92ab286ee27f5a0a72a11d8665f6 Author: Andy Nonaka Date: Thu Nov 4 17:03:34 2021 -0700 E(k) exec/compressible/main_driver.cpp commit a96ca49d4c1d296e60cf53f3ab9a11fe0e29010a Merge: 2a8d1d2f 2a4c8ea1 Author: isriva Date: Thu Nov 4 16:58:43 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 2a8d1d2faf3749a83d4a5c7a8aa4df85af83f744 Author: isriva Date: Thu Nov 4 16:57:53 2021 -0700 set species and individual components of the heat flux to zero at the membrane src_compressible_stag/boundaryStag.cpp src_compressible_stag/timeStepStag.cpp commit 6ff4216a9c3a7f15f4ee57f2258b38cf46fe79f8 Author: isriva Date: Thu Nov 4 16:57:02 2021 -0700 more momentum stats exec/compressible_stag/main_driver.cpp commit 2a4c8ea1bb9200ee2589393457b996b3eb4c3854 Merge: 4c901a37 5af19504 Author: Daniel Ladiges Date: Thu Nov 4 15:49:17 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 4c901a3738bf131202023f5e42fc7cdd79c3ce73 Author: Daniel Ladiges Date: Thu Nov 4 15:48:38 2021 -0700 Added wall mobility func for 6nm full dry src_particles/particle_functions_K.H tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/plotting.ipynb commit 5af195045c65c722cc6b49ddbac9c3a3400c27db Merge: 887f05ce 2355fda8 Author: Andy Nonaka Date: Thu Nov 4 09:31:36 2021 -0700 Merge pull request #88 from AMReX-FHD/taylorgreen Taylor Green Compressible commit 887f05cebdcc7bb2207ec9b95d2f5bd71c888ff9 Author: isriva Date: Wed Nov 3 15:06:36 2021 -0700 prim, vel not initialized -- was giving a FPE in debug mode -- fixed exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.cpp commit 2355fda8fa1b554f8f3e55f0876e103b09b075f7 Author: Andy Nonaka Date: Wed Nov 3 13:13:57 2021 -0700 fix scaling exec/compressible/main_driver.cpp commit c9c51efd671bfc275ec1d2476145b1448c946ba5 Merge: ce73e3c5 a5479263 Author: jbb Date: Wed Nov 3 12:48:38 2021 -0700 Merge branch 'taylorgreen' of github.com:AMReX-FHD/FHDeX into taylorgreen commit ce73e3c551224a19aa98b980c2a3ab30654e6f88 Author: jbb Date: Wed Nov 3 12:47:08 2021 -0700 put in (div u ) squared correction exec/compressible/main_driver.cpp commit a5479263f75423e16f03cc50d929920675232689 Merge: 2ac1d153 6250902e Author: Andy Nonaka Date: Wed Nov 3 11:04:51 2021 -0700 Merge branch 'main' into taylorgreen commit 2ac1d153841e2b7b00b75592e625095bc4ad3856 Merge: 31460dc7 6c49900d Author: jbb Date: Wed Nov 3 10:15:15 2021 -0700 Merge branch 'taylorgreen' of github.com:AMReX-FHD/FHDeX into taylorgreen commit 31460dc7deb50335b71c5f7741f2c72c2bcf0ef0 Author: jbb Date: Wed Nov 3 10:13:22 2021 -0700 added cell centered divergence with centered differences src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit 6250902e43cf0a1a0dc20c053c886d8dec767edd Merge: 358b9a5b ed164e83 Author: isriva Date: Wed Nov 3 10:05:23 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 358b9a5b9c8e7edf69c87cd809462b34cdf204f6 Author: isriva Date: Wed Nov 3 10:04:48 2021 -0700 more RT stuff in compressible_stag exec/compressible_stag/inputs_RT_thermal src_compressible_stag/compressible_functions_stag.cpp commit ed164e83f18e7d42598e41af29449fa2e92239be Merge: 003abe9b 3eb3feba Author: Daniel Ladiges Date: Tue Nov 2 12:58:07 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 003abe9b8d738b519e7471ccc68d7fc14634e4e0 Author: Daniel Ladiges Date: Tue Nov 2 12:57:39 2021 -0700 Added species wise msd measurement src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 6c49900d7917eac369bea37deeaf4efbf0d94f58 Author: Andy Nonaka Date: Tue Nov 2 10:33:52 2021 -0700 add viscosity scaling, nu0 exec/compressible/main_driver.cpp commit 40a587f4819e9866a3bcd88d266f6700f1e1ac78 Author: Andy Nonaka Date: Mon Nov 1 12:10:59 2021 -0700 only print out turbulence diagnostics if turbForcing == 1 exec/hydro/main_driver.cpp commit ae3042dfd0387dda2848afbb6cd8f82d1eb5e377 Author: Andy Nonaka Date: Mon Nov 1 12:06:49 2021 -0700 structfact define that takes in optional element pairs exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 8e3a900a24610d313cd910f77ad4bf70b9a81f01 Author: Andy Nonaka Date: Mon Nov 1 11:51:47 2021 -0700 only compute if turbForcing=1 exec/compressible/inputs_tg exec/compressible/main_driver.cpp commit 88ec0504b7a56572aa448ce2b1de064eb1bc5fa0 Merge: 6406b6f1 3eb3feba Author: isriva Date: Mon Nov 1 11:06:39 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 6406b6f1577f5dbebb84b8fb5c1cd7043bc1186a Author: isriva Date: Mon Nov 1 11:06:09 2021 -0700 new functions for RT with fixed Yk src_compressible_stag/compressible_functions_stag.cpp commit 318fb43d746b0ac6c1608dba95e1c42e496ba430 Author: Andy Nonaka Date: Mon Nov 1 10:27:18 2021 -0700 bug in curl src_common/ComputeDivAndGrad.cpp commit d8cd079c16614d45e6b34896e2e5328b67999417 Author: Andy Nonaka Date: Mon Nov 1 10:20:32 2021 -0700 fixed rhoscale exec/compressible/main_driver.cpp commit 34d32693b1a448bcb2fd0be5cd5880ab37570ca6 Author: Andy Nonaka Date: Mon Nov 1 09:41:59 2021 -0700 comments exec/compressible/main_driver.cpp commit 0cf51d1869533bba0501caa5d6729a5eb4e44a71 Author: Andy Nonaka Date: Fri Oct 29 17:13:55 2021 -0700 more turb diagnostics exec/compressible/main_driver.cpp commit c2cc6eb808c88528ec50b7899634bae45f3e51f1 Author: Andy Nonaka Date: Fri Oct 29 15:43:31 2021 -0700 Lap bug fix implementing form 4 exec/compressible/main_driver.cpp src_common/ComputeDivAndGrad.cpp commit 3c9ee7e366d9e07e610a2594554b7e05e8f4fec1 Author: Andy Nonaka Date: Fri Oct 29 14:38:59 2021 -0700 more diagnostics for compressible exec/compressible/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit b72e1d9d19600fbccaedd3d4e84173656020e526 Merge: 8172c896 3eb3feba Author: Andy Nonaka Date: Fri Oct 29 13:40:09 2021 -0700 Merge branch 'main' into taylorgreen commit 3eb3feba53dc141834a45b35e2d0eb4d87cd1214 Merge: 7bd0144d 2bd7de43 Author: Andy Nonaka Date: Fri Oct 29 13:37:08 2021 -0700 Merge pull request #87 from AMReX-FHD/fix_dissipation Fix dissipation commit 2bd7de4397b9a1090b86e64ccfeb38dfe5bef796 Author: Andy Nonaka Date: Fri Oct 29 13:35:16 2021 -0700 upgraded turb diagnostics in hydro/ exec/hydro/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/NormInnerProduct.cpp src_common/common_functions.H commit 5a37fcbe1a9b65df0d28c48398a2077a3943e332 Merge: 4aaec50a 7bd0144d Author: Andy Nonaka Date: Fri Oct 29 12:53:51 2021 -0700 Merge branch 'main' into fix_dissipation commit 7bd0144d36aca578fbd2b441671dcbaf7124fcb8 Author: Changho Kim Date: Fri Oct 29 04:00:16 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF/zavg.plt exec/compressible_mui/RUN_COadsPt111_eq_SF/zavg.plt commit 64113d6765b29768815ab382c5c253663dd91954 Author: Daniel Ladiges Date: Thu Oct 28 16:39:47 2021 -0700 input parameters to control msd measurements src_common/common_functions.cpp src_common/common_namespace.H tools/notebooks/plotting.ipynb commit 8172c896ad25fd36fdd34ecba58e35845b262352 Merge: 86bf1ade db5da89c Author: Andy Nonaka Date: Thu Oct 28 16:27:24 2021 -0700 Merge branch 'main' into taylorgreen commit 4aaec50ad37f8e6eb4bab1d1a229cfda792a8c89 Merge: c6821ff3 db5da89c Author: Andy Nonaka Date: Thu Oct 28 16:27:14 2021 -0700 Merge branch 'main' into fix_dissipation commit db5da89c1efee7bef15a07bef86a4fef2a9daffb Author: Andy Nonaka Date: Thu Oct 28 16:26:19 2021 -0700 create a SumEdge that properly weights edge (nodal in 2 directions) data simplify interfaces to norm and inner product routines exec/hydro/main_driver.cpp src_common/NormInnerProduct.cpp src_common/common_functions.H src_gmres/GMRES.cpp src_gmres/Precon.cpp src_hydro/AddMFluctuations.cpp src_hydro/advance.cpp src_immersed-boundary/IBGMRES.cpp commit c6821ff3414029c28f758e3149720ed2f35928d5 Merge: 4c014a2c c002e287 Author: Andy Nonaka Date: Thu Oct 28 15:53:10 2021 -0700 Merge branch 'main' into fix_dissipation commit c002e2870bb4036b8ae28120c3645e781e134ec2 Merge: 42527ce4 cce920cd Author: isriva Date: Thu Oct 28 07:42:55 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 42527ce45190a713f70019d58435a7f22fa75628 Author: isriva Date: Thu Oct 28 07:41:59 2021 -0700 added two-fluid RT instability prob_type src_compressible_stag/compressible_functions_stag.cpp commit 63b455d48d1845a66c295cb35d1b890e34a07d8d Author: Jackie Yao Date: Wed Oct 27 15:36:51 2021 -0700 fix conflict in ../DSMC/GNUmakefile exec/DSMC/GNUmakefile commit 268c4d83b31995d88519e219f727c8e3db6057f5 Merge: 7f55725c cce920cd Author: Jackie Yao Date: Wed Oct 27 14:52:38 2021 -0700 fixed conflict in file path commit 4c014a2cb47977865231b55b6c0b19e53fd24b07 Author: Andy Nonaka Date: Tue Oct 26 16:22:47 2021 -0700 start setting up alternative calculation options exec/hydro/main_driver.cpp commit cce920cdf5228a5934993c5044beec582636dfc2 Merge: 27784eeb d4913061 Author: Daniel Ladiges Date: Tue Oct 26 15:32:37 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 27784eebba33ec8c255edf80306650fcf7446dfb Author: Daniel Ladiges Date: Tue Oct 26 15:30:44 2021 -0700 New option in dry mobility function src_common/common_functions.cpp src_common/common_namespace.H src_particles/particle_functions_K.H tools/notebooks/plotting.ipynb commit d49130615cbe55cf87b85e76aa89df8231e7c9ab Author: drladiges Date: Tue Oct 26 15:28:54 2021 -0700 Updated plotting notebook tools/notebooks/plotting.ipynb commit ed3ef718f7b53e5993dcebd5604d954e7507e4bd Author: Andy Nonaka Date: Tue Oct 26 12:54:40 2021 -0700 fix dissipation exec/hydro/inputs_force exec/hydro/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit 0825e65fac36d1807058adb6f936c077ea0464ff Merge: b8b62879 efaf9ebb Author: drladiges Date: Mon Oct 25 13:44:20 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b8b6287976bf30007968da6e19e4a16021319cea Author: drladiges Date: Mon Oct 25 13:43:29 2021 -0700 fixing merge problem with a notebook tools/notebooks/wall_repulsion.nb commit bdc314ed5b7e2f52220d39d12971d791dd1b346a Author: drladiges Date: Mon Oct 25 13:42:44 2021 -0700 updates to post processing tools/notebooks/plotting.ipynb tools/notebooks/units.nb commit efaf9ebb29ccf73ba67e82cccd3908b91a7694c4 Merge: b97cd86e 70db6903 Author: Daniel Ladiges Date: Mon Oct 25 13:41:30 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b97cd86e42a916f490792b2319d0716685641ab1 Author: Daniel Ladiges Date: Mon Oct 25 13:40:54 2021 -0700 updates to notebooks for calculating sim parameters tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/wall_repulsion.nb commit 86bf1ade03cd6365c22036ca50de12855c3b0ecc Author: Andy Nonaka Date: Mon Oct 25 11:43:23 2021 -0700 option 3 for exec/compressible/main_driver.cpp commit 70db6903e3a0fdcc6e260d9b4eaf2d5fe7d1f5b7 Author: isriva Date: Mon Oct 25 10:50:00 2021 -0700 set InitRandom correctly for GPU restarts src_compressible_stag/Checkpoint.cpp commit dc397a42f2b81f3eaa89d7ca3790e422caea089a Author: Changho Kim Date: Mon Oct 25 02:36:57 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF/run.sh: random seed for spparks exec/compressible_mui/RUN_COadsPt111_eq_SF/run.sh commit ba3c49bfc68443fd21db76217cb913dbca999765 Author: Changho Kim Date: Mon Oct 25 02:36:16 2021 -0700 exec/compressible_mui/main_driver.cpp: sequential update, one timer for time advancement exec/compressible_mui/main_driver.cpp commit dfe4d6032a7a8893bc725118853128d79d3ce367 Author: Changho Kim Date: Sun Oct 24 15:47:59 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF/zavg.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/zavg.sh commit 0f337df1a3a353923582e1861b7c6ebdb2c2affd Author: Changho Kim Date: Sun Oct 24 15:44:54 2021 -0700 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 0c75157ee5c2605a7d0cbb416ac162c66bda8c1d Author: Changho Kim Date: Sun Oct 24 15:44:26 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF: updated exec/compressible_mui/RUN_COadsPt111_eq_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py commit 84a7891a9be886552fdd9efeb90f729aeb86aa2a Author: Andy Nonaka Date: Fri Oct 22 13:59:35 2021 -0700 comments exec/compressible/main_driver.cpp commit 45a1f5cb369a6052d52ad4690bc17508b3c9b093 Author: Andy Nonaka Date: Fri Oct 22 11:57:51 2021 -0700 alternative form for energy dissipation exec/compressible/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit 38a6be2e3f03b683226f2b8e2aaf45b2c9eb5dff Author: Daniel Ladiges Date: Thu Oct 21 17:15:08 2021 -0700 Removed message about midpoint rejections when running all dry src_particles/FhdParticleContainer.cpp commit 5023eb9dd7ea8b74ac3f8e9f51767984b66a71f2 Merge: 527c5c61 04689df5 Author: Daniel Ladiges Date: Thu Oct 21 16:40:37 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 527c5c61af0b9dea7d71d8628ddce8f80b5b483e Author: Daniel Ladiges Date: Thu Oct 21 16:40:13 2021 -0700 Added improved msd recording functionality exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit e9c2ab035b86e5b8b7dba3b6ae45ea0af7c12685 Author: Andy Nonaka Date: Thu Oct 21 14:54:13 2021 -0700 first cut at adding energy dissipation calc exec/compressible/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit 521b086563a974ac19505396b867c1f52888a369 Author: Andy Nonaka Date: Thu Oct 21 11:44:58 2021 -0700 tweak dt exec/compressible/inputs_tg commit 03002df915e2e5181f9adf67a38fb0fa65dd6417 Merge: 83c9bcbf 04689df5 Author: Andy Nonaka Date: Thu Oct 21 11:22:21 2021 -0700 Merge branch 'main' into taylorgreen commit 83c9bcbfdffc6add5f2c268b6d7ee8e7ec40a991 Author: Andy Nonaka Date: Thu Oct 21 11:12:39 2021 -0700 larger dt exec/compressible/inputs_tg commit f5849e8a3f631b128961b30437a514696e4f6fdd Author: Andy Nonaka Date: Thu Oct 21 11:02:44 2021 -0700 fix pressure exec/compressible/inputs_tg src_compressible/compressible_functions.cpp commit b52c2494a8179155bc2485bfa7abf6a8de47b0f5 Author: Andy Nonaka Date: Thu Oct 21 10:57:11 2021 -0700 tweaking problem exec/compressible/inputs_tg src_compressible/compressible_functions.cpp commit 04689df58bd98c823d00a54600afa7dfd6ad8027 Author: Andy Nonaka Date: Thu Oct 21 10:41:24 2021 -0700 runiv -> Runiv now that we use only the C++ namespace this matters as far as I can tell all the faulty inputs files were using the correct default anyway exec/compressible/chemistry_inputs_files/inputs_CO_Ar_eq_SF exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF exec/compressible/inputs_RT_3d exec/compressible/inputs_SFtest exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d_mem exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_profiling_gpu exec/compressible/inputs_regression_RT_3d exec/compressible/inputs_regression_equil_3d exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic exec/compressible/inputs_regression_temp_grad exec/compressible/inputs_temp_grad exec/compressible/inputs_test_3d exec/compressible/inputs_test_deterministic exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/cori_coverage/inputs_fhd exec/compressible_mui/pseudo_kmc/inputs_equil_3d exec/compressible_mui/scripts/4spec/compressible/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd exec/compressible_mui/scripts/4spec/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_1+1/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_x/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_y/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_z/inputs_fhd_coverage exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_regression_concentration_3D exec/compressible_stag/inputs_regression_periodic_3D exec/compressible_stag/inputs_regression_reservoir_1D exec/compressible_stag/inputs_regression_reservoir_3D exec/compressible_stag/inputs_regression_slip_adiabatic_3D exec/compressible_stag/inputs_regression_tempgrad_1D exec/compressible_stag/inputs_regression_tempgrad_3D exec/compressible_stag/inputs_reservoir_equil exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify unmaintained/exercises/compressible/inputs_equilibrium_3d unmaintained/exercises/compressible/inputs_temperature_3d unmaintained/exercises/compressible/inputs_temperature_deterministic_3d unmaintained/src_low-density/src_F90/flux_funcs.F90 commit eeb92b2eb0aa37b68d4fdf2995cd951684a11183 Merge: 7c45f84d 99a52218 Author: Ishan Srivastava Date: Wed Oct 20 18:20:31 2021 -0600 Merge pull request #86 from AMReX-FHD/cleanup_init clean up how variables are initialized commit 0af7aef1a2a1fe3345400c37a977ac87ebfcf512 Author: Andy Nonaka Date: Wed Oct 20 16:18:06 2021 -0700 taylor green work exec/compressible/inputs_tg src_compressible/compressible_functions.cpp commit d83bbee774d7a0244e44420aa0f43a856c022b90 Merge: 02e91cd1 99a52218 Author: Andy Nonaka Date: Wed Oct 20 15:21:55 2021 -0700 Merge branch 'cleanup_init' into taylorgreen commit 99a5221832bd19fe28964d46960b018700217824 Author: Andy Nonaka Date: Wed Oct 20 15:21:24 2021 -0700 fix definition of KE src_compressible/compressible_functions.cpp src_compressible_stag/compressible_functions_stag.cpp commit bcd218a190208ea123c9716cc9ad4c4fa8095e3d Author: Andy Nonaka Date: Wed Oct 20 15:15:19 2021 -0700 clean up how variables are initialized initialize only the conserved, then call consToPrim exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp commit 02e91cd14d4413c839a4e743e6014c102b860aef Author: Andy Nonaka Date: Wed Oct 20 14:04:35 2021 -0700 taylor green work exec/compressible/inputs_tg src_compressible/compressible_functions.cpp commit 7c45f84d59e5009721a82bd5889cc448aaf58397 Author: Andy Nonaka Date: Wed Oct 20 12:52:11 2021 -0700 error checking that nvars and nprimvars are set correctly in the inputs files exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/compressible_stag/main_driver.cpp commit 895ba2fc3f9f255cba7def053d272d0073ce73af Merge: 5f4a3aac 90ce9c55 Author: Andy Nonaka Date: Wed Oct 20 12:45:52 2021 -0700 Merge pull request #84 from AMReX-FHD/fix_flattened_SF Fix flattened SF for compressible, compressible_mui, and hydro commit 90ce9c55721d18aac664a7886c7a6942fdbecbf8 Author: Andy Nonaka Date: Wed Oct 20 12:43:36 2021 -0700 final cleanup for flattened SF exec/hydro/main_driver.cpp commit 6df424a3679e11153d170c36c6dbe61f3705ff48 Author: isriva Date: Wed Oct 20 12:09:34 2021 -0700 simplify setting up flat SF exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 8d031d59f387bfa60b04563e6bdb123048777de3 Author: isriva Date: Wed Oct 20 11:30:48 2021 -0700 fixed some more issues exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 5aeb4e830fb34bfb894b964646b704709841c18c Author: isriva Date: Wed Oct 20 10:28:49 2021 -0700 fixed some remaining issues with flat SF setups exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 97f9f50d11a84ef45f231ebf7463fe3c54f83717 Author: isriva Date: Tue Oct 19 20:46:38 2021 -0700 added flattened SF for conserved variables as well in compressible and compressible_mui exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 8c028f85e0cdb2bcd50779bb9017633c41ec7510 Author: Andy Nonaka Date: Tue Oct 19 15:03:05 2021 -0700 finish fixing flattened SF parallel issue exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/hydro/main_driver.cpp commit 6f075cc628af6b857fce1dcee1932435b4ef0cb0 Author: Andy Nonaka Date: Tue Oct 19 13:44:18 2021 -0700 fix compressible flattened SF parallel issue exec/compressible/main_driver.cpp commit 5f4a3aac697572a7a6ab3483e377413d24bd8c01 Author: isriva Date: Tue Oct 19 11:37:36 2021 -0700 some more 1D and 2D consistency checks exec/compressible_stag/main_driver.cpp commit 69b747d09f5aca987d2ca66c4cce4a3a52d17c27 Author: isriva Date: Mon Oct 18 15:56:35 2021 -0700 do covariances only upon request src_compressible_stag/statsStag.cpp commit 62b3c61b57549388c29f6400897fa220bcfb24f8 Author: isriva Date: Mon Oct 18 15:32:02 2021 -0700 fixed a missing bracket exec/compressible_stag/main_driver.cpp commit aa6101b662aa2967bef220de47151ae5bd83e153 Merge: 82f3effb 0c34e137 Author: Ishan Srivastava Date: Mon Oct 18 15:15:27 2021 -0600 Merge pull request #81 from AMReX-FHD/comp_stag_2d 2D simulation enabled in the compressible staggered code. Also introduced support for 2D structure factors. commit 0c34e1373948091c39782c16f8c3fe6837aca22d Merge: 9992acfa 82f3effb Author: isriva Date: Mon Oct 18 13:44:27 2021 -0700 Merge remote-tracking branch 'origin/main' into comp_stag_2d commit 82f3effb995c5505ce58d7711a0cc5849b606d87 Merge: ac6f1a61 9fe63136 Author: Ishan Srivastava Date: Mon Oct 18 14:37:33 2021 -0600 Merge pull request #80 from AMReX-FHD/stats_compressible Capability to do spatial correlations at (fixed) multiple x* in the staggered compressible code commit 9992acfae09ac1e2a26ffbff92b567200f3a0a57 Merge: 683b775b ac6f1a61 Author: Andy Nonaka Date: Mon Oct 18 11:12:23 2021 -0700 Merge branch 'main' into comp_stag_2d commit 9fe63136fdf3c5aa792ccc801dccd98909403746 Merge: 9d54e725 ac6f1a61 Author: isriva Date: Mon Oct 18 10:58:13 2021 -0700 Merge remote-tracking branch 'origin/main' into stats_compressible commit ac6f1a61f4639b94260afabaaf789704e12abaab Author: Changho Kim Date: Mon Oct 18 04:32:39 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage_stat.py: updated exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage_stat.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage_det.py commit bd81ebfa6e5c55c73c285e1527d6efac085dc2ff Author: Changho Kim Date: Mon Oct 18 04:22:24 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage_stat.py: updated exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage_stat.py commit cb9faed12eccfe428c7b0b0658361f2e5e3dbb0f Author: Changho Kim Date: Mon Oct 18 03:49:02 2021 -0700 exec/compressible_mui/SPPARKS_MUI/create_sites.cpp: using round to determine number of cells exec/compressible_mui/SPPARKS_MUI/create_sites.cpp commit 814c7dcf8ed34470718afa1af714f13c6814360c Author: Changho Kim Date: Mon Oct 18 03:47:08 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var: test scripts exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/README exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/analyze_cov_var.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/analyze_cov_var.sh exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/analyze_frac.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/analyze_frac.sh exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/coverage.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/coverage.sh exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/in.kmc_nonmui exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/test_frac_cov_var/run_nonmui.sh commit 83ad63ea882d09e0884088733a646d103617cc47 Author: Changho Kim Date: Mon Oct 18 03:45:05 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/in.kmc_nonmui: rates updated exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/in.kmc_nonmui commit 683b775b3d5fb2a929981114a5b67ad7cbb718d2 Merge: d6783fba 94325cb5 Author: Andy Nonaka Date: Fri Oct 15 18:07:02 2021 -0700 Merge branch 'main' into comp_stag_2d commit 94325cb5ae76b5e4f85c9c0238340b6170126be1 Author: Andy Nonaka Date: Fri Oct 15 18:00:24 2021 -0700 clean up and heavily comment ComputeVerticalAverage to pave way for future improvements src_common/ComputeAverages.cpp src_common/common_functions.H commit d6783fba66ee6690d22241c3fcf04292e92f77f2 Merge: 232c8ec6 35a24d23 Author: Andy Nonaka Date: Fri Oct 15 17:23:32 2021 -0700 Merge branch 'main' into comp_stag_2d commit 35a24d232f2511fc7d5b6bd84fb6d95aedc78760 Author: Andy Nonaka Date: Fri Oct 15 17:20:50 2021 -0700 revert previous commit, but keep comments src_common/ComputeAverages.cpp commit 27b9bc2325d60e5bb1cf08b5a04ef05ae571ac67 Author: Andy Nonaka Date: Fri Oct 15 17:12:09 2021 -0700 ExtractSlice only builds the flattened MultiFab if it needs to src_common/ComputeAverages.cpp commit 232c8ec6004ac44ffc49809881e91245e63a5c28 Author: Andy Nonaka Date: Fri Oct 15 16:57:43 2021 -0700 Remove ExtractSliceI exec/compressible_stag/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H commit 9bbe3e6216185b04aa8fdc3c4d5deeb5c1ab4a37 Merge: 94afec4d 643a9c14 Author: Andy Nonaka Date: Fri Oct 15 16:56:04 2021 -0700 Merge branch 'main' into comp_stag_2d commit 643a9c149fd28da3cdd94809ec1933de05a1f4dd Author: Andy Nonaka Date: Fri Oct 15 16:55:31 2021 -0700 ExtractSlice now requires the coordinate exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/hydro/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H commit 94afec4d9af2aea716e3d4335f6f2f70ee50a642 Merge: b52388bd c2464230 Author: Andy Nonaka Date: Fri Oct 15 16:48:23 2021 -0700 Merge branch 'main' into comp_stag_2d commit b52388bd178ff38e40645efc21ea25b3b105df51 Author: isriva Date: Thu Oct 14 22:56:38 2021 -0700 another small bug fixed exec/compressible_stag/main_driver.cpp commit fe2dc12fb5ea2dba4a83ee06c84fdce052f6d0ee Author: isriva Date: Thu Oct 14 22:04:31 2021 -0700 fixed segfault exec/compressible_stag/main_driver.cpp commit 1f68349a1a3373a21701e79d4db355db8cd7e62f Author: isriva Date: Thu Oct 14 20:32:44 2021 -0700 partially fixed 2D structure factor. getting segfaults. WIP exec/compressible_stag/main_driver.cpp commit c246423076962774a51fd1eb452cc451f019a84f Merge: d2b4f32d 56978357 Author: Daniel Ladiges Date: Wed Oct 13 15:46:44 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit d2b4f32da60e0256ce536249e5dd0d81ca592521 Author: Daniel Ladiges Date: Wed Oct 13 15:46:15 2021 -0700 Added 'real lattice' short range option for walls exec/immersedIons/main_driver.cpp src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H tools/notebooks/EO_Rezaei_parameters.nb commit 31c4b3f283e108da180039e5728779e4c443b417 Merge: d929679a 56978357 Author: Andy Nonaka Date: Wed Oct 13 15:13:34 2021 -0700 Merge branch 'main' into comp_stag_2d commit 56978357fb7c756c65c6a2bf26aa681432d77f59 Author: Andy Nonaka Date: Wed Oct 13 15:13:01 2021 -0700 make cov_real, cov_imag, and cov_mag public src_analysis/StructFact.H commit d929679ae87239edbf94b53933d1f1bd22d048a5 Merge: dcf412c1 12a06884 Author: Andy Nonaka Date: Wed Oct 13 14:51:50 2021 -0700 Merge branch 'main' into comp_stag_2d commit 12a0688482466d85a3e9f9b41ab9bb48206b5208 Author: Andy Nonaka Date: Wed Oct 13 14:50:06 2021 -0700 use same rotated flattened MF to define the flattened boxarray and distributionmap exec/compressible_stag/main_driver.cpp commit dcf412c117ae5b75ade6a3cd8dba6741a87c1af3 Merge: 57c70b28 018569b8 Author: Andy Nonaka Date: Wed Oct 13 14:46:45 2021 -0700 Merge branch 'main' into comp_stag_2d commit 57c70b28a50878bc6116e7320d523244007cba8b Author: isriva Date: Wed Oct 13 11:30:04 2021 -0700 small change to BC sequence src_compressible_stag/timeStepStag.cpp commit 5d739b3b8b9452a7463db01d38e95c1e4b47335e Merge: 9943ace3 d6048fd4 Author: drladiges Date: Wed Oct 13 11:27:21 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 9943ace3a19c373d4037346e8c21290e25749179 Author: drladiges Date: Wed Oct 13 11:25:18 2021 -0700 more notebooks exec/DSMC/test_inputs/input_test tools/notebooks/plotting.ipynb commit aa07dd47a8b10988f5266803f58ca5e3f408d3f1 Author: drladiges Date: Wed Oct 13 11:24:44 2021 -0700 Notebooks for doing useful things tools/notebooks/phononPlotting.ipynb tools/notebooks/plotting_dsmc.ipynb tools/notebooks/units.nb tools/notebooks/wall_repulsion.nb commit d6048fd440db311fc06907b840f9936d8aeb30c9 Author: isriva Date: Wed Oct 13 09:33:20 2021 -0700 small change to BC sequence in compressible_stag src_compressible_stag/timeStepStag.cpp commit bdd1f03906e4886112f88508ea04f68e650020d0 Author: isriva Date: Mon Oct 11 13:20:55 2021 -0700 fixed small bug in 2D structure factor exec/compressible_stag/main_driver.cpp commit 018569b85d36bea0176967c506e0f359c8e79882 Author: Daniel Ladiges Date: Sun Oct 10 15:21:12 2021 -0700 adjustments to time step ramping exec/immersedIons/main_driver.cpp tools/notebooks/EO_Rezaei_parameters.nb commit f2c89ed14ae71354fb7f189d6fc613e443616a42 Author: isriva Date: Sun Oct 10 09:30:44 2021 -0700 fixed a small bug in 2D structure factor exec/compressible_stag/main_driver.cpp commit fbb9901afc43085f2ed79f9188fd3b50e88dcdd9 Author: isriva Date: Fri Oct 8 11:42:52 2021 -0700 small change in SF accumulation logic exec/compressible_stag/main_driver.cpp commit d357bbfda7f703adfde76f03b833937d49b77274 Author: isriva Date: Fri Oct 8 10:54:30 2021 -0700 implemented 2D structure factors in quasi-2D simulations exec/compressible_stag/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_compressible_stag/compressible_functions_stag.H src_compressible_stag/writePlotFileStag.cpp commit 41ae90953a6061247bae0671be0773d7aec3a1c4 Author: isriva Date: Thu Oct 7 13:28:01 2021 -0700 some more cleanup for 2D stats exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit aa2bcf6893b82c885b87bd3e2993784c5896aa7f Author: isriva Date: Thu Oct 7 09:00:38 2021 -0700 fixed small compilation errors exec/compressible_stag/main_driver.cpp commit 80adabde2cfed0e015c90dede135a29a3860cae5 Merge: d8438c98 f4b56a0a Author: isriva Date: Thu Oct 7 08:50:51 2021 -0700 Merge remote-tracking branch 'origin/main' into comp_stag_2d commit d8438c984994d02fc3bbc7fc15088d64ba187ff0 Author: isriva Date: Thu Oct 7 08:49:58 2021 -0700 first pass at 2D. spatial correlation still required to be written (if needed) exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp commit f4b56a0ad20d9a48253e6c77ca3511c23ac881ea Author: isriva Date: Wed Oct 6 13:40:57 2021 -0700 use instantaneous temperature fluctuations for variances and correlations src_compressible_stag/statsStag.cpp commit e4e0160cb63062705fb1cadfda0b80501202ef82 Author: Daniel Ladiges Date: Tue Oct 5 11:48:37 2021 -0700 Another input parameter for Sophie src_common/common_functions.cpp src_common/common_namespace.H commit b1f093a0911b0652c7d80d355a21e59beb8d6c95 Merge: 634622f5 73fd4f76 Author: Daniel Ladiges Date: Mon Oct 4 21:41:02 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 634622f50979e073c04b391fecb061f52ae861eb Author: Daniel Ladiges Date: Mon Oct 4 21:40:42 2021 -0700 Fixed minor bug in ES kernels exec/immersedIons/main_driver.cpp tools/notebooks/plotting.ipynb commit 73fd4f76f7949d199646bdc24743adeef23a89d3 Merge: 62466c31 e56568cf Author: Andy Nonaka Date: Mon Oct 4 16:32:57 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 62466c31c7b32c0396c4774648685bd99d6cfa31 Author: Andy Nonaka Date: Mon Oct 4 16:26:47 2021 -0700 seed now controls RNG random number generators as well abort if trying to restart on the GPU with seed=-1; not supported exec/DSMC/Checkpoint.cpp exec/DSMC/ex_main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMC_granular/Checkpoint.cpp exec/DSMC_granular/ex_main_driver.cpp exec/DSMC_granular/main_DSMC_driver.cpp exec/DSMC_granular/main_driver.cpp exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp exec/immersedIons/Checkpoint.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/Checkpoint.cpp exec/multispec/main_driver.cpp exec/phononDSMC/Checkpoint.cpp exec/phononDSMC/ex_main_driver.cpp exec/phononDSMC/main_driver.cpp src_compressible_stag/Checkpoint.cpp commit e56568cf571a3d52cbc0c77770f823a3b5e88af7 Merge: 9d731075 13d62c5b Author: Daniel Ladiges Date: Mon Oct 4 15:33:56 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 9d7310754f62d2e7eac4615fbdfbaeee570bc0df Author: Daniel Ladiges Date: Mon Oct 4 15:33:42 2021 -0700 Bug in makefile exec/phononDSMC/GNUmakefile commit 13d62c5bfb178d1a39666af8b221f6dcf78c7f6b Author: Andy Nonaka Date: Mon Oct 4 15:10:19 2021 -0700 restart is consistent across codes seed=-1 use saved state seed=0 random seed>0 set the new seed exec/hydro/Checkpoint.cpp exec/multispec/Checkpoint.cpp src_compressible_stag/Checkpoint.cpp commit 014a0a65c088b195de59212668868f81c838bb27 Author: Daniel Ladiges Date: Sun Oct 3 16:14:25 2021 -0700 Added internal scattering and various stat recording things exec/phononDSMC/LocalFunctions.H exec/phononDSMC/delPlots exec/phononDSMC/main_driver.cpp exec/phononDSMC/py/paramPlane.ipynb exec/phononDSMC/stats.cpp exec/phononDSMC/test_inputs/input_test exec/phononDSMC/writePlotFile.cpp src_common/common_functions.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp tools/notebooks/plank.nb commit 3d58559ec29a44d5bab94a2acb8b5b3c3fc8dd7e Merge: 7a55a3f0 f05ee8a8 Author: Daniel Ladiges Date: Sat Oct 2 22:10:01 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7a55a3f0ae91f17ec2c0d72f2f19ec50e3d39577 Author: Daniel Ladiges Date: Sat Oct 2 22:08:35 2021 -0700 Setup phonon input templates. Added internal scattering parameters to namespace. Added recording of particle information at boundaries exec/immersedIons/WritePlotFile.cpp exec/phononDSMC/delPlots exec/phononDSMC/main_driver.cpp exec/phononDSMC/py/paramPlane.ipynb exec/phononDSMC/writePlotFile.cpp src_common/common_functions.cpp src_common/common_namespace.H src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp tools/notebooks/plank.nb commit 2d30b13519191d1347796d627e0a5b3a493edace Author: Daniel Ladiges Date: Fri Oct 1 10:34:10 2021 -0700 Finished phonon source term. Have to figure out correct wat to specift density/flux, just using numbers for now Setup seperate phonon executable directory exec/phononDSMC/Checkpoint.H exec/phononDSMC/Checkpoint.cpp exec/phononDSMC/DsmcCollide.cpp exec/phononDSMC/GNUmakefile exec/phononDSMC/LocalFunctions.H exec/phononDSMC/Make.package exec/phononDSMC/delPlots exec/phononDSMC/ex_main_driver.cpp exec/phononDSMC/externalF.cpp exec/phononDSMC/globalVars.cpp exec/phononDSMC/main_driver.cpp exec/phononDSMC/particleGen.cpp exec/phononDSMC/py/paramPlane.ipynb exec/phononDSMC/py/paramPlane.nb exec/phononDSMC/stats.cpp exec/phononDSMC/updateTimeStep.cpp exec/phononDSMC/writePlotFile.cpp commit 9d54e72560ff0aedd869290eba70ee4d80ea6289 Merge: a7b1715a f05ee8a8 Author: isriva Date: Thu Sep 30 20:22:55 2021 -0700 Merge remote-tracking branch 'origin/main' into stats_compressible commit f05ee8a81c2539cb599c806e9796ed217553ae42 Merge: c4847aa9 0546afa7 Author: isriva Date: Thu Sep 30 20:21:45 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit c4847aa944d3914e6bc21663c3cc805176370248 Author: isriva Date: Thu Sep 30 20:20:52 2021 -0700 fixed a small bug in stochastic viscous heating src_compressible_stag/fluxStag.cpp commit 0546afa7b962634e95fe7a61c04efebbcda48feb Author: Daniel Ladiges Date: Thu Sep 30 14:21:20 2021 -0700 Another bug in z mobility? src_particles/particle_functions_K.H commit 8e80699efdbb6ea0dec2ba68e0a66514507bfb8b Merge: c81df5a4 f0e2fb1e Author: Daniel Ladiges Date: Thu Sep 30 14:03:47 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit c81df5a4d998c56023d954dc1ad09cde2585a329 Author: Daniel Ladiges Date: Thu Sep 30 14:01:50 2021 -0700 fixed bug in mobility when confining bc is set in z axis src_particles/particle_functions_K.H commit a7b1715af3d550afb5a5b15649686c4a0f44a04f Author: isriva Date: Thu Sep 30 13:47:04 2021 -0700 multiple positions for spatial correlations works now exec/compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp commit dcc7a7cc96b381203fddad6c41fd08b11f97f7b9 Merge: d7deac79 f0e2fb1e Author: isriva Date: Thu Sep 30 13:17:28 2021 -0700 Merge remote-tracking branch 'origin/main' into stats_compressible commit d7deac7998c2ee8fa9420c5aae65617214c41415 Author: isriva Date: Thu Sep 30 13:16:54 2021 -0700 moved all_correl to compressible namespace src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H commit f0e2fb1e7dd72345e15a11afd19e38c013818f10 Author: isriva Date: Thu Sep 30 10:22:00 2021 -0700 mean momentum now based on instantaneous values exec/compressible_stag/main_driver.cpp commit ab3e9b3852f1e39f1e832fc8eb2c5e5c23465e9a Author: Changho Kim Date: Thu Sep 30 03:49:49 2021 -0700 src_surfchem_mui/surfchem_mui_functions.cpp: two different temperature defs for sampling of incoming and outgoing velocities src_surfchem_mui/surfchem_mui_functions.cpp commit 5948c69d0acc1d328a65bdd860578ba94ae873df Merge: 8b3d49fa ef8216f1 Author: Daniel Ladiges Date: Wed Sep 29 14:25:26 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 8b3d49faddee339bcee3f65685172ffa44a29823 Author: Daniel Ladiges Date: Wed Sep 29 14:24:13 2021 -0700 Fixed double counting of absolute displacements in particles src_particles/FhdParticleContainer.cpp commit ef8216f1dfd2c7b804fa08416d7ec5fc55a5e3c1 Merge: 56479fcb 2ff45977 Author: Changho Kim Date: Wed Sep 29 03:46:29 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 56479fcbb11abfd9391638ca70a1e79c8830f373 Author: Changho Kim Date: Wed Sep 29 03:45:33 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF: rads = rcol exec/compressible_mui/RUN_COadsPt111_eq_SF/clean.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/comp.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage_det.py exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py commit 2ff459776d19fb745f6f1009bc29ae0ee28fdda6 Author: Daniel Ladiges Date: Tue Sep 28 08:40:17 2021 -0700 started adding phonon inflow boundary condition src_common/common_functions.cpp src_common/common_namespace.H src_particles/DsmcParticleContainer.cpp tools/notebooks/plank.nb commit cf6d403c0fb9b2a9148f5b9f8afc18f65bd70ce3 Author: Daniel Ladiges Date: Mon Sep 27 17:57:15 2021 -0700 Added reduced Plank constant (h_bar) to namespace. Added function to sample Plank distribution src_common/common_functions.cpp src_common/common_namespace.H src_geometry/paramplane_functions_K.H commit 055b5d71b9516b60e307291817f027932bfcdc40 Author: Daniel Ladiges Date: Mon Sep 27 17:06:10 2021 -0700 Finished phonon boundary condition src_geometry/paramplane_functions_K.H commit c4085da8a646a7acb2175e1db83a6e7c397137d1 Author: Daniel Ladiges Date: Mon Sep 27 16:57:45 2021 -0700 notbook deriving sampling method for Plank distribution tools/notebooks/EO_Rezaei_parameters.nb tools/notebooks/plank.nb commit 08d32c7814c0ada84e3a38f20ae60ac4157991a6 Merge: 4d1cecd0 442e0806 Author: Daniel Ladiges Date: Mon Sep 27 15:03:51 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 4d1cecd0d17acd010cc657d5e2e1d10b892ccb07 Author: Daniel Ladiges Date: Mon Sep 27 15:03:12 2021 -0700 Automated particle field labling in plotfile output exec/immersedIons/WritePlotFile.cpp exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H commit 442e0806f0ff9236ca55fd45be2e6135539e2b7d Author: Enrique Mercado Date: Mon Sep 27 13:57:17 2021 -0700 /exec/compressible_mui/SPPARKS_MUI/: updated app.cpp to not recompute propensities between multiple runs exec/compressible_mui/SPPARKS_MUI/app.cpp commit 08744496c3f672a28348b3227f5c2ab2ddb03ebf Author: Daniel Ladiges Date: Mon Sep 27 13:53:50 2021 -0700 MOre phonon stuff and revereted a change that would have broken regressions exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/particle_functions_K.H commit 14143c1910571cc2ed64c8ae532547281d901d5e Merge: 13fa655f 7df9c24a Author: Daniel Ladiges Date: Mon Sep 27 11:26:39 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 13fa655fb977108ec42d26860ad831cb16caf430 Author: Daniel Ladiges Date: Mon Sep 27 11:12:56 2021 -0700 Added namespace parameter to control time step ramping exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_particles/particle_functions_K.H commit 7df9c24a9f0cfe9de17eb8268efb447be11919e0 Merge: e2ee0641 f1d7dadf Author: drladiges Date: Mon Sep 27 11:03:35 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit e2ee0641711d54091fa0b30f73c2a18171ec5fbe Author: drladiges Date: Mon Sep 27 11:03:14 2021 -0700 Some things in the namespace for phonons src_common/common_functions.cpp src_common/common_namespace.H src_geometry/paramplane_functions_K.H commit f1d7dadf0450a1a8d19d483e269afbfc5f8f0dda Author: Changho Kim Date: Mon Sep 27 04:08:25 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF: increase reaction rates by factor of 10 exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py commit e863e32564eca60a022173d89d0c563db75d779e Author: Changho Kim Date: Mon Sep 27 04:04:57 2021 -0700 src_surfchem_mui/surfchem_mui_functions.cpp: use instantaneous temperature for velocity sampling src_surfchem_mui/surfchem_mui_functions.cpp commit 48f2c8a94f0c2983f4aed88bb580d496b8df1eb3 Author: Changho Kim Date: Sat Sep 25 20:36:40 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui: coverage.sh, coverage_det.py exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage_det.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage.sh exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage_det.py commit 89cb424e5802698b289cc1d897ee4efe1ecd30e4 Author: Changho Kim Date: Sat Sep 25 16:35:41 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage.sh exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/coverage_stat.py exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/in.kmc_nonmui exec/compressible_mui/RUN_COadsPt111_eq_SF_nonmui/run_nonmui.sh commit 6a27e3759767e3a9efdc7259b961bc2fea1ce2a6 Author: Changho Kim Date: Sat Sep 25 16:01:39 2021 -0700 compressible_mui/RUN_COadsPt111_eq_SF: rate updated, (in.kmc) run pre no post no exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py commit 6a3511b0475e0dd6dacd2b8ac86f0c360239dfc1 Author: Changho Kim Date: Sat Sep 25 14:22:34 2021 -0700 exec/compressible_mui/RUN_COadsPt111_eq_SF exec/compressible_mui/RUN_COadsPt111_eq_SF/clean.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/comp.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage.sh exec/compressible_mui/RUN_COadsPt111_eq_SF/coverage_stat.py exec/compressible_mui/RUN_COadsPt111_eq_SF/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_eq_SF/havg_stat.py exec/compressible_mui/RUN_COadsPt111_eq_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_eq_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_eq_SF/params_CO_Ar_eq_SF.py exec/compressible_mui/RUN_COadsPt111_eq_SF/run.sh commit 282d08401d675c91fd30a2d1acc25c57492d5a2a Author: Changho Kim Date: Fri Sep 24 02:25:12 2021 -0700 exec/compressible/chemistry_inputs_files: scripts updated exec/compressible/chemistry_inputs_files/params_CO_Ar_eq_SF.py exec/compressible/chemistry_inputs_files/params_NO2_N2O4_eq_SF.py commit 2706852a74536cdb09a01f655fe5622d34c9cb56 Author: Changho Kim Date: Fri Sep 24 02:09:27 2021 -0700 exec/compressible_mui/RUN_COadsPt111_SF: scripts updated/organized exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_SF/run.sh commit 97dd53fe44cc76d1323a5b940341b16908939f07 Author: Changho Kim Date: Fri Sep 24 01:52:46 2021 -0700 exec/compressible_mui/RUN_COadsPt111_SF: scripts updated/organized exec/compressible/chemistry_inputs_files/inputs_CO_Ar_eq_SF exec/compressible/chemistry_inputs_files/params_CO_Ar_eq_SF.py exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_SF/params_CO_Ar_eq_SF.py commit 809c06cc8b2ec06881571152347ee8102cc695af Author: Changho Kim Date: Fri Sep 24 00:47:25 2021 -0700 exec/compressible/chemistry_inputs_files: scripts organized exec/compressible/chemistry_inputs_files/params_CO_He_eq_SF.py exec/compressible/chemistry_inputs_files/run.sh commit 8c7216a1c054473b62382612825a3f0a66fa9800 Author: Changho Kim Date: Fri Sep 24 00:44:09 2021 -0700 exec/compressible/chemistry_inputs_files: scripts organized exec/compressible/chemistry_inputs_files/inputs_CO_Ar_eq_SF exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbAr_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbCO_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbHe_eq_SF exec/compressible/chemistry_inputs_files/params_CO_Ar_eq_SF.py exec/compressible/chemistry_inputs_files/params_NO2_N2O4_eq_SF.py commit 82e52536720291a1cc22128d10b0891d33ec231f Merge: a5290ae3 d2ea6937 Author: drladiges Date: Thu Sep 23 13:16:54 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit a5290ae3e434b5dddb075da7da1d5ec0c432aab7 Author: drladiges Date: Thu Sep 23 13:16:31 2021 -0700 More phonon stuff src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H tools/notebooks/plotting.ipynb commit d2ea69374460dab2a00e760a8b9cabcbebc8c204 Author: Johannes Blaschke Date: Wed Sep 22 21:24:01 2021 -0700 update makefile exec/immersed_boundary/flagellum/GNUmakefile commit a986a1e701bc342ea8a78532a81d6588da8a2f46 Merge: d6988eea e395293a Author: Johannes Blaschke Date: Wed Sep 22 20:52:57 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX commit d6988eea8da2c02ae79f5d06ee25d4ae2af3d89a Author: Johannes Blaschke Date: Wed Sep 22 20:52:51 2021 -0700 this is a simpler taylor line initialization exec/immersed_boundary/flagellum/advance_stokes.cpp exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.cpp commit e395293a23def19053c00b628f6c610a7b31568f Author: Galen Wang Date: Wed Sep 22 17:06:56 2021 -0700 add wetRad tables for 3-point and 7-point ES kernels exec/immersedIons/main_driver.cpp exec/immersedIons/wetRad_KernelES/wetRad_w3.dat exec/immersedIons/wetRad_KernelES/wetRad_w7.dat commit 296fdb13656f7429f7b262ea3f73272bacb450fa Author: Enrique Mercado Date: Wed Sep 22 16:43:16 2021 -0700 exec/compressible_mui/: added call to InitializeCompressibleNamespace(); in main_driver.cpp, added transport_type=2 command to RUN_COadsPt111 dirs inputs_fhd file exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/main_driver.cpp commit f9e55217a4c63959ae093beabb683efe173efe0d Merge: d349b0ff 366c1c23 Author: Andy Nonaka Date: Wed Sep 22 10:15:26 2021 -0700 Merge pull request #79 from AMReX-FHD/rancorn_fix Rancorn fix commit d349b0ff6af04eafb43968975519c1eaa2d5e5b3 Author: Enrique Mercado Date: Tue Sep 21 16:34:57 2021 -0700 exec/compressible_mui/SPPARKS_MUI/: fixed typos in input.cpp exec/compressible_mui/SPPARKS_MUI/input.cpp commit b110be192c12e7f804fabba861d8bf4ffef7afd5 Author: Enrique Mercado Date: Tue Sep 21 16:12:45 2021 -0700 exec/compressible/chemistry_inputs_files/: changed dt to 1.25e-13 in RBtest exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF exec/compressible/chemistry_inputs_files/params_RBtest_eq_SF.py commit 366c1c238dd954c48dc50b1e7681f2f5425de159 Author: Andy Nonaka Date: Tue Sep 21 13:30:59 2021 -0700 formatting src_compressible/flux.cpp commit 529285dc67b7c1982d484fab25e594525598341c Author: Andy Nonaka Date: Tue Sep 21 13:29:25 2021 -0700 rancorn fix for all walls src_compressible/flux.cpp commit d381cb7b79a96d42bbac2d13fe2786baee8977ec Merge: 04cf335f 05c5b051 Author: Andy Nonaka Date: Tue Sep 21 13:19:16 2021 -0700 Merge branch 'main' into rancorn_fix commit 04cf335fa3b53354c6108bb43f0687d267dce17e Author: Andy Nonaka Date: Mon Sep 20 14:51:45 2021 -0700 z walls src_compressible/flux.cpp commit 3d75cedfbca13e481222418e87337abf68c1b214 Author: Andy Nonaka Date: Mon Sep 20 14:45:50 2021 -0700 test Changho y-wall case src_compressible/flux.cpp commit 05c5b051b9d4feb2e42c37d820009e777bd00342 Author: Changho Kim Date: Mon Sep 20 12:17:26 2021 -0700 exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF: physical bc exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF commit 6ba89e828f7f33ff6e0716baacf24f4991717a76 Merge: ccc097aa 62d6ebdf Author: Changho Kim Date: Mon Sep 20 12:12:09 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit ccc097aa242a3e685e0b66e0b805a0ad85847d85 Author: Changho Kim Date: Mon Sep 20 12:11:50 2021 -0700 exec/compressible_mui/RUN_COadsPt111_SF: He->Ar exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_SF/params_CO_He_eq_SF.py commit 62d6ebdfdd0b4252b72ca23ebb61b693d3a5c4bd Merge: 984ec452 ef8315ce Author: etpalmer63 Date: Mon Sep 20 11:16:39 2021 -0400 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit aef5d97958e456af790d4ca714dada869899a8bd Author: isriva Date: Fri Sep 17 12:02:51 2021 -0700 added option for all correlations at various x* src_compressible/compressible_functions.cpp commit d95caec8dd035b48a10700df9d8cebe0f21db242 Merge: 7fdbef1f ef8315ce Author: isriva Date: Fri Sep 17 12:02:25 2021 -0700 Merge remote-tracking branch 'origin/main' into stats_compressible commit ef8315ce8f64b87f5bb96a4e45c6b8fbef8bdaa0 Merge: 386f5473 3e05d5bc Author: isriva Date: Fri Sep 17 11:56:15 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 386f54739922aa644242f4928180c41d1234b09b Author: isriva Date: Fri Sep 17 11:55:36 2021 -0700 temperature variance from conserved variables src_compressible_stag/statsStag.cpp commit 984ec4524ade14a5b43b780392d599233c539da1 Merge: e05ab844 3e05d5bc Author: etpalmer63 Date: Thu Sep 16 12:09:08 2021 -0400 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 3e05d5bc5baf72f15b7da2a05a975b7ad5faa9bf Merge: 3534b8a8 cd1421b6 Author: Changho Kim Date: Thu Sep 16 03:54:40 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3534b8a88e261f6a564770f491df0686ae476c99 Author: Changho Kim Date: Thu Sep 16 03:54:18 2021 -0700 exec/compressible/chemistry_inputs_files/params_RBtest_eq_SF.py exec/compressible/chemistry_inputs_files/params_RBtest_eq_SF.py commit cd1421b62425ceb901f5504964f9b1c3bd8f51a9 Merge: 55f966dc 0caafac9 Author: Daniel Ladiges Date: Wed Sep 15 14:50:14 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 55f966dc7ceec4f3434b270c9196116830bcaf99 Author: Daniel Ladiges Date: Wed Sep 15 14:49:47 2021 -0700 Restored tracking of relative particle positions src_particles/FhdParticleContainer.cpp commit 0caafac9c9a1bc2ffa01c887d5d95488f86c97d3 Author: jgalenwang Date: Wed Sep 15 13:34:46 2021 -0700 fix a typo in Checkpoint exec/immersedIons/Checkpoint.cpp commit a6e4fab6a294b09d42db36a28b353c17b31a0f1b Author: Daniel Ladiges Date: Wed Sep 15 10:56:14 2021 -0700 Accidentally uncommented some debug code exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 02ba9428e7e8b2b8ec12985d64af5a5224f327cd Author: Andy Nonaka Date: Wed Sep 15 10:02:02 2021 -0700 fix inputs files for C++ namespace exec/DSMC/test_inputs/input_periodic_eq exec/DSMC/test_inputs/input_test exec/DSMC/test_inputs/input_therm exec/DSMC/test_inputs/inputs_conc exec/DSMC_granular/input_test exec/DSMC_granular/test_inputs/input_periodic_eq exec/DSMC_granular/test_inputs/input_test exec/DSMC_granular/test_inputs/input_therm exec/compressible_stag/inputs_reservoir_equil exec/immersedIons/test_inputs/inputs_potential_test exec/immersedIons/test_inputs/inputs_test exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip_nowca exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond10 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond11 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond12 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond12a exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond12b exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond12c exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond4 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond5 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond6 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond7 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond8 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond9 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond9a exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond9b exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_cond9c exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_gr1 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_gr2 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_gr3 exec/immersedIons/test_inputs/paper1_inputs/inputs_paper_gr4 exec/lib_hydro/demo/inputs_3d_test commit ff08441a1f07f96a0d9646e6a6801218d0e5fb4b Author: Changho Kim Date: Tue Sep 14 17:18:31 2021 -0700 exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF: simle red/blue monoatomic mixture pbc setup exec/compressible/chemistry_inputs_files/inputs_RBtest_eq_SF commit 5b4cadd05daeebf712d682f26dfed763c3b29f8a Merge: 3c20431c 589b2e9e Author: Daniel Ladiges Date: Tue Sep 14 12:51:53 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 3c20431c013928a41f704661ba9be9dec2a503c6 Author: Daniel Ladiges Date: Tue Sep 14 12:51:24 2021 -0700 Some changes to particle container for sophie's membrane thing exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 589b2e9efa6a610d2a40a6f35d82c54150948347 Author: isriva Date: Tue Sep 14 12:24:46 2021 -0700 small change to regression input files exec/compressible_stag/inputs_regression_concentration_3D exec/compressible_stag/inputs_regression_periodic_3D exec/compressible_stag/inputs_regression_reservoir_1D exec/compressible_stag/inputs_regression_reservoir_3D exec/compressible_stag/inputs_regression_slip_adiabatic_3D exec/compressible_stag/inputs_regression_tempgrad_1D exec/compressible_stag/inputs_regression_tempgrad_3D commit eec11f368d63d9da965eb4773545dc2f9b341c5c Merge: 6aaa3606 bb6a36df Author: isriva Date: Tue Sep 14 10:01:30 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit 6aaa360637df0683d0a79d5e11b620b0369413e6 Author: isriva Date: Tue Sep 14 09:21:09 2021 -0700 added regression tests input files for the staggered compressible code exec/compressible_stag/inputs_regression_concentration_3D exec/compressible_stag/inputs_regression_periodic_3D exec/compressible_stag/inputs_regression_reservoir_1D exec/compressible_stag/inputs_regression_reservoir_3D exec/compressible_stag/inputs_regression_slip_adiabatic_3D exec/compressible_stag/inputs_regression_tempgrad_1D exec/compressible_stag/inputs_regression_tempgrad_3D commit bb6a36dfbe5018d9b6cae2ca44d744dd2afdce89 Author: Changho Kim Date: Mon Sep 13 15:41:06 2021 -0700 exec/compressible/chemistry_inputs_files: updated exec/compressible/chemistry_inputs_files/inputs_CO_He_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbAr_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbCO_eq_SF exec/compressible/chemistry_inputs_files/inputs_rbHe_eq_SF exec/compressible/chemistry_inputs_files/params_CO_He_eq_SF.py commit 4cac27d8757fb4eb477909ae303efaa67096c000 Author: isriva Date: Mon Sep 13 13:01:12 2021 -0700 moved compressible namespace in to src_compressible. also moved some more variables from common into compressible exec/compressible/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/compressible_namespace.H src_compressible/transCoeffs.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/compressible_namespace.H commit 78a226e85f6b778a44a043387c56848c0db71e8a Author: Andy Nonaka Date: Mon Sep 13 11:41:50 2021 -0700 Revert "Revert "Merge pull request #64 from AMReX-FHD/compressible_reservoir"" This reverts commit 59f33475b5f4cc58fd0e238ce67a9c9c20683c9c. exec/compressible_stag/inputs_reservoir_equil exec/compressible_stag/main_driver.cpp src_common/common_namespace.H src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/transCoeffs.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/Make.package src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/compressible_namespace.H src_compressible_stag/fluxStag.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 1ff9780dac6cea361587adc6ba2329418494c439 Author: Andy Nonaka Date: Mon Sep 13 11:41:37 2021 -0700 Revert "Revert "change default value of rho_lo/hi back to -1"" This reverts commit 77bde66657d9ef725c8c4ed6036592372d4123ff. src_common/common_functions.cpp commit 59f33475b5f4cc58fd0e238ce67a9c9c20683c9c Author: Andy Nonaka Date: Mon Sep 13 11:35:15 2021 -0700 Revert "Merge pull request #64 from AMReX-FHD/compressible_reservoir" This reverts commit 64703cb1d3456b7d25d5e1c91e90da9e034daa69, reversing changes made to a176e156118c7a912feded1beb1952a82abc8ab2. exec/compressible_stag/inputs_reservoir_equil exec/compressible_stag/main_driver.cpp src_common/common_namespace.H src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/transCoeffs.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/Make.package src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/compressible_namespace.H src_compressible_stag/fluxStag.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 77bde66657d9ef725c8c4ed6036592372d4123ff Author: Andy Nonaka Date: Mon Sep 13 11:33:08 2021 -0700 Revert "change default value of rho_lo/hi back to -1" This reverts commit 01d85f3e4e4b91490e26835c512e9a6ce66401b7. src_common/common_functions.cpp commit 01d85f3e4e4b91490e26835c512e9a6ce66401b7 Author: Andy Nonaka Date: Mon Sep 13 11:14:03 2021 -0700 change default value of rho_lo/hi back to -1 src_common/common_functions.cpp commit 04ae8be8906744a152693769ea4ec63f87d9674e Merge: 12d887bc 64703cb1 Author: Daniel Ladiges Date: Mon Sep 13 10:59:48 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 12d887bcc9b4cfaf40e617cf0fb5a8590df6f795 Author: Daniel Ladiges Date: Mon Sep 13 10:55:46 2021 -0700 Modified timestep rampup in immersedIons Numerous minor DSMC things exec/DSMC/DsmcCollide.cpp exec/DSMC/particleGen.cpp exec/DSMC/test_inputs/inputs_conc exec/immersedIons/main_driver.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit e05ab844482c4b6c51c12932d49dbabc00c838e5 Merge: bbd46701 64703cb1 Author: etpalmer63 Date: Mon Sep 13 13:36:05 2021 -0400 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 64703cb1d3456b7d25d5e1c91e90da9e034daa69 Merge: a176e156 6fbdc949 Author: Andy Nonaka Date: Mon Sep 13 10:25:23 2021 -0700 Merge pull request #64 from AMReX-FHD/compressible_reservoir Compressible reservoir commit a176e156118c7a912feded1beb1952a82abc8ab2 Merge: 4a54fce1 90a0c457 Author: Andy Nonaka Date: Mon Sep 13 10:20:31 2021 -0700 Merge pull request #68 from AMReX-FHD/basic_ci Basic ci commit 6fbdc94980acb16b505a9fd11dbd721f59cf8db0 Author: isriva Date: Mon Sep 13 00:17:09 2021 -0700 fixed a small bug -- propagated from recent code changes to src_common src_compressible_stag/boundaryStag.cpp commit 63967330ab73a5fbe71ee52512349f40aa98af80 Author: isriva Date: Sun Sep 12 13:10:26 2021 -0700 fix small bug on COM velocity upon restart src_compressible_stag/Checkpoint.cpp commit e3c22ab462d59299db17dc1de409d451c39b4a68 Author: isriva Date: Sun Sep 12 10:20:50 2021 -0700 added function to specify seed at restart src_compressible_stag/Checkpoint.cpp commit 7fdbef1f2666ebf258d1fbc258ea0bc4779c7e0b Author: isriva Date: Sun Sep 12 10:08:18 2021 -0700 added option for multiple spatial correlations within a run exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/compressible_namespace.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 31b3b44cf94e6ad23154ac9d6399addc75013823 Merge: f6aa7053 4a54fce1 Author: isriva Date: Fri Sep 10 11:02:03 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit f6aa7053a03e5eea47ce6df3099e3a744dea10d4 Author: isriva Date: Fri Sep 10 10:33:07 2021 -0700 final cleanups src_common/src_F90/common_namelist.F90 src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp commit 4a54fce1d88f182bd5aa27dbff9dd98814775dcd Author: Andy Nonaka Date: Wed Sep 8 13:20:58 2021 -0700 updated inputs file for C++ namespace exec/compressible/chemistry_inputs_files/inputs_CO_He_eq_SF exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF commit 5f863564cf666ff091fbd082bd831bfb88d895c3 Author: Andy Nonaka Date: Wed Sep 8 11:48:56 2021 -0700 fix comment src_common/common_namespace.H commit 670e78cf982eab92c08aa3d710a87af2e4c0e7b8 Author: Andy Nonaka Date: Wed Sep 8 11:29:38 2021 -0700 clean namespace src_common/common_functions.cpp src_common/common_namespace.H commit dc77b5d07aa2cc39654e385383ce218a6e9c9bfe Author: isriva Date: Wed Sep 8 08:25:00 2021 -0700 infrequent outputs & track avg. momentum exec/compressible_stag/main_driver.cpp commit d2a7cba81ca91b7fd81dd59bb874ba37b90d991b Merge: 737b7c72 1d300eb7 Author: Andy Nonaka Date: Tue Sep 7 19:23:55 2021 -0700 Merge pull request #77 from AMReX-FHD/remove_common_namelist Remove common namelist commit 1d300eb71939f2c0f1b8bf1dbd13c702463d37cc Author: Andy Nonaka Date: Tue Sep 7 19:15:28 2021 -0700 fix inputs to close namelist exec/immersed_boundary/flagellum/inputs_chlamy_data exec/immersed_boundary/flagellum/inputs_regression_chlamy commit 488ebcc137e16b80f493f77361fea865062f0a91 Author: Andy Nonaka Date: Tue Sep 7 17:22:26 2021 -0700 fix inputs files to supply proper number of array elements exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d commit c8c2c69d4d6850e3f1dbbd2a1353fbdc362520f7 Author: Andy Nonaka Date: Tue Sep 7 17:17:48 2021 -0700 error checking for array read src_common/common_functions.cpp src_multispec/multispec_functions.cpp commit 9a0213ea4dbb4d6ddfbbb174b64f6806e199b303 Author: Andy Nonaka Date: Tue Sep 7 16:07:25 2021 -0700 remove commas from array reads exec/compressible/inputs_RT_3d exec/compressible/inputs_SFtest exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d_mem exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_profiling_gpu exec/compressible/inputs_regression_RT_3d exec/compressible/inputs_regression_equil_3d exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic exec/compressible/inputs_regression_temp_grad exec/compressible/inputs_temp_grad exec/compressible/inputs_test_3d exec/compressible/inputs_test_deterministic exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify commit 4dc93bb0677980c4169963276445087e0254a77c Author: Andy Nonaka Date: Tue Sep 7 15:58:52 2021 -0700 fix the optional queries to arrays src_common/common_functions.cpp src_multispec/multispec_functions.cpp commit 465f645217aed8e4a9c60f7f2307b7f41a9bce71 Author: Andy Nonaka Date: Tue Sep 7 15:41:26 2021 -0700 integer read src_common/common_functions.cpp commit ecad774149e63350928b62525137dda2fd3ed7db Author: Andy Nonaka Date: Tue Sep 7 15:23:04 2021 -0700 modify inputs files and source code for C++ namespace exec/DSMC/GNUmakefile exec/DSMC/ex_main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMC/test_inputs/input_periodic_eq exec/DSMC/test_inputs/input_test exec/DSMC/test_inputs/input_therm exec/DSMC/test_inputs/inputs_conc exec/DSMC_granular/GNUmakefile exec/DSMC_granular/ex_main_driver.cpp exec/DSMC_granular/input_test exec/DSMC_granular/main_DSMC_driver.cpp exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/test_inputs/input_periodic_eq exec/DSMC_granular/test_inputs/input_test exec/DSMC_granular/test_inputs/input_therm exec/chemistry_testing/GNUmakefile exec/chemistry_testing/inputs_1 exec/chemistry_testing/inputs_2 exec/chemistry_testing/inputs_3 exec/chemistry_testing/inputs_NO2_N2O4 exec/chemistry_testing/main.cpp exec/compressible/GNUmakefile exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF exec/compressible/inputs_RT_3d exec/compressible/inputs_SFtest exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d_mem exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_profiling_gpu exec/compressible/inputs_regression_RT_3d exec/compressible/inputs_regression_equil_3d exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic exec/compressible/inputs_regression_temp_grad exec/compressible/inputs_temp_grad exec/compressible/inputs_test_3d exec/compressible/inputs_test_deterministic exec/compressible/main_driver.cpp exec/compressible_mui/GNUmakefile exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/SPPARKS_MUI/input.cpp exec/compressible_mui/cori_coverage/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/pseudo_kmc/inputs_equil_3d exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/compressible_mui/scripts/4spec/compressible/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd exec/compressible_mui/scripts/4spec/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_1+1/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_x/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_y/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_z/inputs_fhd_coverage exec/compressible_stag/GNUmakefile exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify exec/compressible_stag/main_driver.cpp exec/hydro/PDF/PDF.cpp exec/hydro/inputs_algtest_2d exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_profiling_discos_3d exec/hydro/inputs_profiling_rtil_3d exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/immersedIons/GNUmakefile exec/immersedIons/inputs_gpu exec/immersedIons/inputs_template exec/immersedIons/main_driver.cpp exec/immersedIons/paper_inputs/inputs_paper_diffusion exec/immersedIons/paper_inputs/inputs_paper_eo exec/immersedIons/paper_inputs/inputs_paper_sf exec/immersedIons/paper_inputs_2/inputs_1_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_0wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift_v2 exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det exec/immersedIons/test_inputs/inputs_3d exec/immersedIons/test_inputs/inputs_3d_poisson exec/immersedIons/test_inputs/inputs_3d_reflect exec/immersedIons/test_inputs/inputs_conductivity_test exec/immersedIons/test_inputs/inputs_density_test exec/immersedIons/test_inputs/inputs_density_test_damp exec/immersedIons/test_inputs/inputs_density_test_dry exec/immersedIons/test_inputs/inputs_density_test_eo_wet exec/immersedIons/test_inputs/inputs_density_test_es_damp exec/immersedIons/test_inputs/inputs_density_test_es_dry exec/immersedIons/test_inputs/inputs_density_test_es_wet exec/immersedIons/test_inputs/inputs_eo_realchannel_test_wet exec/immersedIons/test_inputs/inputs_eo_test_wet exec/immersedIons/test_inputs/inputs_freund_real_eo exec/immersedIons/test_inputs/inputs_gpu exec/immersedIons/test_inputs/inputs_jing_cruz_jcp exec/immersedIons/test_inputs/inputs_mobility_test exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond10 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond11 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond4 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond5 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond6 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond7 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond8 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr1 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr2 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr3 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr4 exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/inputs_3d_test.highres exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_rigid/inputs_2d exec/immersed_boundary/channel_rigid/inputs_3d exec/immersed_boundary/channel_rigid/inputs_3d_test exec/immersed_boundary/channel_rigid/inputs_3d_test.2 exec/immersed_boundary/channel_rigid/inputs_3d_test.3 exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/GNUmakefile exec/immersed_boundary/flagellum/inputs_2d exec/immersed_boundary/flagellum/inputs_3d exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.buddy exec/immersed_boundary/flagellum/inputs_chlamy.cori exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/inputs_chlamy.highres-thin exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/flagellum/inputs_chlamy.large-thin exec/immersed_boundary/flagellum/inputs_chlamy_data exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum/inputs_regression_chlamy exec/immersed_boundary/flagellum/inputs_taylor exec/immersed_boundary/flagellum/main_driver.cpp exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/demo/main_driver.cpp exec/lib_hydro/gnumake/Makefile exec/multispec/GNUmakefile exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_profiling_3d_coriGPU exec/multispec/inputs_profiling_3d_haswell exec/multispec/inputs_regression_cap_2d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_regression_spinodal_2d exec/multispec/inputs_regression_spinodal_3d exec/multispec/inputs_rtil_cap_128V_2d exec/multispec/inputs_rtil_cap_128V_3d exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d exec/multispec/main_driver.cpp exec/structFactTest/GNUmakefile exec/structFactTest/inputs_profiling_3d exec/structFactTest/inputs_regression_2d exec/structFactTest/inputs_regression_3d exec/structFactTest/main_driver.cpp exec/tests/RFDanalysis/GNUmakefile src_chemistry/chemistry_functions.H src_surfchem_mui/surfchem_mui_functions.H commit 737b7c72a4a0ddd6d5b229bab4ccbca57ca6a5ab Merge: 4773411e ee5ebde8 Author: Changho Kim Date: Tue Sep 7 15:09:06 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 4773411e5c7abfddcabe72ee0350d542e86b4fdb Author: Changho Kim Date: Tue Sep 7 15:08:32 2021 -0700 exec/compressible/chemistry_inputs_files: CO/He added exec/compressible/chemistry_inputs_files/inputs_CO_He_eq_SF exec/compressible/chemistry_inputs_files/params_CO_He_eq_SF.py commit a1d5de2fab71e2cb98c01d6a6c9bb1018c8c2b54 Author: Andy Nonaka Date: Tue Sep 7 15:04:49 2021 -0700 remove fortran exec/hydro/GNUmakefile exec/hydro/main_driver.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/common_namelist.F90 commit 0d7221ec99464908edac8d76f60b3dab72e75175 Author: Andy Nonaka Date: Tue Sep 7 14:54:56 2021 -0700 parmparse in all the variables src_common/common_functions.cpp commit 0efb3e4ce2ddcd54fbd9e8a68a3fc08f4b0f148d Merge: f36e26a7 ee5ebde8 Author: isriva Date: Sat Sep 4 15:37:30 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit f36e26a70f4d5d963a3166d16e3592ffd4387e04 Author: isriva Date: Sat Sep 4 15:36:27 2021 -0700 some final cleanups to reservoir BC src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 7c71acb94ee8106d887d49d14fcfeba12d565479 Author: Andy Nonaka Date: Fri Sep 3 17:25:27 2021 -0700 saving progress src_common/common_functions.cpp commit 3feb3fddfc34faba983c5126646996ea55e09243 Author: Andy Nonaka Date: Fri Sep 3 16:55:46 2021 -0700 give default values for C++ common namespace src_common/common_functions.cpp commit 76928935fed92e6da2c0ea74871479e00dbac516 Author: isriva Date: Fri Sep 3 15:56:26 2021 -0700 succesfully added Giovangigli transport equations src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit a2b42377ccd3c969f1ef7ba3e0569223f0541f8a Author: isriva Date: Fri Sep 3 11:18:58 2021 -0700 support for binary transport coefficients from Hirschfelder-Curtiss-Bird exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/compressible_namespace.H commit ee5ebde8428f23acb0d432d2672b171e77eda7b3 Merge: ad1825fa 313056c5 Author: Andy Nonaka Date: Fri Sep 3 09:08:06 2021 -0700 Merge pull request #76 from etpalmer63/remove_redundant_vars Remove redundant vars commit ad1825fa339a972ee6f0e0daf06203656021e0ef Merge: dfc0f0de 3b39330e Author: Changho Kim Date: Fri Sep 3 02:15:06 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit dfc0f0de941228fc6b6d220d664ef4f4b5aaabcf Author: Changho Kim Date: Fri Sep 3 02:14:45 2021 -0700 compressible_mui/RUN_COadsPt111_SF/params_CO_He_eq_SF.py: updated exec/compressible_mui/RUN_COadsPt111_SF/params_CO_He_eq_SF.py commit 3b39330e8156afe82be8453d49629bb5c00cca52 Author: Andy Nonaka Date: Thu Sep 2 15:56:21 2021 -0700 remove tracer support since the lack of physical boundary conditions was generating NaNs exec/hydro/Checkpoint.cpp exec/hydro/Init.cpp exec/hydro/WritePlotFile.cpp exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit e92011efc73f5be787e5e77dcbfa51261223c5c0 Author: Andy Nonaka Date: Thu Sep 2 15:28:40 2021 -0700 replace double precision "d"s with "e"s to prep for elimination of fortran namelists exec/_1d_staggered_comp/inputs exec/_1d_staggered_comp/inputs.eq exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify exec/hydro/inputs_algtest_2d exec/hydro/inputs_force exec/hydro/inputs_profiling_discos_3d exec/hydro/inputs_profiling_rtil_3d exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_profiling_3d_coriGPU exec/multispec/inputs_profiling_3d_haswell exec/multispec/inputs_regression_cap_2d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_regression_spinodal_2d exec/multispec/inputs_regression_spinodal_3d exec/multispec/inputs_rtil_cap_128V_2d exec/multispec/inputs_rtil_cap_128V_3d exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d commit b157d24e13ce08a3e4932c289b0a64345e0094b2 Author: Andy Nonaka Date: Thu Sep 2 12:51:51 2021 -0700 remove need to include the common_namelist by passing in pkernel_fluid src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 30d1730b1a43bf75458f77c48bdf7e0fa43cc09d Author: Andy Nonaka Date: Wed Sep 1 15:52:07 2021 -0700 get random restart in parallel working for multispecies exec/multispec/Checkpoint.cpp exec/multispec/multispec_test_functions.H commit 7dcf113605aedf982445ade5794be599853b9497 Author: isriva Date: Wed Sep 1 12:36:58 2021 -0700 added inital jump conditions src_compressible/compressible_functions.cpp src_compressible_stag/compressible_functions_stag.cpp commit bbd467013ea2f527fe7beb37ca4b9ddc51c50c46 Merge: f600c259 16fa37ef Author: etpalmer63 Date: Tue Aug 31 21:26:24 2021 -0400 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit f600c259b477cd39f18f1f40090c8b9fa4255fc0 Author: etpalmer63 Date: Tue Aug 31 21:25:53 2021 -0400 Remove CI stuff that shouldn't be here. .github/workflows/cuda.disabled .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_clang6.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/dependencies_nofortran.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/dependencies/documentation.sh .github/workflows/docs.disabled .github/workflows/hip.disabled .github/workflows/intel.disabled .github/workflows/linux.yml .github/workflows/macos.disabled .github/workflows/style.yml .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh .github/workflows/style/style/check_tabs.sh .github/workflows/style/style/check_trailing_whitespaces.sh .github/workflows/windows.disabled commit 313056c55fc03d1894ac92fd96a8f520f32f8e76 Author: etpalmer63 Date: Tue Aug 31 21:19:11 2021 -0400 remove files from basic ci. .github/workflows/cuda.disabled .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_clang6.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/dependencies_nofortran.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/dependencies/documentation.sh .github/workflows/docs.disabled .github/workflows/hip.disabled .github/workflows/intel.disabled .github/workflows/linux.yml .github/workflows/macos.disabled .github/workflows/style.yml .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh .github/workflows/style/style/check_tabs.sh .github/workflows/style/style/check_trailing_whitespaces.sh .github/workflows/windows.disabled tempfile.test commit 16fa37ef146a8cabe334d2ea7c4896e32ba2c229 Author: Andy Nonaka Date: Tue Aug 31 15:44:08 2021 -0700 revert exec/structFactTest/main_driver.cpp commit 912ca9d7702a112f2380d123a637c553fc2b7657 Author: Andy Nonaka Date: Tue Aug 31 15:43:21 2021 -0700 test commit to break regression test exec/structFactTest/main_driver.cpp commit 0e7d8e0269e2fb475bb02dcfb7fb8689860d5955 Author: etpalmer63 Date: Tue Aug 31 18:41:48 2021 -0400 Clean up doxygen comments. src_multispec/multispec_functions.H commit c71e2250506d1f2fd0dfc89a87fe260bd0a0fc99 Author: etpalmer63 Date: Tue Aug 31 18:39:33 2021 -0400 Remove chi_iterations_in. Passes my tests. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit ccb4aa630c305e4b97485a6dc7c0e26b1124a421 Author: etpalmer63 Date: Tue Aug 31 18:13:33 2021 -0400 clean up doxy comments src_multispec/multispec_functions.H commit f016d9d51e4a0df1e81ef9f57a847edad06dfe88 Author: etpalmer63 Date: Tue Aug 31 18:08:54 2021 -0400 Changed nspecies to nspecies_in on line 298 -- passes my tests. Confirm with Andy. src_multispec/multispec_functions.H commit 9ffc00666d6aca4f242738b3d3bdc2a1ff3ede9d Author: etpalmer63 Date: Tue Aug 31 18:04:09 2021 -0400 remove nspecies_in from PopulateX_xxT src_multispec/multispec_functions.H commit 401e0ec134545235e3119a9a7f682857fa84bb77 Author: etpalmer63 Date: Tue Aug 31 17:56:58 2021 -0400 remove nspecies_in from GammaIPlusMatmul src_multispec/multispec_functions.H commit 9e73970362650abc3050bd2fda18df2457a8e428 Author: etpalmer63 Date: Tue Aug 31 17:54:39 2021 -0400 Remoce nspecies_in from ComputeGammaLocal src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit b7946c849f5f19088ae433a0311e29b840b2edb8 Author: etpalmer63 Date: Tue Aug 31 17:47:56 2021 -0400 missed a line src_multispec/multispec_functions.H commit 9293660d49436dc23758d093f619f08dabca07de Author: etpalmer63 Date: Tue Aug 31 17:47:08 2021 -0400 Remove nspecies_local from Dbar2chiIterative src_multispec/multispec_functions.H commit 0f01c86aca5478bcfa6a1deeb247fe6e71fd8fbe Author: etpalmer63 Date: Tue Aug 31 16:22:52 2021 -0400 Remove nspecies_in from NonnegativeRhoAv src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 19db924216682f37a6348a5e079e873bd2cae26e Author: etpalmer63 Date: Tue Aug 31 16:05:04 2021 -0400 Remove nspecies_in from ComputeSqrtLOnsagerSub src_multispec/multispec_functions.H commit 48fb8850076fa17fd4c78ee5e82e12fa1f6a9dc1 Author: etpalmer63 Date: Tue Aug 31 16:00:08 2021 -0400 Remove nspecies_in from ComputeSqrtLOnsagerLocal. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit bad2d04463161916a4918c62c7a322fefc982d85 Merge: 62bc74d2 d89f1959 Author: etpalmer63 Date: Tue Aug 31 15:45:40 2021 -0400 Merge branch 'main' of github.com:etpalmer63/FHDeX into main commit d89f19592f6232b3fdaa5f267e5e69e0ac9c524f Merge: 6daf58a7 91d0951d Author: Erik Date: Tue Aug 31 15:44:21 2021 -0400 Merge branch 'AMReX-FHD:main' into main commit 62bc74d2d03bde509dc524910607ba0dff389371 Author: etpalmer63 Date: Tue Aug 31 15:42:49 2021 -0400 Remove nspecies_in from MixturePropsMassLocal and ComputZetaByTempLocal src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 31495bc87ccd0badc4d51e085680dd5fa83790e9 Author: etpalmer63 Date: Tue Aug 31 15:35:13 2021 -0400 Remove nspecies_in from ComputeDbarLocal src_multispec/ComputeMixtureProperties.cpp src_multispec/multispec_functions.H commit 91d0951d35b1cd06a855506c0ef2226ef4ee4001 Author: Changho Kim Date: Mon Aug 30 23:49:00 2021 -0700 compressible_mui/SPPARKS_MUI: temperature dependence of desorption rates implemtend (cp=7/2) exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_coverage/in.kmc exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h commit 6df4b576790c25097b56d68c1b5c5d85171feff9 Author: Changho Kim Date: Mon Aug 30 12:23:09 2021 -0700 compressible_mui/SPPARKS_MUI: temprature-dependenced for r_ads exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_coverage/in.kmc exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp src_surfchem_mui/surfchem_mui_functions.cpp commit 59f8cacbf546b52dcd0cfe6b61dfee8cec2c9cbd Author: Changho Kim Date: Sun Aug 29 16:02:03 2021 -0700 src_surfchem_mui/surfchem_mui_functions.cpp: better logic to restrict non-translational energy sampling to dof=5 and e0 = 0 src_surfchem_mui/surfchem_mui_functions.cpp commit fc5fcf9b76d074a4b7fdd142267db52d053e9e2f Author: isriva Date: Sun Aug 29 10:16:30 2021 -0700 small bugfix in cell-centered reservoir src_compressible/boundary.cpp commit 58c2fdf1d19f4cbb00f72ab154d0edfe4a93018f Author: isriva Date: Sun Aug 29 10:11:51 2021 -0700 reservoir added in cell-centered code -- need to think about stochastic momentum flux at reservoir face src_compressible/boundary.cpp commit 9d785883fa5ef0c99a8bb5e857027cfc4737bfd7 Author: Changho Kim Date: Sun Aug 29 04:51:16 2021 -0700 compressible_mui/src_surfchem_mui: nspec_mui, mom_inertia added, clean-up exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp src_surfchem_mui/surfchem_mui_namespace.H commit 71a529dd7b19f3dc45a24f2edd7d19a7bba8960f Author: Changho Kim Date: Sat Aug 28 22:13:23 2021 -0700 compressible_mui/src_surfchem_mui: clean up exec/compressible_mui/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit fbc9abc621a0cda2b3c4cb805da0b6153cfbc6c9 Author: Changho Kim Date: Sat Aug 28 16:00:04 2021 -0700 compressible_mui: most mui routines moved to src_surfchem_mui exec/compressible_mui/main_driver.cpp src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp commit 3b0473cda4843ffebe3354bae40d1d1372885d36 Merge: faea4afa 1e34ddd6 Author: drladiges Date: Sat Aug 28 08:30:38 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit faea4afabf08173e3d546f2995e6d635b5c38ff2 Author: drladiges Date: Sat Aug 28 08:30:12 2021 -0700 pushing notebook with example of plot formatting we're using for paper tools/notebooks/channel_mob.ipynb commit 1e34ddd6f3608eef02b56697ff4f1ebf18f11a2f Author: Andy Nonaka Date: Fri Aug 27 10:04:30 2021 -0700 tweak for optimal performance on a gpu exec/multispec/inputs_rtil_cap_128V_3d commit 353f4e6f2380af1957869bc620756d1a3e3a3423 Merge: 3e29b7e3 88b91ad5 Author: Andy Nonaka Date: Fri Aug 27 09:46:23 2021 -0700 Merge branch 'remove_multispec_namelist' into main commit 88b91ad54fd43ca5f9617045e99ffa964d967d53 Author: Andy Nonaka Date: Fri Aug 27 09:45:47 2021 -0700 3d cap exec/multispec/inputs_rtil_cap_128V_3d commit 2e0621abd37ff699139e1c3fb125ffba0e31c717 Author: Andy Nonaka Date: Fri Aug 27 09:44:31 2021 -0700 fix comments in inputs file; add new 3D capacitance test exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_profiling_3d_coriGPU exec/multispec/inputs_profiling_3d_haswell exec/multispec/inputs_regression_cap_2d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_regression_spinodal_2d exec/multispec/inputs_regression_spinodal_3d exec/multispec/inputs_rtil_cap_128V_2d exec/multispec/inputs_rtil_cap_128V_3d exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d commit 3e29b7e377004aca970b677907839589055714b6 Author: Changho Kim Date: Fri Aug 27 03:58:03 2021 -0700 compressible_mui: src_surfchem_mui created and mui functions moved exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp src_surfchem_mui/Make.package src_surfchem_mui/surfchem_mui_functions.H src_surfchem_mui/surfchem_mui_functions.cpp src_surfchem_mui/surfchem_mui_namespace.H commit e7bf900d09c9bd722f3622a638fae44646e324f6 Author: Changho Kim Date: Fri Aug 27 03:27:44 2021 -0700 exec/compressible_mui: chemistry (gas) added as in exec/compressible exec/compressible_mui/main_driver.cpp commit 9dd2a45e12bd881946c62826f4858e14ffcb1135 Merge: 7341222d c191da6c Author: Andy Nonaka Date: Thu Aug 26 11:50:39 2021 -0700 Merge pull request #75 from AMReX-FHD/remove_multispec_namelist removing f90 namelist commit c191da6c410b36b7b275512b102b4af9367ef6fe Author: Andy Nonaka Date: Thu Aug 26 11:37:55 2021 -0700 inputs files exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_regression_cap_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_regression_spinodal_2d exec/multispec/inputs_regression_spinodal_3d exec/multispec/inputs_rtil_cap_128V_2d exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d commit a2ed3de6eb13fc49918a7683bae8caee04d54135 Author: Andy Nonaka Date: Thu Aug 26 11:25:49 2021 -0700 inputs exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_profiling_3d_coriGPU exec/multispec/inputs_profiling_3d_haswell commit 1d4383c98a43b1238e69d3a1687077fa1f3c15e7 Author: Andy Nonaka Date: Thu Aug 26 11:18:31 2021 -0700 removing f90 namelist all f90 gone in src_multispec! exec/multispec/GNUmakefile exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_regression_detbubble_2d exec/multispec/main_driver.cpp src_multispec/Make.package src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/multispec_namelist.F90 commit 81f975e01762c93f8164af62ca5af19a7c8899b2 Author: isriva Date: Wed Aug 25 20:48:49 2021 -0700 stochastic stress flux in the reservoir src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit f2ad4b3bda1015ac92b54b723c49da75bfe5066f Merge: e5753820 7341222d Author: isriva Date: Wed Aug 25 15:44:43 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit 7341222de320d02b5cb891a7a3bb85c007e3e945 Merge: c42676c5 924c37dd Author: Ishan Srivastava Date: Wed Aug 25 16:38:34 2021 -0600 Merge pull request #74 from AMReX-FHD/rng_ghost option to fill ghost cells in MultiFabFillRandom() commit c42676c517fbdc7aacbe62d422e1d8b952789d9b Author: emercado9 Date: Wed Aug 25 12:58:22 2021 -0700 exec/compressible_mui/SPPARKS_MUI/: added zigzag lattice, dissocads and assocdes reactions, and MUI directives for mui and nonmui executables into spparks directory exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mui exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.nonmui exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_mui/SPPARKS_MUI/create_sites.cpp exec/compressible_mui/SPPARKS_MUI/diag_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/lattice.cpp exec/compressible_mui/SPPARKS_MUI/main.cpp exec/compressible_mui/SPPARKS_MUI/spparks.h commit 924c37dd8e241fb5906f9b7e0d19e39a06c5b9a1 Author: Andy Nonaka Date: Wed Aug 25 10:16:13 2021 -0700 option to fill ghost cells in MultiFabFillRandom() src_rng/MultiFabFillRandom.cpp src_rng/rng_functions.H commit e5753820e24b07a180e357c25ad09ce029521f4d Author: isriva Date: Tue Aug 24 10:54:14 2021 -0700 added input file for equilibrium reservoir simulation exec/compressible_stag/inputs_reservoir_equil commit ddd4d5bc2696ba212a5129de53447fd354e8b895 Merge: 0e6a41a6 fb8cddff Author: isriva Date: Tue Aug 24 08:36:21 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit fb8cddff72d45028304ffc327707a2344efa5777 Author: Andy Nonaka Date: Mon Aug 23 20:22:35 2021 -0700 move *_namespace_declaration.H contents into *_functions.cpp exec/DSMC/ex_main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMC_granular/ex_main_driver.cpp exec/DSMC_granular/main_DSMC_driver.cpp exec/DSMC_granular/main_driver.cpp exec/chemistry_testing/main.cpp exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/demo/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_chemistry/Make.package src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace_declarations.H src_common/Make.package src_common/common_functions.cpp src_common/common_namespace_declarations.H src_compressible_stag/Make.package src_gmres/Make.package src_gmres/gmres_functions.cpp src_gmres/gmres_namespace_declarations.H src_immersed-boundary/Make.package src_immersed-boundary/MakeBase.package src_immersed-boundary/ib_functions.cpp src_immersed-boundary/immbdy_namespace_declarations.H src_multispec/Make.package src_multispec/multispec_functions.cpp src_multispec/multispec_namespace_declarations.H src_particles/MakeDSMC.package src_particles/dsmc_functions.cpp src_particles/dsmc_namespace_declarations.H unmaintained/DSMC-LDT/main_driver.cpp unmaintained/DiffuisonTest/main_driver.cpp unmaintained/_GL_alt/main_driver.cpp unmaintained/_GL_alt_1D/main_driver.cpp unmaintained/channel_soft/main_driver.cpp unmaintained/exercises/compressible/main_driver.cpp unmaintained/exercises/incompressible/main_driver.cpp commit 0e6a41a647f5796805b75d636f2a5a0a9a6c54bb Author: isriva Date: Mon Aug 23 14:28:21 2021 -0700 fixed reservoir BC (hopefully!) -- inital tests show correct results src_compressible_stag/boundaryStag.cpp src_compressible_stag/fluxStag.cpp commit 5762664dd1a84dc9f4811da0ccc9b36ba61e182a Author: isriva Date: Mon Aug 23 14:27:21 2021 -0700 some more flux stats output -- for debugging src_compressible_stag/timeStepStag.cpp commit 36afc734cc3c8f49f0ebc4d717f582157b27e1a7 Author: isriva Date: Mon Aug 23 14:25:46 2021 -0700 pressure discontinuity simulation setup exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.cpp commit 4559ee98dbee1818f96b50e2e5e42334fe6befdd Author: isriva Date: Mon Aug 23 14:23:59 2021 -0700 added center of mass velocity src_compressible_stag/Checkpoint.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 4a5db144f1120b177365699310f44d62086d7031 Author: Andy Nonaka Date: Mon Aug 23 12:10:25 2021 -0700 add inline src_multispec/multispec_functions.H commit a1b1d523cc9175e896b77e3cf007bea784318b09 Merge: bf12a6f9 53918502 Author: Andy Nonaka Date: Mon Aug 23 11:58:15 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit bf12a6f9d3af73e51ec5233e748950089f467556 Author: Andy Nonaka Date: Mon Aug 23 11:58:02 2021 -0700 cleanup src_multispec/FluidCharge.cpp commit 53918502ceac42df699e75a9a18ecf7f883bde31 Merge: bc3efbb9 f93bc67c Author: Daniel Ladiges Date: Mon Aug 23 11:28:11 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit bc3efbb9c2f86a64619901ebae3db633752dddd9 Author: Daniel Ladiges Date: Mon Aug 23 11:22:21 2021 -0700 Multispecies with inflow/outflow boundaries currently gives weird results for species 2 if the domain is initialized with particles. Starting with empty domain it works fine exec/DSMC/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 4122ce50d1b0665ec00ba2d3b06d77bfede6a309 Merge: 4d18c97f f93bc67c Author: Andy Nonaka Date: Fri Aug 20 17:16:01 2021 -0700 Merge branch 'main' into compressible_reservoir commit 90a0c457a627bc9b3c81fceb6a3c69ab34b1b07e Merge: 50555e73 f93bc67c Author: Andy Nonaka Date: Fri Aug 20 17:15:21 2021 -0700 Merge branch 'main' into basic_ci commit f93bc67c8e583bd4729e2b1a6204262e9fcf6014 Author: Andy Nonaka Date: Fri Aug 20 16:18:30 2021 -0700 optimize inputs exec/hydro/inputs_profiling_discos_3d exec/hydro/inputs_profiling_rtil_3d commit d9268f8dc2719c147b5bcccbf5ca64171496c7ae Author: Andy Nonaka Date: Fri Aug 20 16:02:45 2021 -0700 fix stag_mg_minwidth logic - it didn't work before in the case where max_grid_size = stag_mg_minwidth and could keep coarsening src_gmres/StagMGSolver.cpp commit 0b8855e9a071b1e6f4c15477a441d43b6faa58b3 Author: Andy Nonaka Date: Fri Aug 20 15:35:57 2021 -0700 profiling inputs exec/hydro/inputs_profiling_discos_3d exec/hydro/inputs_profiling_rtil_3d commit 50555e73d117306a37515ab3a326458e117f1440 Author: etpalmer63 Date: Fri Aug 20 15:25:45 2021 -0400 remove debugging stuff .github/workflows/cuda.yml commit 87e56237cd4e02eccad9c8c7b52307d4cdf708f4 Author: etpalmer63 Date: Fri Aug 20 14:02:50 2021 -0400 all the cudas .github/workflows/cuda.yml .github/workflows/dependencies/dependencies_nvcc11.sh commit a08446120965b2a8dc6e870ab8f2982dc6057f6b Author: etpalmer63 Date: Fri Aug 20 13:43:30 2021 -0400 version 11-2 .github/workflows/dependencies/dependencies_nvcc11.sh commit 08a12280fc318d25d111fc617c3da83161924d5a Author: etpalmer63 Date: Fri Aug 20 13:41:15 2021 -0400 still looking for it .github/workflows/cuda.yml commit c3ca53abfc70dd80c2c3ebd79c44c182472866e0 Author: etpalmer63 Date: Fri Aug 20 13:35:30 2021 -0400 change package name .github/workflows/dependencies/dependencies_nvcc11.sh commit 16d8796630f4a3b34ae671eec258bb5b4245d2d8 Author: etpalmer63 Date: Fri Aug 20 13:25:54 2021 -0400 try to locate cufft.h locally .github/workflows/cuda.yml commit deeaa869d83d1783a28698ca7fb849c952765f14 Author: Andy Nonaka Date: Fri Aug 20 10:19:01 2021 -0700 get 2D gpu build working again src_common/common_namespace.H src_common/common_namespace_declarations.H commit 580b05b2ba9fe9857fc85227ea92755326321093 Author: etpalmer63 Date: Fri Aug 20 13:15:18 2021 -0400 start counting down versions until one works .github/workflows/dependencies/dependencies_nvcc11.sh commit a4baff37ca2d20a5f494783f90d8d3ce051fc8a3 Merge: 631705c6 a368d879 Author: Andy Nonaka Date: Fri Aug 20 10:14:45 2021 -0700 Merge pull request #71 from etpalmer63/get_multispec_gpu_compile Cuda now compiles on my machine. commit be7a9e6750ba910152f3ac49c1b56c58d3993f97 Author: etpalmer63 Date: Fri Aug 20 13:05:45 2021 -0400 disable style until we fix all the files .github/workflows/style.disabled commit d4d7ba7a4af5274dff1897e14da30869a08da64d Author: etpalmer63 Date: Fri Aug 20 13:04:06 2021 -0400 test cufft linking .github/workflows/cuda.yml exec/multispec/test.cu commit 1226a06b1a228acc267fabb1f75b243c11482ce7 Author: etpalmer63 Date: Fri Aug 20 12:58:50 2021 -0400 cufft error .github/workflows/cuda.yml commit 9f797816899f65f7532e4abfc21b52809c4c1d45 Author: etpalmer63 Date: Fri Aug 20 12:01:07 2021 -0400 try again. .github/workflows/cuda.yml commit e1515adee82b99d17d9f452cc64147a8c87dd96a Merge: d77e8da9 a368d879 Author: etpalmer63 Date: Fri Aug 20 11:59:25 2021 -0400 Merge branch 'get_multispec_gpu_compile' into basic_ci commit a368d879afb9f46d59e054eea3216c13a9055e15 Author: etpalmer63 Date: Fri Aug 20 11:54:37 2021 -0400 Cuda now compiles on my machine. src_multispec/multispec_namespace.H commit d77e8da91b488b857653d2377c9c151421f50762 Author: etpalmer63 Date: Fri Aug 20 11:29:45 2021 -0400 Try try again. .github/workflows/cuda.yml commit 8608c85b2d7f422b5fa357af9d8da0206705c9fd Author: etpalmer63 Date: Fri Aug 20 11:26:41 2021 -0400 First try at cuda CI .github/workflows/cuda.yml commit 631705c66b9c42f4e7caa64a6a2d41bd72ce3f3a Merge: 8b658e81 d0df7771 Author: Daniel Ladiges Date: Thu Aug 19 15:00:28 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 8b658e814bd1ffdf04af0ea7c9ab0cc35026a791 Author: Daniel Ladiges Date: Thu Aug 19 15:00:10 2021 -0700 Bugfix in cross correlation calulations exec/DSMC/main_driver.cpp exec/DSMC/stats.cpp exec/DSMC/test_inputs/inputs_conc commit a8b97d381d1dec8c88023b22015ee8e41061ff92 Author: Daniel Ladiges Date: Thu Aug 19 14:41:04 2021 -0700 Added cross correlations to plotfiles exec/DSMC/main_driver.cpp exec/DSMC/writePlotFile.cpp commit a8797ae606e02c3d90b44c9615816a64040829f1 Author: Daniel Ladiges Date: Thu Aug 19 13:26:16 2021 -0700 Added spatial cross correlations for John's test case to DSMC stats routine exec/DSMC/main_driver.cpp exec/DSMC/stats.cpp exec/DSMC/test_inputs/inputs_conc src_particles/DsmcParticleContainer.cpp commit d0df7771b84f28220d45ee152a0a8d401ccaa9ea Merge: 1489c8a0 15f15308 Author: Andy Nonaka Date: Thu Aug 19 13:06:12 2021 -0700 Merge pull request #70 from AMReX-FHD/convert_mix_mass Convert mix mass commit 15f1530869292ff3fb948ddbd6d198e9a8224672 Merge: c6e43ed9 1489c8a0 Author: Andy Nonaka Date: Thu Aug 19 13:04:29 2021 -0700 Merge branch 'main' into convert_mix_mass commit 1489c8a0903067b1c006d2849ab7ceb5cff52033 Author: Andy Nonaka Date: Thu Aug 19 12:47:35 2021 -0700 fix an indexing bug in ComputeChiSub don't pass around nspecies when not necessary src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 272ed2e5bdac76e2d157b4cc8ce778b8bb514b67 Merge: 6daf58a7 9abbb47f Author: etpalmer63 Date: Thu Aug 19 11:48:25 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into basic_ci commit c6e43ed973bc9bd746f68df7602bd4f97695fce7 Author: etpalmer63 Date: Thu Aug 19 11:43:31 2021 -0400 Remove deleted file from Make.package. src_multispec/src_F90/Make.package commit 6fc9955b874f9b38e36db35401720e725ae468d6 Author: etpalmer63 Date: Thu Aug 19 11:15:52 2021 -0400 Last Fortran routine in src_F90 removed. src_multispec/multispec_functions_F.H src_multispec/src_F90/compute_mixture_properties.F90 commit c99c60872f424099a1de8549ae3f1c1f8f8f164f Author: etpalmer63 Date: Thu Aug 19 11:08:33 2021 -0400 Changed to match previous logic exactly. Note: Dtherm, H_offdiag, H_diag read from input but have no effect on simulation output. src_multispec/multispec_functions.H commit a015989228ad96e3ea500c2833e7eb8c51da779f Author: etpalmer63 Date: Thu Aug 19 11:01:39 2021 -0400 Testing configuration. src_multispec/multispec_functions.H commit 05751e2c7ecea002c9fdbf7bc83ce0659cee563a Author: etpalmer63 Date: Wed Aug 18 21:58:01 2021 -0400 Current tests not using many of the variables in this function. I will need to pull an old one. src_multispec/multispec_functions.H commit 9abbb47fc2c520b37067494d0cc5c33a78303232 Merge: c5dc88c5 f6f4f263 Author: Andy Nonaka Date: Wed Aug 18 17:58:47 2021 -0700 Merge pull request #67 from AMReX-FHD/convert_LOnsager Convert LOnsager commit f6f4f2631287c56809cb7cef62e9fcfa2c41c00d Merge: eca03099 c5dc88c5 Author: Andy Nonaka Date: Wed Aug 18 17:21:55 2021 -0700 Merge branch 'main' into convert_LOnsager commit c5dc88c5c91f52c4f430613dbf1a7c8f2ba2c308 Author: Andy Nonaka Date: Wed Aug 18 17:16:39 2021 -0700 new regression tests exec/multispec/inputs_regression_cap_2d exec/multispec/inputs_regression_spinodal_2d exec/multispec/inputs_regression_spinodal_3d exec/multispec/inputs_rtil_cap_128V_2d commit 70352e1df5a7046ea92fd0c340a2746f1707729b Merge: 0ba52e5d 3a1d07b0 Author: Andy Nonaka Date: Wed Aug 18 17:14:36 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0ba52e5d1c897d5b40073bf54001557ddf77847e Author: Andy Nonaka Date: Wed Aug 18 17:13:42 2021 -0700 bugfix in gamma computation for multiphase src_multispec/multispec_functions.H commit 3a1d07b0f3451213af2ffe697a4d2d213063bad1 Author: Daniel Ladiges Date: Wed Aug 18 15:56:57 2021 -0700 removed some debugging code exec/immersedIons/main_driver.cpp commit bc934434e6e21f1ee5ff9dd4b23a2cef6d4142da Author: Daniel Ladiges Date: Wed Aug 18 15:46:08 2021 -0700 Fixed another bug in divergence calculation src_particles/particle_functions_K.H commit ce2fd251905df5e212c338f00dbccfb7e0bcc312 Author: Daniel Ladiges Date: Wed Aug 18 14:49:29 2021 -0700 Corrected small error in dry mobility function for 3nm channel src_particles/particle_functions_K.H commit 025e7bb7ba392752427cce69d07409f3bcfb644d Author: etpalmer63 Date: Wed Aug 18 16:42:51 2021 -0400 Remove unused variables. src_multispec/multispec_functions.H commit ca288491bc576a097ff1c4d9b35e787aec8a2ea6 Author: etpalmer63 Date: Wed Aug 18 16:20:59 2021 -0400 Converted mixture_properties_mass, passes defaults now doing additional testing. src_multispec/ComputeMixtureProperties.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H commit b84c1b8aad46b8c0db76b812e86ade475a62a835 Author: Daniel Ladiges Date: Wed Aug 18 12:55:12 2021 -0700 Somehow a line got removed from the Make.package in immersedIons, hence the compile fail on the reg tests exec/immersedIons/Make.package commit c071b7da1e77258373e7fcd3b1fe2bb870bdd1d7 Merge: 05cec088 ca2951ac Author: etpalmer63 Date: Wed Aug 18 14:42:19 2021 -0400 Merge branch 'convert_LOnsager' into convert_mix_mass commit 05cec08823d47de105e5eab6259287d41f6f8a0e Author: etpalmer63 Date: Wed Aug 18 14:39:49 2021 -0400 Getting started porting. src_multispec/ComputeMixtureProperties.cpp src_multispec/multispec_functions.H commit eca03099e86f41928d60a0f173e199a5e34cd89c Author: Andy Nonaka Date: Wed Aug 18 11:23:52 2021 -0700 Update exec/multispec/inputs_rtil_spinodal_charges_2d revert change to inputs file i'm going to set up 2 new regression tests for the spinodal stuff since we are interested in this science problem still exec/multispec/inputs_rtil_spinodal_charges_2d commit ca2951ac9668e5e022b2c499acd090cd110c9865 Author: etpalmer63 Date: Wed Aug 18 13:59:36 2021 -0400 Remove ununsed routine. src_multispec/src_F90/matrix_utilities.F90 commit 6052c484b03eb7a350223d73e1d64b1d08ab81b1 Author: etpalmer63 Date: Wed Aug 18 13:54:49 2021 -0400 Comment out unused functions src_multispec/multispec_functions_F.H commit 9c68ccf1b5e054625fdf56c4afdfaad5672791e5 Author: etpalmer63 Date: Wed Aug 18 13:53:24 2021 -0400 Remove and comment out the unused routines. src_multispec/src_F90/Make.package src_multispec/src_F90/compute_mixture_properties.F90 src_multispec/src_F90/mass_flux_utilities.F90 commit cd5d33b7faac234f49daa591314762438870a2a1 Merge: 68de9dd2 d58cdd99 Author: etpalmer63 Date: Wed Aug 18 13:30:57 2021 -0400 Merge branch 'convert_LOnsager' of https://github.com/AMReX-FHD/FHDeX into convert_LOnsager commit 68de9dd289bb0624f9b67006a2ce566aded96fef Author: etpalmer63 Date: Wed Aug 18 13:27:24 2021 -0400 Comment out unused Fortran. src_multispec/src_F90/mass_flux_utilities.F90 src_multispec/src_F90/matrix_utilities.F90 commit c27f1abcbe85acc3fecc5f120315ef65d0cd2479 Author: etpalmer63 Date: Wed Aug 18 13:03:34 2021 -0400 Abort for case 1&2 in ComputeDBarLocal() -- could not find a test case that used these options & could not verify correctness. src_multispec/multispec_functions.H commit dfe4b58fae21e1f1a5fabb36a76eec52690fef25 Merge: dc46ae8d bceb62e5 Author: Daniel Ladiges Date: Tue Aug 17 13:40:57 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit dc46ae8d2de583972a300282114d2d3be490d49d Author: Daniel Ladiges Date: Tue Aug 17 13:40:35 2021 -0700 Added SSA version of particle inflow exec/DSMC/stats.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit d58cdd99902c53f5c2f5727b5ae3bdce9210be3d Merge: 159c45ba bceb62e5 Author: Andy Nonaka Date: Tue Aug 17 13:23:33 2021 -0700 Merge branch 'main' into convert_LOnsager commit 159c45bab4821d0046b4323742d3f147d9c77168 Merge: e7f1c690 77dcb055 Author: Andy Nonaka Date: Tue Aug 17 13:17:25 2021 -0700 Merge branch 'main' into convert_LOnsager commit bceb62e5e49d2d07616d17c714cdf69dc00e9368 Merge: 77dcb055 9e3a67f0 Author: Andy Nonaka Date: Tue Aug 17 12:45:26 2021 -0700 Merge pull request #69 from AMReX-FHD/convert_MatvecMul Convert matvec mul commit 9e3a67f0d9374152893cf43b3efaa67021fb7166 Author: Andy Nonaka Date: Tue Aug 17 12:42:46 2021 -0700 remove fortran src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/matvec_mul.F90 commit 77dcb0552472db2eb125d6ee61763626095f42a2 Author: Daniel Ladiges Date: Tue Aug 17 12:03:30 2021 -0700 Removed some debugging stuff exec/DSMC/delPlots src_particles/DsmcParticleContainer.cpp commit fd476430e244327f0b115883e300f18bbe2bc406 Merge: 1d51418f bc0ff139 Author: Daniel Ladiges Date: Tue Aug 17 11:31:43 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 1d51418f2043357dfc35db0b0d6dbd85b9394bf0 Author: Daniel Ladiges Date: Tue Aug 17 11:31:22 2021 -0700 Moved input file to subdir exec/DSMC/test_inputs/inputs_conc commit 64ee9488822c861d0fca32b3f45687eae026275d Author: Daniel Ladiges Date: Tue Aug 17 11:30:47 2021 -0700 input file for concentration gradient exec/DSMC/inputs_conc commit f27f33e1adee65bbc7988bb70857cfdfc8a36206 Author: etpalmer63 Date: Tue Aug 17 10:27:34 2021 -0400 Remove call to fortran routine. src_multispec/MatvecMul.cpp commit 6a7fbb1745bccee9a7ca8240c8dce485f64d8aad Author: etpalmer63 Date: Tue Aug 17 10:26:17 2021 -0400 Matmul written in cpp. src_multispec/MatvecMul.cpp commit bc0ff1395ae954c461177d8e1595d7d13cfafdbf Author: Andy Nonaka Date: Mon Aug 16 16:49:48 2021 -0700 comments only src_analysis/StructFact.cpp commit 6dc87736c0fb2dcd46440c86b31b1e47d208a105 Author: Changho Kim Date: Sun Aug 15 00:52:26 2021 -0700 forgot to add exec/compressible/chemistry_inputs_files/run.sh commit 9ad2004bfcafbb0ebfe1032eccb5e25945243770 Merge: 6aab2014 c24cd912 Author: Changho Kim Date: Sun Aug 15 00:42:29 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 6aab20147f40a51b7ba49664349ebcb8f1bd02de Author: Changho Kim Date: Sun Aug 15 00:24:47 2021 -0700 compressible chemistry: corrections due to fluctuating temperature made to rate constants; rate expressions are now in terms of partial pressures exec/compressible/chemistry_inputs_files/inputs_NO2_N2O4_eq_SF exec/compressible/chemistry_inputs_files/params_NO2_N2O4_eq_SF.py exec/compressible/chemistry_inputs_files/params_NO2_N2O4_thermochem.py exec/compressible/chemistry_inputs_files/run.sh src_chemistry/CLE_EM.cpp src_chemistry/CLE_RK3.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H src_chemistry/chemistry_namespace_declarations.H src_compressible/timeStep.cpp commit c24cd912da381f9e19a0de77d16486f1bc07b5ad Author: Daniel Ladiges Date: Thu Aug 12 17:00:21 2021 -0700 parallelised inflow particle generation exec/DSMC/main_driver.cpp exec/DSMC/writePlotFile.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit 4d18c97f96dfe35b671571b073fc39d61a91b97d Author: isriva Date: Thu Aug 12 13:39:36 2021 -0700 setup options to specify rho or T in the reservoirs src_compressible_stag/boundaryStag.cpp commit af364073d7dd3d562f51aafef13ada6009df4d1e Merge: 7a71fbc2 9f7addd0 Author: Daniel Ladiges Date: Thu Aug 12 13:33:07 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 7a71fbc26abed15d6d0fcbf684ab9fa3918aa360 Author: Daniel Ladiges Date: Thu Aug 12 13:25:17 2021 -0700 Integrated/rearranged parts from main and DSMCgranular branches to make complete dsmc in main exec/DSMC/Checkpoint.H exec/DSMC/Checkpoint.cpp exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/LocalFunctions.H exec/DSMC/delPlots exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/updateTimeStep.cpp exec/DSMC/writePlotFile.cpp exec/immersedIons/Make.package src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 9f7addd0229cbca757883b30286746509c6c17b2 Author: Andy Nonaka Date: Thu Aug 12 12:51:00 2021 -0700 renname variables to make future GPU conversion easier src_gmres/StagApplyOp.cpp commit e7a30498cc8d57e4ad20fdcb5118aba3dcad2c2e Author: isriva Date: Thu Aug 12 09:42:44 2021 -0700 fixed bug where reservoir pressure/temp was being set everywhere outside the reservoir as well src_compressible_stag/boundaryStag.cpp commit e7f1c690f0b8490665c99b4bed4494876728a09c Author: Andy Nonaka Date: Thu Aug 12 09:08:55 2021 -0700 remote lapack matmul to make conversion to C++ easier src_multispec/src_F90/matvec_mul.F90 commit 806f0ec9d79c43fe0aa82d91bec5c7031965fb33 Author: Andy Nonaka Date: Thu Aug 12 08:42:08 2021 -0700 get compiling/running on the GPU again src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H commit c04fb3f304073a9014ce0db88994e04837ac7f10 Merge: f7a1ec59 78e9b4f1 Author: Andy Nonaka Date: Thu Aug 12 08:09:21 2021 -0700 Merge branch 'main' into convert_LOnsager commit 6daf58a718ed12e042ea051f47a29ee49278f4e8 Author: etpalmer63 Date: Wed Aug 11 17:52:18 2021 -0400 worked! --now clean up .github/workflows/linux.yml commit 5e3df70ebd541ac723ba354c195f4493ea236cb9 Author: etpalmer63 Date: Wed Aug 11 17:46:36 2021 -0400 try try again .github/workflows/dependencies/dependencies.sh commit 176128f9bddf6095d08df402202a34a07fb77fe2 Author: etpalmer63 Date: Wed Aug 11 17:39:21 2021 -0400 try try again .github/workflows/linux.yml commit ed8f7660d3fb936bae069cf8fbf25397ee92f600 Author: etpalmer63 Date: Wed Aug 11 17:35:43 2021 -0400 try try again .github/workflows/dependencies/dependencies.sh commit e1fc39218b883ac1cd2ce0954946fad6dbcb6870 Author: etpalmer63 Date: Wed Aug 11 17:33:37 2021 -0400 try try again .github/workflows/dependencies/dependencies.sh commit 4bfcd81dde4672409a5b59877d9d93412d17946e Author: etpalmer63 Date: Wed Aug 11 17:31:24 2021 -0400 try try again .github/workflows/dependencies/dependencies.sh commit d423a4b2ea96e2a697210177ea66e7136bc81865 Author: etpalmer63 Date: Wed Aug 11 17:30:04 2021 -0400 whoohoo progress! .github/workflows/dependencies/dependencies.sh commit 870cbf959f33ec74f5a01f74a9df167645ae92b0 Author: etpalmer63 Date: Wed Aug 11 17:26:03 2021 -0400 try try again .github/workflows/linux.yml commit 6539617d86ce4080b92102cf03db2c9dfc284e90 Merge: 4dcedb3e 78e9b4f1 Author: isriva Date: Wed Aug 11 14:23:30 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit 9b1725690515aefb24d687f260cd484ae30fd5a9 Author: etpalmer63 Date: Wed Aug 11 17:22:10 2021 -0400 try try again .github/workflows/linux.yml commit ed271cfa59e0a39fc5f56e7a8f4234ca769e48e0 Author: etpalmer63 Date: Wed Aug 11 17:20:06 2021 -0400 try try again .github/workflows/linux.yml commit 80385fddb42f72cb7a665ee633ca43fe06576ff0 Author: etpalmer63 Date: Wed Aug 11 17:18:57 2021 -0400 try try again .github/workflows/linux.yml commit 4dcedb3e7a8a2161892ed01cf4641a600f3640a8 Author: isriva Date: Wed Aug 11 14:17:29 2021 -0700 compute Xk from Yk in reservoirs src_compressible_stag/boundaryStag.cpp commit cc3b58468c8e36331adc5d7fba9fe4fb8fb0445f Author: etpalmer63 Date: Wed Aug 11 17:16:34 2021 -0400 try try again .github/workflows/linux.yml commit b8cf8a18592ce16bfb60d4a83cd26fa30bd75524 Author: etpalmer63 Date: Wed Aug 11 17:13:57 2021 -0400 try try again .github/workflows/linux.yml commit 6c873bdf356cca6fb35d0e93672d5b3635586a78 Author: etpalmer63 Date: Wed Aug 11 17:11:16 2021 -0400 try try again .github/workflows/linux.yml commit 8e75b5debc6b2ebf91f66dcc8725a41f0cba9312 Author: etpalmer63 Date: Wed Aug 11 17:10:19 2021 -0400 try try again .github/workflows/linux.yml commit 6f8243c8ae2160a02775bfa442c13c6c7ffb14e2 Author: etpalmer63 Date: Wed Aug 11 17:09:13 2021 -0400 try try again .github/workflows/linux.yml commit f85fbf45a2ac1b6870400da31c01694be6d34315 Author: etpalmer63 Date: Wed Aug 11 17:01:29 2021 -0400 try try again .github/workflows/linux.yml commit 6114481d2707a67c159c0a4c02ae613ab9910352 Author: etpalmer63 Date: Wed Aug 11 17:00:56 2021 -0400 try try again .github/workflows/linux.yml commit f0972f8106f9162c153cb6ed0ad008d2859edf67 Author: etpalmer63 Date: Wed Aug 11 16:54:59 2021 -0400 try try again .github/workflows/linux.yml commit 427ce9b362e5aee6bacae6a08324e9bf0d470337 Author: etpalmer63 Date: Wed Aug 11 16:53:09 2021 -0400 try try again .github/workflows/linux.yml commit aeda312a687a525d4299aef5c8c0949c0aef4a27 Author: etpalmer63 Date: Wed Aug 11 16:48:42 2021 -0400 try try again 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15:53:38 2021 -0400 try cloning amrex .github/workflows/linux.yml commit f6c2d6292a0d2b01c5cbcd4918691228aadae4fe Author: etpalmer63 Date: Wed Aug 11 15:52:48 2021 -0400 try cloning amrex .github/workflows/linux.yml commit f9d69d42281d9b2b73c6f4eef95817936f1cfb8c Author: etpalmer63 Date: Wed Aug 11 15:49:07 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 2c605c06f3fd237b973a284360321f30aa9cb728 Author: etpalmer63 Date: Wed Aug 11 15:47:35 2021 -0400 try cloning amrex .github/workflows/linux.yml commit de976d0c66cf8eb9f63943ce6f00518cf6940973 Author: etpalmer63 Date: Wed Aug 11 15:46:24 2021 -0400 try cloning amrex .github/workflows/linux.yml commit b52f3af64294c679708efbbc2986c4c8593ee208 Author: etpalmer63 Date: Wed Aug 11 15:42:03 2021 -0400 try cloning amrex .github/workflows/linux.yml commit cac059479e5c4fdc8319db4e4fd2b2aecc0a73b9 Author: etpalmer63 Date: Wed Aug 11 15:39:17 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 6a25207cf90831770707a74380c1cd080828d1b3 Author: etpalmer63 Date: Wed Aug 11 15:37:54 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 941713ae20e7e8f99e003a4bcc5046250b53f68b Author: etpalmer63 Date: Wed Aug 11 15:25:26 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 3e1c9f1460dc2fab8b0722784ce25f4ea99f27be Author: etpalmer63 Date: Wed Aug 11 15:23:33 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 43662cd4655f93910d260790110ff1471f6d0462 Author: etpalmer63 Date: Wed Aug 11 15:20:27 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 9801f6bd7bb49dddb2b9dcd97e8f14f96929af1c Author: etpalmer63 Date: Wed Aug 11 15:18:25 2021 -0400 try cloning amrex .github/workflows/linux.yml commit 0a6bd98f681b43f67cd0eaa68ba68a5153767805 Author: etpalmer63 Date: Wed Aug 11 15:08:55 2021 -0400 basic compile multispec .github/workflows/cuda.disabled .github/workflows/docs.disabled .github/workflows/hip.disabled .github/workflows/intel.disabled 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f81c9ade80bd6d86685e67eaa5615cceb34ff643 Author: Erik Date: Wed Aug 11 14:49:09 2021 -0400 Create main.yml .github/workflows/main.yml commit 0912f8af568ef79f1a593e3111bdf451e6f67e4d Author: etpalmer63 Date: Wed Aug 11 14:47:02 2021 -0400 CI testing tempfile.test commit 5c211833bc41709d9f53158ce354b53732a46c87 Author: etpalmer63 Date: Wed Aug 11 14:43:54 2021 -0400 CI first test .github/dependencies/dependencies.sh .github/dependencies/dependencies_clang6.sh .github/dependencies/dependencies_dpcpp.sh .github/dependencies/dependencies_gcc10.sh .github/dependencies/dependencies_hip.sh .github/dependencies/dependencies_mac.sh .github/dependencies/dependencies_nofortran.sh .github/dependencies/dependencies_nvcc11.sh .github/dependencies/dependencies_nvcc9.sh .github/dependencies/documentation.sh .github/style.yml .github/style/check_tabs.sh .github/style/check_trailing_whitespaces.sh commit f7a1ec5906fc509c722006a5e7c87bfb0e6e9d51 Author: etpalmer63 Date: Wed Aug 11 14:11:50 2021 -0400 Finding a change in values for RhoN and rhotot_in after first plotfile in comparison with fortran code. src_multispec/multispec_functions.H commit 78e9b4f1780b3c16406204fca5574e3d0bc60d94 Merge: 6d6551ca b32be157 Author: Daniel Ladiges Date: Wed Aug 11 00:37:48 2021 -0700 Merge pull request #65 from AMReX-FHD/merge_granular Merge granular commit 76ea199781386ccfc188ed62bd25f0b22b8dea49 Author: etpalmer63 Date: Tue Aug 10 16:13:19 2021 -0400 edit input file for shorter testing time exec/multispec/inputs_rtil_spinodal_charges_2d commit 92fd3dbf3fcaf9f8efbd0f346e965f686638e49e Author: etpalmer63 Date: Tue Aug 10 16:10:56 2021 -0400 only a few places left to test. src_multispec/multispec_functions.H commit 6d6551ca519ab70eb96f4fb88a7373f23451cd75 Author: Daniel Ladiges Date: Tue Aug 10 12:58:03 2021 -0700 Fixed incorrect merges in discos and compressible. This should fix regression errors src_compressible/writePlotFile.cpp src_geometry/paramPlane.cpp src_particles/FhdParticleContainer.cpp commit d408ec4a4709c889cc3c38e4d5a24ae45ff86bbe Author: Daniel Ladiges Date: Mon Aug 9 18:33:22 2021 -0700 After merge of merge_granular into main: Fixed a couple of typos stopping compilation of discos added 'dsmc_boundary' input into common namespace to switch dsmc boundary conditions 1=on/0=off. Default behaviour preserves discos behaviour exec/immersedIons/Checkpoint.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit c9966f6e28ed492f896a76377a38e76bd46fd639 Merge: 8984052c 08b588eb Author: Daniel Ladiges Date: Mon Aug 9 17:27:03 2021 -0700 Merge branch 'merge_granular' into main commit 08b588eba9966068860f05c85a77e2b497aa6288 Author: Daniel Ladiges Date: Mon Aug 9 17:15:23 2021 -0700 Fixed bug when setting up more than 6 paramPlanes exec/DSMC/main_driver.cpp commit 8984052cd489ae5e8ca5b07453dfb33dac8c4dd9 Author: Daniel Ladiges Date: Mon Aug 9 17:04:22 2021 -0700 updated paramPlane generator exec/DSMC/Make.package exec/DSMC/paramPlane.ipynb commit 091bf9f9c68b1070b49306babb31b1590c61bf57 Merge: df939662 c65952f2 Author: Daniel Ladiges Date: Mon Aug 9 16:31:58 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit df9396626c3e6e98af74736d034bbe73856be168 Author: Daniel Ladiges Date: Mon Aug 9 16:31:26 2021 -0700 merging changes on gigan and kumonga exec/DSMC/Make.package src_particles/DsmcParticleContainer.cpp commit c65952f25088a092b37c24d3d6038a10ac81e92f Author: drladiges Date: Mon Aug 9 16:30:26 2021 -0700 updated paramplane generator exec/DSMC/paramPlane.ipynb exec/DSMC/paramplanes.dat exec/DSMC/particleGen.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp tools/notebooks/plotting.ipynb commit d50b655378e7ab44b0a195ca5672e7430c5f1d06 Merge: 4499da38 1e324db1 Author: drladiges Date: Mon Aug 9 14:48:53 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 1e324db173c14a2fd3d33c3f85e98129c92ff151 Author: Andy Nonaka Date: Mon Aug 9 10:48:30 2021 -0700 fix AMREX_HOME exec/immersedIons/GNUmakefile commit ce396c3d11f23d98048555bd85c6a22a7531cfd3 Author: Andy Nonaka Date: Mon Aug 9 08:53:21 2021 -0700 use twoks = 2*F::ks; instead of [2*ks] so this compiles on cori with the default gcc src_particles/particle_functions_K.H commit 738f2bef08ee878debbbb2a286e4c8d5ab98c79e Author: isriva Date: Mon Aug 9 07:59:52 2021 -0700 fixed some compilation errors src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/timeStepStag.cpp commit 8124b899bf42dc9ef89ce1e4ff44722078d7f4d1 Author: isriva Date: Sun Aug 8 23:16:27 2021 -0700 stochastic momentum at the reservoir src_compressible_stag/boundaryStag.cpp commit 3448137a58bcc93a5c2aa420101f238a47b160a2 Author: isriva Date: Sun Aug 8 23:10:51 2021 -0700 small fix for slip BC src_compressible_stag/boundaryStag.cpp commit b39ec8ad91b25af7d02fa96631e77129ddeb0b23 Merge: a0fee0d7 ef2ff6a3 Author: isriva Date: Sun Aug 8 23:09:18 2021 -0700 Merge remote-tracking branch 'origin/main' into compressible_reservoir commit a0fee0d7efaa98851466eeb26df52299cad9fa08 Author: isriva Date: Sun Aug 8 22:58:32 2021 -0700 first pass at resservoir BCs exec/compressible_stag/main_driver.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit ef2ff6a3c5d4969d06b2c80ab848ce49e19ad158 Author: isriva Date: Sun Aug 8 21:39:47 2021 -0700 fixed a bug in compressible BC src_compressible_stag/boundaryStag.cpp commit b32be15789a01c8234b0fb9e8729f5b0c0d9fae5 Author: andrew Date: Sun Aug 8 15:12:04 2021 -0400 ADD: Boudnaries now accept both mass and number density from input DEBUG: Tested input typ (n0, rho0, total0) and agrees for one species - also tested for two idential species and works Tested Resevoir boundaries for 1 and 2 idential species - Aborts tested and works - Tested case where Yk/Xk do not add to 1 - Tested both rho and n defined at boundaries exec/DSMC_granular/input_test exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/test_inputs/input_test src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit 1fc482496bccaada09d811ba60beb20a5abf30ed Author: andrew Date: Sun Aug 8 11:22:44 2021 -0400 FIX: Number densities (n0) in particle container are now the real number densities DensityLeft and Right are now the real number densities - Corrected bug with neff - Should be consistent with Source now src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit 4d23badb1472728455c2ad34d569bfdafb1da156 Merge: 543e847a c65952f2 Author: andrew Date: Sat Aug 7 19:37:47 2021 -0400 Merge branch 'main' into merge_granular commit 543e847a8dc69b0b66a66853d328147a8f63827f Author: andrew Date: Sat Aug 7 19:18:48 2021 -0400 DSMC Examples exec/DSMC/Checkpoint.H exec/DSMC/Checkpoint.cpp exec/DSMC/DsmcCollide.cpp exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/WritePlotFile.cpp exec/DSMC/ex_main_driver.cpp exec/DSMC/externalF.cpp exec/DSMC/globalVars.cpp exec/DSMC/inputs_template exec/DSMC/inputs_test exec/DSMC/main_DSMC_driver.cpp exec/DSMC/main_driver.cpp exec/DSMC/paramPlane.ipynb exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat exec/DSMC/particleGen.cpp exec/DSMC/stats.cpp exec/DSMC/test_inputs/input_periodic_eq exec/DSMC/test_inputs/input_test exec/DSMC/test_inputs/input_therm exec/DSMC/updateTimeStep.cpp exec/DSMC/writePlotFile.cpp exec/DSMC_granular/ex_main_driver.cpp exec/DSMC_granular/main_DSMC_driver.cpp exec/DSMC_granular/stats_part.cpp commit d61ca8f06fe16319ec9ad0082961d03386d6f596 Merge: c69db1cf 1e324db1 Author: andrew Date: Sat Aug 7 17:41:32 2021 -0400 Merge branch 'main' into merge_granular commit c69db1cfb4f171e58b69899193fbac3d0a75f55b Merge: 62bb29e2 f1cc5b58 Author: andrew Date: Sat Aug 7 09:09:56 2021 -0400 Merge branch 'main' into merge_granular Compiles commit 62bb29e219f6f59b3eb1b477625bd6fc77e5872e Author: andrew Date: Sat Aug 7 08:53:00 2021 -0400 Preparing for merge exec/DSMC_granular/DsmcCollide.cpp exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/particleGen.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit f1cc5b583a69af3f09189cbd8ba508bd72295f28 Author: Matteo Polimeno Date: Fri Aug 6 14:58:40 2021 -0700 CLE_RK3 -> CLE src_compressible/timeStep.cpp commit 55717415f289ff39c0e8dc46a47806d832661616 Author: Matteo Polimeno Date: Fri Aug 6 14:57:56 2021 -0700 CLE_2 -> CLE src_chemistry/CLE_EM.cpp src_chemistry/CLE_RK3.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 922675778be559f44547154952696bf9a0a6e9e8 Author: Matteo Polimeno Date: Fri Aug 6 13:59:20 2021 -0700 exec/chemistry_testing: updated calls to relevant functions in src_chemistry exec/chemistry_testing/main.cpp commit cc0b563eb6c42d05c2160804b1fe13c489dffada Author: Matteo Polimeno Date: Fri Aug 6 13:58:06 2021 -0700 src_chemistry/chemistry_functions.cpp: compute_chemistry_source -> compute_chemistry_source_CLE_1; compute_chemistry_source_CLE_RK3 -> compute_chemistry_source_CLE_2 src_chemistry/CLE_EM.cpp src_chemistry/CLE_RK3.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 1289e8cc4f8e9dabd01c9d69bb4ed9165c3861f0 Author: Matteo Polimeno Date: Fri Aug 6 13:02:49 2021 -0700 src_chemistry/CLE_EM.cpp white noise field passed to function for chemistry_source src_chemistry/CLE_EM.cpp commit d2664ad4c7c4085743a80449cf850e9f2aee556e Author: Matteo Polimeno Date: Fri Aug 6 12:34:20 2021 -0700 exec/chemistry_testing: added prob_type=4 for CLE EM exec/chemistry_testing/inputs_NO2_N2O4 exec/chemistry_testing/main.cpp commit a4e2e8df5da1f259cff4521962749249ba503c76 Author: Matteo Polimeno Date: Fri Aug 6 12:32:40 2021 -0700 src_chemistry: chemistry-only CLE EM implemented src_chemistry/CLE_EM.cpp src_chemistry/Make.package src_chemistry/chemistry_functions.H commit 6021bcd72d225a9d336b745aa0eaea8a82e9b891 Author: Changho Kim Date: Fri Aug 6 04:30:08 2021 -0700 exec/chemistry_testing: chemistry-only CLE RK3 implemented exec/chemistry_testing/GNUmakefile exec/chemistry_testing/inputs_NO2_N2O4 exec/chemistry_testing/main.cpp src_chemistry/CLE_RK3.cpp src_chemistry/Make.package src_chemistry/chemistry_functions.H commit 4ef2b07a20da80c13a71458ad73c880be7b77b3a Author: andrew Date: Thu Aug 5 21:38:26 2021 -0400 ADD: Added additional long range correlations to stats exec/DSMC_granular/stats.cpp commit 5afef24c4be51eade55678f3910de60aa42b3dcd Merge: 6f5326f5 66b08af4 Author: Andy Nonaka Date: Thu Aug 5 14:49:30 2021 -0700 Merge pull request #62 from AMReX-FHD/compressible_CLE_RK3 compressible_CLE_RK3: compute_chemistry_source_CLE_RK3 commit 66b08af4ddd52f7dda33be34e3b85b2e64e860f7 Author: Changho Kim Date: Thu Aug 5 09:49:31 2021 -0700 compressible_CLE_RK3: compute_chemistry_source_CLE_RK3 exec/compressible/main_driver.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_compressible/compressible_functions.H src_compressible/timeStep.cpp commit 7f55725cd675b96480dc9d3d91796581dc6d17bd Merge: 6b90d9cd 18f74f2b Author: Jackie Yao Date: Wed Aug 4 22:11:07 2021 -0700 amrex path fix commit 6b90d9cd910df122de74030108a1dc87f4983d35 Author: Jackie Yao Date: Wed Aug 4 22:10:06 2021 -0700 fix amrex path in exec/DSMC/GNUmakefile exec/DSMC/GNUmakefile commit 4499da383ff7a8d9775e9cbcde2bcf14933a1ab4 Merge: 1841ab47 6f5326f5 Author: drladiges Date: Wed Aug 4 21:55:37 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 18f74f2bda25be9024a489329809aed4970e2ede Merge: e4bcd2af 6f5326f5 Author: jackieyao0114 Date: Wed Aug 4 21:03:06 2021 -0700 fixed conflitc commit e4bcd2afce821abe0085aff7eff7a6ba50fd3d72 Merge: a4268a5a 400686e4 Author: jackieyao0114 Date: Wed Aug 4 21:00:52 2021 -0700 Merge branch 'main' of https://github.com/jackieyao0114/FHDeX into main commit a4268a5aba16a4900bcb72dfd1fd0410020942cd Author: jackieyao0114 Date: Wed Aug 4 21:00:36 2021 -0700 update GNUmakefile in DSMC for cori compilation exec/DSMC/GNUmakefile commit 6f5326f5fb7ced1fb8f9abe135bac214864cbff7 Author: Changho Kim Date: Wed Aug 4 15:41:58 2021 -0700 exec/chemistry_testing/compressible/inputs_eq_SF, params_SF.py: updated exec/chemistry_testing/compressible/inputs_eq_SF exec/chemistry_testing/compressible/params_SF.py commit 1841ab477b91f27153b13ae415be697c4cceaca1 Merge: b2ebe39e 7d30b799 Author: drladiges Date: Wed Aug 4 11:37:11 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b2ebe39e23371f09dbbf4da98ea1bb129d9ebcc9 Author: drladiges Date: Wed Aug 4 11:36:20 2021 -0700 Fiddled with paramPlane input while investigating problem for Jackie src_geometry/paramPlane.cpp commit 7d30b79904f7dc261dce37a07cf2295e230e7344 Merge: d714b29d d84d8b70 Author: Andy Nonaka Date: Wed Aug 4 11:05:19 2021 -0700 Merge pull request #59 from AMReX-FHD/quasi1D_compressible Staggered Compressible Updates: 1D and GPU commit d84d8b700d861a064c0c8daaa70c0cf6f16ac53a Merge: 1696f59b d714b29d Author: Andy Nonaka Date: Wed Aug 4 09:39:23 2021 -0700 Merge branch 'main' into quasi1D_compressible commit 1696f59b55404203ab234271c103810142d22cbd Merge: 883f7b0a d7542d37 Author: Andy Nonaka Date: Wed Aug 4 09:39:01 2021 -0700 Merge branch 'main' into quasi1D_compressible commit d714b29d7bb8d8f0e5a41619efd9d54feb88ef09 Merge: d7542d37 68bede77 Author: Andy Nonaka Date: Wed Aug 4 09:37:45 2021 -0700 Merge pull request #60 from AMReX-FHD/debug_main Debug main commit d7542d37b3a70ba0e56124ea7d87f16736c07941 Author: Andy Nonaka Date: Wed Aug 4 09:30:38 2021 -0700 cleanup unused stuff exec/lib_hydro/cmake/CMakeLists.txt src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H commit 883f7b0a9fd93942e653cf72e550c6f77b7cf163 Merge: f59d6e48 c9e3de4b Author: Andy Nonaka Date: Tue Aug 3 22:31:45 2021 -0700 Merge branch 'main' into quasi1D_compressible commit c9e3de4ba63a395e6ae98750bd0221462441b3a6 Merge: 82417a12 40652a62 Author: Andy Nonaka Date: Tue Aug 3 22:31:12 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 82417a12a46a7b8f7e0aba2c5852c00c6e3294bc Author: Andy Nonaka Date: Tue Aug 3 22:28:56 2021 -0700 fix segfault that can occur when problem is not perfectly load balanced (often happens for flattened multifabs) src_analysis/StructFact.H src_analysis/StructFact.cpp commit f59d6e4892494a7c144f62d7f7df119c465491de Author: Andy Nonaka Date: Tue Aug 3 22:28:56 2021 -0700 fix segfault that can occur when problem is not perfectly load balanced (often happens for flattened multifabs) src_analysis/StructFact.H src_analysis/StructFact.cpp commit 40652a62ccf6e94f6d67749e4ab6abf6afd832e0 Merge: 5fc61615 0b210dbc Author: Daniel Ladiges Date: Tue Aug 3 18:09:10 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 5fc6161582fe45952ebe6cfc0927dabfdaaa768a Author: Daniel Ladiges Date: Tue Aug 3 18:08:18 2021 -0700 Fixed bug in setting number of paramPlanes when reading from input file. I think this is what was crashing the reg tests exec/immersedIons/main_driver.cpp src_geometry/paramPlane.cpp commit 2233236ebe7aa07aa739b62ecbae1fbbb6e8da9d Author: isriva Date: Tue Aug 3 15:51:45 2021 -0700 set correct flag to ParallelReduce sumToLine stuff across MPI procs src_compressible_stag/statsStag.cpp commit d58d4c35f05a473abfe404720c42ea8858299eb1 Author: Andy Nonaka Date: Tue Aug 3 14:56:32 2021 -0700 remove sumToLine and use amrex version src_common/ComputeAverages.cpp src_common/common_functions.H commit da227cafaec114a1a344d76d23996fd8ec58834c Merge: e1c5b126 0b210dbc Author: Andy Nonaka Date: Tue Aug 3 14:37:21 2021 -0700 Merge branch 'main' into quasi1D_compressible commit 0b210dbce0f1b4aafe1041c229f08936acca034b Author: Andy Nonaka Date: Tue Aug 3 14:36:46 2021 -0700 get this compiling again exec/compressible_stag/main_driver.cpp commit 485190d00db1981fa9af36a3e55ceb4ff9855a60 Author: Andy Nonaka Date: Tue Aug 3 14:30:03 2021 -0700 add in src_chemistry to this builds again exec/compressible_stag/GNUmakefile commit 1f9abaf8f58ac0f16b21bcfdcaa9c3032785ba79 Author: Andy Nonaka Date: Tue Aug 3 14:19:13 2021 -0700 get compiling again exec/compressible_mui/main_driver.cpp commit 4d548d4294c80db15a1f4f34df0708608279075d Author: Andy Nonaka Date: Tue Aug 3 14:17:27 2021 -0700 sync compressible and compressibl_mui main_driver's exec/compressible/main_driver.cpp exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp commit 626481c921c7246ff96c5f02b873711107eabec8 Merge: 2eb4acae 494f22bc Author: Andy Nonaka Date: Tue Aug 3 14:09:49 2021 -0700 Merge pull request #57 from AMReX-FHD/compressible_mui Compressible mui commit 494f22bc4b3171796ff9f11e4ec83e453c192db1 Merge: a3395061 2eb4acae Author: Andy Nonaka Date: Tue Aug 3 14:06:26 2021 -0700 Merge branch 'main' into compressible_mui commit 2eb4acae535f95f474802177d91b4b3b76dbc249 Author: Andy Nonaka Date: Tue Aug 3 14:06:09 2021 -0700 eliminate fft_type exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit a3395061433bc45da528e371135b0a7882d48908 Merge: ba1d1f03 d786c4ea Author: Andy Nonaka Date: Tue Aug 3 13:54:45 2021 -0700 Merge branch 'main' into compressible_mui commit e1c5b12613b530c8073b2a759f9aa111e3270758 Merge: 6408b439 d786c4ea Author: isriva Date: Tue Aug 3 10:29:39 2021 -0700 Merge remote-tracking branch 'origin/main' into quasi1D_compressible commit 3417712bb4f1a219e1a5803786e2465e8084adf2 Author: etpalmer63 Date: Mon Aug 2 21:53:18 2021 -0400 Sections that need more testing are noted with 'NOTE'. Remaining code tested and passes. src_multispec/ComputeMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit d840634a7ec8afbaa31b062f2baa96967a2f50f5 Author: etpalmer63 Date: Mon Aug 2 14:52:07 2021 -0400 zeta_by_Temp -- tested and matching, but sometimes all 0 or 1s src_multispec/ComputeMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 50ea527d401326ef54b20509e3ff47e9ae02ef87 Author: etpalmer63 Date: Mon Aug 2 14:21:01 2021 -0400 another error found. Now passes all regression tests! src_multispec/multispec_functions.H commit c11c69418b5025111e003f5b93c615f23c5adbe8 Author: etpalmer63 Date: Mon Aug 2 12:19:42 2021 -0400 found errors, Array2D always need &. DetBubble tests pass, Equil tests fail src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit f95271275d22de15aa760b5d29a259d02cce1a79 Merge: 8dfc76d3 8950d1aa Author: drladiges Date: Sun Aug 1 17:00:31 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit d786c4ea62b1ab3c01614ec6b2160bab086f7042 Merge: b79b62aa 8950d1aa Author: Daniel Ladiges Date: Sun Aug 1 16:47:07 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit b79b62aab4023cb3245624401eb7b2d732d741fe Author: Daniel Ladiges Date: Sun Aug 1 16:46:52 2021 -0700 testing ssh keys for pushing src_particles/FhdParticleContainer.cpp commit 8dfc76d305b4c4e1ca24800cb817c1555eb882c2 Author: drladiges Date: Sun Aug 1 16:42:15 2021 -0700 updated post processing notebook tools/notebooks/plotting.ipynb commit 19109172042a6a7cfe0a6b4c6851fc09d45dd504 Author: etpalmer63 Date: Fri Jul 30 22:08:38 2021 -0400 Isolated an issue with ComputeChi in SqrtLOnsager src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/mass_flux_utilities.F90 commit 8950d1aab8ea76c42b1571056bc58da5009c44e8 Merge: 403a4215 b7fd49fe Author: Galen Wang Date: Fri Jul 30 18:12:08 2021 -0700 Merge branch 'main' into gpu_discos commit b7fd49fe1e6d4a308a9f0cabf4664dcade69ed12 Merge: 87cf1188 86202a27 Author: Matteo Polimeno <40783656+mpolimeno@users.noreply.github.com> Date: Fri Jul 30 16:03:40 2021 -0700 Merge pull request #58 from AMReX-FHD/gpu_chemistry Gpu chemistry commit 86202a276fde9490321bb68a82de986b5a59f071 Merge: b7427ad9 12aabece Author: Andy Nonaka Date: Fri Jul 30 14:59:26 2021 -0700 Merge branch 'compressible_chemistry' into gpu_chemistry commit 12aabece0aec6a68751272d3512e30fc17b5160f Merge: b2a4e4e5 87cf1188 Author: Andy Nonaka Date: Fri Jul 30 14:59:16 2021 -0700 Merge branch 'main' into compressible_chemistry commit b7427ad92d931b7c4f0ac66681ecc985d2ac4dbf Author: Andy Nonaka Date: Fri Jul 30 14:53:21 2021 -0700 formatting only src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 9f69b71639a806be84b7dddcede5432cdee663d4 Author: Andy Nonaka Date: Fri Jul 30 14:49:23 2021 -0700 remove commented code src_chemistry/chemistry_namespace_declarations.H commit 2204dfffeb6bb256b952ea4ebd3d9be100d1f322 Author: Andy Nonaka Date: Fri Jul 30 14:48:06 2021 -0700 Update exec/chemistry_testing/GNUmakefile make default USE_CUDA=FALSE exec/chemistry_testing/GNUmakefile commit 01abf9cf9a22676c3ffc31abbd61dc6593a85929 Author: Matteo Polimeno Date: Fri Jul 30 12:32:36 2021 -0700 update of main.cpp according to gpu-compliance requirements exec/chemistry_testing/main.cpp commit ce171f37c8f88c2fb1dd96aa5d1b7a67dca6669e Author: Matteo Polimeno Date: Fri Jul 30 12:30:29 2021 -0700 gpu-compliant implementation src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 0926bf84c8058d45bd391954feb242aa5e04afae Author: etpalmer63 Date: Fri Jul 30 10:57:05 2021 -0400 Compiles but fails some regression tests. Let the testing begin! src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/mass_flux_utilities.F90 commit 68bede778ef59970c1a4089aa28319f3ca3335b1 Author: andrew Date: Fri Jul 30 06:56:39 2021 -0400 FIX: Removed old lines src_particles/DsmcParticleContainer.cpp commit 40fa02d94762f50731ac71970c7a2a2b4efc4b09 Author: andrew Date: Fri Jul 30 06:54:01 2021 -0400 FIX: Replaced spaces with tabs for ease of reading Removed some old debugging lines Removed unused boundaries exec/DSMC/GNUmakefile exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC_granular/DsmcCollide.cpp exec/DSMC_granular/particleGen.cpp exec/DSMC_granular/stats.cpp exec/DSMC_granular/test_inputs/input_test src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 9d800833c961f3d6b1f41b575bc3b19ae88c1933 Author: andrew Date: Fri Jul 30 03:46:37 2021 -0400 FIX: - Small bug fix for DSMC for Gpuarrays src_particles/DsmcParticleContainer.cpp commit 2d923d84400d7c91e08329c580a273d7e311bd89 Author: andrew Date: Fri Jul 30 02:58:23 2021 -0400 Debugging exec/DSMC_granular/GNUmakefile exec/DSMC_granular/main_driver.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 71700300b37086fe71af6795b94b227a07c4f746 Merge: 30e1b9ea 40652a62 Author: andrew Date: Fri Jul 30 02:12:26 2021 -0400 Merge branch 'main' into DSMCGran commit 30e1b9ea5776201486828a10948734ff38055f1d Author: andrew Date: Fri Jul 30 02:03:41 2021 -0400 Cleaning up files to merge with main exec/DSMC_ContinuousPSD/00/input_test exec/DSMC_ContinuousPSD/01/input_test exec/DSMC_ContinuousPSD/02/input_test exec/DSMC_ContinuousPSD/03/input_test exec/DSMC_ContinuousPSD/Checkpoint.H exec/DSMC_ContinuousPSD/Checkpoint.cpp exec/DSMC_ContinuousPSD/DsmcCollide.cpp exec/DSMC_ContinuousPSD/GNUmakefile exec/DSMC_ContinuousPSD/Make.package exec/DSMC_ContinuousPSD/input_test exec/DSMC_ContinuousPSD/main_driver.cpp exec/DSMC_ContinuousPSD/particleGen.cpp exec/DSMC_ContinuousPSD/stats.cpp exec/DSMC_ContinuousPSD/writePlotFile.cpp exec/DSMC_granular/Checkpoint.H exec/DSMC_granular/Checkpoint.cpp exec/DSMC_granular/DsmcCollide.cpp exec/DSMC_granular/GNUmakefile exec/DSMC_granular/INS_functions.H exec/DSMC_granular/Make.package exec/DSMC_granular/delPlots exec/DSMC_granular/externalF.cpp exec/DSMC_granular/globalVars.cpp exec/DSMC_granular/input_test exec/DSMC_granular/main_driver.cpp exec/DSMC_granular/paramPlane.nb exec/DSMC_granular/particleGen.cpp exec/DSMC_granular/stats.cpp exec/DSMC_granular/stats_part.cpp exec/DSMC_granular/test_inputs/input_periodic_eq exec/DSMC_granular/test_inputs/input_therm exec/DSMC_granular/updateTimeStep.cpp exec/DSMC_granular/writePlotFile.cpp exec/DSMCtest/INS_functions.H exec/DSMCtest/alpha0_95/input_therm_0_95 exec/DSMCtest/alpha0_99/input_therm_0_99 exec/DSMCtest/alpha0_99_zero/input_therm_0_99_zero exec/DSMCtest/conc/input_conc exec/DSMCtest/delPlots exec/DSMCtest/mixed/input_mixed exec/DSMCtest/multi_eq/inputs_eq_multi exec/DSMCtest/paramPlane.nb exec/DSMCtest/periodic/input_periodic exec/DSMCtest/thermgrad/input_therm_long exec/DSMCtest/zeroconcgrad/input_con_zero_grad exec/DSMCtest/zerothermgrad/input_therm_zero_grad src_geometry/paramplane_functions_K.H commit d05403672dd782a8b08f518efcaf900649105171 Author: etpalmer63 Date: Thu Jul 29 17:58:59 2021 -0400 almost finished so kept going, will test later. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 87cf11887ab8c31a949be5699ce51cdd20f472f5 Merge: 60f5b2d1 0f1f50e9 Author: Daniel Ladiges Date: Thu Jul 29 13:57:31 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 60f5b2d111c70edb8f0df6cb9cb814597749559b Author: Daniel Ladiges Date: Thu Jul 29 13:55:51 2021 -0700 Pushing changes to pulldown/up functions from hackathon to main. exec/immersedIons/particles.dat src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp commit 8f24d7236d9cf13f03e48aa52d9b0e16e2a4b2b3 Author: etpalmer63 Date: Thu Jul 29 16:25:17 2021 -0400 Finished porting sqrtLonsager functions. Compiles, needs testing src_multispec/multispec_functions.H commit 6408b43999a960a017053e0fc562f0d6074d0385 Merge: 99858174 46eb2949 Author: Ishan Srivastava Date: Thu Jul 29 12:55:36 2021 -0700 Merge branch 'quasi1D_compressible' of https://github.com/AMReX-FHD/FHDeX into quasi1D_compressible commit 9985817490f51dc38024fd1a4ea06dd0b2745cc4 Author: Ishan Srivastava Date: Thu Jul 29 12:54:52 2021 -0700 added profiling markers src_common/ComputeAverages.cpp commit db352fc80e31a95302edcc0ef38c2f4d82355252 Author: etpalmer63 Date: Thu Jul 29 15:45:51 2021 -0400 compiles and runs src_multispec/multispec_functions.H commit 1400d773993104f0a8e39214d0ffa5fd55da6264 Author: Matteo Polimeno Date: Thu Jul 29 11:37:57 2021 -0700 fixed indexing for 2d arrays src_chemistry/chemistry_namespace.H src_chemistry/chemistry_namespace_declarations.H commit fcc47eba40f46a80cb8b2a2c5a5b1bbdd4c6c475 Merge: c5dd49f2 b2a4e4e5 Author: Andy Nonaka Date: Thu Jul 29 11:28:25 2021 -0700 Merge branch 'compressible_chemistry' into gpu_chemistry commit b2a4e4e5f9ad33765de621a9a6ad4b022dbe6ad6 Merge: 8bf6bc33 0f1f50e9 Author: Andy Nonaka Date: Thu Jul 29 11:28:04 2021 -0700 Merge branch 'main' into compressible_chemistry commit c5dd49f2cacc370d249a4fc9278930936f2fc60c Merge: 34af748a 8bf6bc33 Author: Matteo Polimeno Date: Thu Jul 29 11:23:08 2021 -0700 merging compressible_chemistry with gpu_chemistry commit 34af748ae2ef4537a39fcb8555554a15b1d06c18 Author: Matteo Polimeno Date: Thu Jul 29 11:14:02 2021 -0700 committing gpu-related updates to new branch exec/chemistry_testing/GNUmakefile exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H src_chemistry/chemistry_namespace_declarations.H commit 46eb2949f398d5ef633b122cbcc06ff0a6e32688 Author: isriva Date: Thu Jul 29 10:20:47 2021 -0700 fixed small bug in calculation -- thanks Andrew. src_compressible_stag/statsStag.cpp commit 8bf6bc3345fb05ba49bb5a12af1c770b1e58fcf3 Author: Changho Kim Date: Thu Jul 29 05:19:43 2021 -0700 src_common, src_compressible: e0[k] introduced (initialized to be zeros). e_k(T) = e0[k] + hcv[k]*T, h_k(T) = e0[k] + hcp[k]*T src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/compressible_functions.H commit 9b30ac03d16ca70173ca4eb6b6eb6eb58083ca63 Author: Changho Kim Date: Thu Jul 29 04:21:01 2021 -0700 src_common: variable type of dof changed from amrex::Vector to amrex::GpuArray src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 92e67fe6c183c7aa0a45078ad527fb8f3a46c4ff Author: Changho Kim Date: Thu Jul 29 03:28:18 2021 -0700 compressible_chemistry: andy's suggestions implemented, void compute_chemistry_source(amrex::Real dt, amrex::Real dV, MultiFab& mf_in, int startComp_in, MultiFab& source, int startComp_out) exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_compressible/timeStep.cpp commit 403a4215d739db36590290486182dcd993241784 Author: Galen Wang Date: Wed Jul 28 19:25:00 2021 -0700 switch some vectors to DeviceVector src_particles/FhdParticleContainer.cpp commit 8d1f01718ecab6dba4a3605147c2127bd2de0977 Author: Galen Wang Date: Wed Jul 28 18:25:55 2021 -0700 MoveIons now on GPU exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit f343d415db20bfa4efce7a0e901ea1b354fa171e Author: etpalmer63 Date: Wed Jul 28 21:11:19 2021 -0400 7/9 functions in sqrtLOnsager ported src_multispec/multispec_functions.H src_multispec/src_F90/compute_mixture_properties.F90 src_multispec/src_F90/mass_flux_utilities.F90 commit ba1d1f0395ab34168786b7c6edfefff03d1e001f Author: Andy Nonaka Date: Wed Jul 28 13:52:21 2021 -0700 update comments, makefile exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp commit 6b6c5066f336bf156cd796a47df6b0f397eb083c Merge: 5e36a14e 0f1f50e9 Author: Andy Nonaka Date: Wed Jul 28 13:49:10 2021 -0700 Merge branch 'main' into compressible_mui commit 5e36a14ec259a4430fe74c4c05973d08027d9127 Merge: 47ce4cc6 ee7ba7dc Author: Andy Nonaka Date: Wed Jul 28 13:47:59 2021 -0700 Merge branch 'main' into compressible_mui commit 0f1f50e95b0af986ea40797f2ee559e6ca3582d9 Merge: ee7ba7dc 63177bfe Author: Andy Nonaka Date: Wed Jul 28 13:45:29 2021 -0700 Merge pull request #54 from AMReX-FHD/cuFFT cuFFT commit 63177bfe4b6d7a07b352f97b2133cf29b8a28f0f Author: Andy Nonaka Date: Wed Jul 28 13:42:44 2021 -0700 don't rebuild plan even for FFTW src_analysis/StructFact.cpp commit 09654b2744007589dcd17cfc14de6b8b98a4d0f7 Merge: 6ce7051d ee7ba7dc Author: Andy Nonaka Date: Wed Jul 28 13:15:50 2021 -0700 Merge branch 'main' into cuFFT commit ee7ba7dcb151ef423e21ab340d254efc82cdec16 Author: Andy Nonaka Date: Wed Jul 28 13:13:58 2021 -0700 bugfix - ComputeVerticalAverage was not averaging the final component src_common/ComputeAverages.cpp commit 82dc27dadff476c0d69166845397f6ab9b63ee35 Author: Ishan Srivastava Date: Wed Jul 28 12:25:13 2021 -0700 3D stats routines now on GPU exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit 6ce7051d317312ecc5a17cee6f9fac299a76b708 Merge: 06e3c5a6 7d6c1861 Author: Andy Nonaka Date: Wed Jul 28 12:15:31 2021 -0700 Merge branch 'main' into cuFFT commit 7d6c18615ab47c9ef5e0c86dc95da24343171b89 Author: Andy Nonaka Date: Wed Jul 28 12:14:39 2021 -0700 set max_grid_projection default to 4096. default value of 1 is not a good idea since you end up with a boxarray with n_cell_x*n_cell_y boxes if you don't set this src_common/src_F90/common_namelist.F90 commit 06e3c5a617d5600dacf89ed5e68372ca4d6b9ccc Author: Andy Nonaka Date: Wed Jul 28 12:13:28 2021 -0700 max_grid_size_projection no longer needed removed SWFFT completely fix makefiles to work for FFTW or cuFFT exec/DSMC/GNUmakefile exec/compressible/GNUmakefile exec/compressible/main_driver.cpp exec/compressible_stag/GNUmakefile exec/hydro/GNUmakefile exec/hydro/main_driver.cpp exec/immersedIons/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/multispec/GNUmakefile exec/structFactTest/GNUmakefile exec/tests/RFDanalysis/GNUmakefile src_analysis/StructFact.H src_analysis/StructFact.cpp src_common/common_namespace.H commit e3ff389c85ee9f5dc9e536a043ce68f189e3243e Author: Andy Nonaka Date: Wed Jul 28 12:01:20 2021 -0700 max_grid_size_projection is no longer needed since we don't use SWFFT src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 62ba6b52cafe545b52685ad6d1848ac1ee659838 Author: Andy Nonaka Date: Wed Jul 28 08:08:57 2021 -0700 renname "startOutComp" -> "startComp" exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit f330bde8afe124526b9b71fe68abe8cc9668b034 Author: Andy Nonaka Date: Wed Jul 28 08:01:49 2021 -0700 renname "offset" -> "startOutComp" exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 1e7bc862cbf209dfe3de50b8b47fe97e0cf0d032 Author: andrew Date: Wed Jul 28 08:28:48 2021 -0400 FIX: Bug in update time step fixed where minimum time step was not chosen exec/DSMCtest/periodic/input_periodic exec/DSMCtest/stats.cpp exec/DSMCtest/updateTimeStep.cpp commit 1326790b23abb479f47559c9af92039d45dcd912 Author: Changho Kim Date: Wed Jul 28 05:28:38 2021 -0700 exec/chemistry_testing/compressible: inputs files for exec/compressible (inputs_eq_SF, inputs_neq) exec/chemistry_testing/compressible/inputs_eq_SF exec/chemistry_testing/compressible/run.sh commit 901aeb4038ebc654e51895d6c017a394f115a6f4 Author: Changho Kim Date: Wed Jul 28 04:34:16 2021 -0700 exec/compressible/main_driver.cpp, src_compressible/timeStep.cpp: finally add chemistry source to RK3 exec/compressible/main_driver.cpp src_compressible/timeStep.cpp commit c014e190de0f9775c9c53756c278a5e2ee90b5a3 Author: Changho Kim Date: Wed Jul 28 03:50:52 2021 -0700 src_chemistry/chemistry_functions.cpp: noffset introduced to compute_chemistry_source exec/chemistry_testing/main.cpp src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit bb5918a806e2faf62505615e375ac84b7513fbba Author: Changho Kim Date: Wed Jul 28 03:36:20 2021 -0700 exec/chemistry_testing/main.cpp: small error fixed exec/chemistry_testing/main.cpp commit b58e3aa0f71a79f6acf1855e49aca6e3af0afde4 Author: Changho Kim Date: Wed Jul 28 03:28:40 2021 -0700 exec/chemistry_testing/main.cpp: printing mass densities exec/chemistry_testing/inputs_NO2_N2O4 exec/chemistry_testing/main.cpp commit cd3f52f66af6141a0887181a02d1cf4333b06ec0 Author: Changho Kim Date: Wed Jul 28 03:07:06 2021 -0700 src_chemistry/chemistry_functions.cpp: editted compute_chemistry_source before implementing noffset src_chemistry/chemistry_functions.cpp commit 63445f75976114a7c240a6cd04051b71faad1718 Author: Changho Kim Date: Wed Jul 28 02:54:13 2021 -0700 exec/chemistry_testing: rate constants updated in inputs_NO2_N2O4 and compressible/inputs_fhd exec/chemistry_testing/compressible/inputs_fhd exec/chemistry_testing/inputs_NO2_N2O4 commit dbb714d37fa6950ea2dbf41693866582b45558f7 Author: Changho Kim Date: Wed Jul 28 02:50:18 2021 -0700 FHDeX/exec/compressible/main_driver.cpp: add InitializeChemistryNamespace(), corresponding changes in GNUmakefile exec/compressible/GNUmakefile exec/compressible/main_driver.cpp commit 88c4fa5204b184871b11fb4aa00e6a564f981b5d Author: Changho Kim Date: Wed Jul 28 02:47:40 2021 -0700 src_chemistry/chemistry_functions.cpp: InitializeChemistryNamespace(): nreaction --> pp.query src_chemistry/chemistry_functions.cpp commit b78f23c1c25446ede49f32debf872d052c586ad9 Author: etpalmer63 Date: Tue Jul 27 23:04:59 2021 -0400 Ported Rho average and parts of sqrtLOnsager. Runs, but still missing pieces. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit c4d96e88f403d706d44bea5dc2559626457c4c62 Author: Galen Wang Date: Tue Jul 27 17:50:09 2021 -0700 missed one file src_geometry/paramplane_functions_K.H commit c8291edc6ac3894d2ac7c2404ae316e97ba063dc Author: Galen Wang Date: Tue Jul 27 17:48:36 2021 -0700 a GPU-version of MoveIons() that compiles, but get illegal memory access during runtime src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 9ddff0b4c8c5663066a74c9b5f622ee567129efc Author: Andy Nonaka Date: Tue Jul 27 16:01:56 2021 -0700 1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT1D cuFFT src_analysis/StructFact.cpp commit c42395d78542925d765a030c48bbf73a56857d7f Author: Andy Nonaka Date: Tue Jul 27 15:23:10 2021 -0700 build plan once per time step for CUDA build src_analysis/StructFact.cpp commit 985eacfa34aeeafda4da50cc8a045fbf6a48269a Author: andrew Date: Tue Jul 27 11:23:10 2021 -0400 ADD: - Inputs from gigan - Ignore spatial files in gitignore .gitignore exec/DSMCtest/alpha0_99_zero/input_therm_0_99_zero exec/DSMCtest/alpha1_0_zero/input_therm_1_0_zero exec/DSMCtest/periodic/input_periodic exec/DSMCtest/periodic/spatialCross1D_000000000 exec/DSMCtest/periodic/spatialCross1D_000000005 exec/DSMCtest/periodic/spatialCross1D_000000010 exec/DSMCtest/thermgrad/input_therm_long commit afe8f89abe8516ffa795b6a4a95b1dd5727f8629 Author: andrew Date: Tue Jul 27 09:33:05 2021 -0400 FIX: - Small bug in - Added more vars to make stats more readable exec/DSMCtest/stats.cpp commit 2472ed11adb97ae1d27f8c1c5c716a34332e4eff Author: Changho Kim Date: Tue Jul 27 04:22:44 2021 -0700 /exec/chemistry_testing/compressible: small changes exec/chemistry_testing/compressible/inputs_fhd exec/chemistry_testing/compressible/run.sh commit 328a04ffe06aa4229e44dfc46748d37937dbe9d3 Author: Changho Kim Date: Tue Jul 27 03:07:53 2021 -0700 exec/chemistry_testing/compressible: inputs_fhd, params_SF.py exec/chemistry_testing/compressible/inputs_fhd exec/chemistry_testing/compressible/params_SF.py commit b3730e4507835e7d069f700e805b498da9e63c71 Author: Changho Kim Date: Tue Jul 27 02:33:57 2021 -0700 exec/chemistry_testing/params_NO2_N2O4.py: updated exec/chemistry_testing/params_NO2_N2O4.py commit f85b2a67ee61a7aa7598a12ddc6d20c431275101 Author: andrew Date: Tue Jul 27 04:22:10 2021 -0400 ADD: - Reverted impact sampling use angles exec/DSMCtest/DsmcCollide.cpp exec/DSMCtest/main_driver.cpp commit ee20e0f0303ce29005ce24fbd31a0c2d599bc8d9 Author: andrew Date: Tue Jul 27 04:10:57 2021 -0400 ADD: - Added heat flux and heat capactiy for long range corr -- Compiles and runs - Uncommented the temperature related long range corrs exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/periodic/input_periodic exec/DSMCtest/periodic/spatialCross1D_000000000 exec/DSMCtest/periodic/spatialCross1D_000000005 exec/DSMCtest/periodic/spatialCross1D_000000010 exec/DSMCtest/stats.cpp src_particles/DsmcParticleContainer.H commit 9de7e25691ae555f2541be49ea91cefb97085f6f Author: Galen Wang Date: Mon Jul 26 19:52:17 2021 -0700 add ReduceOp on GPU; still need a way to handle RNG engines src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit b860e283669fd8377d445ecf470d421d00774046 Author: etpalmer63 Date: Mon Jul 26 22:51:02 2021 -0400 first step running src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 581c48d0fccb50950b0f66a2eba9359c08c1a5d4 Author: Matteo Polimeno Date: Mon Jul 26 16:45:04 2021 -0700 exec/chemistry_testing: updated call to compute_chemistry_source exec/chemistry_testing/main.cpp commit 45e52b9cba77698eaea09122d9a1852ed6e405dc Author: Matteo Polimeno Date: Mon Jul 26 16:43:49 2021 -0700 src_chemistry/chemistry_functions.cpp: computing chemistry source term both for deterministic chemistry and for CLE as MultiFab src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit f5d751cdb888275fa60c55c2f3f2e7f00682e21d Author: Andy Nonaka Date: Mon Jul 26 15:49:47 2021 -0700 cuFFT exec/hydro/GNUmakefile commit ca58738076165626fbbc40a503f212ac23af3b02 Author: Andy Nonaka Date: Mon Jul 26 15:32:18 2021 -0700 update makefile exec/compressible/GNUmakefile commit 0f8022cffebfce8afe1c940665131bc6606c09ad Author: Andy Nonaka Date: Mon Jul 26 14:55:42 2021 -0700 profiling inputs exec/structFactTest/inputs_profiling_3d commit 21cb1896d8bfd0709585f4999176a7d76ff61a98 Author: Andy Nonaka Date: Mon Jul 26 14:46:43 2021 -0700 cuFFT src_analysis/StructFact.H src_analysis/StructFact.cpp commit c3c5fb689044fa5a5d8c5c3d16bbd76b552949f2 Author: andrew Date: Mon Jul 26 17:16:47 2021 -0400 ADD: Testing time step updating (useful when particles heated) - Will also add option to always update timestep for when particles cool signif. External forces added - Will add thermostat as option for fluctuating gas in future .gitignore exec/DSMCtest/Make.package exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats_part.cpp exec/DSMCtest/updateTimeStep.cpp src_particles/DsmcParticleContainer.H commit f9109a048e41bc2b24d50a6a6eb275f2ccec5b18 Author: Matteo Polimeno Date: Mon Jul 26 14:15:35 2021 -0700 exec/chemistry_testing: Omega -> source; call to compute_chemistry_source from src_chemistry/ exec/chemistry_testing/main.cpp commit a3bccd8228a7fdbd7cc6de0a9c77c9d0310f6f29 Author: Matteo Polimeno Date: Mon Jul 26 14:13:38 2021 -0700 src_chemistry/chemistry_functions.cpp compute_Omega -> compute_chemistry_source; Omega -> source; src_chemistry/chemistry_functions.cpp: declared compute_chemistry_source src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit b288e417277ea42777ad2bbdd9b64044cebd64d1 Author: Ishan Srivastava Date: Mon Jul 26 11:43:32 2021 -0700 added Weiqun's 3D to 1D average of MutiFab to src_common/ src_common/ComputeAverages.cpp src_common/common_functions.H commit 8f47d43bd78e31abfa10f75557fdf7711b77eefd Merge: 7202e43e ba6e9ce3 Author: isriva Date: Mon Jul 26 11:04:12 2021 -0700 Merge remote-tracking branch 'origin/main' into quasi1D_compressible commit 7202e43ea344efcb43edfb1050fae57b49d4c6d9 Author: isriva Date: Mon Jul 26 11:03:17 2021 -0700 fixed a small error in stochastic stress tensor in 1D src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp commit ba6e9ce398a0fcf3c00c3fd71a984e8d0ed67adf Merge: 28dd03a5 4e6f51fa Author: Daniel Ladiges Date: Mon Jul 26 10:31:57 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 28dd03a5b20ecf7e42f5dc32ab1c457433de31dd Author: Daniel Ladiges Date: Mon Jul 26 10:31:22 2021 -0700 Removed some debug code to hopefully fix discos regressions exec/immersedIons/main_driver.cpp exec/immersedIons/test_inputs/inputs_gpu commit 2e8622d635a43fad5f757da2625d99b3b8976edd Merge: 40487391 4e6f51fa Author: isriva Date: Sun Jul 25 20:51:49 2021 -0700 Merge remote-tracking branch 'origin/main' into DSMCGran commit 404873916dd6be4a6c48b78e5d3d1bb334572d0a Author: isriva Date: Sun Jul 25 20:49:58 2021 -0700 spatial correlations for granular DSMC implemented -- needs testing exec/DSMCtest/Checkpoint.H exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/writePlotFile.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_particles/DsmcParticleContainer.H commit 4e6f51fabd840612f0502d6eb2772f85b46a44fe Merge: 6b218071 b7b40fe1 Author: Changho Kim Date: Sun Jul 25 04:41:13 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 6b218071b19cd6b48eb793419bbb580a20808dcf Author: Changho Kim Date: Sun Jul 25 04:41:01 2021 -0700 exec/chemistry_testing/params_NO2_N2O4.py: replaced by NIST thermo/kinetic data exec/chemistry_testing/params_NO2_N2O4.py commit 041521b16ea4bbb4dcc18c81589afb087eba4a21 Author: Andy Nonaka Date: Fri Jul 23 21:46:38 2021 -0700 cuFFT progress exec/structFactTest/GNUmakefile src_analysis/StructFact.H src_analysis/StructFact.cpp commit a7c72ccbfe6df5f6a14a27cb0f724a7789884d38 Author: Andrew Hong Date: Fri Jul 23 16:45:50 2021 -0700 FIX: - Small bug in checkpoint where not enough indices defined for covars exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_99/input_therm_0_99 exec/DSMCtest/alpha0_99_zero/input_therm_0_99_zero exec/DSMCtest/alpha1_0/input_therm_1_0 exec/DSMCtest/thermgrad/input_therm_long commit f136affdfb625d968a90d37e7d497fd40a944087 Author: Andy Nonaka Date: Fri Jul 23 13:25:57 2021 -0700 double precision src_multispec/multispec_functions.H commit 7332f776497af81d7512a282e9ecf7415dc1f008 Author: etpalmer63 Date: Fri Jul 23 14:34:01 2021 -0400 Doesn't compile with gpu. src_multispec/multispec_functions.H src_multispec/multispec_namespace.H commit d73813be597c41acce2ba789192f39d6b5369418 Author: etpalmer63 Date: Fri Jul 23 14:07:12 2021 -0400 removed WIP inputs exec/multispec/inputs_regression_equil_3d commit 8d9504a37c3854ae5ed557ad77932dbf44cd49d2 Author: etpalmer63 Date: Fri Jul 23 11:52:41 2021 -0400 remove my comments/questions. Noted untested parts of code. src_multispec/multispec_functions.H commit 3d811d641f2f6f6fad4b8a8d17111130b8a642ca Author: etpalmer63 Date: Fri Jul 23 11:45:58 2021 -0400 UNTESTED: use_multiphase=1 and nspecies=2. Otherwise good. exec/multispec/inputs_regression_detbubble_3d src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 24097377d48ae67265900d629f0eda3137581271 Merge: 09de8c56 b7b40fe1 Author: etpalmer63 Date: Thu Jul 22 15:22:20 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into remove_converted_fortran commit b7b40fe1891f6541604efb3afe86c5f911efbe46 Merge: fafa0516 2ef2d000 Author: Erik Date: Thu Jul 22 15:04:01 2021 -0400 Merge pull request #46 from etpalmer63/f90_cpp_convert_fix tested against commit 6140960. Tests touch molmass and nspecies incom… commit 09de8c56a1a9c7386700ace0e2299808323d1d23 Author: etpalmer63 Date: Thu Jul 22 14:59:16 2021 -0400 remove more working comments src_multispec/MassFluxUtil.cpp src_multispec/src_F90/matrix_utilities.F90 commit 22aa7825ed46ff79193ee86f228566c2a15cf9f1 Merge: 0a6e8b2f fafa0516 Author: Daniel Ladiges Date: Thu Jul 22 11:35:52 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit fafa051623070ffb14b88da4069b5ae4f178655b Author: Galen Wang Date: Thu Jul 22 11:35:23 2021 -0700 gpu test inputs exec/immersedIons/test_inputs/inputs_gpu commit 0a6e8b2f66e73b224934e84ba518342257e37432 Merge: 04458816 85a780d9 Author: Daniel Ladiges Date: Thu Jul 22 11:22:32 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 044588167cf87f655da905a3d4bc68087821ab7e Author: Daniel Ladiges Date: Thu Jul 22 11:22:16 2021 -0700 updated particle mobility src_particles/particle_functions_K.H commit 12abbb040ea6359b10a36dba8bde3bc92912f1f2 Author: etpalmer63 Date: Thu Jul 22 13:19:21 2021 -0400 remove error searching comments src_multispec/multispec_functions.H commit 279dcbb36fe609105aef27c4e7296c968a4e25c4 Author: Andy Nonaka Date: Thu Jul 22 10:15:58 2021 -0700 starting cuFFT work src_analysis/StructFact.H src_analysis/StructFact.cpp commit 85a780d95f0da025672ea23ad3b9f7ead6024b4e Merge: 9f7809e9 e4d586f5 Author: Andy Nonaka Date: Thu Jul 22 09:56:21 2021 -0700 Merge branch 'gpu_discos' into main commit d56404f7adf69aaf34dd610a80cca5d10765c97a Author: etpalmer63 Date: Thu Jul 22 12:56:00 2021 -0400 found error in previous merge. With that fix, matches first plotfile. Misses second. src_multispec/multispec_functions.H commit e4d586f5cfd154d248ec9ce3fc868317d7af0f95 Author: Andy Nonaka Date: Thu Jul 22 09:55:46 2021 -0700 clean up makefiles exec/DSMC/GNUmakefile exec/chemistry_testing/GNUmakefile exec/compressible/GNUmakefile exec/hydro/GNUmakefile exec/hydro/PDF/GNUmakefile exec/immersedIons/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/multispec/GNUmakefile exec/structFactTest/GNUmakefile exec/tests/RFDanalysis/GNUmakefile commit 9f7809e9799ae597ff48a93ae80833ba3f66b303 Merge: f79a1ea6 49e53b8d Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Thu Jul 22 09:25:57 2021 -0700 Merge pull request #51 from AMReX-FHD/gpu_discos DISCOS GPU Fixes commit 49e53b8dd6c5088108d110f63ec72ed2b7c3c4e5 Author: Andy Nonaka Date: Thu Jul 22 08:17:56 2021 -0700 cleanup src_particles/FindCoords.cpp commit 1a266fd6d2f19d5f9efa894da63cc423ba104243 Author: Andy Nonaka Date: Thu Jul 22 07:53:51 2021 -0700 use gpuarray instead of regular array within parallelfor src_particles/FindCoords.cpp commit a73e5d2053e2c98f805a451b0cc26d1f48315edb Author: etpalmer63 Date: Wed Jul 21 23:06:03 2021 -0400 found and fixed one issue! still have more errors. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 99a87f71b022bf295d57a19fee3e59e8194c41af Author: Galen Wang Date: Wed Jul 21 17:17:31 2021 -0700 create a new branch for discos gpu exec/immersedIons/inputs_gpu src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H commit f79a1ea61e7c1fd082d049e85fcfc38747ac9dea Author: Galen Wang Date: Wed Jul 21 16:31:32 2021 -0700 Revert "immersedIons now compiles on GPU" This reverts commit 02cdd44f5a1c6b3d7d5ee47aa1f03d92949b0019. src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H commit 07501a77c5545476c91218c13cae23005c3c2395 Author: isriva Date: Tue Jul 20 16:27:31 2021 -0700 sqrt(3) term for stochastic stress in 1D src_compressible_stag/fluxStag.cpp commit 02cdd44f5a1c6b3d7d5ee47aa1f03d92949b0019 Author: Galen Wang Date: Tue Jul 20 16:10:31 2021 -0700 immersedIons now compiles on GPU src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H commit 11258a291f0f6c9a39aba33808bd6663adf00070 Author: etpalmer63 Date: Tue Jul 20 18:08:17 2021 -0400 need to double check adding 4th index, shows promise. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit a42537ddf8fbb6e84fad5347f277fa507a4e7b8e Author: etpalmer63 Date: Tue Jul 20 16:57:09 2021 -0400 still trying to isolate the error. Found initializing to 0 helpful to compare output. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit c430ffada608b88928d7f53f86b41b1ccbf37179 Author: isriva Date: Mon Jul 19 21:00:03 2021 -0700 small output changes exec/compressible_stag/main_driver.cpp commit 9091309b98ffa375ef44a442814af472a796c828 Author: Ishan Srivastava Date: Mon Jul 19 20:44:09 2021 -0700 1D stats routine now on GPU src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit d4dc047528aaf8b0a156c77b4593a086c1f2af62 Author: etpalmer63 Date: Mon Jul 19 19:14:10 2021 -0400 isolated a (hopefully) small error to Dbar2chi_iterative, and other errors to ComputeChiSub. src_multispec/multispec_functions.H commit 47ce4cc6bacbfa4faa692536ceda8c6b3d425970 Merge: c05990c2 2b60a667 Author: Andy Nonaka Date: Mon Jul 19 15:40:29 2021 -0700 Merge branch 'main' into compressible_mui commit fafb7a445b7947fad57894042102c3f7971dd025 Author: Andy Nonaka Date: Mon Jul 19 14:36:04 2021 -0700 profiling exec/compressible/inputs_profiling_gpu commit 2b60a667d23c6a8c36be944ddfbb95dae4c7c2b3 Merge: 33d17ebb 2ff31d5d Author: Andy Nonaka Date: Mon Jul 19 14:28:39 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 33d17ebba1d7e6beb607ad9c81a80b6dfe6ee163 Author: Andy Nonaka Date: Mon Jul 19 14:28:24 2021 -0700 add timers to structure factor code src_analysis/StructFact.cpp commit 22b0400b02a570ae6bc164fffcfbd7a4064a11ce Merge: b7938885 2ff31d5d Author: etpalmer63 Date: Mon Jul 19 17:03:03 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into remove_converted_fortran commit 2ef2d000725f93c84946fc3427a25b0d0cb8bfc0 Merge: cfca884f 2ff31d5d Author: etpalmer63 Date: Mon Jul 19 16:55:32 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert_fix commit 2ff31d5d01696090d4286a00323dd2223f6e2805 Author: Andy Nonaka Date: Mon Jul 19 12:52:23 2021 -0700 remove file exec/multispec/inputs_profiling_3d commit dd832226159ef938552386dcbaaac69a397be9d3 Author: etpalmer63 Date: Mon Jul 19 15:45:29 2021 -0400 input files for comparing haswell and cori gpu exec/multispec/inputs_profiling_3d_coriGPU exec/multispec/inputs_profiling_3d_haswell commit 29c3bb68c546d44d9a196be5c1dfc6d6e7955d0d Author: Andy Nonaka Date: Mon Jul 19 12:25:21 2021 -0700 max_step=3 exec/multispec/inputs_profiling_3d commit e727470dff9a2b164d7ce7b8dc7cbbef588d97f5 Author: Andy Nonaka Date: Mon Jul 19 11:33:43 2021 -0700 profiling exec/multispec/inputs_profiling_3d commit a259b507b376c351fc7421edbb201bb8c0f5180c Author: andrew Date: Mon Jul 19 07:39:23 2021 -0400 ADD: - Working on timestep updating in cases where particles speed up over time - Working on measuring global vars in globalVars.cpp FIX: - Small bug in pressure exec/DSMCtest/Checkpoint.H exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/Make.package exec/DSMCtest/alpha0_99/input_therm_0_99 exec/DSMCtest/alpha1_0/input_therm_1_0 exec/DSMCtest/globalVars.cpp exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/updateTimeStep.cpp commit 1ae2c04ecdc050f4bc1751a697b5bd4d4799ff72 Author: andrew Date: Mon Jul 19 01:07:48 2021 -0400 ADD: Inputs for shear exec/DSMC_ContinuousPSD/00/input_test exec/DSMC_ContinuousPSD/01/input_test exec/DSMC_ContinuousPSD/02/input_test exec/DSMC_ContinuousPSD/03/input_test exec/DSMC_ContinuousPSD/DsmcCollide.cpp exec/DSMC_ContinuousPSD/input_test exec/DSMC_ContinuousPSD/main_driver.cpp exec/DSMC_ContinuousPSD/stats.cpp exec/DSMC_ContinuousPSD/writePlotFile.cpp commit c14de66eb77a382d3f9bf8da19f54445fcf52eb3 Author: andrew Date: Sun Jul 18 20:34:16 2021 -0400 ADD: - Tested the external forces - Fixed variances to be unbiased -- Cleaned up stats -- Tested and ran exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/externalF.cpp exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/writePlotFile.cpp commit 87271228622d5504c340b74bd6e45be968984f0d Author: isriva Date: Sun Jul 18 14:41:02 2021 -0700 major refactor of the stats routine: now works with both 3D and quasi-1D 3D results unchanged -- checks ongoing for 1D compiles on GPU exec/compressible_stag/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 8026a368ca0e35f25e466c1e1bc1d420624cbc5c Merge: 4bebe248 fafb7a44 Author: andrew Date: Sun Jul 18 07:11:55 2021 -0400 Merge branch 'main' into DSMCGran commit 4bebe248bf6c8c30b04cf998c7a1e411ccc75f76 Author: andrew Date: Sun Jul 18 07:10:48 2021 -0400 ADD: - External forces to simulate Pouseuille flow exec/DSMC_ContinuousPSD/input_test exec/DSMC_ContinuousPSD/main_driver.cpp exec/DSMC_ContinuousPSD/writePlotFile.cpp exec/DSMCtest/Make.package exec/DSMCtest/externalF.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/stats_unbiased.cpp src_particles/DsmcParticleContainer.H commit 3a5ac12d613dfaf7f8c13c373083334270e2842f Author: andrew Date: Sun Jul 18 02:05:19 2021 -0400 ADD: Continuous PSD DSMC runs in periodic/shear with Lee-Ed TODO: Verify flow behavior is correct exec/DSMC_ContinuousPSD/Checkpoint.H exec/DSMC_ContinuousPSD/Checkpoint.cpp exec/DSMC_ContinuousPSD/DsmcCollide.cpp exec/DSMC_ContinuousPSD/GNUmakefile exec/DSMC_ContinuousPSD/Make.package exec/DSMC_ContinuousPSD/checkpoint.cpp exec/DSMC_ContinuousPSD/input_test exec/DSMC_ContinuousPSD/inputs_thermalconcBC exec/DSMC_ContinuousPSD/main_driver.cpp exec/DSMC_ContinuousPSD/particleGen.cpp exec/DSMC_ContinuousPSD/stats.cpp exec/DSMC_ContinuousPSD/writePlotFile.cpp exec/DSMCtest/input_test src_particles/DsmcParticleContainer.cpp commit bd94b89f05274adee199b608a578a72270eace24 Author: andrew Date: Sat Jul 17 01:20:23 2021 -0400 test thermal BC with explicit directions (no rotation) exec/DSMC_ContinuousPSD/DsmcCollideCont.cpp exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp src_geometry/paramplane_functions_K.H commit b79388852d893eae9dcb3021eb1651711232dcfc Author: etpalmer63 Date: Fri Jul 16 23:25:36 2021 -0400 still looking for the error exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_3d src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/matrix_utilities.F90 commit bec2a1753b2f239a437bb23bd734e658f96eda99 Author: etpalmer63 Date: Fri Jul 16 12:57:56 2021 -0400 looks like an issue maybe in rhoN -- still tracking exec/multispec/inputs_regression_equil_3d src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 02e70b71f8a5b371215bf8409f2bc229aa053c57 Author: isriva Date: Thu Jul 15 20:18:15 2021 -0700 fixed a small bug for 1D concerning pressure gradients -- code works now src_compressible_stag/fluxStag.cpp commit 8f4eda12365471fe1f379bd703e49b487d353e5d Author: etpalmer63 Date: Thu Jul 15 22:57:05 2021 -0400 runs but fails only touching regression test. Also, converted many Array1D to GpuArray. Miss the Array1D. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 434dfef44d8f6d9ed26ec389f4d3eb215f0bb887 Author: Changho Kim Date: Thu Jul 15 15:41:13 2021 -0700 exec/chemistry_testing/params_NO2_N2O4.py exec/chemistry_testing/params_NO2_N2O4.py commit e509d8d9f3f2d0e023970e2139f7d7fbf5683d23 Author: etpalmer63 Date: Thu Jul 15 17:03:21 2021 -0400 first draft ComputeRowWChiLocal src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit b1a0f72180a4a0914c927b082aa9c717d6d403ca Merge: 6dce448c b4a9cc3c Author: etpalmer63 Date: Thu Jul 15 14:04:03 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into remove_converted_fortran commit 6dce448cf7b878001725c886965a71614b588f31 Author: etpalmer63 Date: Thu Jul 15 11:46:40 2021 -0400 working on ComputeRowChi src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit cfca884f971983e7b996b6de23a10614982fd6c9 Merge: 93a58dd6 b4a9cc3c Author: etpalmer63 Date: Thu Jul 15 09:45:26 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert_fix commit b4a9cc3c3eeb52408a161c770e17bf039d038d4e Author: Changho Kim Date: Thu Jul 15 05:24:46 2021 -0700 exec/chemistry_testing: inputs_NO2_N2O4 exec/chemistry_testing/inputs_1 exec/chemistry_testing/inputs_NO2_N2O4 commit b729ede642a085816e2b622649097c46b6a2fa65 Author: Changho Kim Date: Thu Jul 15 04:20:14 2021 -0700 exec/chemistry_testing: inputs_1 updated exec/chemistry_testing/inputs_1 commit 38de8acb36fdbdac9fa42bad1e2bb165f75cecc6 Author: Changho Kim Date: Thu Jul 15 04:14:27 2021 -0700 src_chemistry: clean up chemistry_functions.cpp src_chemistry/chemistry_functions.cpp commit 7174cbbea353fdd2cc3c6201dff13593e93806ca Author: Changho Kim Date: Thu Jul 15 02:37:23 2021 -0700 exec/chemistry_testing: cleaning up main.cpp exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp commit d5556e3aae342a698b278cc79f0f82bb1015982c Author: Matteo Polimeno Date: Wed Jul 14 22:23:18 2021 -0700 exec/chemistry_testing: adding prob_lo and prob_hi arrays to inputs_1; DIM=2 -> DIM=3 exec/chemistry_testing/GNUmakefile exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp commit 556409ff24e8ec5e8f84995aa85089eeab484b9c Author: isriva Date: Wed Jul 14 20:04:20 2021 -0700 quasi 1D enabled for staggered compressible; need to modify stats routine src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 385d5505308af8fa1fb374e4676ac355161dd9af Author: Matteo Polimeno Date: Wed Jul 14 19:11:49 2021 -0700 exec/chemistry_testing: added prob_type to inputs_1 and main.cpp exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp commit 32e811010e8b3597653b592ec96b1c4b35e6cc2b Author: Matteo Polimeno Date: Wed Jul 14 19:09:50 2021 -0700 src_chemistry: adding routine to compute source term Omega (MultiFab) src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp commit 5188bc4d4542595474f85c82b9374d7f895985e6 Merge: d8326696 f1b269df Author: Matteo Polimeno Date: Wed Jul 14 16:17:16 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d8326696021b336dfa57350949638327f6f07aea Author: Matteo Polimeno Date: Wed Jul 14 16:16:31 2021 -0700 exec/chemistry_testing: phi(number density) -> rho(mass density) exec/chemistry_testing/main.cpp commit f1b269df01075459281f048c05b8596da263d90b Author: drladiges Date: Wed Jul 14 15:35:26 2021 -0700 Some plotting and modified mobility funcs exec/DSMC/paramPlane.ipynb exec/immersedIons/main_driver.cpp exec/immersedIons/paper_inputs_2/inputs_1_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_0wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift_v2 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H tools/notebooks/channel_mob.ipynb tools/notebooks/plotting.ipynb commit 8e5bb1807d05211f38ac792e9c282f688584c652 Author: Matteo Polimeno Date: Wed Jul 14 13:38:05 2021 -0700 exec/chemistry_testing: initializing number density with rhos from src_common. NOTE: inputs_2 and inputs_3 need to yet be updated accordingly exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp commit 9d2c20d1d530489f831bfc76649122ce898d9201 Author: jgalenwang Date: Tue Jul 13 16:31:51 2021 -0700 re-calculate wetRad for ES kernel on a 256^3 domain to eliminate periodic effect (still need more testing) exec/immersedIons/wetRad_KernelES/wetRad_w4.dat exec/immersedIons/wetRad_KernelES/wetRad_w5.dat exec/immersedIons/wetRad_KernelES/wetRad_w6.dat commit 33f89aa47473b94642406aee58b093f396fe5e9a Merge: 0eb23c05 c7d9d2a3 Author: drladiges Date: Tue Jul 13 14:37:31 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0eb23c05ec09a7e1f734721535953488b407d963 Author: drladiges Date: Tue Jul 13 14:37:12 2021 -0700 paramPlane python update exec/DSMC/paramPlane.ipynb commit 93a58dd63d41b49c466178205168e7cec1dca0eb Author: etpalmer63 Date: Tue Jul 13 13:30:22 2021 -0400 tested against commit 6140960. Tests touch molmass and nspecies incompute_molconc_molmtot_local. Passes. src_multispec/multispec_functions.H commit 39b52d6bb6296aa427460338176f179057d256af Author: etpalmer63 Date: Tue Jul 13 11:14:48 2021 -0400 Got carried away deleting fortran functions [WIP] src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/mass_flux_utilities.F90 commit c7d9d2a396696ec715e7330ae092256d86fd5e24 Merge: fb6a0aed 7f09dcfb Author: Erik Date: Tue Jul 13 09:02:38 2021 -0400 Merge pull request #45 from AMReX-FHD/multispecies_gpu_fix get multispecies compiling on the gpu commit fb6a0aed95f95d7add44e7bd5090c3c7f3a42b3a Author: Matteo Polimeno Date: Mon Jul 12 14:32:17 2021 -0700 exec/chemistry_testing: updated main.cpp ComputeMean -> ComputeSpatialMean exec/chemistry_testing/main.cpp commit 088224a60fb03e80dfbab7aa973a96547d211e59 Author: Matteo Polimeno Date: Mon Jul 12 14:30:14 2021 -0700 src_common/ComputeBasicStats.cpp and src_common/common_functions.H ComputeMean -> ComputeSpatialMean src_common/ComputeBasicStats.cpp src_common/common_functions.H commit ff7eefc8ff95b82067e23bcce8bead8b525bbd74 Author: Matteo Polimeno Date: Mon Jul 12 13:42:08 2021 -0700 chemistry_testing/main.cpp: updated to output mean exec/chemistry_testing/main.cpp commit 39051e66be5ed3eba61069f8fa4679a1e33d6c80 Author: Matteo Polimeno Date: Mon Jul 12 13:39:41 2021 -0700 src_common: adding the function declaration for mean src_common/common_functions.H commit 7a9e8ac193e41f25042b20881722c4243bb0d655 Author: Matteo Polimeno Date: Mon Jul 12 11:51:10 2021 -0700 src_common: adding routine to compute mean src_common/ComputeBasicStats.cpp commit 7f09dcfbf220158ed2c7f8b17161f84a2d733c18 Author: Andy Nonaka Date: Mon Jul 12 10:19:03 2021 -0700 get multispecies compiling on the gpu src_common/common_namespace.H src_common/common_namespace_declarations.H src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H commit 848e778cbeff9814b646fb17d4804f73e8d925c2 Author: Andy Nonaka Date: Mon Jul 12 09:23:13 2021 -0700 get structFactTest compiling on corigpu exec/structFactTest/GNUmakefile commit 806dc4755774adf26e280bda50324adab19d32bc Author: andrew Date: Fri Jul 9 22:38:58 2021 -0400 ADD: - Debugged Lees-Edwards BC -- Checked that velocities were adjusted accordingly exec/DSMC_ContinuousPSD/Make.package exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp src_geometry/paramplane_functions_K.H commit 8127831a05eeedb0678ec945590f50801f80a146 Author: Andrew Hong Date: Thu Jul 15 19:03:02 2021 -0700 FIX: - Angles mixed up when determining the unit vector at impact - Implemented Gaussian sampling instead exec/DSMCtest/DsmcCollide.cpp exec/DSMCtest/conc/input_conc exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/zeroconcgrad/input_con_zero_grad exec/DSMCtest/zerothermgrad/input_therm_zero_grad commit d09c9835d098284b05df55b8d129622191c876a0 Merge: 8e7a5502 14d5fae6 Author: Andy Nonaka Date: Fri Jul 9 17:13:48 2021 -0700 Merge pull request #44 from AMReX-FHD/fix_max_species Fix max species commit 14d5fae602ce042000b083b346806e595ad9a055 Author: Andy Nonaka Date: Fri Jul 9 17:11:59 2021 -0700 move MAX_ELEMENT into common namespace/namelist src_common/common_namespace.H src_common/src_F90/common_namelist.F90 src_multispec/multispec_functions.H src_multispec/src_F90/multispec_namelist.F90 commit 127b1bfc2df9fd5d468ff754ed002b6e2e72a126 Author: andrew Date: Fri Jul 9 18:48:19 2021 -0400 ADD: - Routine to zero out VCOM in each cell exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp commit 20735cbcc4b52c24a4ee19c233da325d4ad3bb7d Author: Andrew Hong Date: Thu Jul 15 14:14:05 2021 -0700 Most recent version exec/DSMCtest/mixed/input_mixed exec/DSMCtest/periodic/input_therm_periodic exec/DSMCtest/stats.cpp commit 8e7a55027216cadc149cecc3e2d2fb49446a5b01 Author: Matteo Polimeno Date: Fri Jul 9 14:58:28 2021 -0700 updating inputs_2 and inputs_3 in accordance with the design of inputs_1 exec/chemistry_testing/inputs_2 exec/chemistry_testing/inputs_3 commit 6c5cff1fcb1ec01cebcced79a2f225682791dbb8 Author: Matteo Polimeno Date: Fri Jul 9 14:12:46 2021 -0700 src_chemistry: nspecies, MAX_SPECIES deleted, exec/chemistry_testing: nspecies and MAX_SPECIES used from src_common exec/chemistry_testing/GNUmakefile exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp exec/chemistry_testing/myfunc.H src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H src_chemistry/chemistry_namespace_declarations.H commit 26afad903acc227808230a14a868f0abf5d14743 Author: Andy Nonaka Date: Fri Jul 9 13:54:18 2021 -0700 MAX_SPECIES work src_common/common_namespace.H commit 61067dbb6a9a576280130dcf19de7a1e038bc58d Author: Andy Nonaka Date: Fri Jul 9 13:46:39 2021 -0700 MAX_SPECIES consistent in F90 and C++ eliminated LOHI src_common/common_functions.H src_common/common_functions.cpp src_common/common_namespace.H src_common/src_F90/common_namelist.F90 src_compressible/compressible_functions.H src_compressible_stag/compressible_functions_stag.H src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit da22677b4121f17878e10905228e4f0025820939 Author: andrew Date: Fri Jul 9 09:39:06 2021 -0400 FIX: - Debugged temperature calculations - Mean velocities, stresses, densities calculated correctly exec/DSMCtest/alpha1_0/input_therm_1_0 exec/DSMCtest/alpha1_0_unbiased/input_therm_1_0_unbiased exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats_unbiased.cpp exec/DSMCtest/zerograd/input_therm_zero_grad exec/stats_unbiased.cpp commit 754dbc9083fb5a627dee4a3c7d32b366f7b41a09 Author: andrew Date: Fri Jul 9 08:54:34 2021 -0400 FIXED: -Added new stats routine where hydro vars calculated from conserved vars ADD: - Inputs to compare each stats and to zero grad wall TODO: - Still need to include heat flux in stats (follow Gallis) exec/DSMCtest/DsmcCollide.cpp exec/DSMCtest/Make.package exec/DSMCtest/alpha1_0/input_therm_1_0 exec/DSMCtest/alpha_1_0_unbiased/input_therm_1_0_unbiased exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/stats_unbiased.cpp exec/DSMCtest/zerograd/input_therm_zero_grad exec/stats_unbiased.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit e92a8c24991e7d33bc1aff6714ebcbfa86070a8f Author: Andrew Hong Date: Wed Jul 14 06:09:42 2021 -0700 FIXED: - Added timeFrac = 1 to all newly generated particles and particles read from checkpoint -- Previously saw that the runtime in move routine was a vey large number at times and stalled TODO: There is a mean u velocity in the temperature gradient case. - Tried to change collision acceptance to reject non-approaching pairs - Checked momentum conserved in the fully periodic and isothermal case exec/DSMCtest/DsmcCollide.cpp exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp src_analysis/StructFact.cpp commit 3651a1031d66e4cf8975d1666ae93e7a88d97f73 Merge: 0366f2a3 b5ecb7b3 Author: Ishan Srivastava Date: Thu Jul 8 18:02:16 2021 -0600 Merge pull request #38 from AMReX-FHD/fixBC_compressible Correct energy flux in the staggered compressible code for various BCs commit b5ecb7b330dcb48414a2e6c61bb96553849b559b Merge: d432f611 0366f2a3 Author: Andy Nonaka Date: Thu Jul 8 16:23:47 2021 -0700 Merge branch 'main' into fixBC_compressible commit 0366f2a375bd84fd30fbf15128582c2f4d9ae7e0 Author: Andy Nonaka Date: Thu Jul 8 16:22:08 2021 -0700 weiner -> wiener src_compressible_stag/fluxStag.cpp commit d432f611ab78e1cc64e2f2d65e401023ad19b47f Merge: a3d8b7fb 191e0d1b Author: isriva Date: Thu Jul 8 15:54:03 2021 -0700 Merge remote-tracking branch 'origin/main' into fixBC_compressible commit 191e0d1bafa9a429bd7fb7a4865d7f62446a7982 Merge: 400686e4 032d8982 Author: Andy Nonaka Date: Thu Jul 8 14:17:49 2021 -0700 Merge pull request #43 from etpalmer63/add_comments added comments, fixed spelling commit 1b1c98ec241757c442403d792dcc3f5e9e6b04ea Author: andrew Date: Thu Jul 8 10:02:08 2021 -0400 TODO: Pushing to debug on minilla - Thermal BC showing incorrect bulk momentum Lees-Edwards still in development Cleaned up some files Collision stages in the exec dir exec/DSMCGran/GNUmakefile exec/DSMCGran/INS_functions.H exec/DSMCGran/Make.package exec/DSMCGran/checkpoint.cpp exec/DSMCGran/delPlots exec/DSMCGran/input_therm exec/DSMCGran/inputs_bi_gran exec/DSMCGran/inputs_ex exec/DSMCGran/inputs_thermalBC exec/DSMCGran/inputs_thermalconcBC exec/DSMCGran/main_driver.cpp exec/DSMCGran/paramPlane.nb exec/DSMCGran/particleGen.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp exec/DSMC_ContinuousPSD/DsmcCollideCont.cpp exec/DSMCtest/DsmcCollide.cpp exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/multi_eq/inputs_eq_multi exec/DSMCtest/particleGen.cpp src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 97da526f8048ebe7ccd9ac0065d23e6ca7cec30a Author: Andrew Hong Date: Mon Jul 12 16:51:39 2021 -0700 FIX: Small bug where particle tried to change species in thermal BC only - Added flag and works nowy src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 868ae3fcd2b5d60bd7e00a3f8d1ce3051a0eae6f Author: andrew Date: Wed Jul 7 18:16:05 2021 -0400 ADD: Inputs to test thermal and conc gradients Added solid wall concentration inputs - Tested in serial for 3-AR gas DEBUG: Bulk velocities now only zero'd at restart Bulk velocities now zero VCOM when initializing particles exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_9/input_therm_09 exec/DSMCtest/alpha0_95/input_therm_095 exec/DSMCtest/alpha0_95/input_therm_0_95 exec/DSMCtest/alpha0_99/input_therm_099 exec/DSMCtest/alpha0_99/input_therm_0_99 exec/DSMCtest/alpha1_0/input_therm exec/DSMCtest/alpha1_0/input_therm_1_0 exec/DSMCtest/bialpha1_0/input_therm_bi exec/DSMCtest/biconc/input exec/DSMCtest/conc/input exec/DSMCtest/input_test exec/DSMCtest/main_driver.cpp exec/DSMCtest/mixed/input_mixed exec/DSMCtest/particleGen.cpp exec/DSMCtest/smallTGrad/input_therm_smallT exec/DSMCtest/therm/input_therm exec/DSMCtest/therm_conc/input exec/DSMCtest/writePlotFile.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 400686e434d20f418d3c69f26c8882a9ba8cbf88 Author: Matteo Polimeno Date: Wed Jul 7 14:52:25 2021 -0700 adding inputs_2 and inputs_3 exec/chemistry_testing/inputs_2 exec/chemistry_testing/inputs_3 commit 66340eee86bde248d1f4d881181f8ccd8716d231 Author: Matteo Polimeno Date: Wed Jul 7 12:23:45 2021 -0700 exec/chemistry_testing: to test src_chemistry/ exec/chemistry_testing/GNUmakefile exec/chemistry_testing/Make.package exec/chemistry_testing/README exec/chemistry_testing/inputs_1 exec/chemistry_testing/main.cpp exec/chemistry_testing/myfunc.H exec/chemistry_testing/params_1.py commit 222eb68bc28461e62de05af104b9c49f157bb430 Author: Matteo Polimeno Date: Wed Jul 7 12:16:46 2021 -0700 adding src_chemistry/ directory src_chemistry/Make.package src_chemistry/chemistry_functions.H src_chemistry/chemistry_functions.cpp src_chemistry/chemistry_namespace.H src_chemistry/chemistry_namespace_declarations.H commit 5c3330104c3f6142731a7f8aeea787b39f31bb73 Author: andrew Date: Wed Jul 7 11:25:28 2021 -0400 ADD: In process of adding new BCs: - Solid wall with concentration - Lees Edwards (bc_vel==3) In process of adding optional collision routine for ... continuous size distributions exec/DSMCtest/alpha0_9/input_therm_09 exec/DSMCtest/input_test src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 946bc5789bd079384277e6e5be931b733a5ff23b Author: Andrew Hong Date: Sun Jul 11 20:04:41 2021 -0700 ADD: - Partially added tabs for readable code (few more need to be corrected) DEBUG: Corrected stats and plotfile indexing .gitignore exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_99/input_therm_099 exec/DSMCtest/alpha1_0/input_therm exec/DSMCtest/stats.cpp exec/DSMCtest/writePlotFile.cpp commit 95e6c9fc4ce6ea434fa1769ffb7c49aea5551aab Merge: 7be14b86 c53b7640 Author: Andrew Hong Date: Sat Jul 10 22:16:56 2021 -0700 Merge branch 'DSMCGran' of https://github.com/AMReX-FHD/FHDeX into DSMCGran commit 7be14b86e83af86eeb92ef069178eeb48b357d9f Author: Andrew Hong Date: Sat Jul 10 22:16:04 2021 -0700 FIX: Main driver was corrupted in parallel but now works correctly after ... fix to particleGen ADD: Checkpointing for particles and field data verified - Can proceed with all DSMC routines implemented so far ReInitParticles also sets vrmax - vrmax set in InitCollisionCells unnecssary (remove) .gitignore exec/DSMCGran/input_therm exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_9/input_therm_09 exec/DSMCtest/alpha0_95/input_therm_095 exec/DSMCtest/alpha0_99/input_therm_099 exec/DSMCtest/alpha1_0/input_therm exec/DSMCtest/bialpha1_0/input_therm_bi exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp commit c53b764064be5d26d944ed94a642891ed446c1d2 Author: Andrew Hong Date: Sat Jul 10 22:12:00 2021 -0700 FIX: Main driver was corrupted in parallel but now works correctly after ... fix to particleGen ADD: Checkpointing for particles and field data verified - Can proceed with all DSMC routines implemented so far ReInitParticles also sets vrmax - vrmax set in InitCollisionCells unnecssary (remove) .gitignore exec/DSMCGran/input_therm exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_9/input_therm_09 exec/DSMCtest/alpha0_95/input_therm_095 exec/DSMCtest/alpha0_99/input_therm_099 exec/DSMCtest/alpha1_0/input_therm exec/DSMCtest/bialpha1_0/input_therm_bi exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp commit 33439913c9f9dab842fa6ae75872701274f1b2bf Author: andrew Date: Wed Jul 7 03:24:53 2021 -0400 DEBUG: - False boundary at proc boundaries when running in parallel. in process of fixing exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/writePlotFile.cpp src_geometry/paramplane_functions_K.H commit 5db78859f74cab94c837c0e5530638ad0d807d92 Author: andrew Date: Tue Jul 6 17:55:10 2021 -0400 FIX: Verified particle restart is working correctly in serial TODO: Verify particle restart in parallel ADD: Added heat fluxes to MFs - Verified via plotfiles - Set up Fourier probs for weak temp. grad. and small dissipation REMOVE: exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/alpha0_9/input_therm exec/DSMCtest/alpha0_95/input_therm exec/DSMCtest/alpha0_99/input_therm exec/DSMCtest/alpha1_0/input_therm exec/DSMCtest/bialpha1_0/input_therm exec/DSMCtest/main_driver.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/therm/input_therm exec/DSMCtest/writePlotFile.cpp src_particles/DsmcParticleContainer.cpp commit 9d3e3a83a8480dfd4b872ddf70ca340bbaed04af Author: isriva Date: Fri Jul 9 16:09:48 2021 -0700 capability to reset stats upon restart; negative seed works for restarting from saved rng state exec/DSMCtest/Checkpoint.H exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/main_driver.cpp commit 032d8982cadba8244782c25d67a6cfee0898fd64 Author: etpalmer63 Date: Tue Jul 6 15:00:23 2021 -0400 added comments, fixed spelling src_multispec/multispec_functions.H commit 8ce54aa2f2e594661f17f600ef07410694efa68d Merge: 2eda69ae 7f9a303a Author: Andy Nonaka Date: Tue Jul 6 07:35:08 2021 -0700 Merge pull request #40 from etpalmer63/f90_cpp_convert F90 cpp convert commit 7f9a303a0d0c816226d8f3293f990f8153cdfa08 Author: Andy Nonaka Date: Tue Jul 6 07:32:29 2021 -0700 cleanup only src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 68f78bf7fdaacb06ba709bda0643c2029222045d Merge: 820890c7 255f5c16 Author: Andy Nonaka Date: Tue Jul 6 07:28:36 2021 -0700 Merge branch 'f90_cpp_convert' of https://github.com/etpalmer63/FHDeX into f90_cpp_convert commit 820890c7322d5560aa65b727e65a16467f4c48cf Author: Andy Nonaka Date: Tue Jul 6 07:28:29 2021 -0700 remove swp file src_multispec/src_F90/.mass_flux_utilities.F90.swp commit 255f5c1679ac07446267f8cc6dbfbab2a86c94cb Author: Andy Nonaka Date: Tue Jul 6 07:28:18 2021 -0700 Update exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_regression_equil_3d commit 4932628bfaec533f1456d2a0f30dd741dcf38491 Author: etpalmer63 Date: Tue Jul 6 09:39:44 2021 -0400 remove my debug comments exec/multispec/inputs_regression_detbubble_3d commit c281cca4c8812853a42dcd970e1181c85449de79 Author: etpalmer63 Date: Tue Jul 6 09:31:02 2021 -0400 clean up debug, add comments src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit a4e58bd07cd5988331b78231512cd187119b965e Author: etpalmer63 Date: Tue Jul 6 09:18:30 2021 -0400 flipped indicies to correctly account for column-major order of MultiFabs src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 2277a417943d0a12f2cb2263f202ba3bb0815285 Author: andrew Date: Tue Jul 6 07:04:31 2021 -0400 Added checkpointing/restart and runs - Still need to check correct read for MFs and particle data exec/DSMC_ContinuousPSD/GNUmakefile exec/DSMC_ContinuousPSD/INS_functions.H exec/DSMC_ContinuousPSD/Make.package exec/DSMC_ContinuousPSD/checkpoint.cpp exec/DSMC_ContinuousPSD/delPlots exec/DSMC_ContinuousPSD/input exec/DSMC_ContinuousPSD/inputs_thermalconcBC exec/DSMC_ContinuousPSD/main_driver.cpp exec/DSMC_ContinuousPSD/paramPlane.nb exec/DSMC_ContinuousPSD/particleGen.cpp exec/DSMC_ContinuousPSD/stats.cpp exec/DSMC_ContinuousPSD/writePlotFile.cpp exec/DSMCtest/Checkpoint.H exec/DSMCtest/Checkpoint.cpp exec/DSMCtest/GNUmakefile exec/DSMCtest/Make.package exec/DSMCtest/biconc/input exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp exec/DSMCtest/therm/input_therm exec/immersedIons/Checkpoint.cpp src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcCollide.cpp src_particles/DsmcCollideCont.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 519c13db85ee8ac812c758ed2a4bd655c8e4eeb5 Author: andrew Date: Mon Jul 5 15:17:54 2021 -0400 BUG: Small domain -> negative particle flux (w/ var) - fixed Increased dimensions normal to gradient in inputs exec/DSMCtest/biconc/input exec/DSMCtest/conc/input exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp exec/DSMCtest/therm/input exec/DSMCtest/therm_conc/input src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit 4e89a93c520a33da118df98ccd0106eda2ed619e Author: andrew Date: Mon Jul 5 07:21:35 2021 -0400 Debugged concentration (not fully tested) Test inputs for gigan exec/DSMCGran/inputs_thermalBC exec/DSMCtest/conc/input exec/DSMCtest/inputs_thermalconcBC exec/DSMCtest/main_driver.cpp exec/DSMCtest/particleGen.cpp exec/DSMCtest/therm/input exec/DSMCtest/therm_conc/input src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 9e304f527d043fad87e6874cef3cd264bbdb0666 Author: andrew Date: Sun Jul 4 21:24:05 2021 -0400 Debugged concentration BC's - Added new inputs for user (rho0, Yk0) - Added mixed boundary conditions for thermal/concentration (no velocity atm) Tested case of homogeneous, full conc. boundary (same conc.) for constant n Needs further testing for mixed boundaries and multispecies exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/inputs_thermalBC exec/DSMCGran/inputs_thermalconcBC exec/DSMCtest/GNUmakefile exec/DSMCtest/INS_functions.H exec/DSMCtest/Make.package exec/DSMCtest/checkpoint.cpp exec/DSMCtest/delPlots exec/DSMCtest/inputs_thermalconcBC exec/DSMCtest/main_driver.cpp exec/DSMCtest/paramPlane.nb exec/DSMCtest/particleGen.cpp exec/DSMCtest/stats.cpp exec/DSMCtest/writePlotFile.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 06b47e2b9a3fb569d33c301833b58bf5ce227cc3 Merge: 594ac5ac 8ce54aa2 Author: andrew Date: Sun Jul 4 11:35:46 2021 -0400 Merge branch 'main' into DSMCGran commit 594ac5ac9c64970ac3d2256ea13975433f54d7d0 Author: andrew Date: Sun Jul 4 11:34:54 2021 -0400 Added inputs for total density in reservoirs Added concentration BC - Mixed BC also implemented as well Everything Compiles / nothing tested yet (will do later today) exec/DSMCGran/Make.package exec/DSMCGran/checkpoint.cpp exec/DSMCGran/inputs_ex exec/DSMCGran/inputs_single exec/DSMCGran/inputs_thermalBC exec/DSMCGran/inputs_thermalconcBC exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit d546b9603274dabfb798ffacd3e74cbddc4b5170 Author: etpalmer63 Date: Sat Jul 3 23:26:49 2021 -0400 Within epsilon of all regression tests. Error due to column vs. row major counting -- still needs fix src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 76888d1f582614f17cfe15c1d4ea762fa3db8a46 Merge: 954e7ebd 624c459b Author: etpalmer63 Date: Fri Jul 2 20:46:11 2021 -0400 Merge branch 'f90_cpp_convert' of https://github.com/etpalmer63/FHDeX into f90_cpp_convert commit 954e7ebdd1988140e2d3aef00a3c4e813a285e67 Author: etpalmer63 Date: Fri Jul 2 15:55:24 2021 -0400 Does not pass equil 3d regression test, but ideal mixture flag confirmed working src_multispec/multispec_functions.H commit 624c459b5649c39861f41463e24c982daefaed45 Author: etpalmer63 Date: Fri Jul 2 15:55:24 2021 -0400 Does not pass detbubble 3d regression test, but ideal mixture flag confirmed working src_multispec/multispec_functions.H commit b208031f5422d5ddb3ca3a645039e4169e213fee Author: etpalmer63 Date: Fri Jul 2 15:01:43 2021 -0400 passes my tests. Note change to regression test inputs exec/multispec/inputs_regression_equil_3d src_multispec/multispec_functions.H commit 500b114d46ff8ec7c5551c8bfd641336a1f96f9f Author: andrew Date: Thu Jul 1 22:02:24 2021 -0400 small bug in temperature output - divided by total part instead of by species - verified with elastic case exec/DSMCGran/inputs_bi_gran exec/DSMCGran/inputs_ex exec/DSMCGran/stats.cpp commit cfa620a69f064c85758c3572c0f8bb58dad6fb9b Merge: 2fc0abfa 2eda69ae Author: etpalmer63 Date: Thu Jul 1 16:15:41 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 2eda69ae31e0446e9bd9f555f1ea278bf298f4ff Author: Galen Wang Date: Wed Jun 30 13:32:04 2021 -0700 particle files for static results exec/immersedIons/paper_inputs_2/particles_1_1.dat exec/immersedIons/paper_inputs_2/particles_2_1.dat exec/immersedIons/paper_inputs_2/particles_3_1.dat commit 2fc0abfaba492b694c3036b69eef00043465b4d6 Author: etpalmer63 Date: Wed Jun 30 09:21:04 2021 -0400 large function into smaller functions. Compiles, needs testing src_multispec/multispec_functions.H commit 0d3440c5e25c0af35e5abad8afa098eb16835cb7 Author: etpalmer63 Date: Mon Jun 28 21:37:27 2021 -0400 Had to remove unused to get rid of compile error. exec/multispec/inputs_regression_detbubble_3d src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 19f1154e45393d1fd8d00cb2d1f82974c593a4c1 Merge: 7b7d5765 e4ffff2b Author: etpalmer63 Date: Mon Jun 28 16:41:04 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 7b7d57658c849347bcd6e7ea3b638ff9f12995ca Author: etpalmer63 Date: Mon Jun 28 16:35:26 2021 -0400 starting to kernels to separate functions src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit c33ed0ae133b531af420f8c49c39568d97f6555c Author: etpalmer63 Date: Mon Jun 28 15:37:30 2021 -0400 testing method. matches fortran output src_multispec/MassFluxUtil.cpp commit 6c1bdc89344f9365fcb3a3a29ec16bd22d0cb592 Author: etpalmer63 Date: Mon Jun 28 15:05:29 2021 -0400 modified input file for better cpp fortran comparison. exec/multispec/inputs_regression_detbubble_3d commit e4ffff2bf6d0f88936570da792ce48abf83dde7b Author: drladiges Date: Mon Jun 28 09:45:45 2021 -0700 Added dsmc namespace for additional input parameters exec/DSMC/paramPlane.ipynb src_particles/DsmcParticleContainer.H src_particles/MakeDSMC.package src_particles/dsmc_functions.H src_particles/dsmc_functions.cpp src_particles/dsmc_namespace.H src_particles/dsmc_namespace_declarations.H commit 929dd1207a81c739b86fb2d94477f8cb616ce53a Author: etpalmer63 Date: Fri Jun 25 22:53:20 2021 -0400 Suddenly tests start matching. I cannot explain it. src_multispec/MassFluxUtil.cpp commit 31ebca00e0f38b01b378439a4bbca6a82ef23855 Merge: 9c3ca044 410783e0 Author: etpalmer63 Date: Fri Jun 25 16:21:42 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 410783e0871b94960dd1681455b59f4aac64e3d6 Merge: 8047bc91 cdfb64f4 Author: drladiges Date: Fri Jun 25 13:14:11 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 8047bc914f4343bf213cb5bfc57e2c48bbc25911 Author: drladiges Date: Fri Jun 25 13:13:31 2021 -0700 DSMC mathematica input now completely switched over to python exec/DSMC/paramPlane.ipynb exec/DSMC/paramplanes.dat exec/DSMC/particles.dat src_geometry/paramplane_functions_K.H commit 9c3ca0448aecfa4803e7c14082661f94082e064d Merge: a1a20fb9 cdfb64f4 Author: etpalmer63 Date: Fri Jun 25 15:31:32 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit a1a20fb9c8aae1d3cd55e3d72ddb28aa178573a1 Author: etpalmer63 Date: Fri Jun 25 15:31:26 2021 -0400 first output match in testing src_multispec/MassFluxUtil.cpp commit cdfb64f489623bff2e4a83e373652cc21ed0d8b0 Merge: 34717dac a6fac053 Author: Johannes Blaschke Date: Fri Jun 25 08:19:21 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX commit 34717dac248faf657e755b8edbaa5a34c178d685 Author: Johannes Blaschke Date: Fri Jun 25 08:19:10 2021 -0700 resurrect the taylor line swimmer exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/inputs_taylor exec/immersed_boundary/flagellum/main_driver.cpp commit a6fac0534411e2e28bbabf9de78f7c379b7bfc55 Author: drladiges Date: Thu Jun 24 19:20:18 2021 -0700 more work on python notebook for geometry input exec/DSMC/paramPlane.ipynb commit f13705aa56c07b59efbfca3bac8e43f4303fdaf7 Merge: bd50c470 813d0c4c Author: drladiges Date: Thu Jun 24 17:37:13 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit bd50c47075047a142532b46a90ccaa12da3ba7cd Author: drladiges Date: Thu Jun 24 17:36:34 2021 -0700 Started replacing mathematica notebook for geometry definition with jupyter notebook exec/DSMC/paramPlane.ipynb commit 9a21336554fbcb8fb34565492e18fbb9ccf1be89 Author: etpalmer63 Date: Thu Jun 24 16:50:03 2021 -0400 passes regression tests. further investigation needed. Also, still need to move code around src_multispec/MassFluxUtil.cpp commit d3141220d5e3440c56dca37b4e656d67834042aa Merge: 5d976be7 813d0c4c Author: etpalmer63 Date: Thu Jun 24 08:50:40 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 813d0c4cb609b25135540b1d04c6ce4cd4cf8d7e Merge: 9e823dcd 65651443 Author: Changho Kim Date: Wed Jun 23 13:36:49 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 9e823dcdf715bdfca32901d4a57e513e6b4cb7ea Author: Changho Kim Date: Wed Jun 23 13:36:09 2021 -0700 src_common/ComputeBasicStats.cpp: in ComputeSpatialVariance, avg divided by npts, var divided by npts-1 src_common/ComputeBasicStats.cpp commit a3d8b7fb09cdf306fc2492095238f5b09c8d2346 Author: isriva Date: Wed Jun 23 12:10:51 2021 -0700 more correlations stats exec/compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 65651443cf56fba30a797f81ee262309832adba1 Merge: 05a2ea8d 558bd305 Author: drladiges Date: Wed Jun 23 11:52:05 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 05a2ea8da0edcac1a173207e77b2b1e82ce647e1 Author: drladiges Date: Wed Jun 23 11:51:37 2021 -0700 Finally fixed DSMC inflow bug exec/DSMC/inputs_test exec/DSMC/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 558bd305b4f796f8291abdfc931a45ab8f1d194a Author: Galen Wang Date: Tue Jun 22 16:35:48 2021 -0700 input files for static ionic structure exec/immersedIons/paper_inputs_2/inputs_1_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_0wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift exec/immersedIons/paper_inputs_2/inputs_3_1_50wet_noDrift_v2 commit 5d976be7649e59ae2159a1cb3901a6ce3523ea07 Merge: 7a22d036 827d9ed0 Author: etpalmer63 Date: Tue Jun 22 08:25:38 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit e01dcfd5ae4cc861f094a0850c94d34608a29d9e Author: isriva Date: Mon Jun 21 22:21:47 2021 -0700 restarts work properly now in cell-centered code + ability to reset stats upon restart exec/compressible/main_driver.cpp src_compressible/checkpoint.cpp commit c82b5ffc533add0e73ae7809a1713fad03c56b5a Author: isriva Date: Mon Jun 21 22:20:37 2021 -0700 remove k=0 values from structure factor for better viewing + remove additional diagnostics outputs exec/compressible_stag/main_driver.cpp commit 827d9ed04b74984cde33c2645a302b3d86607243 Author: Andy Nonaka Date: Mon Jun 21 15:18:06 2021 -0700 MultiFab::Subtract src_common/ComputeBasicStats.cpp commit 7a22d036bd27a8d3a3a0148f3fefb41197cbae5b Author: etpalmer63 Date: Mon Jun 21 15:22:02 2021 -0400 First attempt at ComputeGamma. Array2D, 6-dim array, Array4, so many questions. src_multispec/MassFluxUtil.cpp commit af552810a97bd814bda0e5d681b7bc09103ee842 Author: Andy Nonaka Date: Mon Jun 21 12:04:47 2021 -0700 fix bug src_common/ComputeBasicStats.cpp commit a570e1b58cc51d755996c7d04da5a7001e4dff60 Author: Andy Nonaka Date: Mon Jun 21 11:23:32 2021 -0700 ComputeSpatialVariance routine src_common/ComputeBasicStats.cpp src_common/common_functions.H commit f23cadccf66e05fce3abfc5394d638bdbc4fd3dd Author: etpalmer63 Date: Mon Jun 21 11:18:51 2021 -0400 molmtot should be an in/out variable src_multispec/multispec_functions.H commit 5f25f01d4a47dbdb7fc6a7fd8262bd918679a83c Author: etpalmer63 Date: Mon Jun 21 10:10:06 2021 -0400 added MACRO src_multispec/multispec_functions.H commit befb27af9a7ab03ae8c4d0d322b954973ab5008d Merge: 4be86440 89246d4b Author: etpalmer63 Date: Mon Jun 21 09:45:28 2021 -0400 Merge branch 'f90_cpp_convert' of https://github.com/etpalmer63/FHDeX into f90_cpp_convert commit 4be864401c41c37d6944abbeb5eb2a9267453301 Author: etpalmer63 Date: Mon Jun 21 09:37:57 2021 -0400 Corrected RhoN[n] = rhotot( ... typo. Passes my tests. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 89246d4b3f8e354b850571a3baaa383e98b994be Author: etpalmer63 Date: Mon Jun 21 09:37:57 2021 -0400 Corrected RhoN[n] = molmtot( ... typo. Passes my tests. src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 79a187ece87afd1a6629cfcb247d982287d93151 Author: isriva Date: Sun Jun 20 19:11:55 2021 -0700 move ncross as a function argument -- better extensibilty exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit 88d61f2eb200ef90138226417c4024f6134b549b Merge: 7ba8e823 019ff731 Author: isriva Date: Sun Jun 20 18:52:51 2021 -0700 Merge remote-tracking branch 'origin/main' into fixBC_compressible commit c13b0bf54cc1a48d46568f17c926078624ce3c6e Merge: 3443b1bb 2eda69ae Author: andrew Date: Sun Jun 20 03:34:25 2021 -0400 Merge branch 'main' into DSMCGran commit 3443b1bbf5675f6094bbf37ca9cccaabc1061a94 Author: andrew Date: Sun Jun 20 02:44:46 2021 -0400 Added flag where dissipation added after n_steps_skip Recreated bidisperse granular case so Lcell < lambda Small bug in temperature output fixed exec/DSMCGran/inputs_bi_gran exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/stats.cpp src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.cpp commit c4ea74e6008f63a9389b1417d29c0e829836049e Author: andrew Date: Sat Jun 19 23:45:17 2021 -0400 Temperature outputs correctly Set up input for bidisperse granular case exec/DSMCGran/inputs_bi_gran exec/DSMCGran/inputs_eq_multi exec/DSMCGran/writePlotFile.cpp src_particles/DsmcCollide.cpp commit 932e890d1fa92f95d9243139317b865c30d1dbf9 Author: andrew Date: Sat Jun 19 22:37:30 2021 -0400 Added temperature outputs (verify works in parallel) exec/DSMCGran/inputs_bi_gran exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/stats.cpp commit c135c1e19a4434578730bc60c62f29d3a080fea2 Author: andrew Date: Sat Jun 19 20:26:34 2021 -0400 Began writing routins for measuring global temperature exec/DSMCGran/Inputs_bi_gran exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/surfaces.dat src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H commit 221f3900ac5d339d314cd386e9d85ce478a29fc7 Author: isriva Date: Wed Jun 30 15:24:36 2021 -0700 more edits to stats and structure factor calculations exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp commit 45a5ddceb84ff88bce46d783517af0773f667ab2 Author: isriva Date: Wed Jun 30 14:39:19 2021 -0700 fixed structure factor for DSMC exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp commit 36e4aad065bbae89ccc384eaba1d87896d675431 Author: andrew Date: Sat Jun 19 07:54:54 2021 -0400 Renamed multifabs for plotfiles to be more readable Debugged plotfiles (looks much better) Separated plotfiles for cons, prim, and vars exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp src_particles/DsmcParticleContainer.H commit 12436cf1761a44428b2f6657386707d9892a633b Author: andrew Date: Fri Jun 18 22:50:47 2021 -0400 debug fft exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/stats.cpp commit c426fa528d46af4cfbbb6e9b037c35325387f7a3 Author: andrew Date: Fri Jun 18 18:46:02 2021 -0400 Reverted the evaluate stats so prim means are from instananeous prims Compiles and runs (checked the first few plotfiles) NEed to verify sf plotfiles still... exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp commit e334c990b58e968eabd59a6ea2bddd65eb7f0410 Author: etpalmer63 Date: Fri Jun 18 16:24:08 2021 -0400 Compiles once again. Misses regression tests src_multispec/multispec_functions.H commit 2446e1cceb5e3cfa876d7b519eab72e2f9d5af93 Author: andrew Date: Fri Jun 18 03:52:39 2021 -0400 Divided cu into prim and cons Primitives now calculated from conserved vars Mean and variance of energy density needs to be corrected still Plotfiles appropriately modified - Compiled and confiremd in amrvis exec/DSMCGran/Make.package exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp src_particles/DsmcParticleContainer.H commit e75f7399e6096eeb9b9228bcdff9df15ce266bd7 Author: etpalmer63 Date: Thu Jun 17 15:20:11 2021 -0400 Passes regression tests src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 6b7baff0fe159bb6aaab2bcc58c7752e953a5c68 Merge: 6518785f 019ff731 Author: etpalmer63 Date: Thu Jun 17 09:39:44 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 6518785f3cad1d2b925f09e7e882c78b75e93e97 Author: etpalmer63 Date: Wed Jun 16 22:33:48 2021 -0400 need to pass 4th dimension of an array4 to a function as a 1dim array, not working src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/.mass_flux_utilities.F90.swp commit 019ff7310177bd93fdcd2ae3a548ff6cd4bca7ec Merge: e241a803 2621b53b Author: Andy Nonaka Date: Wed Jun 16 15:37:51 2021 -0700 Merge pull request #41 from AMReX-FHD/implement_fftw FlattenedMF Structure Factor with FFTW commit 2621b53bd4d878a70afcdb23a9568618a0481541 Author: Andy Nonaka Date: Wed Jun 16 15:37:19 2021 -0700 turn on FFTW exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp commit 389a630218f411f5b4ad7c45e9ee1217f0ac16a1 Author: Andy Nonaka Date: Wed Jun 16 15:31:01 2021 -0700 fix brace position src_analysis/StructFact.cpp commit 3ffbabd0210b16f5d47c22fbfde9f79d2fb971af Author: Andy Nonaka Date: Wed Jun 16 15:27:59 2021 -0700 index bugfix src_analysis/StructFact.cpp commit 9fb5275eccfdaf67ff5118293d30890b6225b05b Author: Andy Nonaka Date: Wed Jun 16 15:04:58 2021 -0700 flattened MF with FFTW WIP exec/compressible/main_driver.cpp src_analysis/StructFact.cpp commit e241a8037faf928bd65647c5bd62ca7475cb26d3 Merge: d15e1081 1e46478d Author: Daniel Ladiges Date: Wed Jun 16 15:02:57 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d15e1081611ef883a2fa6e726540b7125d12ed47 Author: Daniel Ladiges Date: Wed Jun 16 15:02:20 2021 -0700 still trying to fix dsmc inflow bug. Pushing because this machine is going back to the lab exec/DSMC/paramplanes.dat src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit e36ea45237d1b77a434670f4329f0992e0de7707 Author: etpalmer63 Date: Wed Jun 16 17:52:37 2021 -0400 removed my comments src_compressible/.conservedPrimitiveConversions.cpp.swp src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_multispec/multispec_functions.H src_multispec/src_F90/mass_flux_utilities.F90 commit 1e46478d7b9a4301e9a17861444606a260f679ff Merge: 3f75dc19 faf0227c Author: Andy Nonaka Date: Wed Jun 16 14:28:50 2021 -0700 Merge pull request #39 from AMReX-FHD/implement_fftw Implement serial fftw option in structure factor commit faf0227c75cf0fb19d89b360bd2e5699fee51cc2 Author: Andy Nonaka Date: Wed Jun 16 14:23:03 2021 -0700 2D implementation src_analysis/StructFact.cpp commit 60e2dbd1a640a323bd3b8ddbd27804a84e3ac5b7 Author: Andy Nonaka Date: Wed Jun 16 14:10:34 2021 -0700 2d abort message src_analysis/StructFact.cpp commit 6fa06c2c342e9a629395c0dc6d176eca229bc0d4 Merge: c80fc452 7599c35b Author: andrew Date: Wed Jun 16 17:06:38 2021 -0400 Merge branch 'DSMCGran' of https://github.com/AMReX-FHD/FHDeX into DSMCGran commit 7599c35b6745d3e67fc79cda2c99698fa4ad1af5 Author: Andrew Hong Date: Thu Jun 24 23:12:47 2021 -0700 working version exec/DSMCGran/inputs_eq_multi exec/DSMCGran/particleGen.cpp commit c80fc452e4f2967268a4c6a1826e47309739bfef Merge: 7f5b3b44 a6fac053 Author: andrew Date: Wed Jun 16 16:55:10 2021 -0400 Merge branch 'main' into DSMCGran commit 7f5b3b4409c453c84217c3a3b9381a24e8faa881 Author: andrew Date: Wed Jun 16 16:53:54 2021 -0400 Broadcast timestep exec/DSMCGran/particleGen.cpp commit 6ddadd05bfc0f8e2b8337a950155fbf2114aaef0 Author: andrew Date: Wed Jun 16 16:17:38 2021 -0400 DSMC is running in serial but not proceeding in parallel - stalls within MoveParticles - if move routine commented out, can proceed normally... exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit c05990c22fd4815ec23a90e24ce28618ea86f1f4 Author: Changho Kim Date: Wed Jun 16 11:43:55 2021 -0700 exec/compressible_mui: sav before re-org exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/sav_src/202106_before_summer/app_surfchemtest.cpp exec/compressible_mui/sav_src/202106_before_summer/app_surfchemtest.h exec/compressible_mui/sav_src/202106_before_summer/diag_surfchemtest.cpp exec/compressible_mui/sav_src/202106_before_summer/diag_surfchemtest.h exec/compressible_mui/sav_src/202106_before_summer/main_driver.cpp commit 6134fb70c2abdaf02f45d919bb992a621e790b4d Author: etpalmer63 Date: Wed Jun 16 14:42:30 2021 -0400 directly pass molmtot(i,j,k) src_multispec/.MassFluxUtil.cpp.swp src_multispec/.multispec_functions.H.swp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 73f6eeb6d5fb3ab57b017e4b1cd1f1aeeec15cb9 Author: andrew Date: Wed Jun 16 14:42:11 2021 -0400 Fixed bug where bulk velocities not zerod during particle gen Fixed bug where temperatures were not being correctly measured Fixed bug where particles were given same speed but not same energy - far from equilibrium at start -> longer to equilibrate Fixed solid fraction for eq_multi - now mass and mol fractions are same as Balakrishnan(2014) Fixed time step so now Courant number is 0.2 Tested and confirmed using inputs_ex exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp src_particles/DsmcCollide.cpp commit 913ef56ecb06ac822595f497a1c20f2f1596bd96 Author: etpalmer63 Date: Wed Jun 16 11:34:43 2021 -0400 file clean-up .gitignore exec/multispec/Reg_Equil_2d_Diffile/Header exec/multispec/Reg_Equil_3d_Diffile/Header exec/multispec/myfile/Header exec/multispec/reg_equil_2d_diffile/Header src_compressible/.conservedPrimitiveConversions.cpp.swp src_multispec/.MassFluxUtil.cpp.swp src_multispec/.multispec_functions.H.swp commit ccf79bd05351c5e3c7d7fd9cc6c0dfc094199fc7 Author: etpalmer63 Date: Wed Jun 16 11:26:06 2021 -0400 Moved some calculations to GPU function src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit 0e864b6685866f6882f6e2505989ba1340debf75 Author: Andy Nonaka Date: Wed Jun 16 08:16:11 2021 -0700 syntax error src_analysis/StructFact.cpp commit 0f111fce06855eb9c13de4de7b30fe973cb104e6 Author: Andy Nonaka Date: Wed Jun 16 08:15:31 2021 -0700 function argument order fix exec/hydro/main_driver.cpp src_analysis/StructFact.cpp commit 4baa6cfec6b5e2a3e535f8e69300b7d6aa13fab5 Author: Andy Nonaka Date: Wed Jun 16 08:07:56 2021 -0700 fix header src_common/common_functions.cpp src_common/common_functions_F.H commit 42aa822820c162e73e912e7d967a1fa31ff06636 Author: Andy Nonaka Date: Wed Jun 16 08:04:23 2021 -0700 fft_type to common_namespace/namelist 1=fftw (default); 0=swfft exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_analysis/StructFact.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 58c5aaaa2de80fe0059f4d45dd341d2ea476e129 Author: Andy Nonaka Date: Wed Jun 16 07:31:29 2021 -0700 fft cleanup exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp commit 7ba8e8238ef27feefd619a134f51e17ac8062e48 Author: isriva Date: Wed Jun 16 07:29:58 2021 -0700 ability to reset stats upon restart in cell-centered compressible code exec/compressible/main_driver.cpp commit 13ceee83ecbd59ccf3265e09bd7b578c0ffd16ee Author: Andy Nonaka Date: Wed Jun 16 07:27:45 2021 -0700 fft cleanup src_analysis/StructFact.H src_analysis/StructFact.cpp commit c08b1710540bca897d5e51ea3844c6b845573876 Author: etpalmer63 Date: Wed Jun 16 09:16:12 2021 -0400 removed WIP comments .gitignore src_multispec/MassFluxUtil.cpp commit 0ecffcd64cfd47d2cb521a8a88893c7ea481d721 Author: etpalmer63 Date: Wed Jun 16 09:06:23 2021 -0400 Runs and passes comparison to regression tests. exec/multispec/Reg_Equil_2d_Diffile/Header exec/multispec/Reg_Equil_3d_Diffile/Header exec/multispec/reg_equil_2d_diffile/Header commit 9d5941c7bba64466d9287d9acd7622c567df3654 Merge: 7e0272c7 3f75dc19 Author: etpalmer63 Date: Wed Jun 16 08:42:09 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into f90_cpp_convert commit 3f75dc190b8e2cf2fde12e2ecaf6ab1680b131eb Merge: a9547317 460e011d Author: Daniel Ladiges Date: Wed Jun 16 00:46:35 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit a954731720d88744f015f418714f4f20fe93b684 Author: Daniel Ladiges Date: Wed Jun 16 00:46:06 2021 -0700 still trying to find inflow bug for DSMC exec/DSMC/inputs_test exec/immersedIons/GNUmakefile src_particles/DsmcParticleContainer.cpp commit 25fc007d939f3166d6ff819df2d0a80041aa691c Merge: c456936d 813d0c4c Author: andrew Date: Wed Jun 16 00:42:08 2021 -0400 Merge branch 'main' into DSMCGran commit c456936d82e887fdf1dec681b86b919ceae87ac9 Author: andrew Date: Wed Jun 16 00:40:56 2021 -0400 Small bugs in stats with indexing/using old names Set up input for the multispecies eq case Commented particle input because size too big exec/DSMCGran/GranularTemp.txt exec/DSMCGran/Make.package exec/DSMCGran/inputs_eq_multi exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/particles.dat exec/DSMCGran/stats.cpp exec/DSMCGran/writePlotFile.cpp src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit 1f3bfdf82f0ea024202edd5ebd0fddbece9fe17d Merge: 2d4b3b7f 2acfe520 Author: isriva Date: Wed Jun 23 16:56:42 2021 -0700 Merge remote-tracking branch 'origin/DSMCGran' into DSMCGran commit 2d4b3b7ff9a1029c4cd09e32069fa98e7b80121d Author: isriva Date: Wed Jun 23 16:51:02 2021 -0700 setup stats and writeplotfile for DSMC exec/DSMCGran/WritePlotFile.cpp exec/DSMCGran/main_driver.cpp exec/DSMCGran/stats.cpp src_particles/DsmcParticleContainer.H commit 7e0272c754ef02af14498d89659c5e1304601205 Author: etpalmer63 Date: Tue Jun 15 23:27:10 2021 -0400 WIP: Purposely incorrect code of fortran func port to cpp src_multispec/.MassFluxUtil.cpp.swp src_multispec/MassFluxUtil.cpp commit 460e011d2f9b6f273b77d003b290cc62308a4697 Author: Daniel Ladiges Date: Tue Jun 15 17:28:30 2021 -0700 Fixed neighborlist bug in main src_particles/FhdParticleContainer.cpp commit 07eb683ba939d7a453bbd459de4c836e0092a29d Merge: a5dc28a8 a3a6c389 Author: isriva Date: Tue Jun 15 16:19:47 2021 -0700 Merge remote-tracking branch 'origin/main' into fixBC_compressible commit a5dc28a847d2bb84af3c091e00beb47aa08bc749 Author: isriva Date: Tue Jun 15 16:18:17 2021 -0700 density-momentum and density-energy correlations in cell-centered code exec/compressible/main_driver.cpp src_compressible/stats.cpp src_compressible/writePlotFile.cpp commit bda0fc9d0ae06450386f032f3f928a5b334d0c00 Author: Andy Nonaka Date: Tue Jun 15 15:59:48 2021 -0700 fix fftw bug when nranks > 1 case src_analysis/StructFact.cpp commit f1457105755b631d198d2fdfa4fd4a682ca44e0a Author: Andy Nonaka Date: Tue Jun 15 15:48:20 2021 -0700 fix multicomponent debugging output for swfft src_analysis/StructFact.cpp commit ca9c5668b6a353139a112a595c23085408e05cb9 Author: Andy Nonaka Date: Tue Jun 15 15:29:25 2021 -0700 fix scaling of FFTW - need to divide by sqrt(npts) to match previous result from SWFFT src_analysis/StructFact.cpp commit a3a6c3896b46a3aa7f7d316f008e44b322c69da2 Author: Daniel Ladiges Date: Tue Jun 15 13:48:44 2021 -0700 Fixed compile bug in immmersed ions exec/immersedIons/GNUmakefile src_particles/FhdParticleContainer.cpp commit 2acfe520b495b8af84245a4fe6be82dc43c7fbea Merge: dae0938c 65651443 Author: andrew Date: Tue Jun 15 15:48:53 2021 -0400 Merge branch 'main' into DSMCGran commit dae0938cf8efc9fee71b897af3edfc2341b03d64 Author: andrew Date: Tue Jun 15 15:06:22 2021 -0400 Changed for loops within stats.cpp to a parallelfor (temporary fix for particle) - Compiles and runs exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particles.dat exec/DSMCGran/stats.cpp commit 73c71f6ea2548abb53f63d5d6ab8f16fc18d5ca7 Author: andrew Date: Tue Jun 15 14:51:46 2021 -0400 plotfiles added (for covar and means) and workign exec/DSMCGran/IO.cpp exec/DSMCGran/WritePlotFile.cpp exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particles.dat exec/DSMCGran/stats.cpp src_particles/DsmcParticleContainer.H commit 575b871f36d49e52e762e0e2ba7fd39ac5bc6567 Author: Andy Nonaka Date: Tue Jun 15 08:10:43 2021 -0700 FFTW WIP exec/structFactTest/main_driver.cpp src_analysis/StructFact.cpp commit a1a487270f3137b40cb61d77ed68f11598d82431 Author: Andy Nonaka Date: Tue Jun 15 07:42:06 2021 -0700 begin implementaton of serial fftw exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/multispec/main_driver.cpp exec/structFactTest/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 22cf4c9a53d62ea5345d5a8aad63c5fede13aaa9 Author: isriva Date: Tue Jun 15 07:37:58 2021 -0700 cell-centered fluxes require a ghost cell value -- fixed a small bug that affected only periodic systems src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit d3c4d85332110ca55f2e434ca815501542f752aa Author: isriva Date: Tue Jun 15 07:37:23 2021 -0700 added functions for sinusoidal density/temperature initializations src_compressible_stag/compressible_functions_stag.cpp commit a42a70a648b8c9310bd0c61edd851c8fbfcd5d42 Author: andrew Date: Tue Jun 15 09:57:46 2021 -0400 Revisit tomorrow. Error while using Amrvis (tried dim=1-3). May need to check each component in MF is valid number exec/DSMCGran/WritePlotFile.cpp exec/DSMCGran/inputs_ex exec/DSMCGran/particles.dat commit d72c3da96d2a9c4d6dae627c91433c6086c7bd6b Author: andrew Date: Tue Jun 15 08:17:53 2021 -0400 Added plotfiles/checkpoints Compiles (untested) exec/DSMCGran/Make.package exec/DSMCGran/WritePlotFile.cpp exec/DSMCGran/checkpoint.cpp exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/miscValid.txt exec/DSMCGran/particleGen.cpp exec/DSMCGran/particles.dat exec/DSMCGran/stats.cpp exec/DSMCGran/virial.txt src_compressible/writePlotFile.cpp src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H commit 195f0b7b9a2579c11ab12539732ce988caed6d86 Author: andrew Date: Mon Jun 14 20:33:10 2021 -0400 added stats for instant, mean, and covars exec/DSMC/main_driver.cpp exec/DSMCGran/IO.cpp exec/DSMCGran/Make.package exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/miscValid.txt exec/DSMCGran/particles.dat exec/DSMCGran/stats.cpp src_particles/DsmcCollide.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit eee270105df51a2a28d24510ca0c3db75996ad48 Author: etpalmer63 Date: Mon Jun 14 19:19:44 2021 -0400 added comments to describe task exec/multispec/myfile/Header src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_multispec/.MassFluxUtil.cpp.swp src_multispec/src_F90/mass_flux_utilities.F90 commit 7df15570a8936efebf350fc48ec023a692b7f73d Author: Andy Nonaka Date: Mon Jun 14 11:12:02 2021 -0700 sync up with main exec/compressible_mui/main_driver.cpp commit 44ce284f1405e0673e40f79286cc8073382de38a Merge: 9bbb5795 17c8838e Author: Andy Nonaka Date: Mon Jun 14 11:06:53 2021 -0700 Merge branch 'main' into compressible_mui commit f0795d981962dc661a9e5bb0c96ce142ef77f2e1 Author: isriva Date: Mon Jun 14 08:18:26 2021 -0700 added routines for flux diagnostics src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp commit d992ddc4ef83fbbbd3dcd279f04bf951f52d2b21 Author: isriva Date: Sun Jun 13 23:14:37 2021 -0700 compiles on GPU + fixed random shear stress at the walls src_compressible_stag/boundaryStag.cpp commit 65ab5e18e222622f4db44c54779b811fe18aa4c4 Merge: 5e59b35e 61409601 Author: isriva Date: Sun Jun 13 21:52:28 2021 -0700 Merge remote-tracking branch 'origin/main' into fixBC_compressible commit 5e59b35e9d36ef4e5dff3db53b866c7798db875a Author: isriva Date: Sun Jun 13 21:51:32 2021 -0700 staggered code works for isothermal walls; fixed Dufour corrections; checks ongoing exec/compressible_stag/main_driver.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 51a496f2bf72b754223a9b20bc4e012b9102523e Author: andrew Date: Sun Jun 13 14:15:13 2021 -0400 Set up evaluate stats, still need to organize variances and validate exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particles.dat src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 18402129834f34ba39009196cacf434c0e3d46d8 Author: andrew Date: Sun Jun 13 10:35:23 2021 -0400 Forgot to extract vrmax each time in species. Results previously did not change since system ... was fully periodic with elastic particles exec/DSMCGran/inputs_ex exec/DSMCGran/particles.dat src_particles/DsmcParticleContainer.cpp commit 3582e4a47e152cb579ba73cfd08a597b84259d40 Author: andrew Date: Sun Jun 13 10:32:26 2021 -0400 Fixed bug where in two species with identical species was baising more collisions for the second even ... when setting different seeds Implemented collisions to not be grouped by species but be randomly selected from total selections exec/DSMCGran/GranularTemp.txt exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/particles.dat exec/DSMCGran/virial.txt src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit ee9739ec0ecbde6653430095730b68c88e38f00d Author: andrew Date: Sat Jun 12 04:36:24 2021 -0400 Verified haff's law collision rule changed exec/DSMCGran/GranularTemp.txt exec/DSMCGran/main_driver.cpp exec/DSMCGran/particles.dat src_particles/DsmcParticleContainer.cpp commit d098158239dedc2c31a429769dad5c8f4cd065c3 Author: andrew Date: Sat Jun 12 04:02:20 2021 -0400 Cooling rate correct - change the probability to include impact vector (look at collide scheme) exec/DSMCGran/inputs_ex exec/DSMCGran/particles.dat src_particles/DsmcParticleContainer.cpp commit 89e6fa7ae449a127cbd5ace89c362aca70a66cd3 Merge: 89d40ba2 61409601 Author: andrew Date: Sat Jun 12 02:13:00 2021 -0400 Merge branch 'main' into DSMCGran - Did not resolve main driver in exec/DSMC since we are using exec/DSMCGran (copy paste later) Checked that every compiles and runs (Compatible) commit 89d40ba296daf871a19885b7a6e23a2343536151 Author: andrew Date: Sat Jun 12 02:00:57 2021 -0400 Confirmed vel. distr. equilibrates from a uniform velocity distr. Confiemd that the collision frequency is correct for elastic particles The cooling rate does not seem to agree with Haff's Law (fix) exec/DSMCGran/GranularTemp.txt exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp exec/DSMCGran/particles.dat src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 614096016ff01aafaac0428e3055061f6c365963 Merge: b7106f6d 17c8838e Author: Daniel Ladiges Date: Fri Jun 11 17:21:10 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit b7106f6d8507467321882851df76b3bce8fe89cd Author: Daniel Ladiges Date: Fri Jun 11 17:20:45 2021 -0700 Added outflow, still a bug in inflow exec/DSMC/inputs_test exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit 17c8838ee09b3cf75595a09707cf0d0f84c474e0 Author: Andy Nonaka Date: Fri Jun 11 16:40:38 2021 -0700 new periodic regression test exec/compressible/inputs_regression_equil_3d commit 93a59256117f468876188081b610aec6d146dda5 Author: jbb Date: Thu Jun 10 16:27:45 2021 -0700 fix shift exec/hydro/PDF/PDF.cpp commit d96726d0c662bc770aff4fd8862f2fff4d4a53c8 Author: jbb Date: Thu Jun 10 16:22:04 2021 -0700 Fixed bias in binning exec/hydro/PDF/PDF.cpp commit 25c8bc5f84665919f8e7958361b9957e2bc59480 Merge: 52fa9a47 70635108 Author: Daniel Ladiges Date: Thu Jun 10 12:19:59 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 52fa9a47d28f3b0af2ada4aeb2bccd804d14dede Author: Daniel Ladiges Date: Thu Jun 10 11:51:54 2021 -0700 Particle inflow now working exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 70635108f97aad5d530334c0b84ae0ab761c20b1 Author: jbb Date: Thu Jun 10 11:04:22 2021 -0700 fixed measure exec/hydro/PDF/PDF.cpp commit 98369fac97b66e9a4898a97d17c7d5c0e5279170 Author: Andy Nonaka Date: Thu Jun 10 07:40:37 2021 -0700 comments; fixed a parallel bug for the last bin reduction exec/hydro/PDF/PDF.cpp commit 515f42efd7bfb48aa50d63b1bed1a59e2316a98b Author: andrew Date: Thu Jun 10 03:22:54 2021 -0400 particle velocities not being updated during collisions - verified that granular temperature does not drop exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 64b503232505ae00e1e7f1d1d7fa49186a74b60f Merge: f4ffb8ec 3525d69e Author: jbb Date: Wed Jun 9 19:56:10 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit f4ffb8ecaa474f0a68e0af33919455dde5708968 Author: jbb Date: Wed Jun 9 19:55:42 2021 -0700 minor tweak exec/hydro/PDF/PDF.cpp commit 3525d69e32ae787534a6f54ac4dbe0bc8757035c Merge: 233686b7 e6323170 Author: Daniel Ladiges Date: Wed Jun 9 19:31:34 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit e63231704c1bc99a1daf5d8c49df9f46bf15f8d7 Author: jbb Date: Wed Jun 9 19:31:34 2021 -0700 fixed up program to generate pdf of laplacian to various powers exec/hydro/PDF/PDF.cpp commit 233686b71bac55a41521fed898d8e3d3f6688dcd Author: Daniel Ladiges Date: Wed Jun 9 19:31:21 2021 -0700 More work on particle inflow exec/DSMC/inputs_test exec/DSMC/main_driver.cpp exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.cpp commit 171a5fd86e77fa57bc5524197ac8c4dad688e774 Merge: 5fdcf068 94849f8d Author: jbb Date: Wed Jun 9 14:40:33 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 94849f8dedab839541af550635de97b0e5b56e99 Author: Andy Nonaka Date: Wed Jun 9 14:16:39 2021 -0700 PDF work exec/hydro/PDF/PDF.cpp commit 36ea39a17205aee1d116d48e396f5c62c06d6607 Author: Andy Nonaka Date: Wed Jun 9 14:05:30 2021 -0700 PDF WIP exec/hydro/PDF/PDF.cpp commit b6708ca4df397da4ed45ba5f52169ba51a053c24 Author: Andy Nonaka Date: Wed Jun 9 13:55:15 2021 -0700 PDF WIP exec/hydro/PDF/PDF.cpp commit 2bb33e49c3083c285bbd0c9493190fcbb306300d Author: Andy Nonaka Date: Wed Jun 9 13:21:59 2021 -0700 turbulence diagnostics exec/hydro/PDF/GNUmakefile exec/hydro/PDF/Make.package exec/hydro/PDF/PDF.cpp commit 3990bf245f6ce3c670065c23d1db570c05569110 Merge: ee040d9d 3784e44e Author: Andy Nonaka Date: Wed Jun 9 12:57:40 2021 -0700 Merge pull request #37 from AMReX-FHD/fixBC_compressible Fix bc compressible commit 3784e44e577e638bb297f437fec397e1ab4ef73d Author: Ishan Srivastava Date: Wed Jun 9 12:31:40 2021 -0600 Update src_compressible/flux.cpp Co-authored-by: Andy Nonaka src_compressible/flux.cpp commit c08c4db817df47a88f79ff0e3256a9c0b5bf52a7 Author: Andy Nonaka Date: Wed Jun 9 10:19:53 2021 -0700 formatting only src_compressible/flux.cpp commit c54994e5aeb515ed47e968211860f1b1d5140991 Merge: ee047b79 ee040d9d Author: Andy Nonaka Date: Wed Jun 9 10:18:27 2021 -0700 Merge branch 'main' into fixBC_compressible commit ee040d9d8455de75cd4905366fcd10e40d732780 Author: Andy Nonaka Date: Wed Jun 9 10:16:11 2021 -0700 weiner -> wiener in flux.cpp to make the fixBC_compressible PR a little easier to see src_compressible/flux.cpp commit b7b3ec1190b59879b160b7e2d1bbfaa93e0c2334 Author: Andy Nonaka Date: Wed Jun 9 09:48:56 2021 -0700 get DSMC compiling again don't put kernels inline on the gpu until they are in a launch region src_geometry/paramplane_functions_K.H commit 57da6b6c752e6af2b37b03bfc32c7d03ad735f17 Author: andrew Date: Wed Jun 9 10:09:33 2021 -0400 changed ParallelFor -> ParallelForRNG(engine) when random was called src_particles/DsmcParticleContainer.cpp commit a9c227af4cb7085ecec1b01845efcd4b13b001ed Author: andrew Date: Wed Jun 9 09:59:04 2021 -0400 Alpha input now takes all matrix elements Added boost velociites and inelasticity to collisions (checked) Runs over 20k time steps with no issues Need to test bulk quantities for validation exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 89bef4a1119088eafffd0dacfe3f88af34f197ec Author: andrew Date: Wed Jun 9 00:53:56 2021 -0400 Added granular temperature output and shows no change over 20k steps with ... collisions enabled. Energy seemse to be conserved. exec/DSMCGran/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 385af78ee53b669420f92b231c71aa34cb0aa560 Author: andrew Date: Wed Jun 9 00:27:21 2021 -0400 All collision routines run (tested with 20k timesteps) Elastic collisions conserve energy and momentum from center of mass frame - small energy loss when summing individual particle energies during coll. -- must fix exec/DSMCGran/inputs_ex src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit cfa02d78a3225014adc23151543a0f6cfa533baa Author: andrew Date: Tue Jun 8 22:36:35 2021 -0400 Selections loop tested Excluding the collision themselves (latter of collide), compiles exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp src_particles/DsmcParticleContainer.cpp commit 24dc69dfd4917b9df9dd8711e67fb0cc58621359 Merge: fbb80099 e73fd8ba Author: Daniel Ladiges Date: Tue Jun 8 19:18:11 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit fbb80099c0801824dbd7e8f57fc95448708fd672 Author: Daniel Ladiges Date: Tue Jun 8 19:17:51 2021 -0700 More source boundary stuff src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.cpp commit f9420b300831deb142bc9bec6bbb291e883f3c79 Author: andrew Date: Tue Jun 8 18:13:17 2021 -0400 Tested radial distribution function (compiles and runs) Tested selections (compiles and runs) Need to test collisions exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp exec/DSMCGran/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit e73fd8bade19cc19a4c294cc90f421759b5aeaa8 Author: Andy Nonaka Date: Tue Jun 8 13:10:12 2021 -0700 use ParallelForRNG instead of ParallelFor src_rng/MultiFabFillRandom.cpp commit f47df7c368d6a8c453495765452a2e9a555050e7 Author: Andy Nonaka Date: Tue Jun 8 13:09:58 2021 -0700 calling fprint instead of Print() inside GPU kernel src_compressible/transCoeffs.cpp commit ee047b797fc7fcdfac7e0872af7848258740de9b Author: isriva Date: Tue Jun 8 09:47:46 2021 -0700 added function for sinusoidal temperature variation initialization (constant pressure) src_compressible/compressible_functions.cpp commit 3ef988769b53b2376e0beb7b34fc326c879352c0 Author: isriva Date: Mon Jun 7 14:43:45 2021 -0700 more fixes src_compressible/boundary.cpp commit 60b8df0012ab0b94f85774c15121f3ada1c9806c Author: isriva Date: Mon Jun 7 14:16:32 2021 -0700 remove double operation of increased variance at the wall for viscous heating src_compressible/boundary.cpp commit 6018bcf235cac0b1be95d81fd47206b120dc93c0 Author: Andy Nonaka Date: Mon Jun 7 13:52:10 2021 -0700 comments and whitespace cleanup only src_compressible/boundary.cpp src_compressible/flux.cpp commit 534ce839f9747bd58333374d6309c17cb62c6dc0 Author: Daniel Ladiges Date: Mon Jun 7 12:40:27 2021 -0700 Outline for sources in DSMC exec/DSMC/paramPlane.nb src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 375707fb4ab7adced3c5880a575c5cbcb0b28692 Author: isriva Date: Sun Jun 6 23:30:17 2021 -0700 minor fixes src_compressible/boundary.cpp src_compressible/flux.cpp commit 19341fff86b03e3ccc0ef993fcd363a4230c0a85 Author: isriva Date: Sun Jun 6 23:25:28 2021 -0700 weiner --> wiener, with apologies to the hot dog :-) src_compressible/flux.cpp commit a26107748a515e4fd20709cc0f8f0e5a560c7d28 Author: isriva Date: Sun Jun 6 23:20:36 2021 -0700 separated various contributions to energy flux with appropriate BCs for each [cell-centered compressible] exec/compressible/main_driver.cpp src_compressible/boundary.cpp src_compressible/flux.cpp src_compressible/timeStep.cpp commit 1142641c8f3fb4b700a422bd25a606bf5db0f2b3 Merge: e70099ee 0c876705 Author: isriva Date: Fri Jun 4 16:55:18 2021 -0700 Merge remote-tracking branch 'origin/main' into main commit e70099ee44a53f26c2d846f99d17f37816087d17 Author: isriva Date: Fri Jun 4 16:54:39 2021 -0700 warning for negative mole fractions src_compressible/transCoeffs.cpp commit 0c876705d028d4aabb48db0102ba8ec919bc86c0 Author: Daniel Ladiges Date: Fri Jun 4 15:06:46 2021 -0700 one more paramater that I forgot... exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat src_geometry/paramPlane.H src_geometry/paramPlane.cpp commit 92cc2f1a04a0131247ba78e2f9b7c84de4db00d1 Author: Daniel Ladiges Date: Fri Jun 4 14:28:28 2021 -0700 Added source/sink parameters to surfaces for DSMC exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat src_geometry/paramPlane.H src_geometry/paramPlane.cpp commit 5fdcf0681dfe993913a8fd824e8221050e599dc7 Merge: 0add6049 663457af Author: jbb Date: Thu Jun 3 15:54:19 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main t# Please enter a commit message to explain why this merge is necessary, commit 663457afc06fd48c41f1c763fe4c110de3a2f76b Merge: c865ae6d 24808243 Author: Daniel Ladiges Date: Thu Jun 3 15:44:54 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit c865ae6de4f14f2e8842a395f070916bb714b13c Author: Daniel Ladiges Date: Thu Jun 3 15:44:31 2021 -0700 Added multispecies particle lists exec/DSMC/inputs_test exec/DSMC/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 0add6049c07a531fc9e09eead278c59fde8fa4ab Author: jbb Date: Thu Jun 3 15:12:38 2021 -0700 allowed for diatomic gas exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/inputs.eq commit 24808243c058644a687f8b2c7bb55554e86bf85f Author: jbb Date: Thu Jun 3 15:01:17 2021 -0700 fixing mess with 1d exec/_1d_staggered_comp/Makefile exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/flux.f exec/_1d_staggered_comp/inputs exec/_1d_staggered_comp/stats.c commit e02feb52c9100913f531d4c230f5223f391e9fa9 Merge: b6602897 7ba751ca Author: jbb Date: Thu Jun 3 14:56:27 2021 -0700 M rge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b66028979c001e6460f2d9b964fcaa8d85714376 Author: jbb Date: Thu Jun 3 14:55:47 2021 -0700 added temperature variance exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/inputs commit 7ba751ca9ff7eac24b2a4cdd4e4bea29dc406e2d Merge: 80711c1f f0c94811 Author: Andy Nonaka Date: Thu Jun 3 14:22:02 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 80711c1fa2c45e77677c1812b246c6c41ef5036c Author: Andy Nonaka Date: Thu Jun 3 14:21:33 2021 -0700 add some error checking to make sure that either mass or mole fractions sum to 1 if we are using a mass reservoir src_compressible/boundary.cpp commit f0c948112c9ce240da16c3b5e8ee4d013eff37fa Author: Changho Kim Date: Thu Jun 3 13:31:35 2021 -0700 src_compressible/stats.cpp: compute cell vairance of temp using instantaneous temp (i.e. not using the long formula based on conservative variables) src_compressible/stats.cpp commit 4811f28b200c43a41d153dd5f51a732bf5ed181a Author: Changho Kim Date: Thu Jun 3 13:29:36 2021 -0700 exec/compressible/main_driver.cpp: not using yzAverage for WritePlotFile exec/compressible/main_driver.cpp commit 9bbb57951c608602d1bfc26617c15cde2b3be2f6 Merge: 847703f2 ac227c1e Author: Andy Nonaka Date: Thu Jun 3 12:35:39 2021 -0700 Merge branch 'main' into compressible_mui commit ac227c1ec66dafcb41abaae8711ae05108492734 Author: Daniel Ladiges Date: Wed Jun 2 21:18:57 2021 -0700 added outline of stats functions exec/DSMC/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 6676140ef05edb1b6ed615eee9b52f91bdd332f4 Author: Daniel Ladiges Date: Wed Jun 2 21:04:10 2021 -0700 dsmc geometry now reads from file exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/delPlots exec/DSMC/inputs_test exec/DSMC/main_driver.cpp exec/DSMC/paramPlane.nb exec/DSMC/paramplanes.dat exec/DSMC/particles.dat src_geometry/paramPlane.cpp src_geometry/paramplane_functions_K.H commit 2a653e8884bf806d460a6a57a892be506b472a0f Author: Daniel Ladiges Date: Wed Jun 2 16:34:24 2021 -0700 surface generating notebook exec/DSMC/paramPlane.nb commit 97ddbe48bfa609dd69a1a4f80e303dd8664e94c4 Merge: f7ef65fc cfd69065 Author: Daniel Ladiges Date: Tue Jun 1 19:14:00 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit f7ef65fcf1c37719d65f2abaa5ea4665e23f9165 Author: Daniel Ladiges Date: Tue Jun 1 19:13:39 2021 -0700 some dsmc plotfile stuff exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/paramPlane.nb commit cfd690655a35b5df9b90554a6c9f56ccc309c7a0 Merge: 3b75ffef 70ad4671 Author: isriva Date: Tue Jun 1 12:15:14 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3b75ffef77fa7699158b3daaca1749c2d7176523 Author: isriva Date: Tue Jun 1 12:13:35 2021 -0700 fixed a subtle bug -- spurious momentum flux from pressure gradient in staggered formulation -- see comments in timeStepStag.cpp src_compressible_stag/timeStepStag.cpp commit 5da35c40acaa238e1331aa038993fd190ff21721 Author: isriva Date: Tue Jun 1 12:10:55 2021 -0700 direct computation of temperature fluctuations [temporary] src_compressible_stag/statsStag.cpp commit 1173dcd404c67418601decd8d355fdda25d5394e Author: isriva Date: Tue Jun 1 12:10:03 2021 -0700 remove abort for negative mass fractions src_compressible/transCoeffs.cpp commit 5fcb89d35db2c4812579769eaff6f78120d53b8a Author: isriva Date: Tue Jun 1 12:09:11 2021 -0700 high precision output in outMFAscii src_common/Debug.cpp commit 29e35dbf93104915ad7cc71006e150007db3c5f7 Author: isriva Date: Tue Jun 1 12:08:12 2021 -0700 Makefile path change exec/immersedIons/GNUmakefile commit 70ad4671f5bf2e1851b40efa3b9d5b112b8e2c46 Author: Daniel Ladiges Date: Tue Jun 1 10:19:58 2021 -0700 removed unecessary stuff from makefile for DSMC exec/DSMC/GNUmakefile exec/DSMC/delPlots exec/DSMC/paramPlane.nb exec/DSMC/surfaces.dat commit 66ff8d41db5617509e19cd5e3e44108d193dddc0 Author: Daniel Ladiges Date: Mon May 31 17:51:49 2021 -0700 commented out some debugging code src_particles/DsmcParticleContainer.cpp commit abcad759778ebd128d730b97c13d6681cb1b6c25 Author: Daniel Ladiges Date: Mon May 31 17:47:14 2021 -0700 Added cell list functionality to DSMC exec/DSMC/inputs_template exec/DSMC/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 0802fcd70f551436ad07c70a020358b114ef025d Author: Daniel Ladiges Date: Fri May 28 16:12:15 2021 -0700 Added particle mover function exec/DSMC/inputs_template exec/DSMC/main_driver.cpp src_geometry/paramPlane.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit fdff9422391469d161083b5f586dd37d81a22918 Merge: aa4389cf 69b79e54 Author: Daniel Ladiges Date: Fri May 28 11:54:23 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit aa4389cf3bde6366d885b21395fb4c0cff1b87e6 Author: Daniel Ladiges Date: Fri May 28 11:54:04 2021 -0700 DSMC framework exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/inputs_template exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_common/common_namespace.H src_geometry/paramplane_functions_K.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/Make.package src_particles/MakeDSMC.package commit 07b8506dec48a32d12674d5158e8c2b6d80d8ad4 Merge: c1fcce6e 1142641c Author: andrew Date: Fri May 28 00:19:41 2021 -0400 Merge branch 'main' into DSMCGran commit c1fcce6efac47c01eac99b52d584d3a4a90e7809 Author: andrew Date: Fri May 28 00:04:06 2021 -0400 Partial implementation of no species order selections Compiles (collisions untested) Tested InitCollision cells exec/DSMCGran/inputs_ex exec/DSMCGran/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 847703f233e69ba944e5aaaacd86a4a05bbfd247 Merge: 62d24c60 69b79e54 Author: Andy Nonaka Date: Thu May 27 17:40:20 2021 -0700 Merge branch 'main' into compressible_mui commit 69b79e540c9552f32a14dba183293f44e3ac6777 Author: Andy Nonaka Date: Thu May 27 17:39:43 2021 -0700 fix parallelizaton of stats for multiple grids in the slice plane src_compressible/stats.cpp commit 1928be717f1a2c81bb357601977a150ff376a062 Author: Andy Nonaka Date: Thu May 27 15:47:00 2021 -0700 fix one of the stats routines to work with multiple grids in the yz-plane. more fixes to come src_compressible/stats.cpp commit 84d983ffda798ab203db70854e4f08f5fff6cb5b Author: andrew Date: Thu May 27 10:01:07 2021 -0400 Compiles exec/DSMCGran/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit a2df8fe0d293f05d3418d80c568c1bb64d555246 Author: andrew Date: Thu May 27 09:09:05 2021 -0400 Finished writing first draft of to prep and carry out collisions within cells Also implemented the radial distribution function HAVE NOT TESTED/COMPILED (need to do) Still issues with reading new inputs Also need to finish InitCollision cells - on related note, will need to fix Neff and calc np based on given phi -- unclear if Neff can be different by species exec/DSMCGran/main_driver.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit 7762b8d2badb4483da889b84dbbac4c13023f80c Merge: dff1d532 ac227c1e Author: andrew Date: Thu May 27 07:29:05 2021 -0400 Merge branch 'main' into DSMCGran commit dff1d532e0d502a011bf678578a30de2b5bcbcac Author: isriva Date: Thu Jun 3 11:46:26 2021 -0700 minor change to inputs_ex to get it to work exec/DSMCGran/inputs_ex commit 54bbf8791164dcf2d589aa8b7091ead8bf5c2bec Merge: 92d2ed8e 66ff8d41 Author: andrew Date: Tue May 25 21:54:43 2021 -0400 Merge branch 'main' into DSMCGran commit 5a77014cd83faa04aa14d9549816243f4e012c9d Merge: a0c18bd3 0150c489 Author: Daniel Ladiges Date: Mon May 24 13:25:45 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit a0c18bd3b14a5bed8146d30da0deded85fb42999 Author: Daniel Ladiges Date: Mon May 24 13:25:30 2021 -0700 more dsmc framework src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/Make.package commit 62d24c60d986aeeab3ac4bc97ccd444be651fb24 Merge: e85a5df6 0150c489 Author: Andy Nonaka Date: Mon May 24 12:22:14 2021 -0700 Merge branch 'main' into compressible_mui commit 0150c489ed63d6a2ec47b5ca68fc3a7cd5e48a52 Author: Andy Nonaka Date: Mon May 24 12:21:43 2021 -0700 formatting; add in pressure to struct fact variable names exec/compressible/main_driver.cpp commit e85a5df666b6913bd94fa1ff0ed180ba7f8c70bb Author: Andy Nonaka Date: Mon May 24 12:21:01 2021 -0700 sync up with compressible exec/compressible_mui/main_driver.cpp commit 878e22221083d830d0f800ed34ed292e84d05f05 Merge: 1eb6cac5 ad322919 Author: Andy Nonaka Date: Mon May 24 11:45:17 2021 -0700 Merge branch 'main' into compressible_mui commit ad3229199598ae5f75284527e59b010b49781cbc Author: Andy Nonaka Date: Mon May 24 09:55:19 2021 -0700 RIP fortran exec/multispec/Init.cpp exec/multispec/Make.package exec/multispec/init_funcs.F90 exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions_F.H commit 92d2ed8e18efff277335cb4de8715e0cc7fea04e Author: andrew Date: Mon May 24 05:37:12 2021 -0400 05_28_21 - first commit for DSMC Granular exec/DSMC/inputs_template exec/DSMC/main_driver.cpp exec/DSMCGran/.particleGen.cpp.swp exec/DSMCGran/GNUmakefile exec/DSMCGran/INS_functions.H exec/DSMCGran/Make.package exec/DSMCGran/delPlots exec/DSMCGran/inputs_template exec/DSMCGran/main_driver.cpp exec/DSMCGran/paramPlane.nb exec/DSMCGran/particleGen.cpp exec/DSMCGran/surfaces.dat src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp unmaintained/DSMC-LDT/inputs_3d commit c3b525550c4cec3c7820d64042f99cb6719012e8 Merge: fabcee0f 7d2f1d67 Author: Daniel Ladiges Date: Sun May 23 18:37:58 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit fabcee0f11137e712bb0252e960079a974676012 Author: Daniel Ladiges Date: Sun May 23 17:12:48 2021 -0700 framework for dsmcParticleContainer src_particles/Make.package commit 774acd543bc22fade7e463d2968b49c078c7a3c7 Author: Daniel Ladiges Date: Sun May 23 16:04:19 2021 -0700 Some setup for DSMC exec/DSMC/bashscript exec/DSMC/delPlots exec/DSMC/inputs_2d exec/DSMC/inputs_3d commit 1eb6cac58e11d64eb7555c6c6c2e240233c317ee Author: Changho Kim Date: Sat May 22 17:59:56 2021 -0700 exec/compressible_mui: rm gnuplot_cmd, update info/how_to exec/compressible_mui/gnuplot_cmd exec/compressible_mui/info/how_to commit 699a5bca38cbbb95337c9ef240fa7d6bd7ad411e Merge: 8dfba882 7d2f1d67 Author: Changho Kim Date: Sat May 22 17:49:34 2021 -0700 Merge branch 'main' into compressible_mui commit 7d2f1d67b18fcf84a2582c90ffaccf97d992a2ed Author: Andy Nonaka Date: Fri May 21 21:07:15 2021 -0700 Init... tolerance changes to regression exec/multispec/Init.cpp exec/multispec/main_driver.cpp commit 80a5087260125e454b8403932bf7740e4cf0b16c Author: Andy Nonaka Date: Fri May 21 20:38:53 2021 -0700 Init function exec/multispec/Init.cpp exec/multispec/Make.package exec/multispec/multispec_test_functions.H commit f78bb2414a95103e6f1c56c0847845013cd5e723 Author: Andy Nonaka Date: Fri May 21 19:47:14 2021 -0700 don't need src_immersed-boudary/src_F90 exec/immersedIons/GNUmakefile commit d5838e5d9e1b3b4a945ab6732943390ee87aed97 Author: Andy Nonaka Date: Fri May 21 19:40:50 2021 -0700 code cleanup exec/immersed_boundary/flagellum/Make.package exec/immersed_boundary/flagellum/init_funcs.F90 exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum/main_driver_F.H exec/multispec/Make.package exec/tests/RFDanalysis/Make.package exec/tests/RFDanalysis/init_funcs.F90 src_common/common_functions_F.H src_common/src_F90/Make.package src_compressible_stag/Checkpoint.cpp commit a730d1d3aa7e8e8d710d87f0f0521055fbc0ce3a Author: Andy Nonaka Date: Fri May 21 18:51:47 2021 -0700 get this compiling again exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp exec/multispec/Checkpoint.cpp commit 0af5b2528ebe8a78760cf5675ff31ab31634f52c Author: Andy Nonaka Date: Fri May 21 18:39:55 2021 -0700 remove rng f90 code; regressions tests are changing clean up seed initialization in main_driver.cpp exec/immersedIons/Checkpoint.cpp exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersed_boundary/flagellum/GNUmakefile exec/immersed_boundary/flagellum/main_driver.cpp src_particles/FhdParticleContainer.cpp src_rng/Make.package src_rng/rng_functions.H src_rng/rng_functions_F.H src_rng/src_F90/Make.package src_rng/src_F90/bl_random.F90 src_rng/src_F90/rng_functions.F90 commit 5e521535a72f281c3291880856c121cec7744fec Author: Andy Nonaka Date: Fri May 21 18:20:32 2021 -0700 RIP more fortran exec/DSMC/GNUmakefile exec/immersedIons/GNUmakefile exec/lib_hydro/cmake/CMakeLists.txt exec/tests/RFDanalysis/GNUmakefile src_particles/particle_functions.H src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/particle_type.F90 unmaintained/DSMC-LDT/GNUmakefile commit cdd70ec3f68451c52e9e3cc075d8ab39cdbaf8a1 Author: Andy Nonaka Date: Fri May 21 18:05:35 2021 -0700 remove src_geometry/src_F90 exec/DSMC/GNUmakefile exec/immersedIons/GNUmakefile exec/tests/RFDanalysis/GNUmakefile src_geometry/paramplane_functions_F.H src_geometry/src_F90/Make.package src_geometry/src_F90/paramplane_functions.F90 src_geometry/src_F90/paramplane_type.F90 src_geometry/src_F90/precheck.F90 unmaintained/DSMC-LDT/GNUmakefile commit 8dfba882834d20610d977a2e083d9b0b3b6843ba Author: Andy Nonaka Date: Fri May 21 15:28:15 2021 -0700 remove f90 rng and add seed=0 (clock) exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp commit 809168b7558011c25222fa3dc5f4372bc4eb39ed Merge: 13bd410f 0c2f5453 Author: Andy Nonaka Date: Fri May 21 15:26:56 2021 -0700 Merge branch 'main' into compressible_mui commit 0c2f5453a4dbb9e5bba6e298e5224523686906e4 Author: Andy Nonaka Date: Fri May 21 15:25:47 2021 -0700 clock-based seed=0 enabled exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/main_driver.cpp exec/multispec/main_driver.cpp commit b66a55740d2b535f1ef866f30ef057054c09ee5e Author: Andy Nonaka Date: Fri May 21 15:12:59 2021 -0700 remove compilation and inclusion of F90 RNG exec/compressible/GNUmakefile exec/compressible/main_driver.cpp exec/compressible_stag/GNUmakefile exec/compressible_stag/main_driver.cpp exec/hydro/Checkpoint.cpp exec/hydro/GNUmakefile exec/hydro/main_driver.cpp exec/multispec/Checkpoint.cpp exec/multispec/GNUmakefile exec/multispec/main_driver.cpp src_compressible/checkpoint.cpp src_compressible_stag/Checkpoint.cpp commit 43718b38f1f55f873b363a964112a40fb9252b4e Author: Andy Nonaka Date: Fri May 21 13:50:26 2021 -0700 make problem domain larger to avoid negative mass fractions exec/compressible/inputs_regression_noslip_reservoir_isothermal commit c2eb70b2998f8a7911dd6fad2327062b2f635eda Author: Andy Nonaka Date: Fri May 21 13:30:29 2021 -0700 add Reset() function to SF so we can manually reset outside of FortStructure() src_analysis/StructFact.H src_analysis/StructFact.cpp commit 60c442ff2dd58229531e171303df1cbaea99229c Merge: e2069680 2b43c2a2 Author: Andy Nonaka Date: Fri May 21 13:14:29 2021 -0700 Merge pull request #35 from AMReX-FHD/sf_stag Several improvements and additions to the staggered compressible code commit 2b43c2a24cc84c533535c1b80ddef5d37f40c6c6 Author: Andy Nonaka Date: Fri May 21 13:09:30 2021 -0700 Combine ComputeVerticalAverage and ComputeVerticalAverageSlab exec/compressible_stag/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H commit c2c41cd9901aae72db730945a56c76933a6093c2 Merge: e8f51c3d e2069680 Author: isriva Date: Fri May 21 12:24:38 2021 -0700 Merge remote-tracking branch 'origin/main' into sf_stag commit e8f51c3d25b2c745d1699960e83a1fe9fa9df34f Author: isriva Date: Fri May 21 11:48:22 2021 -0700 removed unecessary diagnostics src_common/Debug.cpp src_common/common_functions.H commit c2aef1dd0aae4c1deec535307f630ea2115a8a7d Author: isriva Date: Fri May 21 10:37:12 2021 -0700 several new stats routines exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 1b018bc9bf90bc9336b9e9abc25c71a9e8ad52f3 Author: isriva Date: Thu May 20 14:05:59 2021 -0700 restart from single proc -- enable SF for non-cubic domains (erroneous on mutiple procs) exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H commit 1ddbfbcb7d04e0acb4412494371c8ad5922d54d1 Author: Daniel Ladiges Date: Thu May 20 12:47:30 2021 -0700 reorganizing for new dsmc directory exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/Make_precheck.package exec/DSMC/TimeStep.cpp exec/DSMC/WritePlotFile.cpp exec/DSMC/amrex_to_vtp.py exec/DSMC/cellvols.F90 exec/DSMC/convertSeries exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/precheck.F90 exec/DSMC/write_pview_file.py unmaintained/notebooks/particle_calcs.nb unmaintained/notebooks/velcocityCalc.nb commit 3758829356eed693563004c13c1a5791af21598d Author: Daniel Ladiges Date: Thu May 20 12:18:20 2021 -0700 renamed old dsmc files src_particles/DsmcParticleContainer.H.old src_particles/DsmcParticleContainer.cpp.old commit ef926ceb86a86c6fb92655e998c3d63118223acd Author: isriva Date: Thu May 20 09:24:01 2021 -0700 remove old membrane code src_compressible/src_F90/Make.package commit c75ff0d6bd146bb8d0d9b638df5ebe3e6183e435 Author: isriva Date: Thu May 20 09:23:44 2021 -0700 small changes to the SF routine exec/compressible_stag/main_driver.cpp commit 13bd410f90155a6923a5787623b406431da72c08 Author: Andy Nonaka Date: Wed May 19 16:25:25 2021 -0700 remove src_compressible/src_F90 exec/compressible_mui/GNUmakefile commit dc008c4cc264fd33078ac62fe583c7e4d10d3b1e Merge: 3a4a8269 e2069680 Author: Andy Nonaka Date: Wed May 19 16:24:11 2021 -0700 Merge branch 'main' into compressible_mui commit e20696800ab01f21c1cb57955befe96607c6ae49 Author: Andy Nonaka Date: Wed May 19 16:23:51 2021 -0700 remove src_compressible/src_F90 exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/membrane.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/membrane_funcs.F90 src_compressible_stag/compressible_functions_stag.H commit 1928142287f74c1be3d8884a42df0ff2cc39afc2 Merge: 8271341c d148f984 Author: isriva Date: Wed May 19 14:43:15 2021 -0700 Merge remote-tracking branch 'origin/main' into sf_stag commit 8271341c51279a0f093138bd2f4690bc05df7839 Author: isriva Date: Wed May 19 14:08:36 2021 -0700 small changes to slab SF exec/compressible_stag/main_driver.cpp commit d6d8f2377a172eedb49a7052e0c05f4b6d78514e Author: isriva Date: Wed May 19 13:32:35 2021 -0700 now calculates structure factors on two sides of a membrane (do_slab_sf keyword) exec/compressible_stag/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit d148f984e94c9bd0c96471314831fcdfd8332ba0 Author: Jailun Wang Date: Wed May 19 13:16:12 2021 -0700 parallel version of pairwise coulomb (currently hard-coded for y-wall) exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 3a4a82699f7018ac27481998dec14d04a6937057 Author: Andy Nonaka Date: Tue May 18 14:43:50 2021 -0700 sync up with main for compilation exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/cori_coverage/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/pseudo_kmc/inputs_equil_3d exec/compressible_mui/scripts/4spec/compressible/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd exec/compressible_mui/scripts/4spec/inputs_fhd_SF exec/compressible_mui/scripts/4spec/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_1+1/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_x/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_y/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_z/inputs_fhd_coverage commit baaf586f03ea784528fcd307f5a739bd961c8d81 Author: isriva Date: Tue May 18 13:59:04 2021 -0700 option to reset stats upon restart: keyword: 'reset_stats' exec/compressible_stag/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit dd97a2da41960a7065f1be9d62b33353653e75ac Merge: 9a2d8889 cda98452 Author: Andy Nonaka Date: Tue May 18 13:45:16 2021 -0700 Merge branch 'main' into compressible_mui commit cda98452f25133b29f65ac1b26d3f09f96c3e374 Author: Andy Nonaka Date: Tue May 18 13:43:59 2021 -0700 get rid of compressible namespace and namelist exec/compressible/inputs_RT_3d exec/compressible/inputs_SFtest exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d_mem exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic exec/compressible/inputs_regression_temp_grad exec/compressible/inputs_temp_grad exec/compressible/inputs_test_3d exec/compressible/inputs_test_deterministic exec/compressible/main_driver.cpp exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_equil_3d exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/inputs_test_verify exec/compressible_stag/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/Make.package src_compressible/src_F90/compressible_namelist.F90 src_compressible_stag/compressible_functions_stag.H commit b4fbd6276e43eeb2113d784c159f4394ddf1e3a1 Author: Andy Nonaka Date: Tue May 18 13:28:41 2021 -0700 sync up with 3d exec/hydro/inputs_incomp_equil_fluct_2d commit c2e61b902da0ca03f65bb6f0fc14ff37a3429559 Merge: 0068f39a a2a51fa1 Author: Andy Nonaka Date: Tue May 18 13:19:47 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0068f39ae02937d254490215dd3791930285f63a Author: Andy Nonaka Date: Tue May 18 13:19:35 2021 -0700 eliminate more F90 exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 commit a2a51fa1a82bc0b390ca60090d4259fd5080cbd2 Merge: 55ca799b debc5014 Author: Jailun Wang Date: Tue May 18 12:51:44 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 55ca799b8f6f065f8ef4d9137aa5d55996feaa47 Author: Jailun Wang Date: Tue May 18 12:50:36 2021 -0700 fix bug in restart; now works with new kernel exec/immersedIons/Checkpoint.cpp exec/immersedIons/particleGen.cpp commit debc501434fbcb4f4c01c69855c938102855843e Author: Andy Nonaka Date: Mon May 17 16:47:59 2021 -0700 implement flattened SF for hydro and 2d ComputeVerticalAverage() exec/hydro/main_driver.cpp src_common/ComputeAverages.cpp commit fbd0d989dbc79bcf798f520103df26e2a7a86ab6 Author: Andy Nonaka Date: Mon May 17 15:40:00 2021 -0700 re-org, move unused stuff to unmaintained unmaintained/channel_soft/Explore Data.ipynb unmaintained/channel_soft/Explore_Chemistry_checkpoint.ipynb unmaintained/channel_soft/GNUmakefile unmaintained/channel_soft/Make.package unmaintained/channel_soft/Test Sphere Markers.ipynb unmaintained/channel_soft/WritePlotFile.cpp unmaintained/channel_soft/advance.cpp unmaintained/channel_soft/compute_convfact_2.sh unmaintained/channel_soft/init_funcs.F90 unmaintained/channel_soft/init_s_funcs.F90 unmaintained/channel_soft/inputs_2d unmaintained/channel_soft/inputs_3d unmaintained/channel_soft/inputs_3d_test unmaintained/channel_soft/inputs_3d_test.2 unmaintained/channel_soft/inputs_3d_test.3 unmaintained/channel_soft/inputs_incomp_equil_fluct_2d unmaintained/channel_soft/inputs_incomp_equil_fluct_3d unmaintained/channel_soft/main_driver.H unmaintained/channel_soft/main_driver.cpp unmaintained/channel_soft/main_driver_F.H unmaintained/channel_soft/run_conv_tests_2.sh unmaintained/channel_soft/sphere_markers.txt unmaintained/src_chem/AmrCoreAdv.H unmaintained/src_chem/AmrCoreAdv.cpp unmaintained/src_chem/AmrCoreAdv_F.H unmaintained/src_chem/CMakeLists.txt unmaintained/src_chem/Make.package unmaintained/src_chem/README unmaintained/src_chem/src_F90/Adv_2d.F90 unmaintained/src_chem/src_F90/Adv_3d.F90 unmaintained/src_chem/src_F90/Make.package unmaintained/src_chem/src_F90/Prob.F90 unmaintained/src_chem/src_F90/SurfGrad_2d.F90 unmaintained/src_chem/src_F90/SurfGrad_3d.F90 unmaintained/src_chem/src_F90/Tagging_nd.F90 unmaintained/src_chem/src_F90/bc_fill_nd.F90 unmaintained/src_chem/src_F90/compute_flux_2d.F90 unmaintained/src_chem/src_F90/compute_flux_3d.F90 unmaintained/src_chem/src_F90/ptsource_fill_2d.F90 unmaintained/src_chem/src_F90/ptsource_fill_3d.F90 unmaintained/src_chem/src_F90/slope_2d.F90 unmaintained/src_chem/src_F90/slope_3d.F90 commit 53f547b289097c61f6dd7c9b0896e75c6790af38 Author: Daniel Ladiges Date: Mon May 17 15:16:19 2021 -0700 Bug in the WriteParticleAscii function crashes program. Appears to originate from within AMReX. We don't actully need it so commented out for now exec/immersedIons/WritePlotFile.cpp tools/notebooks/positionGenerator.nb commit 9a2d8889866111ad00d20e83eb5796e441afa77c Merge: 29f5a0b7 6ddae51d Author: Andy Nonaka Date: Mon May 17 14:52:17 2021 -0700 Merge pull request #33 from AMReX-FHD/main Testing merging main into compressible_mui commit 29f5a0b75a3b50f30cc01bdac0d0ae8d435524e7 Author: Andy Nonaka Date: Mon May 17 14:47:19 2021 -0700 fix pressure in SF exec/compressible_mui/main_driver.cpp commit 5d97f963b78c73122cf8c0811e721f83cbbcbb30 Merge: 1e17a418 be0d3970 Author: Ishan Srivastava Date: Sun May 16 21:07:29 2021 -0700 Merge branch 'sf_stag' of https://github.com/AMReX-FHD/FHDeX into sf_stag commit 1e17a418431c61724f235ea746af43e63b74c7fb Author: Ishan Srivastava Date: Sun May 16 21:06:32 2021 -0700 makefile for CUDA compile on cori exec/compressible_stag/GNUmakefile commit be0d39703142eb4fac33d6a6705d54ae6701e666 Author: isriva Date: Sun May 16 20:49:49 2021 -0700 fixed bug in structure factor -- in old compressible code too --> to be fixed exec/compressible_stag/main_driver.cpp commit d4634468c4fe1770f6312af4c4d533221d9e3a52 Author: isriva Date: Sun May 16 13:03:32 2021 -0700 added some functions for concentration gradients exec/compressible_stag/main_driver.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H commit 6ddae51d0c4d9d7b6da34b7453a469b5d968e9d5 Author: Daniel Ladiges Date: Fri May 14 19:24:08 2021 -0700 Change reinit particles to possibly fix problem with restart exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp commit 894b942f8d4e6110f5767c3ffd062e514593d32a Author: Jailun Wang Date: Fri May 14 16:35:17 2021 -0700 update inputs_template exec/immersedIons/inputs_template commit 6ac20638ad728507b5f72594f1ea285d9ba8c77b Author: Jailun Wang Date: Fri May 14 16:24:31 2021 -0700 add back slicepoint src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 4050b18f6430e8f1e5a2f8e61f927aad4ce3fd06 Merge: 4747cfd6 ec227242 Author: Jailun Wang Date: Fri May 14 16:12:07 2021 -0700 Merge branch 'past_commit' into main commit ec2272420215f3116da6357dfb928d3b1b95e076 Author: Jailun Wang Date: Fri May 14 16:11:16 2021 -0700 white space src_common/common_namespace.H commit 4747cfd61d3703922037661a60e8ef28d51210e5 Merge: 54f8d36b 6fcc9e74 Author: Daniel Ladiges Date: Fri May 14 15:44:28 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 54f8d36b1d2142179d8d8388c4b73811e0bdca5c Author: Daniel Ladiges Date: Fri May 14 15:43:25 2021 -0700 Added functionality to do mobility matrix inversion within discos exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersedIons/particles.dat src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/Make.package tools/notebooks/mobility_calc.nb tools/notebooks/positionGenerator.nb commit 6fcc9e74ab5251d5d6cc1216030e8e3a4c86dc6e Author: Jailun Wang Date: Fri May 14 15:31:20 2021 -0700 add exponential of a semicircle kernel exec/immersedIons/main_driver.cpp exec/immersedIons/wetRad_KernelES/wetRad_w4.dat exec/immersedIons/wetRad_KernelES/wetRad_w5.dat exec/immersedIons/wetRad_KernelES/wetRad_w6.dat src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/kernel_functions_K.H commit bbf6a1b888c20e657e7ab0e17d015b421cb78aef Author: Andy Nonaka Date: Thu May 13 17:25:29 2021 -0700 remove more fortran exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/conv_funcs.F90 unmaintained/exercises/compressible/main_driver.cpp commit 15334f268504be30b0dd845e745f3580af6d7ce3 Author: Andy Nonaka Date: Thu May 13 17:09:45 2021 -0700 remove fortran src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 commit 5d6fc720cbc7d7ec231e0128204790a8d729a870 Author: isriva Date: Thu May 13 13:42:31 2021 -0700 2D structure factor now works on staggered compressible code exec/compressible_stag/inputs_SFtest commit 9560d0237c40105f244638413e567749a0d962a0 Merge: 9b3c765c 46bd9cd3 Author: isriva Date: Thu May 13 13:36:47 2021 -0700 Merge remote-tracking branch 'origin/main' into sf_stag commit 9b3c765cb8a156ddfe5213137fdbe0bd082688b8 Merge: 093f9a60 eb4bf8e6 Author: isriva Date: Thu May 13 13:36:07 2021 -0700 Merge remote-tracking branch 'origin/main' into sf_stag 2D SF in compressible staggered code commit 46bd9cd39cc4e9e680b431ec4d3b1688072fac47 Author: Andy Nonaka Date: Thu May 13 13:17:11 2021 -0700 comments exec/compressible/main_driver.cpp commit b92c289bb17fef996af200f767ee71d56267e63d Author: Andy Nonaka Date: Thu May 13 13:11:30 2021 -0700 comments exec/compressible/main_driver.cpp commit f583d760189a5a518abc7391e178219212cb6344 Author: Andy Nonaka Date: Thu May 13 13:05:40 2021 -0700 added option for compressible code to either do vertical averaging, or slicing. in both cases project_dir needs to be >=0 and max_grid_projection defined to create the same number of boxes as MPI ranks if slicepoint < 0, we do vertical averating. Otherwise, we do a planar slice at slicepoint with normal project_dir exec/compressible/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 749d05dc4dc75bb895ed44ae9b0e1e7e7978e724 Author: Andy Nonaka Date: Thu May 13 12:17:21 2021 -0700 remove unmaintained findredistribution for vertical averaging, and force user to use max_grid_projection src_common/ComputeAverages.cpp src_common/common_functions.H commit 8065338b88aac18aed301b58469870304b34b25c Author: Andy Nonaka Date: Thu May 13 10:54:13 2021 -0700 comments exec/compressible/main_driver.cpp commit 5ad74cc0a5eafbcad31fa50afc48e7e2080c5fe1 Author: Andy Nonaka Date: Thu May 13 10:36:30 2021 -0700 fix bugs in vertically averaged SF code src_analysis/StructFact.H src_analysis/StructFact.cpp commit eb4bf8e68e58d29b4294817f5aab7718a4778a10 Author: Andy Nonaka Date: Wed May 12 15:42:37 2021 -0700 fix the project_dir = AMREX_SPACEDIM-1 case exec/compressible/main_driver.cpp commit 9608af26550bd884732114b5771c3636d45687ff Author: Andy Nonaka Date: Wed May 12 15:29:01 2021 -0700 vertical average SF - WIP exec/compressible/main_driver.cpp commit 8937b0557fa6be8f8b14a98a5e76a0b13083cb84 Author: Andy Nonaka Date: Wed May 12 14:20:36 2021 -0700 rotation of a flat multifab src_common/Make.package src_common/RotateFlattenedMF.cpp src_common/common_functions.H commit 40bdc7ebd72548ed3789b8ad5fa5519a10f885dc Author: Andy Nonaka Date: Tue May 11 12:59:06 2021 -0700 fix error messages; relax grid requirements src_analysis/StructFact.cpp commit 4201145311b5a1ac9fccd8fbcfa66f6ae69cd051 Author: Andy Nonaka Date: Tue May 11 12:54:58 2021 -0700 more elaborate error message src_analysis/StructFact.cpp commit 211018fd3084d6514b7f493dd69618bced49e5ea Author: Andy Nonaka Date: Tue May 11 11:20:54 2021 -0700 make code more readable src_common/ComputeAverages.cpp commit 46fbad3b50bf520681dd2b292257c138e5bbc86c Author: Andy Nonaka Date: Tue May 11 10:09:32 2021 -0700 use init_function for SF exec/compressible/main_driver.cpp commit 1dedb64edb9ec1f0b693c7159daafe39e1a193ac Author: Andy Nonaka Date: Tue May 11 10:00:45 2021 -0700 quiet compiler warning src_analysis/StructFact.cpp commit 6ad26342f67b7d23e8e69c77fe83fd1d4dd7f19a Author: Andy Nonaka Date: Tue May 11 09:58:06 2021 -0700 add define function src_analysis/StructFact.H src_analysis/StructFact.cpp commit 093f9a60c072b6a6fea50ccdc2faecb69c6bd8f2 Author: isriva Date: Mon May 10 20:45:24 2021 -0700 small changes to structure factor calculations + Makefile changes for corigpu exec/compressible_stag/GNUmakefile exec/compressible_stag/main_driver.cpp src_compressible/src_F90/Make.package commit 40c2caa5e0aac4d972f3606e47b765d024a0b9d7 Author: Andy Nonaka Date: Mon May 10 16:55:34 2021 -0700 rewrite stoch bc multipliers -> C++ / GPU src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 3939819cbce5d429cdd369ad2f3a12c9004b8b2b Merge: e7ba8c7d 47d76329 Author: Andy Nonaka Date: Mon May 10 16:24:47 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit e7ba8c7ddb7dfa41a959f4085ee3f14114cc0dee Author: Andy Nonaka Date: Mon May 10 16:24:29 2021 -0700 sqrt(2.d0) needed in double precision src_compressible/src_F90/flux_funcs.F90 commit 47d76329b8dfceae96a5b592ddbc894d002931e9 Author: Andy Nonaka Date: Mon May 10 12:24:21 2021 -0700 corigpu fftw fix exec/compressible_stag/GNUmakefile commit f5a253f24cbbd467b1277e49b74a8c12dc31088c Merge: e14dd829 7a163bd1 Author: isriva Date: Mon May 10 08:53:59 2021 -0700 Merge remote-tracking branch 'origin/main' into stag_membrane commit e14dd8293188bcfe32a59121a8bec717d976b577 Author: isriva Date: Sun May 9 23:06:19 2021 -0700 minor changes to stats routine src_compressible_stag/statsStag.cpp commit 7a163bd16bb05c5f5874d9fdba373bda28893a9a Author: Jailun Wang Date: Fri May 7 18:21:39 2021 -0700 switch back 12-6 and 9-3 lj src_particles/particle_functions_K.H commit 9014bf2326b448f5e79b972547466c573bd30b5a Author: isriva Date: Fri May 7 13:44:25 2021 -0700 some more stats routines exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/statsStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit d5e600e44409f67debe1bb0bb8c5c9469fbb3238 Author: isriva Date: Fri May 7 13:43:50 2021 -0700 added some debug functions src_common/Debug.cpp src_common/common_functions.H commit 641ca6d7b6d27f4e44930aceefdfd30560c1f015 Author: Andy Nonaka Date: Fri May 7 10:32:42 2021 -0700 3 steps exec/immersed_boundary/flagellum/inputs_regression_chlamy commit 36e7b1c215c5775df03f9285ed76de2f95a818e5 Author: Andy Nonaka Date: Fri May 7 10:04:52 2021 -0700 new regression test for immersed_boundary exec/immersed_boundary/flagellum/inputs_regression_chlamy commit 3330e3933620d83ea9e438b16a5f55eb91583c7b Author: Andy Nonaka Date: Fri May 7 09:58:38 2021 -0700 minor tidy src_compressible/src_F90/conv_funcs.F90 commit 063172a5471118fd4e7a5d1da43e0352b1299247 Author: Jailun Wang Date: Thu May 6 17:38:04 2021 -0700 fixed bug in 12-6 lj potential src_particles/particle_functions_K.H commit c35abcf7d9061758109e0fe7f5962983b585838c Author: Andy Nonaka Date: Thu May 6 16:59:28 2021 -0700 GetHcGas exec/compressible_stag/main_driver.cpp commit 93c883309ed42d64f9fc67d9fcb156f5236c350a Author: Andy Nonaka Date: Thu May 6 16:57:05 2021 -0700 more code cleanup, eliminate fortran, convert routines to C++ exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 commit 6080f4001776ab5742435a54e220c30c16cd6334 Author: Andy Nonaka Date: Thu May 6 16:45:22 2021 -0700 move SetBC C++ code into a function exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp src_compressible/boundary.cpp src_compressible/compressible_functions.H commit 695288c833b26dedcb6b4412637c3d6610d8b998 Author: Andy Nonaka Date: Thu May 6 16:20:24 2021 -0700 C++ version of SetupCWall exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 commit 140d97f4ae8a25386f2ed0533b1d93f012e0ec68 Author: Andy Nonaka Date: Thu May 6 15:27:37 2021 -0700 rewrote yzavg function so it's in C++ (not GPU) and fixed a parallel bug if there is more than 1 grid in yz at any particular x coordinate will update regression tests src_common/ComputeAverages.cpp src_common/common_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_compressible_stag/statsStag.cpp commit 15c562eb44dabef32618fc62440c64edd31f40aa Author: Andy Nonaka Date: Thu May 6 13:46:36 2021 -0700 get this compiling again using pkernel_fluid[0] src_immersed-boundary/IBParticleContainer.cpp commit efe011b5a3bb73c61fbbce9fb01dfdc3a6a157d8 Author: Andy Nonaka Date: Thu May 6 13:46:29 2021 -0700 timers src_analysis/StructFact.cpp commit 06bb024ecf7016e5ac10339cf93058faafbbb453 Merge: 9bbff8e9 b24d3a66 Author: Jailun Wang Date: Wed May 5 14:18:43 2021 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 9bbff8e9e6f108dfb0943e8532ff3b71566cbda8 Author: Jailun Wang Date: Wed May 5 14:17:08 2021 -0700 minor bug fixes exec/immersedIons/WritePlotFile.cpp src_particles/FhdParticleContainer.cpp commit b24d3a66a1efce1b6db03a30dc543caea9179166 Author: Andy Nonaka Date: Tue May 4 12:08:51 2021 -0700 put F90 into the attic src_particles/src_F90/Make.package src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/species_type.F90 commit 508834a6fed74f5499867a2fe4dbc22d9ebbbc32 Author: Andy Nonaka Date: Tue May 4 11:53:16 2021 -0700 move precheck.F90 to src_geometry/src_F90 since it's only called by F90 routines in there exec/immersedIons/GNUmakefile exec/immersedIons/Make_precheck.package src_geometry/src_F90/Make.package src_geometry/src_F90/precheck.F90 commit 44cd904198d42da9e4c946031a449f69442e62ca Author: isriva Date: Mon May 3 15:55:43 2021 -0700 further cleanup of stats routine src_compressible_stag/statsStag.cpp commit 888ba8ff8e52374966151bef8965627949ca8cba Author: Andy Nonaka Date: Mon May 3 15:19:45 2021 -0700 F90 -> C++ exec/hydro/Init.cpp exec/hydro/init_funcs.F90 exec/hydro/main_driver.cpp commit a61a067c8f0e5368790957fb64320e07e3eeec0b Author: isriva Date: Mon May 3 15:02:20 2021 -0700 renamed a staggered function src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/timeStepStag.cpp commit 58d0294cb27e26873b35a7d48481d57cffddcb97 Merge: 3fc43396 cc013730 Author: isriva Date: Mon May 3 14:48:36 2021 -0700 Merge remote-tracking branch 'origin/main' into stag_membrane commit 3fc43396b3cfe50040b749c9b7379c8664e889da Author: isriva Date: Mon May 3 13:35:49 2021 -0700 added methods for various spatial correlation calculations exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit cc0137306c5a281411bfb5c178c42731f5062785 Author: Andy Nonaka Date: Mon May 3 12:37:29 2021 -0700 add Init.cpp exec/hydro/Init.cpp commit 7b0103e348864ea23967df9271901519c6f8b6da Author: Andy Nonaka Date: Mon May 3 10:09:48 2021 -0700 cleanup; convert some init routines to C++ exec/hydro/Make.package exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp exec/hydro/WritePlotFile.cpp exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/hydro_test_functions_F.H exec/hydro/init_s_funcs.F90 exec/hydro/main_driver.cpp commit bb409288881a8f6dc538bc2483e9a3a5878d23e2 Author: Andy Nonaka Date: Fri Apr 30 18:32:41 2021 -0700 remove unused fortran exec/immersedIons/init_funcs.F90 exec/immersedIons/main_driver.cpp commit 4c402e446c2a12a3b55d2174d08fc46fe71e3ba3 Author: Daniel Ladiges Date: Fri Apr 30 17:53:51 2021 -0700 fixed typo in last push exec/immersedIons/main_driver.cpp commit 9be7ecd8f4fcbaecbcd49c032d455975f40db335 Merge: 4add8c9d 5e2e546f Author: Daniel Ladiges Date: Fri Apr 30 17:49:44 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 4add8c9de91c7a96d4d23622c2586ba4c4d13eac Author: Daniel Ladiges Date: Fri Apr 30 17:48:34 2021 -0700 REmoved bug zeroing unititialized multifab (which is being removed) Added 1 point option to hydro interp and spread operations exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat src_immersed-boundary/IBMarkerContainerBaseI.H tools/notebooks/channel_mobility.nb tools/notebooks/mobility_calc.nb tools/notebooks/positionGenerator.nb commit 5e2e546faef0f00fb06a76cd49d0b1b44a155e11 Author: Andy Nonaka Date: Fri Apr 30 17:37:49 2021 -0700 remove variance calculation and variance from plotfiles and checkpoints exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/main_driver.cpp exec/tests/RFDanalysis/INS_functions.H exec/tests/RFDanalysis/WritePlotFile.cpp exec/tests/RFDanalysis/WritePlotFileHydro.cpp exec/tests/RFDanalysis/main_driver.cpp src_common/ComputeBasicStats.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/compute_basic_stats.F90 commit 77c6e2e0b563a8957a6893903fdea0264bc75d27 Author: Andy Nonaka Date: Fri Apr 30 16:50:56 2021 -0700 remove unused functions src_common/ComputeBasicStats.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_basic_stats.F90 commit 16708103a7481d0b67920f76cd67ae2cfa3cd723 Author: Andy Nonaka Date: Fri Apr 30 16:45:12 2021 -0700 remove unused code find_nodal_coords exec/lib_hydro/cmake/CMakeLists.txt src_common/FindNodalValues.cpp src_common/Make.package src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/find_nodal_values.F90 src_common/src_F90/init_funcs.F90 src_particles/particle_functions.H commit db642605b6e60b2f0932e15b8b08d2270878ff95 Merge: b98690b1 8b082fb0 Author: Andy Nonaka Date: Fri Apr 30 15:50:34 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit b98690b1cbc0c618f80e7adfffeacea753bd52db Author: Andy Nonaka Date: Fri Apr 30 15:50:19 2021 -0700 find_center_coords -> C++ src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/find_coords.F90 src_particles/FindCoords.cpp commit 75098d641424f11b9a55ef55c3aa649f74f4e9cd Author: Andy Nonaka Date: Fri Apr 30 15:33:02 2021 -0700 find_face_coords F90 -> C++ src_common/common_functions_F.H src_common/src_F90/find_coords.F90 src_particles/FindCoords.cpp commit 95f97316d51c67c4f5e2b096cbeeb8c889ea33d9 Author: Andy Nonaka Date: Fri Apr 30 15:07:09 2021 -0700 convert Debug F90 -> C++ src_common/Debug.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/debug_mod.F90 commit 8b082fb0e90134910b872ce0ef4caf41e8507f45 Author: Daniel Ladiges Date: Fri Apr 30 14:21:38 2021 -0700 fixed bug in 9-3 wall potential src_particles/particle_functions_K.H commit a68d4b53d212d63a2dd82e873f79b534fd1f2948 Merge: 32a98393 0fbeddeb Author: Daniel Ladiges Date: Wed Apr 28 18:59:34 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 32a98393b8e9c9e13361c44a1f09b37daef7ae03 Author: Daniel Ladiges Date: Wed Apr 28 18:12:45 2021 -0700 removed some debugging code src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 23a7a9765d0131d5e88c4a41290a085a0871e5e2 Author: Daniel Ladiges Date: Wed Apr 28 17:26:56 2021 -0700 modified calculation of dry mobility divergence for stochastic drift src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H tools/notebooks/channel_mobility.nb commit 89d0c21af9d565c5afb6054b98ae3313255ce649 Author: isriva Date: Wed Apr 28 13:37:26 2021 -0700 fixed bug in the plot routine src_compressible_stag/writePlotFileStag.cpp commit fc1a09aeb51b751cdfe5f49baec02871d458b061 Author: isriva Date: Wed Apr 28 13:36:51 2021 -0700 most of the stats routine now on GPU exec/compressible_stag/main_driver.cpp src_compressible_stag/statsStag.cpp commit a48ddebc7499fecb5208547035cfc1ec9ce7ca9d Author: isriva Date: Wed Apr 28 13:35:54 2021 -0700 reset MAX_SPECIES=4 src_common/common_namespace.H src_common/src_F90/common_namelist.F90 commit 0fbeddebdb85c5c2276b307b85a57eff306353f9 Author: Andy Nonaka Date: Wed Apr 28 09:22:31 2021 -0700 use MAX_SPECIES from the common_namespace instead of having to re-declare it here src_multispec/multispec_namespace.H commit 8b89dc74bc8bfde028bb95ad4bbf4667c64d85bd Author: isriva Date: Tue Apr 27 22:54:23 2021 -0700 set MAX_SPECIES=2 for binary gases src_common/common_namespace.H src_common/src_F90/common_namelist.F90 commit 043da952a577bd3dc25d1ced8261ba7774d15408 Author: isriva Date: Tue Apr 27 22:53:37 2021 -0700 implemented logic for block averaging exec/compressible_stag/main_driver.cpp commit b19e720df0f84c08ac956cfde3a63061c1264a18 Author: isriva Date: Tue Apr 27 21:41:44 2021 -0700 fixed small bug for checkpointing exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/statsStag.cpp commit 28dff7838e7976de19b1c47faf3085e2f2c989a3 Author: Andy Nonaka Date: Tue Apr 27 17:31:47 2021 -0700 port compute_vertical_average to C++ src_common/ComputeAverages.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/compute_averages.F90 commit df55aa28bf5c57dc426d8f930c9dce1bf773cfb8 Author: Changho Kim Date: Mon Apr 26 23:05:40 2021 -0700 exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd: boundary condition corrected exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd commit 69bf1e837b1436d25b47c95b30723fa3f5835940 Merge: deff01fb c6dc4ef9 Author: Changho Kim Date: Mon Apr 26 22:54:24 2021 -0700 Merge branch 'main' into compressible_mui commit 1d5e37da4da290ddf81572aa86c3b7e13fabdb19 Author: isriva Date: Mon Apr 26 20:57:50 2021 -0700 checkpoint compiles on GPU and host. now need to run tests exec/compressible_stag/main_driver.cpp src_compressible_stag/Checkpoint.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H commit c6dc4ef9e0feb28cf49d3c04094852b84beefd06 Merge: afee1df2 bcbf916c Author: Daniel Ladiges Date: Mon Apr 26 20:28:13 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit afee1df270c55d2c4ce3f9d97f7a40e9fc1502c9 Author: Daniel Ladiges Date: Mon Apr 26 20:27:48 2021 -0700 Bugfix in short range wall caclulation exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H tools/notebooks/densityAnalysis.nb tools/notebooks/velAnalysisX.nb commit bcbf916c33c1fb30dfc2b7fa6eb09ca6a14e730e Merge: 609c197f fd225837 Author: Andy Nonaka Date: Mon Apr 26 16:53:56 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 609c197f12c2b3d1c609ec27e0858b3b7447237c Author: Andy Nonaka Date: Mon Apr 26 16:53:46 2021 -0700 code cleanup exec/lib_hydro/cmake/CMakeLists.txt src_common/src_F90/Make.package src_particles/src_F90/Make.package src_particles/src_F90/species_type.F90 commit 8f101d3b102301f3ae9a79080655ce86ae85c6c7 Author: Andy Nonaka Date: Mon Apr 26 16:47:17 2021 -0700 port fortran -> C++ exec/DSMC/TimeStep.cpp exec/lib_hydro/cmake/CMakeLists.txt src_common/common_functions_F.H src_common/src_F90/time_step.F90 commit fd22583794e12c3e9a302e062979a802e16d4a92 Merge: ec4b5ba9 8f101d3b Author: Daniel Ladiges Date: Mon Apr 26 16:46:46 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit ec4b5ba94b10a7d47ac78e5f4a75ce762bfcb7ac Author: Daniel Ladiges Date: Mon Apr 26 16:45:58 2021 -0700 particle redistribute and neighbourlist building now only happen when it is detected a particle has changed boxes exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit f33b597acc0b84d51d0ebb743fe281d449bd00f9 Merge: fdbeb8f8 894ba54b Author: Andy Nonaka Date: Mon Apr 26 14:04:25 2021 -0700 Merge pull request #31 from AMReX-FHD/wall_bc_compressible Set correct BC for isothermal walls commit 894ba54b44c9f727a87b5f739738708b7f585f29 Author: isriva Date: Mon Apr 26 13:34:01 2021 -0700 species flux set to 0 at the walls src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/timeStep.cpp commit fdbeb8f846458fb9792c1728ba72cb8aea16f453 Author: Andy Nonaka Date: Mon Apr 26 12:03:22 2021 -0700 replace comments in c++ namespace with "#" instead of "!" exec/DSMC/inputs_2d exec/hydro/inputs_algtest_2d exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_profiling_3d exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/immersedIons/inputs_template exec/immersedIons/paper_inputs/inputs_paper_diffusion exec/immersedIons/paper_inputs/inputs_paper_eo exec/immersedIons/paper_inputs/inputs_paper_sf exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det exec/immersedIons/test_inputs/inputs_3d exec/immersedIons/test_inputs/inputs_3d_poisson exec/immersedIons/test_inputs/inputs_3d_reflect exec/immersedIons/test_inputs/inputs_conductivity_test exec/immersedIons/test_inputs/inputs_density_test exec/immersedIons/test_inputs/inputs_density_test_damp exec/immersedIons/test_inputs/inputs_density_test_dry exec/immersedIons/test_inputs/inputs_density_test_eo_wet exec/immersedIons/test_inputs/inputs_density_test_es_damp exec/immersedIons/test_inputs/inputs_density_test_es_dry exec/immersedIons/test_inputs/inputs_density_test_es_wet exec/immersedIons/test_inputs/inputs_eo_realchannel_test_wet exec/immersedIons/test_inputs/inputs_eo_test_wet exec/immersedIons/test_inputs/inputs_freund_real_eo exec/immersedIons/test_inputs/inputs_jing_cruz_jcp exec/immersedIons/test_inputs/inputs_mobility_test exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond10 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond11 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond4 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond5 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond6 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond7 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond8 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr1 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr2 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr3 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr4 exec/immersedIons/test_inputs/inputs_potential_test exec/immersedIons/test_inputs/inputs_test exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip_nowca exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/inputs_3d_test.highres exec/immersed_boundary/channel_rigid/inputs_2d exec/immersed_boundary/channel_rigid/inputs_3d exec/immersed_boundary/channel_rigid/inputs_3d_test exec/immersed_boundary/channel_rigid/inputs_3d_test.2 exec/immersed_boundary/channel_rigid/inputs_3d_test.3 exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft/inputs_2d exec/immersed_boundary/channel_soft/inputs_3d exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/inputs_3d_test.2 exec/immersed_boundary/channel_soft/inputs_3d_test.3 exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum/inputs_2d exec/immersed_boundary/flagellum/inputs_3d exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.buddy exec/immersed_boundary/flagellum/inputs_chlamy.cori exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/inputs_chlamy.highres-thin exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/flagellum/inputs_chlamy.large-thin exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/lib_hydro/demo/inputs_3d_test exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_rtil_cap_128V exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d exec/tests/RFDanalysis/inputs_3d commit 3bef9ef518d3ec66d8eceeac3d1effb96448da14 Author: Daniel Ladiges Date: Sun Apr 25 17:09:31 2021 -0700 Converted computeBasicStats to GPU src_common/ComputeBasicStats.cpp src_common/common_functions.H commit a10a4c739e3f33651ccac99956d25c502216a607 Merge: cbcbbf5d 4e7ee9bd Author: Daniel Ladiges Date: Sun Apr 25 16:50:15 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit cbcbbf5d6d5cbcf18a9ebf09ca480715de87ff5e Author: Daniel Ladiges Date: Sun Apr 25 16:50:03 2021 -0700 start conversion of basicStats exec/immersedIons/main_driver.cpp src_common/ComputeBasicStats.cpp commit deff01fb61b1baf274d879dd140983d6afea53c9 Author: Changho Kim Date: Sun Apr 25 01:49:43 2021 -0700 FHDeX/exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd: bc_Yk_z_hi not needed for SF exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd commit faa5ec622c8a31d5eae6e52c04f36a5eba55b950 Author: Changho Kim Date: Sat Apr 24 23:44:08 2021 -0700 FHDeX/exec/compressible_mui/RUN_COadsPt111_SF: updated exec/compressible_mui/RUN_COadsPt111_SF/clean.sh exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_SF/inputs_fhd commit 4ec9cd5abeb5e96bf6b21600a9ee2f7bb8da79dc Author: Changho Kim Date: Sat Apr 24 17:18:13 2021 -0700 exec/compressible_mui: use t_lo[3] for veleocity sampling exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/main_driver.cpp commit 4e7ee9bdc8a342632003c6a4ea72991e4da5dce6 Merge: c7627745 d211ecfd Author: Andy Nonaka Date: Fri Apr 23 18:26:42 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit c7627745999849ccee4bb9038dcf11fe19f3ca27 Author: Andy Nonaka Date: Fri Apr 23 18:26:24 2021 -0700 add initialization timer exec/immersedIons/main_driver.cpp commit d211ecfd7267df5aa959ba99f160ad952eddcc16 Merge: 51aa7b95 f7e4b474 Author: Daniel Ladiges Date: Fri Apr 23 16:25:26 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 51aa7b954050c12386c6f943cab2800d0a12a441 Author: Daniel Ladiges Date: Fri Apr 23 16:24:43 2021 -0700 Interim state working on neighbourlist optimization. Still not right yet, talking to Andrew on Monday exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp commit 11fdc659504f09173bf4aa063e4bfb3e7a06066e Author: Daniel Ladiges Date: Fri Apr 23 14:58:19 2021 -0700 Cleared out old refs to cell lists exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp commit f7e4b47494dbf9a09bb49ecd4548130e95b666c8 Author: Andy Nonaka Date: Fri Apr 23 14:12:55 2021 -0700 add std out timers to plotfile exec/hydro/WritePlotFile.cpp exec/multispec/WritePlotFile.cpp src_compressible/writePlotFile.cpp src_compressible_stag/writePlotFileStag.cpp commit ff2a5a5665dc769a0c3cca091300b0a42e73eff7 Author: Andy Nonaka Date: Fri Apr 23 14:09:05 2021 -0700 write out plotfile writing wallclock exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp commit 23f819c98911c785280dc0ab736bec47ccdd749c Author: Andy Nonaka Date: Fri Apr 23 14:01:44 2021 -0700 fix timers for plotfile writing exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp src_compressible_stag/writePlotFileStag.cpp commit 7e520540938d859f6dd1ffd98b9a0e5269b9403a Merge: 1fcae314 2b856153 Author: isriva Date: Thu Apr 22 21:21:33 2021 -0700 Merge remote-tracking branch 'origin/main' into stag_membrane commit 1fcae314ff517d442c69d70d1c8d9dfcbe71bc55 Author: isriva Date: Thu Apr 22 21:20:22 2021 -0700 membranes now entirely uses C++ src_compressible/transCoeffs.cpp src_compressible_stag/membraneStag.cpp commit 2b8561534e6fd81015be8d901e228c28234d66e1 Merge: e5c09c3b a7a98523 Author: Andy Nonaka Date: Thu Apr 22 20:24:13 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit e5c09c3bc08c766c66ccb80915926ec4e39b0d8f Author: Andy Nonaka Date: Thu Apr 22 20:23:57 2021 -0700 add timer for esSolve src_electrostatic/electrostatic.cpp commit a7a985232caba60454ee4dff0796d187a38169c6 Author: Daniel Ladiges Date: Thu Apr 22 17:37:25 2021 -0700 Particle stats calculation now on GPU Also removed about half the particle stats and a couple more unnecessary fabs exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit b7cb04c603ea5a1389ef708a6c60c2ddb80a244b Merge: 798783d2 9353c1a8 Author: Daniel Ladiges Date: Wed Apr 21 16:16:46 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 798783d2f542416fcb2e4303e8a265e0137b829c Author: Daniel Ladiges Date: Wed Apr 21 16:16:21 2021 -0700 started gpu conversion of stats funcs src_particles/FhdParticleContainer.cpp commit 9353c1a8d2ce2dc7afce3e0e961dfa045e0bc8bc Merge: 1a643fdc 1ba91d05 Author: Andy Nonaka Date: Wed Apr 21 18:37:33 2021 -0400 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 1a643fdc5de69db5b0b69d393f9c51cdeafec951 Author: Andy Nonaka Date: Wed Apr 21 18:37:08 2021 -0400 don't initialize turblence stuff unless you need it this goes for checkpoint/restart as well exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp commit 1ba91d05e8361870f9fbeb5d0bb39394adf246cf Author: Andy Nonaka Date: Wed Apr 21 13:55:19 2021 -0700 clean up inputs files exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det commit bcdb6aa949e78f42b509cd322685846c92716170 Merge: 62f6018a e6e366cc Author: Daniel Ladiges Date: Tue Apr 20 17:45:23 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 62f6018a1efd5eea4bf44bfcef69df40a7f8fa49 Author: Daniel Ladiges Date: Tue Apr 20 17:41:58 2021 -0700 added 1 point kernel src_immersed-boundary/kernel_functions_K.H commit e6e366cc4e4dbe37ea6da769e5ead798184c4a86 Merge: 62e27972 1efddaaf Author: Daniel Ladiges Date: Tue Apr 20 16:32:56 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 62e27972f573a801151ab5b6dce84a9192416d66 Author: Daniel Ladiges Date: Tue Apr 20 16:32:46 2021 -0700 cleanup src_particles/FhdParticleContainer.cpp commit 1efddaaf826ad2f77e22791d61af9b06171b8a27 Merge: 9132876e f9cc5475 Author: Andy Nonaka Date: Tue Apr 20 14:53:34 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 9132876e5dd17c41e3713c301a82e83ac1498dbd Author: Andy Nonaka Date: Tue Apr 20 14:53:07 2021 -0700 fix bug in GPU implementation of staggered prolongation stencil src_gmres/StagMGSolver.H src_gmres/StagMGSolver.cpp commit 650cec4b3475442ccef59b6510c38326282a1534 Merge: bc4c5737 f9cc5475 Author: Daniel Ladiges Date: Tue Apr 20 13:57:36 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit bc4c5737255bd0ff3a73275a9abbd04868e0a886 Author: Daniel Ladiges Date: Tue Apr 20 13:57:29 2021 -0700 merging exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersedIons/particles.dat src_particles/particle_functions_K.H tools/notebooks/mobility_calc.nb tools/notebooks/positionGenerator.nb tools/notebooks/velAnalysisX.nb commit 6d1a1a0e290e10a6c506731f6359bff578a13dbc Author: Changho Kim Date: Mon Apr 19 10:38:59 2021 -0700 RUN_COadsPt111_coverage: changed accordingly exec/compressible_mui/RUN_COadsPt111_coverage/clean.sh exec/compressible_mui/RUN_COadsPt111_coverage/in.kmc commit 6c04e657ba6f3173cdeb781d357dfb31d491a936 Author: Changho Kim Date: Mon Apr 19 10:37:06 2021 -0700 exec/compressible_mui/main_driver.cpp: now getting only density1 and no mui_span exec/compressible_mui/main_driver.cpp commit 968c69d885c7b0378c082e1f4f442346e6c1b709 Author: Changho Kim Date: Mon Apr 19 10:35:22 2021 -0700 SPPARKS_MUI app_surfchemtest aggregated MUI fetch/push exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h commit f810464df2ccc8fd98b5667302153e4f4589f2d1 Merge: 5265076b f9cc5475 Author: Changho Kim Date: Sat Apr 17 02:29:08 2021 -0700 Merge branch 'main' into compressible_mui commit f9cc5475c377adcd0ddd36eeef00d0dd52abe353 Author: Andy Nonaka Date: Fri Apr 16 17:14:46 2021 -0700 get compiling on gpu again exec/immersedIons/particleGen.cpp commit 6704fd46237a45123b97549d920eacbc14e70031 Merge: accdc746 3902aec9 Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:40:10 2021 -0700 Merge pull request #30 from AMReX-FHD/c++_rng_seed0_init implement seed=0 for C++ rng engine commit 3902aec92019c3855db1b6fecf42204e48d42200 Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:37:04 2021 -0700 Update exec/immersedIons/main_driver.cpp Co-authored-by: Andy Nonaka exec/immersedIons/main_driver.cpp commit a98eb087dcbf858f5d6a693509ebd27e4aa9ebf8 Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:36:43 2021 -0700 Update exec/immersedIons/main_driver.cpp Co-authored-by: Andy Nonaka exec/immersedIons/main_driver.cpp commit b8e6e239269aa0833267282645d3fbc5e6822e3a Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:36:34 2021 -0700 Update exec/immersedIons/main_driver.cpp Co-authored-by: Andy Nonaka exec/immersedIons/main_driver.cpp commit 055a854ff79d4fdda29be460a4caf609e779736d Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:36:18 2021 -0700 Update exec/immersedIons/main_driver.cpp Co-authored-by: Andy Nonaka exec/immersedIons/main_driver.cpp commit accdc746518bfc7d6901491926ac12e27b45c7c8 Author: Andy Nonaka Date: Fri Apr 16 15:35:31 2021 -0700 fix typos in comments exec/immersedIons/Checkpoint.cpp commit 24c4ac150a51e8bc8da36e4c4353a1eb77b9894b Author: Jailun Wang Date: Fri Apr 16 15:25:52 2021 -0700 implement seed=0 for C++ rng engine exec/immersedIons/main_driver.cpp commit 9e2cfe2242d1d8a646ca3125e47d8f1001835df9 Merge: 7755a7a8 e021116e Author: jgalenwang <74326987+jgalenwang@users.noreply.github.com> Date: Fri Apr 16 15:06:56 2021 -0700 Merge pull request #29 from AMReX-FHD/checkpoint_PR Checkpoint pull request commit e021116e049160557007b7f83a9eca1fc8fae1a5 Merge: 7241f0f6 7755a7a8 Author: Andy Nonaka Date: Fri Apr 16 14:58:48 2021 -0700 Merge branch 'main' into checkpoint_PR commit 7755a7a809d96ed22bfe1ae003d9fabb82481fb9 Merge: 0e35db7f 2ada2612 Author: Daniel Ladiges Date: Fri Apr 16 14:55:34 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0e35db7f437fa64a1aec2eb85bd623146e810c0e Author: Daniel Ladiges Date: Fri Apr 16 14:54:46 2021 -0700 Fixed bug causing out of bounds error in debug mode. Incorrect settiong of es grid ghost cell ranges exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp commit 7241f0f60660f3dadaf558501e15f266085e6a5c Author: Andy Nonaka Date: Fri Apr 16 14:53:21 2021 -0700 change seed restart logic - only loop over ranks if seed<0 exec/immersedIons/Checkpoint.cpp commit 7ac9194fd3a76c7ed75fad0cc1f4d425afa28b6d Author: Jailun Wang Date: Fri Apr 16 14:18:53 2021 -0700 Checkpoint pull request exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/particleGen.cpp exec/immersedIons/test_inputs/inputs_conductivity_test src_particles/FhdParticleContainer.H commit a495aec38ac873bca01cfa32e543b7164e2d9f0b Author: isriva Date: Fri Apr 16 14:02:07 2021 -0700 multispecies with isothermal walls works correctly now exec/compressible_stag/main_driver.cpp src_common/common_functions.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/timeStepStag.cpp commit ff2211cfd63942157488b431ec572684d2899072 Merge: b63aa838 2ada2612 Author: isriva Date: Thu Apr 15 11:54:23 2021 -0700 Merge remote-tracking branch 'origin/main' into stag_membrane set species fluxes to zero at the walls commit 2ada26124b05370ae9ae25738b3f7a80c302d040 Merge: 62fedbb0 7a874f65 Author: Andy Nonaka Date: Thu Apr 15 07:52:51 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 62fedbb03f5783792007a4030e734a3ed0371cc0 Author: Andy Nonaka Date: Thu Apr 15 07:52:31 2021 -0700 switch to C++ rng for MultiFabFillRandom src_rng/MultiFabFillRandom.cpp src_rng/rng_functions.H src_rng/rng_functions_F.H src_rng/src_F90/Make.package src_rng/src_F90/multifab_fill_random.F90 commit 7a874f658797718d7960f19d739f11006bf2dc3f Merge: 8906d631 36b20ad1 Author: Daniel Ladiges Date: Wed Apr 14 18:12:36 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 8906d631a38c03ceabc9939d7d2a1d19dffd15f0 Author: Daniel Ladiges Date: Wed Apr 14 18:12:02 2021 -0700 DISCOS now compiles with CUDA=TRUE exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp tools/notebooks/mobility_calc.nb tools/notebooks/positionGenerator.nb commit 36b20ad1d673df9b6995c44d524a4c767c6c370e Author: Andy Nonaka Date: Wed Apr 14 15:45:52 2021 -0700 generalize the structure factor code so it works as long as mod(n_boxes, n_mpi) = 0 (i.e. perfect load balancing) If you are perfectly load balanced, and if there are less MPI ranks than boxes, the code will abort unless you add max_grid_size_structfact(1:3) = X Y Z to your inputs file. max_grid_size_structfact must divide up the domain into the number of boxes equal to the number of MPI ranks or the code will abort It will use this altered grid structure for the SWFFT call and copy the result back to your original multifabs src_analysis/StructFact.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 93d48bdc9e4293336509354d5e7ec8b09de57425 Author: Daniel Ladiges Date: Wed Apr 14 12:57:04 2021 -0700 Added basic C++ rng init (I need it now), we can discuss better version this afternoon exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H tools/notebooks/densityAnalysis.nb tools/notebooks/positionGenerator.nb tools/notebooks/velAnalysisX.nb commit a7559467e293a9df8c73b7455abff0621db1eb08 Author: Daniel Ladiges Date: Tue Apr 13 15:46:58 2021 -0700 Fixed cRange calculation for case where 'short range' distance is larger than p3m cutoff exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat src_particles/particle_functions_K.H commit c102983e61677921cee0e3c02253a6e96a3857cd Merge: 95081aef 59a0ccef Author: Daniel Ladiges Date: Tue Apr 13 13:50:03 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 95081aef94d4eec9c278bdfca3f279e7320ae051 Author: Daniel Ladiges Date: Tue Apr 13 13:49:33 2021 -0700 Added correct mobility function for Freund problem exec/immersedIons/particles.dat src_particles/particle_functions_K.H tools/notebooks/channel_mobility.nb tools/notebooks/positionGenerator.nb commit 59a0ccef6e9304bc0ade04739dc6ee637060c979 Author: Andy Nonaka Date: Tue Apr 13 13:24:12 2021 -0700 clean unused fortran src_compressible/boundary.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 commit d6af2247f8d97b29c120059b40c9291f20407803 Author: Andy Nonaka Date: Tue Apr 13 13:19:57 2021 -0700 move src_low-density to unmaintained unmaintained/src_low-density/Make.package unmaintained/src_low-density/boundary.cpp unmaintained/src_low-density/compressible_functions.H unmaintained/src_low-density/compressible_functions_F.H unmaintained/src_low-density/flux.cpp unmaintained/src_low-density/src_F90/Make.package unmaintained/src_low-density/src_F90/bound_funcs.F90 unmaintained/src_low-density/src_F90/flux_funcs.F90 unmaintained/src_low-density/src_F90/stats_funcs.F90 unmaintained/src_low-density/src_F90/time_step_funcs.F90 unmaintained/src_low-density/stats.cpp unmaintained/src_low-density/timeStep.cpp commit 637f8dd605e2a8603f4b9b30d798121347d84c0a Merge: 3a1cec05 c28d3f54 Author: Daniel Ladiges Date: Mon Apr 12 18:48:53 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3a1cec05aefe9cbd62b32dab10f6f6ef8b65592e Author: Daniel Ladiges Date: Mon Apr 12 18:48:13 2021 -0700 mathematica calculation of channel mobility tools/notebooks/channel_mobility.nb commit c28d3f549174341061e0149c8c75467d2398c381 Author: Andy Nonaka Date: Mon Apr 12 14:46:37 2021 -0700 move kc_tension to AMREX_GPU_MANAGED src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H commit c9661061b7d1c7c8cd13120eef10c6dd5e1fa035 Author: Andy Nonaka Date: Mon Apr 12 14:37:53 2021 -0700 remove timer from GPU kernel (not allowed on summit) src_compressible/compressible_functions.H commit ce106c5dbea700da4c9757d6c2014560c2ad0b89 Author: Andy Nonaka Date: Mon Apr 12 14:33:31 2021 -0700 move p_lo/hi to GpuArray src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit c6434147298c7e14bdadd074773b714b7f472f49 Merge: 2ebc385e 4ec1ac72 Author: Andy Nonaka Date: Mon Apr 12 14:30:45 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 2ebc385ed896ed361210746ddc96489a56504a44 Author: Andy Nonaka Date: Mon Apr 12 14:30:07 2021 -0700 make pkernel_fluid and pkernel_es both GpuArrays src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit 4ec1ac72f77fe334358b260e928b51fb2da31020 Author: Daniel Ladiges Date: Mon Apr 12 14:10:31 2021 -0700 moved pre/post processing mathematica notebooks tools/notebooks/NeumannCond.nb tools/notebooks/channel_mobility.nb tools/notebooks/chargeAnalysis.nb tools/notebooks/densityAnalysis.nb tools/notebooks/energyAnalysis.nb tools/notebooks/eo_analysis.nb tools/notebooks/mobility_calc.nb tools/notebooks/positionGenerator.nb tools/notebooks/potentialAnalysis.nb tools/notebooks/velAnalysis.nb tools/notebooks/velAnalysisX.nb tools/notebooks/velAnalysisY.nb commit 84a5116b9f931ab187fcc7f7f431a045ab4c9162 Merge: 15448d19 fa289aaf Author: Daniel Ladiges Date: Mon Apr 12 14:08:10 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 15448d19744df499516a626953558707e99709f7 Author: Daniel Ladiges Date: Mon Apr 12 14:07:02 2021 -0700 Minor edit to wall mobility stuff exec/immersedIons/WritePlotFileHydro.cpp exec/notebooks/densityAnalysis.nb exec/notebooks/potentialAnalysis.nb src_particles/particle_functions_K.H commit 5265076b25b11474545621c34a4f5504beefd937 Author: Andy Nonaka Date: Fri Apr 9 18:46:21 2021 -0700 remove src_analysis/src_F90 from makefile exec/compressible_mui/GNUmakefile commit 7e64a67fa2fe432aa82cf2824f791883ce34ff1e Merge: 1077a706 fa289aaf Author: Andy Nonaka Date: Fri Apr 9 18:43:36 2021 -0700 Merge branch 'main' into compressible_mui commit fa289aaf53a8fce9b8f0592af1fdb6e8f2369805 Author: Andy Nonaka Date: Fri Apr 9 18:42:44 2021 -0700 remove fortran in structure factor code exec/compressible/GNUmakefile exec/compressible_stag/GNUmakefile exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/multispec/GNUmakefile exec/structFactTest/GNUmakefile exec/tests/RFDanalysis/GNUmakefile exec/tests/RFDanalysis/main_driver.cpp src_analysis/Make.package src_analysis/StructFact.cpp src_analysis/StructFact_F.H src_analysis/src_F90/Make.package src_analysis/src_F90/struct_fact.F90 unmaintained/exercises/compressible/GNUmakefile unmaintained/exercises/incompressible/GNUmakefile commit 08ec4870c9eb3452460111355b4afeaf794ae6ef Author: Andy Nonaka Date: Fri Apr 9 18:12:54 2021 -0700 some prep work for eliminating f90 shift routine src_analysis/StructFact.cpp src_analysis/StructFact_F.H src_analysis/src_F90/struct_fact.F90 commit f71c4dcca296db95143b85c3061439c3853206da Author: Andy Nonaka Date: Fri Apr 9 18:00:43 2021 -0700 2d regression test exec/structFactTest/inputs_regression_2d commit c8b27d22bcdd261cd56d47fd20c376b9ab2e8f99 Merge: fcdff38e c9e550aa Author: Andy Nonaka Date: Fri Apr 9 11:09:57 2021 -0700 Merge pull request #26 from AMReX-FHD/remove_gmres_namelist Remove gmres namelist commit c9e550aa418aecdbed64da37efd85efbd0b91a87 Author: Andy Nonaka Date: Fri Apr 9 11:08:54 2021 -0700 first line of inputs file must use # as a comment instead of ! exec/DSMC/inputs_2d exec/hydro/inputs_algtest_2d exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_profiling_3d exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/immersedIons/inputs_template exec/immersedIons/paper_inputs/inputs_paper_diffusion exec/immersedIons/paper_inputs/inputs_paper_eo exec/immersedIons/paper_inputs/inputs_paper_sf exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det exec/immersedIons/test_inputs/inputs_3d exec/immersedIons/test_inputs/inputs_3d_poisson exec/immersedIons/test_inputs/inputs_3d_reflect exec/immersedIons/test_inputs/inputs_density_test exec/immersedIons/test_inputs/inputs_density_test_damp exec/immersedIons/test_inputs/inputs_density_test_dry exec/immersedIons/test_inputs/inputs_density_test_eo_wet exec/immersedIons/test_inputs/inputs_density_test_es_damp exec/immersedIons/test_inputs/inputs_density_test_es_dry exec/immersedIons/test_inputs/inputs_density_test_es_wet exec/immersedIons/test_inputs/inputs_eo_realchannel_test_wet exec/immersedIons/test_inputs/inputs_eo_test_wet exec/immersedIons/test_inputs/inputs_freund_real_eo exec/immersedIons/test_inputs/inputs_jing_cruz_jcp exec/immersedIons/test_inputs/inputs_mobility_test exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond10 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond11 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond12c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond4 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond5 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond6 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond7 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond8 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9a exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9b exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_cond9c exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr1 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr2 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr3 exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr4 exec/immersedIons/test_inputs/inputs_potential_test exec/immersedIons/test_inputs/inputs_test exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip_nowca exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/inputs_3d_test.highres exec/immersed_boundary/channel_rigid/inputs_2d exec/immersed_boundary/channel_rigid/inputs_3d exec/immersed_boundary/channel_rigid/inputs_3d_test exec/immersed_boundary/channel_rigid/inputs_3d_test.2 exec/immersed_boundary/channel_rigid/inputs_3d_test.3 exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft/inputs_2d exec/immersed_boundary/channel_soft/inputs_3d exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/inputs_3d_test.2 exec/immersed_boundary/channel_soft/inputs_3d_test.3 exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum/inputs_2d exec/immersed_boundary/flagellum/inputs_3d exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.buddy exec/immersed_boundary/flagellum/inputs_chlamy.cori exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/inputs_chlamy.highres-thin exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/flagellum/inputs_chlamy.large-thin exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/lib_hydro/demo/inputs_3d_test exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_rtil_cap_128V exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d exec/tests/RFDanalysis/inputs_3d unmaintained/exercises/incompressible/inputs_diffusion_2d commit 67d62b25ad8189ab484724efbae4f40de91a13c8 Author: Andy Nonaka Date: Fri Apr 9 10:59:20 2021 -0700 fix inputs files to eliminate &gmres exec/immersedIons/inputs_template exec/immersedIons/paper_inputs/inputs_paper_diffusion exec/immersedIons/paper_inputs/inputs_paper_eo exec/immersedIons/paper_inputs/inputs_paper_sf exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet 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exec/immersed_boundary/flagellum/inputs_chlamy.buddy exec/immersed_boundary/flagellum/inputs_chlamy.cori exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/inputs_chlamy.highres-thin exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/flagellum/inputs_chlamy.large-thin exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/multispec/inputs_compare_equil_3d unmaintained/DSMC-LDT/inputs_3d commit d5a7f7f097d5ab7a0b3a19c6f37b546369266baf Author: Andy Nonaka Date: Fri Apr 9 10:06:13 2021 -0700 update some inputs files to remove gmres namelist remove calls to read_gmres_namelist remove fortran header for gmres f90 code exec/DSMC/inputs_2d exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/hydro/inputs_algtest_2d exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_profiling_3d exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/demo/inputs_3d_test exec/lib_hydro/demo/main_driver.cpp exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d exec/multispec/inputs_Seawater_structure_2d exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_rtil_cap_128V exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d exec/multispec/main_driver.cpp exec/tests/RFDanalysis/inputs_3d exec/tests/RFDanalysis/main_driver.cpp src_gmres/Make.package src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H unmaintained/DSMC-LDT/main_driver.cpp unmaintained/DiffuisonTest/inputs_2d unmaintained/DiffuisonTest/inputs_debug_multigrid_2d unmaintained/DiffuisonTest/main_driver.cpp unmaintained/exercises/incompressible/inputs_diffusion_2d unmaintained/exercises/incompressible/main_driver.cpp commit 90a9fd099b6da0233e7192078f940ded59e40f40 Author: Andy Nonaka Date: Thu Apr 8 20:33:27 2021 -0700 do not put "mg_bottom_solver=4" in a comment after a valid parameter - parmparse gets confused exec/DSMC/inputs_2d src_gmres/gmres_functions.cpp src_gmres/gmres_namespace.H commit ac6fa3edf0ac37a4e44afd830c1a61a19ff5fb05 Author: Andy Nonaka Date: Thu Apr 8 20:25:29 2021 -0700 remove src_gmres/src_F90 from makefiles exec/DSMC/GNUmakefile exec/immersedIons/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/lib_hydro/gnumake/Makefile exec/multispec/GNUmakefile exec/tests/RFDanalysis/GNUmakefile unmaintained/DSMC-LDT/GNUmakefile unmaintained/DiffuisonTest/GNUmakefile unmaintained/exercises/incompressible/GNUmakefile commit ff774327f2f20fe19f017acd93c44f4ef69b2ca2 Author: Andy Nonaka Date: Thu Apr 8 20:18:27 2021 -0700 WIP - removing fortran namelist from gmres the src_gmres/src_F90 directory has been eliminated What still needs to happen is the inputs files need to change in the following ways: The "&gmres" and terminating "/" need to be deleted Scientific format must us a "e" instead of "d" exec/DSMC/inputs_2d exec/hydro/GNUmakefile exec/hydro/inputs_algtest_2d exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_profiling_3d exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/hydro/main_driver.cpp exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres 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exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/inputs_rtil_cap_128V exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d src_gmres/gmres_functions.cpp src_gmres/gmres_namespace.H src_gmres/src_F90/Make.package src_gmres/src_F90/gmres_namelist.F90 unmaintained/DiffuisonTest/inputs_2d unmaintained/DiffuisonTest/inputs_debug_multigrid_2d unmaintained/exercises/incompressible/inputs_diffusion_2d commit fcdff38e653338d5b9b2004e4cf8d964961c6ec9 Merge: 453602d5 b4056658 Author: Daniel Ladiges Date: Thu Apr 8 16:35:50 2021 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 453602d5bd0a02e8d508df29b93228e4eecce103 Author: Daniel Ladiges Date: Thu Apr 8 16:34:18 2021 -0700 reorganized directories exec/DSMCstatcheck/GNUmakefile exec/DSMCstatcheck/INS_functions.H exec/DSMCstatcheck/Make.package exec/DSMCstatcheck/Make_precheck.package exec/DSMCstatcheck/TimeStep.cpp exec/DSMCstatcheck/WritePlotFile.cpp exec/DSMCstatcheck/amrex_to_vtp.py exec/DSMCstatcheck/cellvols.F90 exec/DSMCstatcheck/convertSeries exec/DSMCstatcheck/delPlots exec/DSMCstatcheck/inputs_2d exec/DSMCstatcheck/inputs_3d exec/DSMCstatcheck/main_driver.cpp exec/DSMCstatcheck/makeBoth exec/DSMCstatcheck/paramPlane.nb exec/DSMCstatcheck/particleCheck.cpp exec/DSMCstatcheck/particleGen.cpp exec/DSMCstatcheck/precheck.F90 exec/DSMCstatcheck/surfaces.dat exec/DSMCstatcheck/write_pview_file.py exec/overdamped/GNUmakefile exec/overdamped/Make.package exec/overdamped/WritePlotFile.cpp exec/overdamped/advance.cpp exec/overdamped/hydro_test_functions.H exec/overdamped/hydro_test_functions_F.H exec/overdamped/init_funcs.F90 exec/overdamped/inputs_incomp_equil_fluct_2d 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unmaintained/exercises/incompressible/multispec_test_functions.H unmaintained/exercises/incompressible/multispec_test_functions_F.H commit b405665872f6baae940d94025a562f3d76fca852 Author: Andy Nonaka Date: Thu Apr 8 15:37:00 2021 -0700 Remove the function SetPressureBCs (set pressure to Dirichlet values p_lo/hi[]) and instead equip and use MultiFabPhysBC to do the same thing Remove src_hydro/src_F90 (all fortran is now gone from src_hydro) exec/exercises/incompressible/GNUmakefile exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/flagellum/GNUmakefile exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/advance_midpoint.cpp exec/immersed_boundary/flagellum/advance_stokes.cpp exec/multispec/GNUmakefile exec/overdamped/GNUmakefile exec/tests/RFDanalysis/GNUmakefile src_common/BCPhysToMath.cpp src_common/InhomogeneousBCVal.H src_hydro/HydroBCs.cpp src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/src_F90/Make.package src_hydro/src_F90/hydro_bounds_mod.F90 commit 1077a706065f054d87b122e6a693f8bf5e59c32d Author: Changho Kim Date: Mon Apr 5 04:15:39 2021 -0700 exec/compressible_mui/RUN_COadsPt111_SF/params.py: dEsq, dTsq exec/compressible_mui/RUN_COadsPt111_SF/params.py commit 2aa13c3248278b7e3f7b96251051a4a2c7d6b0bc Author: Daniel Ladiges Date: Fri Apr 2 14:54:43 2021 -0700 Fixed bugs in wall repulsion and dry move src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 279a964a7a4b3585434193ec5448e8603e69600b Author: Changho Kim Date: Sun Mar 28 14:42:26 2021 -0700 exec/compressible_mui/main_driver.cpp: diatomic molecules, rotational energy exec/compressible_mui/main_driver.cpp commit dd180728bf68f1bf514db51588dfecd4206eefcb Author: Changho Kim Date: Sun Mar 28 01:42:25 2021 -0700 RUN_COadsPt111_SF/havg_stat.py exec/compressible_mui/RUN_COadsPt111_SF/havg_stat.py commit 80d32025b9b71e051e12e9d6f894b7fe177a79b9 Author: Changho Kim Date: Sun Mar 28 01:41:42 2021 -0700 SPPARKS_MUI/app_surfchemtest.cpp: adsorption = adsrate * num_dens exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 76038d24f180203ef120b35716caa1ee7294e33b Author: Daniel Ladiges Date: Wed Mar 24 14:18:21 2021 -0700 Changes to pre-processing notebooks exec/notebooks/mobility_calc.nb exec/notebooks/positionGenerator.nb commit dfd3ccb69fd5b91fab667eb5914e21dfe9231af4 Author: Daniel Ladiges Date: Wed Mar 24 11:04:27 2021 -0700 Fixed various bugs in process to build fixed particle boundaries exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat exec/notebooks/mobility_calc.nb exec/notebooks/positionGenerator.nb src_particles/FhdParticleContainer.cpp commit 6b5cc465b680893b301f71c9930967ecd94427d5 Author: Andy Nonaka Date: Fri Mar 19 17:08:19 2021 -0700 read/write out each of the C++ AMReX rng states to checkpoint directory, one at a time, to different ASCII files this is in anticipation of later eliminating the f90 rng calls exec/hydro/Checkpoint.cpp exec/hydro/hydro_test_functions.H commit 1b8c8aa97c0263b70215b47704ca606247e94ca2 Author: Andy Nonaka Date: Fri Mar 19 16:09:03 2021 -0700 initialize seeds for C++ random number generator exec/hydro/main_driver.cpp exec/multispec/main_driver.cpp commit fc4cb2dd2fd1a9b66d6deff6b1359d7bac0a4941 Author: Andy Nonaka Date: Fri Mar 12 19:51:21 2021 -0800 deterministic restart for multispecies code working exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/Checkpoint.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit 22c37a98ac1bb2023c156ffeb1e22fd1455f422f Author: Andy Nonaka Date: Fri Mar 12 16:15:44 2021 -0800 now using boxarray and dmap from checkpoint to build all multifabs exec/hydro/Checkpoint.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 8da18147ebb1cf1fd8cf706cc63438589693218f Author: Andy Nonaka Date: Fri Mar 12 16:00:07 2021 -0800 fix checkpoint to work properly now with boxarray for turbforcing pulled from restart file exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp commit 0a456925a898123c11d8e02fdbd088a2d78dfa26 Author: Andy Nonaka Date: Fri Mar 12 15:37:54 2021 -0800 changes to turbforce class for more restart flexibility exec/hydro/Checkpoint.cpp exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 28c5533a040f9eb99c53f06ff10786c881d5e842 Author: Andy Nonaka Date: Fri Mar 12 15:17:08 2021 -0800 checkpoint routine for multispecies (not calling it yet) exec/multispec/Checkpoint.cpp exec/multispec/Make.package exec/multispec/multispec_test_functions.H commit b63aa83877d091ba490697de401b6b7a06905174 Author: isriva Date: Mon Mar 8 20:10:03 2021 -0800 corrected BCs for the membrane -- changed order of setBC and fillBoundary src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp commit 5ab438826df7a6c692553b035f3fc30bd94b33fc Author: isriva Date: Sun Mar 7 21:33:21 2021 -0800 fixed boundary conditions at the membrane src_common/common_namespace.H src_common/common_namespace_declarations.H src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp commit defcd8215db9c5482027bc5d3629f4e6fe538149 Author: isriva Date: Thu Mar 4 09:21:32 2021 -0800 setting up membrane without fluctuations src_compressible_stag/membraneStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 9a8daa3957bdaf9a6644260e76c791928cb8c5ee Author: Andy Nonaka Date: Tue Mar 2 11:47:40 2021 -0800 turn back on struct fact plotfiles for non-turb runs src_analysis/StructFact.cpp commit eed197467d5d283255dea9988948b8e47a8f00f4 Author: John Bell Date: Sat Feb 27 15:54:07 2021 -0800 got rid of unnecessary turbulence outputs src_analysis/StructFact.cpp commit 47c389c4f77b87fd57596c07b5e96d8763c41d52 Author: Andy Nonaka Date: Thu Feb 25 17:22:02 2021 -0800 change MultiFabPhysBC so it fills in ALL the ghost cells, not just one. Note all ghost cells receive the same value, which is the value on the boundary src_common/MultiFabPhysBC.cpp src_common/README_FILLROUTINES commit 9fa77ef94ec9a2673be0f2d377f8f9d3a9e7b0fe Author: Andy Nonaka Date: Wed Feb 24 15:50:26 2021 -0800 bugfix in 3d div_reversible_stress src_multispec/ComputeDivReversibleStress.cpp commit 016541f30eecb802545bda915112e91ba8c9d975 Author: Andy Nonaka Date: Wed Feb 24 15:50:12 2021 -0800 update spinodal inputs 2d, 3d exec/multispec/inputs_rtil_spinodal_charges_2d exec/multispec/inputs_rtil_spinodal_charges_3d commit 0bef94f798dc42a01bb6da3bb6603f4dc3ffa6f3 Author: Andy Nonaka Date: Wed Feb 24 08:43:09 2021 -0800 nonideal exec/multispec/inputs_rtil_cap_128V commit bd4e77becfaa03330f025a9799b7348c6ad26184 Author: isriva Date: Tue Feb 23 23:30:56 2021 -0800 small bugfix src_compressible_stag/membraneStag.cpp commit 9c82ce35e98ba4be458d510000bf1aaaa6921b9c Author: Andy Nonaka Date: Tue Feb 23 16:46:45 2021 -0800 cleanup exec/multispec/inputs_Seawater_structure_2d commit 166a280ad2291e01d658cf434bfb83b15048edcd Author: Andy Nonaka Date: Tue Feb 23 16:27:12 2021 -0800 include higher-order term src_multispec/DiffusiveMassFluxdiv.cpp commit 38539419e8b8d23c01f1c10d09019b3bfd88c0bf Author: Andy Nonaka Date: Tue Feb 23 15:38:34 2021 -0800 nonideal mixture exec/multispec/inputs_rtil_spinodal_charges_2d commit 2cb1c2a3e74ceb6212476d16daac767648cf8937 Author: Daniel Ladiges Date: Tue Feb 23 15:07:16 2021 -0800 Mod to allow dry stochastic drift to be seperately turned off exec/immersedIons/inputs_template src_particles/FhdParticleContainer.cpp commit a8fee94ce726d6ff610056936873de4dc1c762db Author: isriva Date: Tue Feb 23 14:36:47 2021 -0800 improvements to setting the BCs src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp commit 6d5bc77a9c91df096e9904a5bda0697d2225152c Author: Daniel Ladiges Date: Tue Feb 23 12:46:19 2021 -0800 Dry wall mobility model now selectable input rather than hard coded. exec/immersedIons/inputs_template exec/immersedIons/regression_inputs/inputs_regression_cond exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit c308da2493651e76f89a37919514e32e4646c33c Author: isriva Date: Tue Feb 23 12:45:57 2021 -0800 small bugfixes to membrane calculations src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp commit ac26428c658278e9662ce133f2f325dd381025bd Author: isriva Date: Tue Feb 23 08:06:11 2021 -0800 set additional stochastic fluxes to 0 at membrane (check for wall conditions too) src_compressible_stag/boundaryStag.cpp commit f33c0c7a95761c0b24b6cfab646ded00cc919f44 Author: isriva Date: Mon Feb 22 21:41:49 2021 -0800 setup right membrane condition src_compressible_stag/timeStepStag.cpp commit 76560e3dde00ac5b70fe37ea7b844e99a35133fe Author: isriva Date: Mon Feb 22 17:49:47 2021 -0800 first pass at multi-species membranes in the staggered code src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/src_F90/Make.package src_compressible_stag/Make.package src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/membraneStag.cpp src_compressible_stag/timeStepStag.cpp commit 96b689552e94d0b13a1ad6025d1184661c9a2302 Author: Daniel Ladiges Date: Mon Feb 22 16:17:02 2021 -0800 changed wall model back to infinite plane src_particles/particle_functions_K.H commit f80c1970d55740f803a9a0bb1e829e083631d9d3 Author: Daniel Ladiges Date: Mon Feb 22 15:50:21 2021 -0800 fixed makefule exec/immersedIons/GNUmakefile commit 1f9a7dbdbd1333f8a6b530956b54b80b54b1c63f Author: Daniel Ladiges Date: Mon Feb 22 15:47:47 2021 -0800 Removed some old project directories exec/brownian/GNUmakefile exec/brownian/INS_functions.H exec/brownian/INS_functions.cpp exec/brownian/Make.package exec/brownian/Make_paramPlane.package exec/brownian/Make_precheck.package exec/brownian/TimeStep.cpp exec/brownian/WritePlotFile.cpp exec/brownian/WritePlotFileHydro.cpp exec/brownian/advance.cpp exec/brownian/amrex_to_vtp.py exec/brownian/convertSeries exec/brownian/delPlots exec/brownian/hydro_test_functions.H exec/brownian/hydro_test_functions_F.H 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exec/immersedIons/regression_inputs/inputs_regression_eo exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann exec/immersedIons/regression_inputs/inputs_regression_noslip_neumann_det exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet exec/immersedIons/regression_inputs/inputs_regression_slip_dirichlet_det exec/immersedIons/test_inputs/inputs_freund_real_eo exec/immersedIons2/Checkpoint.cpp exec/immersedIons2/Eanalysis.nb exec/immersedIons2/GNUmakefile exec/immersedIons2/INS_functions.H exec/immersedIons2/Make.package exec/immersedIons2/Make_debug.package exec/immersedIons2/Make_precheck.package exec/immersedIons2/WritePlotFile.cpp exec/immersedIons2/WritePlotFileHydro.cpp exec/immersedIons2/channel_mobility.nb exec/immersedIons2/delPlots exec/immersedIons2/init_funcs.F90 exec/immersedIons2/inputs_3d exec/immersedIons2/main_driver.cpp exec/immersedIons2/particleGen.cpp exec/immersedIons2/precheck.F90 exec/low_density/GNUmakefile exec/low_density/Make.package exec/low_density/delPlots exec/low_density/exec_functions.H exec/low_density/inputs_3d exec/low_density/interpAnalysis.nb exec/low_density/main_driver.cpp exec/low_density/stressTensor.nb exec/low_density/writePlotFile.cpp commit dc85f9e15c5cd516eb49bc812d8d90e0b5009cbd Merge: 05112c73 42b032b1 Author: Daniel Ladiges Date: Mon Feb 22 15:45:37 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 05112c736555f331b939d67af4e3e3f32e2426d9 Author: Daniel Ladiges Date: Mon Feb 22 15:44:28 2021 -0800 Updated regression input files to contain all parameters Re orged the rest of the input files exec/immersedIons/Data.ipynb exec/immersedIons/Eanalysis.nb exec/immersedIons/Electrolyte_Data.xlsx exec/immersedIons/amrex_to_vtp.py exec/immersedIons/analysis.ipynb exec/immersedIons/analysis.nb exec/immersedIons/channel_mobility.nb exec/immersedIons/convertSeries exec/immersedIons/inputs_template exec/immersedIons/p3mcalc.nb 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exec/immersedIons/test_inputs/inputs_paper1/inputs_paper_gr4 exec/immersedIons/test_inputs/inputs_potential_test exec/immersedIons/test_inputs/inputs_test exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip exec/immersedIons/test_inputs/inputs_test_fullywet_neutral_noslip_nowca exec/immersedIons/varAnalysis.nb exec/immersedIons/velAnalysis.nb exec/immersedIons/write_pview_file.py exec/immersedIons/write_pview_file.pyc commit b5252b8586626be194e416778261aa6ad5370e58 Author: Daniel Ladiges Date: Mon Feb 22 14:54:08 2021 -0800 Consolidated short range functions. Set new input parameters for short range functions Stripped out some more Fortran. exec/immersedIons/inputs_freund_real_eo exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/Make.package src_particles/particle_functions_K.H src_particles/src_F90/Make.package commit 42b032b1b489f63a3973c07aeda6bc13c7898d8f Author: Andy Nonaka Date: Mon Feb 22 14:08:02 2021 -0800 fix typo in inputs file exec/multispec/inputs_rtil_spinodal_charges_2d commit 6377e2aa214ab25843708148d7257e0e35132ada Author: Daniel Ladiges Date: Mon Feb 22 11:54:08 2021 -0800 Whoopsie exec/immersedIons/main_driver.cpp commit ea2fd028d61e104344f66651a0cff019f97e6505 Merge: 0681bc66 067f3622 Author: Daniel Ladiges Date: Fri Feb 19 16:02:50 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0681bc66bc5b8ed17efed744a96c5f32899e0c03 Author: Daniel Ladiges Date: Fri Feb 19 16:01:13 2021 -0800 Rolled in changes from Galen's branch implementing seperate kernels for different species. Removed old fortran versions from FHDParticleContainer Removed need to enter crange parameter in input file exec/immersedIons/Checkpoint.cpp exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/FhdParticleContainer_WF.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 067f36227c78d48a5f8d8bc60c6aab619e749ced Merge: a438da36 185495ae Author: Andy Nonaka Date: Fri Feb 19 14:03:25 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit a438da36bd32be2778ab57e4de2b0535e6555388 Author: Andy Nonaka Date: Fri Feb 19 14:03:15 2021 -0800 new test problem exec/multispec/inputs_rtil_spinodal_charges_2d commit 185495ae5bffe97bc71623d9f8fcaa8dd1b04ebc Author: Daniel Ladiges Date: Thu Feb 18 15:04:12 2021 -0800 Removed some more debugging code exec/immersedIons/inputs_test exec/immersedIons/main_driver.cpp exec/notebooks/mobility_calc.nb commit 024def83bd6b773572e09d7eec339c52bd46a83e Merge: 2a388cb2 3886e30c Author: Daniel Ladiges Date: Wed Feb 17 12:50:01 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 2a388cb2b371fe4920764fb8c996cacdb43bcfd5 Author: Daniel Ladiges Date: Wed Feb 17 12:48:40 2021 -0800 Removed some debug code exec/immersedIons/main_driver.cpp commit b27d06296ff5744d4b5118eb3178497e9cca0ee8 Author: isriva Date: Fri Feb 12 08:33:17 2021 -0800 fixed a bug in spatial correlation calculations src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 3886e30c09249e84f5e4e02f3b7037460e727bbc Author: Andy Nonaka Date: Thu Feb 11 15:58:30 2021 -0800 fixed turb forcing restart (needed to save C++ rng engine in addition to f90 engine) exec/hydro/Checkpoint.cpp commit b55df7df18d98b35bd913890adc14e7b0d32d706 Author: isriva Date: Tue Feb 9 22:04:54 2021 -0800 cleaned up spatial correlation calculations exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 9384ebace719132c08c17e26f586ec405475cbb5 Author: isriva Date: Mon Feb 8 20:41:52 2021 -0800 added routines for spatial correlations of conserved variables across a plane exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/compressible_namelist.F90 src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 2bd88d2a7bc8b5ee98fbc363b2d28f43a78a4535 Author: Andy Nonaka Date: Thu Feb 4 15:35:22 2021 -0800 added algorithm_type=-1 (inertial backward euler) exec/hydro/advance.cpp exec/hydro/inputs_algtest_2d exec/hydro/main_driver.cpp commit bbdb8b102d3618318e79256687a11e409372cc88 Author: Andy Nonaka Date: Thu Feb 4 15:17:43 2021 -0800 fix overdamped case exec/hydro/advance.cpp exec/hydro/main_driver.cpp commit 51be065a95195fda05047ac403572d60b112469b Author: Andy Nonaka Date: Thu Feb 4 11:36:37 2021 -0800 fix relative tolerance exec/immersedIons2/inputs_3d commit 12873d49b36734e62ea0ffc5f69802616cd1899b Author: Andy Nonaka Date: Thu Feb 4 10:50:15 2021 -0800 fix a ghost cell issue add sum of averaged velocitie exec/hydro/main_driver.cpp commit 772a0e056c333fd1c4d0cae92848a185c6330019 Author: Andy Nonaka Date: Thu Feb 4 10:31:26 2021 -0800 fix a timer src_common/NormInnerProduct.cpp commit 042fb52d2cf367ef713c70f6b8b26f313961e412 Author: Andy Nonaka Date: Thu Feb 4 07:16:28 2021 -0800 forgot to define a multifab exec/multispec/AdvanceTimestepBousq.cpp commit 3d9892c88cc635647110fa057fb2ea17986142c2 Merge: 8ed8fa87 033f5556 Author: Andy Nonaka Date: Thu Feb 4 06:44:18 2021 -0800 Merge branch 'charged_integrator' into main commit 8ed8fa87049b4b78d3710b702fe9200430e8e3f7 Author: Andy Nonaka Date: Wed Feb 3 20:41:35 2021 -0800 theta_alpha=0 for overdamped exec/hydro/advance.cpp commit c06e8111abd16225944f6c2a004cf90dfe1e1bb8 Author: Andy Nonaka Date: Wed Feb 3 20:25:54 2021 -0800 point force test problem exec/hydro/inputs_algtest_2d commit 91c1822b1950a6d96f3f92fccf9d29900caa09cf Author: Andy Nonaka Date: Wed Feb 3 18:53:24 2021 -0800 ability to add external force exec/hydro/ExternalForce.cpp exec/hydro/Make.package exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/inputs_force exec/hydro/inputs_incomp_equil_fluct_2d commit 79d35274e909ad3b93a680a3d36c850a51ce0539 Author: Andy Nonaka Date: Wed Feb 3 18:37:37 2021 -0800 overdamped option need to reset regression benchmarks as order of operations has changed exec/hydro/advance.cpp commit 033f555667a3af132d3601b1c2a5b00fbf1d3ab4 Merge: a941c555 d7f2ab26 Author: Andy Nonaka Date: Wed Feb 3 12:45:08 2021 -0800 Merge branch 'main' into charged_integrator commit a941c555651b6ad247d5d97af40741cbaac7e485 Author: Andy Nonaka Date: Wed Feb 3 09:41:00 2021 -0800 get rid of Epot_wall and Epot_wall_bc_type. These have been replaced with bc_es_lo/hi and potential_lo/hi in the common namespace src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 40489e46597f0ae888f0beb8a4ce2777b35bc8de Author: Andy Nonaka Date: Wed Feb 3 09:38:30 2021 -0800 setting up rtil exec/multispec/inputs_rtil_cap_128V commit dce3d2439f4c9900f9fd2b910605008f5d57613b Author: Andy Nonaka Date: Wed Feb 3 08:14:08 2021 -0800 first cut at ComputeHigherOrderTerm start adding reservoir bc support for mole fractions src_common/BCPhysToMath.cpp src_common/InhomogeneousBCVal.H src_common/common_functions.H src_multispec/DiffusiveMassFluxdiv.cpp commit ddabdf4ed002cd34bcd10f18bd8371fe2d43b472 Author: Andy Nonaka Date: Tue Feb 2 17:47:08 2021 -0800 saving ComputeHigherOrderTerm progress src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H commit 0b1dde7ea24abd49687357db443d77d1c2ff1f65 Author: Andy Nonaka Date: Tue Feb 2 16:29:00 2021 -0800 DivReversibleStress stuff exec/multispec/AdvanceTimestepBousq.cpp commit 4104155c3a4463c50a4bb8c734dca03bf05d0a70 Author: Andy Nonaka Date: Tue Feb 2 16:26:06 2021 -0800 added ComputeDivReversibleStress exec/multispec/AdvanceTimestepBousq.cpp src_multispec/ComputeDivReversibleStress.cpp src_multispec/Make.package src_multispec/multispec_functions.H commit 8de00e35532321a6b1030a7033fbbba44fb16c12 Author: Andy Nonaka Date: Mon Feb 1 15:39:41 2021 -0800 LimitEMF function src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H commit 069a1b22add43e7e826ab3ae4553c86781c84a4b Author: Andy Nonaka Date: Mon Feb 1 15:17:13 2021 -0800 a bunch of use_multiphase routines src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/mass_flux_utilities.F90 src_multispec/src_F90/multispec_namelist.F90 commit 9ef6153e5e3aa8719f56a55dc779e91f0a0084ed Author: isriva Date: Sun Jan 31 22:45:54 2021 -0800 added routines for covariances calcaulations exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/compressible_namelist.F90 src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 705bf00bfd33ea012063bec1064738e16830ea36 Author: Andy Nonaka Date: Sat Jan 30 17:24:44 2021 -0800 first cut at Bousq alg exec/multispec/AdvanceTimestepBousq.cpp commit 699ff59d651a5680b986a582e0e0ab7cecd67a9f Author: Andy Nonaka Date: Sat Jan 30 09:35:53 2021 -0800 Bousq updates exec/multispec/AdvanceTimestepBousq.cpp commit 718eb72a3a3ad83203099096f1628b08dcf1b566 Author: Andy Nonaka Date: Sat Jan 30 09:35:43 2021 -0800 fixes to charged inertial alg exec/multispec/AdvanceTimestepInertial.cpp commit 0c53ca2dbb500e06e601f7d9234bcaeb3f40bb4c Author: Andy Nonaka Date: Sat Jan 30 09:27:21 2021 -0800 add ProjectOntoEOS for Bousq algorithm src_multispec/ProjectOntoEOS.cpp src_multispec/multispec_functions.H commit bd2cdf9260f027b0524d31aedff2b15af9891d62 Author: Andy Nonaka Date: Fri Jan 29 10:13:31 2021 -0800 more bousq algorithm progress exec/multispec/AdvanceTimestepBousq.cpp commit 9cd8acd7c8aec20287cc3f60f7ac8cb477e1a579 Author: Andy Nonaka Date: Fri Jan 29 09:13:05 2021 -0800 saving progress exec/multispec/AdvanceTimestepBousq.cpp commit 12e65e04179d77d8e2625a4868861d95563298c0 Author: Andy Nonaka Date: Thu Jan 28 20:06:52 2021 -0800 saving progress exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp commit fccfd7d0a01ab0e5b288cb667d863f77b02fb258 Author: Andy Nonaka Date: Thu Jan 28 19:01:33 2021 -0800 saving progress Bousq integrator exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/AdvanceTimestepInertial.cpp commit d7f2ab26274a2faa95e5b88c1a18fa4e2f7aac46 Merge: 03eecea4 841106a8 Author: Daniel Ladiges Date: Thu Jan 28 11:43:15 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 03eecea400202639206b63299b0cab4a017bd228 Merge: d0558842 0ab73732 Author: Daniel Ladiges Date: Thu Jan 28 11:42:07 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 841106a8620456cc448dde37300e3f4c70dec97e Author: Daniel Ladiges Date: Thu Jan 28 11:40:50 2021 -0800 Definitely fixed it this time exec/immersedIons/main_driver.cpp commit 0ab73732470da00691c340d2bd20dc076460bca7 Author: Daniel Ladiges Date: Thu Jan 28 11:36:34 2021 -0800 Fixed bug in applying close range forces to pinned particles. (Thanks Ishan) src_particles/particle_functions_K.H commit f28ae1282c86134033350d2b00bc416006598b0f Merge: d17cd846 a532358f Author: Daniel Ladiges Date: Thu Jan 28 11:31:48 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d055884282d80ad5d62f093c2d76a6a776c9ff5c Author: Daniel Ladiges Date: Thu Jan 28 10:37:05 2021 -0800 Hopefully fixed reason for regression failures exec/immersedIons/main_driver.cpp commit f61a78bbec96f7365538ba8ced3ea7e7bfed0a5f Author: Andy Nonaka Date: Wed Jan 27 13:58:20 2021 -0800 remove unused variable exec/multispec/AdvanceTimestepInertial.cpp commit 948769dcc6020827ae6b8cf150b5fc3b2747f3ff Author: Andy Nonaka Date: Tue Jan 26 16:15:43 2021 -0800 boussinesq boundary condition support for total rho exec/multispec/main_driver.cpp src_common/InhomogeneousBCVal.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit 240d998873e96df3f331b14d12d2bfae46070922 Merge: 79969634 a532358f Author: Andy Nonaka Date: Tue Jan 26 15:09:35 2021 -0800 Merge branch 'main' into charged_integrator commit a532358f944b25388c8a5378dbbfe16fd464e61d Author: Andy Nonaka Date: Tue Jan 26 13:18:13 2021 -0800 put in some protection about using 0 density when cross cell is not in a particular grid src_compressible/stats.cpp commit b84271494fd13129ab34944e64c2bf986acd4977 Merge: d75e5351 091d94ef Author: Andy Nonaka Date: Tue Jan 26 12:57:45 2021 -0800 Merge pull request #20 from AMReX-FHD/comp_stag_BC_corr Comp stag bc corr commit 091d94ef639d7c8cab150a43c2630245413e457b Author: isriva Date: Tue Jan 26 12:53:12 2021 -0800 some more small changes to flux.cpp src_compressible/flux.cpp src_compressible_stag/fluxStag.cpp commit 210c10a8d0148d0e026e2313e9eefa0f6e5effd2 Author: isriva Date: Tue Jan 26 12:34:02 2021 -0800 fixed small error for primitive interpolation for advection_type=2 src_compressible/flux.cpp src_compressible_stag/fluxStag.cpp commit d848b8fc411e825ffa8bb01b2c865e0d1dc33bad Merge: c6d364bc d75e5351 Author: isriva Date: Tue Jan 26 11:50:10 2021 -0800 Merge remote-tracking branch 'origin/main' into comp_stag_BC_corr commit d75e535129d563ef8c1462911d5403d2be9ba579 Merge: bcab09f4 5d6aa7b7 Author: Ishan Srivastava Date: Tue Jan 26 12:32:18 2021 -0700 Merge pull request #22 from AMReX-FHD/fix_T_P_stats fix computation of "mean" temperature and pressure in stats.cpp commit 5d6aa7b7c7dc5d565ab7325cc4c3b0f344bdc403 Author: Andy Nonaka Date: Tue Jan 26 10:36:43 2021 -0800 remove unused variable src_compressible/stats.cpp commit 51e5d62fc86c7055f10501fc8f60ce964f061522 Author: Andy Nonaka Date: Tue Jan 26 10:34:37 2021 -0800 fix computation of "mean" temperature and pressure in stats.cpp src_compressible/stats.cpp commit 79969634919fbc8111ae88631430541062659a98 Author: Andy Nonaka Date: Tue Jan 26 10:17:15 2021 -0800 remove notion of algorithm_type=6 src_multispec/InitialProjection.cpp commit 5e78c3a9ec3c247b444e293fcf3465445888af49 Author: Changho Kim Date: Tue Jan 26 09:37:06 2021 -0800 exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp_0126_bc commit 5a7cb349005c82e15e7af0360291d89975381a5d Author: Changho Kim Date: Tue Jan 26 09:36:40 2021 -0800 exec/compressible_mui: RUN_COadsPt111_SF/clean.sh RUN_COadsPt111_coverage/clean.sh exec/compressible_mui/RUN_COadsPt111_SF/clean.sh exec/compressible_mui/RUN_COadsPt111_coverage/clean.sh commit c6d364bca43c199b8e6c0d0c892f8fcf42d1649f Author: isriva Date: Mon Jan 25 20:26:28 2021 -0800 fixed mean T and P calculations. possible error in the old code. added comments. exec/compressible_stag/main_driver.cpp src_compressible/stats.cpp src_compressible_stag/statsStag.cpp commit 45aafe847fdd0db829e0616cdd4b261db1d1c806 Author: Changho Kim Date: Mon Jan 25 19:04:42 2021 -0800 exec/compressible_mui: main.cpp is needed exec/compressible_mui/main.cpp commit 447d7fb73aadc547f1211ea8539a4b92460ddf93 Author: Changho Kim Date: Mon Jan 25 17:31:27 2021 -0800 exec/compressible_mui: made the codes copilable after merging to main exec/compressible_mui/GNUmakefile exec/compressible_mui/main.cpp exec/compressible_mui/main_driver.cpp commit d12bffaecb8a407809fe60780271dc9ccfc341e9 Merge: a52ca88e bcab09f4 Author: Changho Kim Date: Mon Jan 25 16:42:20 2021 -0800 Merge branch 'main' into compressible_mui commit a52ca88ef1b364cb6c31cd7f7d9fd2e49af51201 Author: Changho Kim Date: Mon Jan 25 16:41:05 2021 -0800 compressible_mui/RUN_COadsPt111_coverage/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_coverage/gnuplot_cmd commit bcab09f4a1e8df2cee9cd4d108baf2757805e684 Merge: bba7aa83 5cad2849 Author: John Bell Date: Mon Jan 25 16:37:23 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit bba7aa83dea8cdb14083db15d833b91c9418f18d Author: John Bell Date: Mon Jan 25 16:35:14 2021 -0800 added functionality to compute skewness and kurtosis exec/hydro/main_driver.cpp src_common/NormInnerProduct.cpp src_common/common_functions.H commit bee67bfa2619c889faf1f65b9bf026b46b3917f3 Author: Andy Nonaka Date: Mon Jan 25 12:26:14 2021 -0800 add shifted and averaged vel/mom to SF output exec/compressible_stag/main_driver.cpp commit 205805623416f755f640305d4ba7da3d87863e23 Author: isriva Date: Sun Jan 24 23:21:33 2021 -0800 added routines for means/covariances in the staggered scheme. cleaned up writeplotfile functions. exec/compressible_stag/main_driver.cpp src_compressible/stats.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp src_compressible_stag/writePlotFileStag.cpp commit b284bcff695617e104e5afd3e0e17a2bc936749f Author: Changho Kim Date: Sun Jan 24 04:03:14 2021 -0800 exec/compressible_mui/RUN_COadsPt111_SF: scripts exec/compressible_mui/RUN_COadsPt111_SF/comp.sh exec/compressible_mui/RUN_COadsPt111_SF/coverage.sh exec/compressible_mui/RUN_COadsPt111_SF/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_SF/in.kmc exec/compressible_mui/RUN_COadsPt111_SF/params.py exec/compressible_mui/RUN_COadsPt111_SF/run.sh commit 1cfd19a6a8462400004daa3a87a7baf3033fa8ba Author: Changho Kim Date: Sat Jan 23 19:31:06 2021 -0800 exec/compressible_mui: mui_span as default exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/main_driver.cpp exec/compressible_mui/sav_src/2020/README exec/compressible_mui/sav_src/2020/m00.cpp exec/compressible_mui/sav_src/2020/m01-cutemp_jsq.cpp exec/compressible_mui/sav_src/2020/m01.cpp exec/compressible_mui/sav_src/2020/m02.cpp exec/compressible_mui/sav_src/2020/m10.cpp exec/compressible_mui/sav_src/2020/m11.cpp exec/compressible_mui/sav_src/2020/m12.cpp exec/compressible_mui/sav_src/202101_before_mui_span/app_surfchemtest.cpp exec/compressible_mui/sav_src/202101_before_mui_span/app_surfchemtest.h exec/compressible_mui/sav_src/202101_before_mui_span/main_driver.cpp commit c3767c6b7237f061b881748c38b8690a514b6d8f Author: Changho Kim Date: Sat Jan 23 17:49:27 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage/mass_cons.py exec/compressible_mui/RUN_COadsPt111_coverage/mass_cons.py commit 710aa577c9f8b1107e461982143e055435ec01a3 Author: Changho Kim Date: Sat Jan 23 17:12:53 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: correct setting exec/compressible_mui/RUN_COadsPt111_coverage/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/params.py exec/compressible_mui/RUN_COadsPt111_coverage/run.sh commit 2eb8a5a776a293b29b4c7f39c12cc762410aea05 Author: Changho Kim Date: Sat Jan 23 16:34:19 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: correct setup exec/compressible_mui/RUN_COadsPt111_coverage/comp.sh exec/compressible_mui/RUN_COadsPt111_coverage/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/mass_cons.py commit ed1fec644329018e796e44132c03c7a6dd255b48 Author: Changho Kim Date: Sat Jan 23 10:30:43 2021 -0800 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp_mui_span: name change exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp_mui_span commit 7d5b6f95a28cf6fc570eb472eb37df73a00d925d Author: Changho Kim Date: Sat Jan 23 10:29:10 2021 -0800 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest_mui_span.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest_mui_span.cpp commit 8b244add089afece05bd3358bbecbc1052e65f43 Author: Changho Kim Date: Sat Jan 23 10:22:55 2021 -0800 exec/compressible_mui/main_driver_mui_span.cpp exec/compressible_mui/main_driver_mui_span.cpp commit a36135b9dd7e2e8edd8adb852d9676dc11fce4c8 Author: Changho Kim Date: Sat Jan 23 10:15:18 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: setup exec/compressible_mui/RUN_COadsPt111_coverage/coverage.sh exec/compressible_mui/RUN_COadsPt111_coverage/gnuplot_cmd exec/compressible_mui/RUN_COadsPt111_coverage/in.kmc exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/mass_cons.py exec/compressible_mui/RUN_COadsPt111_coverage/run.sh commit 5cad284917dba9c003c073f6572e777f256526c0 Author: Andy Nonaka Date: Fri Jan 22 16:21:12 2021 -0800 ComputeDiv now takes a Real for the increment Change the external electric field so it's subtracted from the Poisson RHS instead of added src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit ff07c163f9d64f3740ca4db1688a4fd0eb79b5aa Author: Andy Nonaka Date: Fri Jan 22 15:44:23 2021 -0800 comment src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit abbb760b430e39ff575519b32b9c64f9627bfe3b Author: Andy Nonaka Date: Fri Jan 22 15:42:17 2021 -0800 update lorentz comments src_multispec/FluidCharge.cpp commit cdfa2812004b347babadbc7539ddf12b152d42f0 Author: Andy Nonaka Date: Fri Jan 22 09:08:21 2021 -0800 more setup for boussinesq exec/multispec/AdvanceTimestepBousq.cpp exec/multispec/Make.package exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H src_multispec/InitialProjection.cpp commit b01a8b4dc722441e5e13a32b0b836c8dd75ee483 Author: Andy Nonaka Date: Fri Jan 22 08:50:12 2021 -0800 setup declaration for ProjectOntoEOS exec/multispec/AdvanceTimestepInertial.cpp src_multispec/Make.package src_multispec/ProjectOntoEOS.cpp src_multispec/multispec_functions.H commit d17cd846d864528d5f03af9ccdd5cbed7d9f7149 Merge: 3cb75b6c df34f1e5 Author: Daniel Ladiges Date: Thu Jan 21 12:02:27 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3cb75b6c5f7018f4a84d29027db0abbfd796837b Author: Daniel Ladiges Date: Thu Jan 21 12:02:12 2021 -0800 commit to change branch exec/immersedIons/main_driver.cpp exec/notebooks/mobility_calc.nb src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 9faef340531db15a3d6ca8b8a3f28fe5d9dba3b6 Merge: f619b895 df34f1e5 Author: Andy Nonaka Date: Thu Jan 21 09:11:58 2021 -0800 Merge branch 'main' into charged_integrator commit df34f1e5a950b56d3c643d2040af1e7c8a733e9c Author: Andy Nonaka Date: Thu Jan 21 09:11:34 2021 -0800 don't add stoch update unless the variance>0 exec/multispec/AdvanceTimestepInertial.cpp commit f619b895b6a46f6afd84e31f86e1092b9cd9c4d7 Author: Andy Nonaka Date: Thu Jan 21 08:15:36 2021 -0800 3D init and testing exec/multispec/init_funcs.F90 exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_convergence_3d commit ae58058fad6fcd24046f44949ef34b72279c052d Merge: 6c2d37ab 6ad6a7bc Author: Andy Nonaka Date: Thu Jan 21 07:54:59 2021 -0800 Merge pull request #19 from AMReX-FHD/charged_integrator Charged integrator commit 6ad6a7bcc3bb42050b864a089d5658e01e37f290 Author: Andy Nonaka Date: Wed Jan 20 14:09:24 2021 -0800 update convergence test exec/multispec/inputs_Seawater_convergence_2d commit df99d5dbdf932c2fcd114bd26aa4e950852c9049 Merge: b1f47243 6c2d37ab Author: Andy Nonaka Date: Wed Jan 20 14:07:04 2021 -0800 Merge branch 'main' into charged_integrator commit 6c2d37abfa4c3d75b86816238f678ebccf13fd64 Author: Andy Nonaka Date: Wed Jan 20 14:06:07 2021 -0800 added BiCGStab with Agglomeration for Poisson multigrid src_gmres/MacProj.cpp src_gmres/gmres_namespace.H src_gmres/src_F90/gmres_namelist.F90 commit b1f47243a2d505800e0dc18a8110d0ab6f1052ca Author: Andy Nonaka Date: Wed Jan 20 10:21:29 2021 -0800 add rho-rho correlation exec/multispec/main_driver.cpp commit 964642d0a927d75bec216ab8a1a487cbdadd6ed9 Author: Johannes Blaschke Date: Mon Jan 18 21:35:53 2021 -0800 fix cmake -- a semicolon was creeping into the cxx flags 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factor of 2 exec/hydro/advance.cpp commit b6ccffdf42aef680d03b473fbc67c13960d0ebf5 Merge: e1f5b611 b0c9bd88 Author: Andy Nonaka Date: Fri Jan 15 14:16:14 2021 -0800 Merge branch 'main' into charged_integrator commit b0c9bd88abe132c06f8eb8a037086bbfbe5e0a86 Author: Andy Nonaka Date: Fri Jan 15 14:14:37 2021 -0800 bugfix in stag_mg_update 2d stencils for visc_type=2 that was slowing down gmres convergence src_gmres/StagMGSolver.cpp commit e1f5b6117e64e0e76281e0ef7d96037e8459a176 Author: Andy Nonaka Date: Fri Jan 15 12:38:54 2021 -0800 update test problem exec/multispec/inputs_Seawater_convergence_2d commit 1a7b574e965f89d9819d437b60e2a5198447b884 Merge: e2e15133 ac425640 Author: Andy Nonaka Date: Fri Jan 15 12:29:23 2021 -0800 Merge branch 'main' into charged_integrator commit ac425640f0797d7ecd93132a32cd2b3b1f3f13f2 Author: Andy Nonaka Date: Fri Jan 15 12:28:34 2021 -0800 add BiCGStab verbosity for mac projection src_gmres/MacProj.cpp commit e2e15133d632fc837fc043de3c07d79ef2d348db Merge: 60b348f2 d19f8d70 Author: Andy Nonaka Date: Fri Jan 15 12:26:28 2021 -0800 Merge branch 'main' into charged_integrator commit cc712f6b976a298539d58179baccc386073dcc73 Author: Changho Kim Date: Sun Jan 10 05:36:19 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage/run.sh: typo exec/compressible_mui/RUN_COadsPt111_coverage/run.sh commit d7ea9eb873fcb3171e28b40568c71bba4cfbeaf6 Author: Changho Kim Date: Sun Jan 10 05:22:20 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: small change exec/compressible_mui/RUN_COadsPt111_coverage/run.sh commit ed29885bd55a90bb069a036b2ae8f5072cd8e303 Author: Changho Kim Date: Sun Jan 10 05:08:05 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: coverage.sh exec/compressible_mui/RUN_COadsPt111_coverage/coverage.sh commit 9be8205a829621b6be06bcf933cc160f4076ca30 Author: Changho Kim Date: Sun Jan 10 04:52:27 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage and SF: corrections 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2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: params.sh, coverage.sh exec/compressible_mui/RUN_COadsPt111_coverage/coverage.sh exec/compressible_mui/RUN_COadsPt111_coverage/params.py commit 9ebe9c5e9033910ab8b5fd83cad1aa4154b06589 Author: Changho Kim Date: Sat Jan 9 22:32:02 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage: small changes exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/run.sh commit aed510631da3de875c27cbfcd36b32c3d5df5b8c Author: Changho Kim Date: Sat Jan 9 22:03:15 2021 -0800 /exec/compressible_mui: delete READMDE and create info/how_to instead exec/compressible_mui/README exec/compressible_mui/info/how_to commit e521e4e530ddb6d55a3b44c92efc70de1ea749c2 Author: Changho Kim Date: Sat Jan 9 22:00:10 2021 -0800 exec/compressible_mui/RUN_COadsPt111_coverage exec/compressible_mui/RUN_COadsPt111_coverage/coverage.sh exec/compressible_mui/RUN_COadsPt111_coverage/in.kmc exec/compressible_mui/RUN_COadsPt111_coverage/inputs_fhd exec/compressible_mui/RUN_COadsPt111_coverage/params.py exec/compressible_mui/RUN_COadsPt111_coverage/run.sh exec/compressible_mui/run.sh commit d19f8d70a099704c432d0e3c63b993e7135059b2 Author: Daniel Ladiges Date: Fri Jan 8 14:41:07 2021 -0800 Update regression input files for immersedIons to hopefully fix failed reg tests. exec/immersedIons/inputs_regression_cond exec/immersedIons/inputs_regression_eo exec/immersedIons/inputs_regression_noslip_neumann exec/immersedIons/inputs_regression_noslip_neumann_det exec/immersedIons/inputs_regression_slip_dirichlet exec/immersedIons/inputs_regression_slip_dirichlet_det commit 1542ce52cf2a7aa230d15c5ee0ad6ae779a4bd71 Author: isriva Date: Fri Jan 8 12:07:45 2021 -0800 interpolate primitive variables in staggered code src_compressible_stag/fluxStag.cpp commit fa1effc8c9f8646eaeb187b92c7aaf2531d1b0b9 Author: Changho Kim Date: Thu Jan 7 17:00:14 2021 -0800 exec/compressible_mui: CO ads on 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for fixing particle positions using inverse mobility matrix exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_freund_real_eo exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersedIons/particles.dat exec/notebooks/mobility_calc.nb exec/notebooks/positionGenerator.nb exec/notebooks/velAnalysis.nb src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_type.F90 commit bdf013f238cafc26faa2d9f22a519885808b6ee3 Author: Changho Kim Date: Thu Jan 7 03:09:56 2021 -0800 exec/compressible_mui: struct factor setup exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/params.py commit 6e803eadb075f645e2331304f45c2510ccc96d68 Author: Changho Kim Date: Wed Jan 6 16:07:34 2021 -0800 exec/compressible_mui: CO+He/Pt(111) 8x8x8 exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd commit 5d046be5bd01fc73bddf390968e8af65408f4719 Merge: 7e748ba7 64d78cae Author: Andy Nonaka Date: Wed Jan 6 14:59:32 2021 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 7e748ba76129c4e926bcca2d5b26bbd5fcbdc1ab Author: Andy Nonaka Date: Wed Jan 6 14:58:37 2021 -0800 define the primVerticalAvg MultiFab in scope when needed exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp commit 64d78cae48480f699180647519e3069f5b2181ae Merge: 9913dfe1 5bcca829 Author: Johannes Blaschke Date: Wed Jan 6 08:28:26 2021 -0800 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 9913dfe1afba7b6f6098e7962a277a27127a060a Author: Johannes Blaschke Date: Wed Jan 6 08:28:19 2021 -0800 clean up libhydro build script exec/lib_hydro/cmake/build.fish commit 4a6a30cc68804d1445cac4901ce87386f5162db1 Author: Changho Kim Date: Wed Jan 6 05:57:25 2021 -0800 exec/compressible_mui: CO ads/des on Pt(111) + He exec/compressible_mui/coverage.sh exec/compressible_mui/gnuplot_cmd exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/params.py exec/compressible_mui/run.sh commit b0b80b6dc097edd236ba50ad92fa5fb7fbaa687b Author: Changho Kim Date: Wed Jan 6 05:18:38 2021 -0800 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp: simpler rate exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp commit 909deb15e43e39c869d9e4344ad1097d998d06ba Author: Changho Kim Date: Tue Jan 5 03:09:03 2021 -0800 exec/compressible_mui: forgot to move prev run scripts to scripts/4spec exec/compressible_mui/scripts/4spec/run_SF.sh exec/compressible_mui/scripts/4spec/run_coverage.sh exec/compressible_mui/scripts/4spec/run_coverage_multi.sh commit 95562beb93d80afc4028fd9593b2ea9a8101f726 Author: Changho Kim Date: Tue Jan 5 02:57:57 2021 -0800 exec/compressible_mui: mv 4spec under scripts 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exec/compressible_mui/scripts/4spec/test/test_4+1_x/run.sh exec/compressible_mui/scripts/4spec/test/test_4+1_y/in.kmc exec/compressible_mui/scripts/4spec/test/test_4+1_y/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_y/run.sh exec/compressible_mui/scripts/4spec/test/test_4+1_z/in.kmc exec/compressible_mui/scripts/4spec/test/test_4+1_z/inputs_fhd_coverage exec/compressible_mui/scripts/4spec/test/test_4+1_z/run.sh exec/compressible_mui/scripts/4spec/vert_stat.py commit 4251dd96a666461f64c14a66e25b55edcaf3900d Author: Changho Kim Date: Tue Jan 5 02:40:12 2021 -0800 exec/compressible_mui/SPPARKS_MUI/create_sites.cpp exec/compressible_mui/SPPARKS_MUI/create_sites.cpp commit 0319a1032433f7c0bdc2f0d7be889b0b1159e4a9 Author: Andy Nonaka Date: Mon Jan 4 16:27:52 2021 -0800 tolerance for initial projection 1d-12 to match old code exec/multispec/inputs_Seawater_convergence_2d commit a03e903d1edaa14c043d5020066810b169598bf3 Author: Andy Nonaka Date: Mon Jan 4 15:55:11 2021 -0800 add beta (epsilon) scaling to Poisson solver LHS src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit 54bd40e7bac7a063904b1d2143f6c0239d4bb9d1 Author: Andy Nonaka Date: Mon Jan 4 15:51:54 2021 -0800 remove inadvertant Aborts exec/multispec/AdvanceTimestepInertial.cpp commit 900ead20179621c692449a4df34ff9c664eedb7d Author: Andy Nonaka Date: Mon Jan 4 15:07:58 2021 -0800 typo in output diagnostic exec/multispec/main_driver.cpp commit 653f1a03d6ca2c613755d63f851509d9d1cc0f3c Author: isriva Date: Mon Jan 4 09:49:59 2021 -0800 fixed error in hyperbolic flux (from Balakrishnan et al) src_compressible_stag/fluxStag.cpp commit a1d55d71d1166d7b82279021aa71f4371f4be9f1 Author: Andy Nonaka Date: Wed Dec 23 10:46:10 2020 -0800 set Epot=0 by default before electrostatic solver exec/multispec/AdvanceTimestepInertial.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/multispec_functions.H commit 863b37f6002b50a1a9e3f010f46569185385853f Merge: 8f3250cb 5bcca829 Author: Andy Nonaka Date: Wed Dec 23 09:51:51 2020 -0800 Merge branch 'main' into charged_integrator commit 5bcca8291314b01fe3ecf47b970dba8e941de8d9 Author: Andy Nonaka Date: Wed Dec 23 09:51:11 2020 -0800 fix calling sequence to ComputeDiv src_multispec/InitialProjection.cpp commit 8f3250cb408f61400dd7adf857ccb33422ae7439 Merge: 73d65ea6 c6c92cdd Author: Andy Nonaka Date: Wed Dec 23 09:49:35 2020 -0800 Merge branch 'main' into charged_integrator commit c6c92cdd1257159b3a0fcedb6c2f31cb50d79842 Author: Andy Nonaka Date: Wed Dec 23 09:46:25 2020 -0800 bugfix in initial projection; divu was uninitialized src_multispec/InitialProjection.cpp commit 73d65ea630922d5a3a7babcd71ab778f8cabdde5 Author: Andy Nonaka Date: Tue Dec 22 06:52:36 2020 -0800 Seawater deterministic strip convergence test exec/multispec/init_funcs.F90 exec/multispec/inputs_Seawater_convergence_2d exec/multispec/inputs_Seawater_structure_2d commit 63a3ae75f3fcd028c533dda45b59ba3808246f71 Author: Johannes Blaschke Date: Mon Dec 21 17:44:54 2020 -0800 ensure compiler optimization exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/demo/CMakeLists.txt commit c4e92cec62b1c3087a9fb1b92a8ddfd859beaeda Author: Johannes Blaschke Date: Mon Dec 21 17:42:12 2020 -0800 update cmake to track changes in amrex exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/cmake/test/CMakeLists.txt exec/lib_hydro/demo/CMakeLists.txt exec/lib_hydro/demo/build.fish commit 19925aa5d3120906ec416efce3ce5f38aaf281fa Author: Johannes Blaschke Date: Mon Dec 21 17:41:45 2020 -0800 track changes in amrex: spacedim defined via AMReX_Config.H src_common/src_F90/common_namelist.F90 src_common/src_F90/debug_mod.F90 src_common/src_F90/find_coords.F90 src_hydro/src_F90/hydro_bounds_mod.F90 src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 6f08de51ef6bd27e062accf2979adc9a7476a820 Author: Daniel Ladiges Date: Sun Dec 20 21:01:54 2020 -0800 notebook that generates inverse mobility matrix exec/notebooks/mobility_calc.nb commit 1d8d1954909b563edc27dc8ab1991647793bf795 Author: Andy Nonaka Date: Thu Dec 17 12:17:10 2020 -0800 remove epot_mg_verbose, _abs_tol, and _rel_tol from the multispecies namespace instead use the common namespace objects: poisson_verbose, poisson_bottom_verbose, poisson_max_iter, poisson_rel_tol src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit fe88acb18c7fa50746f3f773bd29958ca0ec1ff7 Author: Andy Nonaka Date: Thu Dec 17 11:54:35 2020 -0800 give sensible default values to Poisson solver parameters exec/multispec/main_driver.cpp src_common/src_F90/common_namelist.F90 commit 55dec6f54a19522ca441f825939acea048feaa8b Author: Andy Nonaka Date: Thu Dec 17 11:12:41 2020 -0800 ghost cell copy issue fixed src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit 22b0961da05d83c2d75d1190a0ae19db7ac9dcb0 Author: Andy Nonaka Date: Thu Dec 17 11:00:05 2020 -0800 plotfile bugfix exec/multispec/WritePlotFile.cpp commit 9f4f8442632cc3c78c3f000986c6e3ac0d4b0ef8 Author: Andy Nonaka Date: Thu Dec 17 10:57:33 2020 -0800 add bc_es exec/multispec/inputs_charged_equil_2d commit 9d1ade1f2c5b313de76269a47b4c0adbd37f8879 Author: Andy Nonaka Date: Wed Dec 16 16:08:15 2020 -0800 write out charge and Epot to plotfile fix inputs file to new C++ format exec/multispec/WritePlotFile.cpp exec/multispec/inputs_charged_equil_2d exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit b7f7482697ca61ae3e39944127cff0b21c97b801 Merge: 0e109e40 6ccfd95f Author: Andy Nonaka Date: Wed Dec 16 15:49:57 2020 -0800 Merge branch 'main' into charged_integrator commit 6ccfd95ff3acea7640b67e893ee353b261ef9e0a Author: Andy Nonaka Date: Wed Dec 16 15:49:31 2020 -0800 charged test file exec/multispec/inputs_charged_equil_2d commit 41211aa5ab59cbeb38890926c7db308e11c29cb4 Author: isriva Date: Wed Dec 16 15:27:02 2020 -0800 fixed subtle bugs that causes stack smashing crashes in both compressible codes. also cleaned up GPU variables. exec/compressible_stag/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 6c7e19cbf2df5bc374a94024b6613e81be52ff4c Author: isriva Date: Mon Dec 14 15:51:20 2020 -0800 fixed small changes for GPU compilation src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit ac85fa29e173dee46a6bdd2ae00fd98e07595763 Merge: 914b8df9 e54743de Author: Daniel Ladiges Date: Thu Dec 10 18:49:32 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 914b8df966d08bd172009f4a24bc22d166dfa36a Author: Daniel Ladiges Date: Thu Dec 10 18:48:51 2020 -0800 Update to make neighbourlist referencing compatible with latest AMReX src_immersed-boundary/IBMarkerContainer.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit e54743def123bb64c92f44cd082fc47fe3077b01 Merge: 91db931b 6d20a02d Author: Daniel Ladiges Date: Wed Dec 9 11:12:08 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 91db931bb34003b6ea4e4365aab12ec4a3e2dc69 Author: Daniel Ladiges Date: Wed Dec 9 11:11:39 2020 -0800 Some notebooks for analysis exec/notebooks/NeumannCond.nb exec/notebooks/channel_mobility.nb exec/notebooks/chargeAnalysis.nb exec/notebooks/densityAnalysis.nb exec/notebooks/energyAnalysis.nb exec/notebooks/eo_analysis.nb exec/notebooks/potentialAnalysis.nb exec/notebooks/velAnalysis.nb commit 6d20a02d2f66b7bc527d49ca8eea08bc85280d87 Author: Daniel Ladiges Date: Tue Dec 8 23:39:18 2020 -0800 Bugfix to spring force function. Now uses absolute position instead of periodic exec/immersedIons/inputs_eo_test_wet exec/immersedIons/inputs_freund_real_eo exec/immersedIons/particleGen.cpp exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb src_common/common_functions.cpp src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 4098e3a01466df2647e43a198e1edf78d27b6136 Author: Daniel Ladiges Date: Fri Dec 4 23:12:15 2020 -0800 bugfix to interpolation in ghost cells and setup for real eo problem exec/immersedIons/inputs_freund_real_eo exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/collision_functions.F90 commit 03bbf1270440a9c85efea12bc249a3e5aa752afe Author: isriva Date: Fri Dec 4 13:49:40 2020 -0800 added BC for stochastic flux in staggered scheme. fully C++ on GPU src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp commit 5dc2ac75be45cb4293a5579ac77cb670812e0e83 Author: Daniel Ladiges Date: Fri Dec 4 01:01:55 2020 -0800 Setup for 'real' eo flow exec/immersedIons/inputs_freund_real_eo exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb commit 0e109e40bff579b4411251dcd38dfc4e879a2e8d Author: Andy Nonaka Date: Thu Dec 3 19:24:47 2020 -0800 first cut at charged integrator exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/InitialProjection.cpp src_multispec/multispec_functions.H commit 6c9a5ef509fb114dee6ea5cc73efdfca9ac6e70b Author: Daniel Ladiges Date: Thu Dec 3 17:32:53 2020 -0800 temporary hack to add full range LJ to main branch. exec/notebooks/positionGenerator.nb src_particles/particle_functions_K.H commit 9206eb571e0b86591a5f4ac3bf4901a08fe35512 Merge: 710bd779 64145b28 Author: Daniel Ladiges Date: Thu Dec 3 15:20:42 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 710bd77938cad578fd1954ade4e9d2eac39b4994 Author: Daniel Ladiges Date: Thu Dec 3 15:14:41 2020 -0800 Saving input file for branch change exec/immersedIons/inputs_eo_test_wet commit 5e3033376a2f2ef174f775986de2677dceb7c8d2 Author: Andy Nonaka Date: Thu Dec 3 13:14:13 2020 -0800 saving progress exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp src_multispec/FluidCharge.cpp src_multispec/multispec_functions.H commit 64145b28262383730221c98b6080f0067e09308f Author: isriva Date: Thu Dec 3 12:19:56 2020 -0800 fixed bug in BC for old compressible code in main branch src_compressible/boundary.cpp commit c34e517ddf70001f18cc6c7bda2cabfaf6d10494 Author: Andy Nonaka Date: Thu Dec 3 11:46:14 2020 -0800 split c_init(:,:) into c_init_1(:) and c_init_2(:) and put on GPU exec/exercises/incompressible/init_funcs.F90 exec/exercises/incompressible/inputs_diffusion_2d exec/multispec/init_funcs.F90 exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_incomp_3d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d exec/multispec/main_driver.cpp src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 2fcf2591913be240388b995cd062216ac0535347 Author: Andy Nonaka Date: Thu Dec 3 11:13:53 2020 -0800 starting charged inertial work exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit 5f5848f2b05f2e97672a9bba14da5278fa645f4d Author: isriva Date: Thu Dec 3 11:10:01 2020 -0800 fixed bug in BC for old compressible code src_compressible/boundary.cpp commit e1761fc2fc30fc0992cfacec96946a1ec0fdacd5 Author: isriva Date: Thu Dec 3 11:05:12 2020 -0800 implemented BCs for staggered grid ... needs testing exec/compressible_stag/main_driver.cpp src_compressible_stag/Make.package src_compressible_stag/boundaryStag.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/timeStepStag.cpp commit e93c3d34311547769d790d6f78f90ec8c48bc1b9 Merge: a8884a2a 285ecea9 Author: Daniel Ladiges Date: Wed Dec 2 12:07:53 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit a8884a2a49700abe93c47c690fe59387cfd50667 Author: Daniel Ladiges Date: Wed Dec 2 12:07:30 2020 -0800 Implemented 'invisible particles' exec/immersedIons/WritePlotFile.cpp exec/immersedIons/particleGen.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_type.F90 commit 285ecea97910c1e2e29dbef1f8092e36d84825d2 Author: Andy Nonaka Date: Wed Dec 2 11:20:26 2020 -0800 remove extra plot variables exec/compressible/inputs_regression_noslip_reservoir_isothermal commit 0b87e8fc344d7ad6e49a2c7f3a9d96ec876dd86e Author: Andy Nonaka Date: Wed Dec 2 10:55:43 2020 -0800 add plotting stuff back to this test exec/compressible/inputs_regression_noslip_reservoir_isothermal commit d25ed2eb3387bc03c1ebf3574f9166e0a78ce0c4 Merge: 1cc9db90 240c3f42 Author: Andy Nonaka Date: Wed Dec 2 10:52:56 2020 -0800 Merge pull request #18 from AMReX-FHD/comp_stag_BC_corr Moved all mass boundary conditions to common namespace commit 240c3f427fa5a064240fe0a764ecf9015937e086 Merge: eab67481 1cc9db90 Author: Andy Nonaka Date: Wed Dec 2 10:52:35 2020 -0800 Merge branch 'main' into comp_stag_BC_corr commit eab67481562b291831792c80e628ad933425b977 Author: Andy Nonaka Date: Wed Dec 2 10:48:21 2020 -0800 update bc's exec/compressible/inputs_regression_noslip_reservoir_isothermal commit 1cc9db9063dfed6a6a24cf2f360bb32f07e079a5 Author: Andy Nonaka Date: Wed Dec 2 10:45:00 2020 -0800 tweak bc's for more robust test. need to update regression exec/compressible/inputs_regression_noslip_reservoir_isothermal commit 4528c8edb78fa429fd5a0c689496ef5e7ddda24d Author: Andy Nonaka Date: Wed Dec 2 10:36:34 2020 -0800 copy Xk's to C++ src_compressible/src_F90/bound_funcs.F90 commit 5cafecc400e33a3d79c413ae1be9424b9dbe1ac5 Author: Andy Nonaka Date: Wed Dec 2 10:15:07 2020 -0800 update C++ copies of bc_X/Yk_x/y/z_lo/hi in setup_cwall() exec/compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp exec/exercises/compressible/main_driver.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 commit 5e43fb4677d9304a84e15cbf9edbee5ef203bcee Author: Andy Nonaka Date: Wed Dec 2 09:46:57 2020 -0800 Bugfix in accessing Yk bc's src_common/InhomogeneousBCVal.H commit 0dcab962d297b7496a17c2bc9c85a09283fa298d Author: isriva Date: Tue Dec 1 09:36:15 2020 -0800 all compressible BCs in common namespace exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/main_driver.cpp src_common/InhomogeneousBCVal.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/boundary.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible_stag/boundaryStag.cpp commit d58cc1ae77d62226729f1cd221c331833afab203 Merge: 0c42d56e e85a3203 Author: isriva Date: Tue Dec 1 07:36:12 2020 -0800 Merge remote-tracking branch 'origin/main' into comp_stag_BC_corr commit e85a3203a901f9e96040b96d2746edabbdcfb604 Author: Andy Nonaka Date: Mon Nov 30 15:34:52 2020 -0800 move c_bc to src_common update InhomogeneousBCVal to support reservoirs for low Mach src_common/InhomogeneousBCVal.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 6865e3cc1d3f8dcacca506cbd98f6d1643196f3a Author: Andy Nonaka Date: Mon Nov 30 15:05:15 2020 -0800 c_bc onto GPU src_multispec/multispec_functions.cpp src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H commit 2f024241fa90aca1020eb7d5b613dcae90d19925 Author: Andy Nonaka Date: Mon Nov 30 14:50:46 2020 -0800 split up c_bc into c_bc_x_lo, c_bc_x_hi, etc. src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 0c42d56e327060a9c5cda77a82df16110ebd62ae Author: isriva Date: Mon Nov 30 12:32:37 2020 -0800 fixed small bugs for compressible BCs src_compressible/boundary.cpp commit 906aa2fbc51f15bbcaac19eca535af769e85123f Author: isriva Date: Mon Nov 30 10:40:20 2020 -0800 all compressible BCs now on GPU src_compressible/boundary.cpp src_compressible/src_F90/bound_funcs.F90 commit d8cf8166351bc2e952fc6b18d49dfff71c2a31b8 Author: Andy Nonaka Date: Wed Nov 25 12:52:55 2020 -0800 first cut at complete electrodiffusive flux routines src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 6b66511d58fbf8b5d8ab732ce8581148fccf9cbd Author: Andy Nonaka Date: Wed Nov 25 12:14:34 2020 -0800 es progress src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit ea57b18aba40467a4233a664b438805c82daec7a Author: Daniel Ladiges Date: Wed Nov 25 12:10:26 2020 -0800 switching beanch exec/immersedIons/inputs_eo_realchannel_test_wet exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb commit 28e49ffbcbc61e8a22bfa47ecc0d03f75d800964 Merge: 2c865dfb ce11e6a3 Author: jbbel Date: Wed Nov 25 11:15:49 2020 -0800 Merge pull request #17 from AMReX-FHD/dev_compressible_stag Merging Staggered Compressible into Main commit 2c865dfb7b64d69713a8fa7c02ca198fd0f70bb8 Author: Andy Nonaka Date: Wed Nov 25 11:12:33 2020 -0800 add pressure BC src_common/InhomogeneousBCVal.H commit 3b52f0b1ddae7aa6e584f30004bd6df4cf0410d6 Author: Andy Nonaka Date: Wed Nov 25 10:36:02 2020 -0800 increased inhomogeneous BC support for incompressible/low Mach codes src_common/InhomogeneousBCVal.H src_common/MultiFabPhysBC.cpp src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit ce11e6a33b5f8820dc5c59bd8dbd2155225a219d Author: Ishan Srivastava Date: Tue Nov 24 16:06:35 2020 -0700 Update src_compressible_stag/compressible_functions_stag.H Co-authored-by: Andy Nonaka src_compressible_stag/compressible_functions_stag.H commit e44df05638df19ca90a0bd598d3982eb1f677111 Merge: 81c06925 52eb873e Author: Andy Nonaka Date: Tue Nov 24 14:41:59 2020 -0800 Merge branch 'main' into dev_compressible_stag commit 52eb873e82afde8a60b5010aae009f321d6eb32f Author: Daniel Ladiges Date: Tue Nov 24 02:30:40 2020 -0800 Bugfix in particle plotfile writing plus misc exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_eo_realchannel_test_wet exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_type.F90 commit ad6b41023eb7d74addb37532a87ef9e2f408656d Author: Daniel Ladiges Date: Tue Nov 24 02:04:05 2020 -0800 Bugfix for pinned particle displacement calc. Mathematica notebook for generating particle starting positions. Sample input and particle.dat file for 'real' eo channel. exec/immersedIons/inputs_eo_realchannel_test_wet exec/immersedIons/main_driver.cpp exec/immersedIons/particles.dat exec/notebooks/positionGenerator.nb src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit de9e41faed77af3b7a76ffef8820766d648fe1b4 Author: Daniel Ladiges Date: Mon Nov 23 23:34:43 2020 -0800 input now takes matrix to turn interactions on/off between different species. particles can now be 'fixed in place' using an harmonic potential of specified stiffness exec/immersedIons/inputs_eo_realchannel_test_wet exec/immersedIons/particleGen.cpp src_common/common_functions.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_type.F90 commit 61193d33a0cab126d5ec98017b1683387925d000 Author: Andy Nonaka Date: Mon Nov 23 09:36:24 2020 -0800 move MAX_SPECIES to common_namelist.H so it compiles src_common/common_functions.H src_common/common_namespace.H commit e346551fd097065a66e3cb7e915fa51174020877 Author: Andy Nonaka Date: Mon Nov 23 09:15:19 2020 -0800 gpu WIP src_common/common_functions.cpp src_common/common_namespace_declarations.H commit f4f793bf3aac9007f0526ab8413ce33c7effb426 Author: Andy Nonaka Date: Mon Nov 23 09:09:48 2020 -0800 GPU WIP. Still doesn't compile on gigan due to namelist stuff not being on GPU src_common/common_namespace.H commit 991f4707e4c5741f1ea11c3d7e84a31f4f645aa2 Author: Andy Nonaka Date: Mon Nov 23 08:15:35 2020 -0800 forgot to add file src_common/InhomogeneousBCVal.H commit 0460ae9d4e2d4ed138be08ec7d4159f902198af3 Author: Andy Nonaka Date: Mon Nov 23 08:08:39 2020 -0800 testing cleanup of GPU namespace stuff (WIP) exec/compressible/main_driver.cpp src_common/Make.package src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_common/common_namespace.H src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp commit 87ba73e43273b7bf924fa3ed5bfad76e8308ddc9 Author: Andy Nonaka Date: Mon Nov 23 07:19:34 2020 -0800 testing MultiFabPhysBC only filling 1 ghost cells (comments updated). Misleading to fill all the ghost cells with the same value - if those extra (beyond the 1st) ghost cells are ever accessed, MultiFabPhysBC is not the routine that should be filling those ghost cells src_common/BCPhysToMath.cpp src_common/MultiFabPhysBC.cpp src_common/README_FILLROUTINES commit 647e80530442ea83958ad9cae7e7f354846bbefe Author: Andy Nonaka Date: Sun Nov 22 10:46:58 2020 -0800 testing new bc functionality; will run regression test and revert immediately if broken src_common/common_functions.H commit acd9f84c0a9b6990e62952056d1720c9119af904 Author: Andy Nonaka Date: Fri Nov 20 15:27:54 2020 -0800 begin overhaul of scalar bc's no changes to results expected exec/channel/advance.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/advance_midpoint.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/lib_hydro/demo/main_driver.cpp exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp src_chem/AmrCoreAdv.cpp src_common/BCPhysToMath.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp src_gmres/Utility.cpp src_hydro/AddMFluctuations.cpp src_hydro/MacProj_hydro.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/FluidCharge.cpp src_multispec/InitialProjection.cpp src_multispec/RhoUtil.cpp commit d767c49c3c011b70ada8df0e5e2d14ec86601598 Author: Andy Nonaka Date: Fri Nov 20 14:50:55 2020 -0800 cleanup; move definition of NUM_EDGE to src_common only src_common/common_functions.H src_gmres/gmres_functions.H src_immersed-boundary/ib_functions.H commit 0ddabdb414e6a268cfb8565a0fccb20f3a2f5f3d Author: Andy Nonaka Date: Fri Nov 20 13:25:44 2020 -0800 detailed description of all ghost cell, boundary value, and folding routines src_common/README_FILLROUTINES commit 36380342a38d7e42f085ff72672773ff69168811 Author: Andy Nonaka Date: Fri Nov 20 13:24:55 2020 -0800 update/fix comments on all filler routines src_common/MultiFabPhysBC.cpp src_multispec/RhoUtil.cpp src_particles/particle_physbc.cpp commit e90f02296863c46b0075d5a65305f6b505f444d2 Author: Johannes Blaschke Date: Fri Nov 20 10:39:32 2020 -0800 make FindCoords available to IB codes exec/immersed_boundary/flagellum/GNUmakefile src_particles/MakeKernels.package commit 351c0c0254d4037e48d7cf59d8a991187fcc642a Author: Andy Nonaka Date: Fri Nov 20 08:01:26 2020 -0800 fixed the surface charge exec/immersedIons/inputs_regression_eo commit 0b6476c5987feeee9c3360fb56b3a18a5ba59e0c Author: Andy Nonaka Date: Thu Nov 19 19:55:50 2020 -0800 move FindCoords to particle source (out of common) src_common/Make.package src_common/common_functions.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FindCoords.cpp src_particles/Make.package src_particles/particle_functions.H commit a97243b48687e820124ea8a3e2a70a3d1719f9e3 Author: Andy Nonaka Date: Thu Nov 19 19:18:03 2020 -0800 move particle-specific physbc routines into their own file "particle_physbc.cpp" in src_particles clean up header file includes src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/Make.package src_particles/particle_functions.H src_particles/particle_mobility.cpp src_particles/particle_physbc.cpp commit 8685257ddca7f37f2caf5b42bdf72fbdcb1d575b Author: Andy Nonaka Date: Thu Nov 19 16:16:59 2020 -0800 turn on singularity check/abort for Neumann and periodic problems src_electrostatic/electrostatic.cpp commit b21dbced402a8730f5e245655c90c377cece54cc Author: Andy Nonaka Date: Tue Nov 17 16:13:16 2020 -0800 corigpu fftw exec/compressible/GNUmakefile exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/immersedIons2/GNUmakefile exec/multispec/GNUmakefile commit c6c00967d04df39c86ff4dd27c2d9d51ca3d004d Author: Andy Nonaka Date: Tue Nov 17 16:07:49 2020 -0800 testing corigpu build stuff exec/hydro/GNUmakefile commit 79e855ea3de459293c951e4ddbabd8bfdddd7e39 Author: Andy Nonaka Date: Tue Nov 17 15:17:03 2020 -0800 updates so this compiles/runs on GPU exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp commit b4da905b9ae77219e9ade4ce225666c3be14ade6 Author: Andy Nonaka Date: Mon Nov 16 12:37:59 2020 -0800 bugfix in Dirichlet gradient at walls - will check regression but I don't think any of our codes touched this yet? src_common/ComputeDivAndGrad.cpp commit de59a9150ac0642091c70e06ad93d2cdecaa2664 Author: Andy Nonaka Date: Mon Nov 16 12:35:33 2020 -0800 charged updates src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit cca2474cb8dfe4f5230d70793cade5012a1fdd50 Merge: 8718af6a 886d5d4e Author: John Bell Date: Fri Nov 13 17:22:33 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 8718af6a1f6a15ccdc2bea896834074df2122605 Author: John Bell Date: Fri Nov 13 17:21:31 2020 -0800 fixed intervals and added two alternative for spectrum src_analysis/StructFact.cpp commit 886d5d4efda1372f1e6fd29237b7a6792bc30f14 Author: Andy Nonaka Date: Fri Nov 13 16:13:10 2020 -0800 Move initialization into separate routine out of constructor so it compiles on GPU exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp exec/hydro/main_driver.cpp commit 9cc02941abe9a5b1cf034578cb4b17fde33fb909 Author: Andy Nonaka Date: Fri Nov 13 15:51:22 2020 -0800 forgot a ;. how did this compile? src_hydro/Vorticity.cpp commit 058976cbb7c5c1c1547d1a87adea0893519f1e26 Author: Andy Nonaka Date: Fri Nov 13 13:56:24 2020 -0800 finished GPU conversion of x boundary ghost cells src_compressible/boundary.cpp src_compressible/src_F90/bound_funcs.F90 commit c231fd480cca52ba84c92cced1bb9a5286cf77da Author: Andy Nonaka Date: Fri Nov 13 11:26:02 2020 -0800 more gpu bc progress src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/src_F90/bound_funcs.F90 commit c5982bff6bb153c9b4ca0537c2bf6bac671eb2ba Merge: f93d953d c0260e58 Author: Daniel Ladiges Date: Fri Nov 13 02:21:26 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit f93d953dd04ff080e39a6e11d72c6cc17b4607b0 Author: Daniel Ladiges Date: Fri Nov 13 02:10:13 2020 -0800 Merging two different versions of particleGen which do file inputs exec/immersedIons/particleGen.cpp commit 64b463e551eefbba2a0a37c6f8ee1402c32377c5 Author: Daniel Ladiges Date: Fri Nov 13 02:08:34 2020 -0800 Moved the last of Donev/Sophie's stuff out of FHDeX into FluctuatingMembrane src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/membrane_forces.F90 commit c0260e58f97538446bb1f14a282dcca78f488f60 Author: Andy Nonaka Date: Thu Nov 12 17:45:14 2020 -0800 more GPU conversion; had to copy bc_Yk and bc_Xk from F90 to C++ in setup_cwall exec/compressible/main_driver.cpp src_compressible/boundary.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 commit 0d91d369d4c2cc4e4c897a434007db94c0b9d8f1 Author: Andy Nonaka Date: Thu Nov 12 17:22:59 2020 -0800 change this test to have reservoirs at all walls to help with testing exec/compressible/inputs_regression_noslip_reservoir_isothermal commit c22be02a3c55aeb07d7c47264612baebb6a09966 Author: Andy Nonaka Date: Thu Nov 12 15:58:20 2020 -0800 converted 1 boundary routine to GPU as an example/guide src_compressible/boundary.cpp src_compressible/src_F90/bound_funcs.F90 commit 11234127b242bc71df0bf0d2199324bf2354edc2 Author: Andy Nonaka Date: Thu Nov 12 07:53:47 2020 -0800 comments, and change gmres_max_inner to 5 to save memory exec/immersedIons/inputs_eo_test_wet commit 5dbbe63f73935fc54dc505e76c9ad4b9055021ea Merge: 2086614a a2ea8180 Author: Daniel Ladiges Date: Thu Nov 12 01:21:57 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 2086614aa4bcaa0aab9e97069ebdd742ccd45ae4 Author: Daniel Ladiges Date: Thu Nov 12 01:10:20 2020 -0800 particle file input and eo test input exec/immersedIons/inputs_eo_test_wet exec/immersedIons/particleGen.cpp commit a2ea818085c969c43d8a05136ecfd64cf7665c42 Author: Andy Nonaka Date: Wed Nov 11 16:22:28 2020 -0800 change dt to 1e13. e_external to x-direction exec/immersedIons/inputs_eo_test_wet exec/immersedIons/inputs_paper_eo commit e2a79781860abdade72e9ddfb68f0f00e3fc35d1 Merge: c9e73c69 89223b93 Author: Andy Nonaka Date: Wed Nov 11 15:55:35 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit c9e73c69442b802843ab1178b8e04068bdc50d43 Author: Andy Nonaka Date: Wed Nov 11 15:54:49 2020 -0800 clean up inputs files. no changes exec/immersedIons/inputs_eo_test_wet exec/immersedIons/inputs_paper_eo commit 89223b93332caba256813aca58d7140255eb3c8a Author: John Bell Date: Wed Nov 11 11:57:12 2020 -0800 fix typo exec/hydro/main_driver.cpp commit 7a0080b592083f4ab886ffd029296d8efd1256a8 Merge: d4b1eb25 f68cbb96 Author: John Bell Date: Wed Nov 11 11:35:53 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d4b1eb256fc2c84198b7c46771b08fdf8cc93b76 Author: John Bell Date: Wed Nov 11 11:34:39 2020 -0800 fix shell volume and normalization for energy dissipation exec/hydro/main_driver.cpp src_analysis/StructFact.cpp commit f68cbb9676b30cac4197cf1d52e235d85c35c8b4 Author: isriva Date: Wed Nov 11 09:19:55 2020 -0800 added capability to read particles from file requires a "particles.xyz" in executable folder format of the file: "x y z species_index" exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.H commit 2a56079f92554fbc39cdfdd9b0a8ca0a2214b3cc Author: Andy Nonaka Date: Wed Nov 11 09:01:23 2020 -0800 initial plotfile should be plt0000 not plt0001 exec/hydro/main_driver.cpp commit 625c36f9e60f0a685585032a5341e14f0e8afd24 Author: Daniel Ladiges Date: Tue Nov 10 12:41:38 2020 -0800 input files for DISCOS #2 exec/immersedIons/inputs_density_test_damp exec/immersedIons/inputs_density_test_dry exec/immersedIons/inputs_density_test_eo_wet exec/immersedIons/inputs_density_test_es_damp exec/immersedIons/inputs_density_test_es_dry exec/immersedIons/inputs_density_test_es_wet exec/immersedIons/inputs_eo_test_wet commit 28de164ccf068467c529cd3bb8dba6b86ee2cb5c Author: Andy Nonaka Date: Tue Nov 10 10:23:11 2020 -0800 bugfix in turbulent energy calculation src_analysis/StructFact.cpp commit a58852c40d123ee13e7dae9efc102b7cd4c43da3 Author: John Bell Date: Tue Nov 10 10:04:57 2020 -0800 inputs for forcing exec/hydro/inputs_force commit 563670775ef2958525397ed8894424fb12c7d6b9 Merge: 94cd4c28 3170b25a Author: John Bell Date: Tue Nov 10 08:48:05 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3170b25ae9969e0b525ea3c97fbea1cac487e631 Author: Andy Nonaka Date: Tue Nov 10 07:45:43 2020 -0800 turbForcing=1 in the common namelist now enables the turbulent forcing addition to the RHS and the output of the turblent energy spectrum to text files based on plot_int exec/hydro/advance.cpp exec/hydro/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit d0715d81205513779815c51849134bc62e37017a Author: Changho Kim Date: Mon Nov 9 05:21:09 2020 -0800 exec/compressible_mui: ad-hoc fix for memory leakage exec/compressible_mui/cori_coverage/cori_slurm.sh exec/compressible_mui/main_driver.cpp commit 81c069258017ad887f0a1a32bef29cf495d674ee Author: isriva Date: Fri Nov 6 16:26:48 2020 -0800 added shifted momemtun and velocity variance - still incomplete exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/statsStag.cpp commit abd6b3aba6fb26b327eba4475a8ebed68bbbb613 Author: Andy Nonaka Date: Fri Nov 6 13:29:17 2020 -0800 GPU fixes exec/hydro/TurbForcing.H commit e61aac01fe8d3e44b374167769bc68a3c964aba8 Author: Andy Nonaka Date: Fri Nov 6 13:26:21 2020 -0800 GPU fix exec/hydro/TurbForcing.cpp commit dd8b3bdc43f11845dfd33f61a98664f995fb9b08 Author: Andy Nonaka Date: Fri Nov 6 13:06:15 2020 -0800 parallel turblent energy spectrum calculator - writes to text files now on plot_int exec/hydro/inputs_turbtest_2d exec/hydro/inputs_turbtest_3d exec/hydro/main_driver.cpp src_analysis/StructFact.cpp commit 8e932e1f7bbe7606ae1527bb7ee23128dd4f693e Merge: dee34444 6a182fbf Author: Andy Nonaka Date: Thu Nov 5 17:41:43 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit dee34444a76867e1d1447b646e389768fdf4c85f Author: Andy Nonaka Date: Thu Nov 5 17:41:31 2020 -0800 scaling on spectrum src_analysis/StructFact.cpp commit 6a182fbfadd8f095928cfdc01dc667b0236bc9ff Author: Daniel Ladiges Date: Thu Nov 5 16:33:39 2020 -0800 Modifications for Sophie's membrane src_particles/particle_functions_F.H commit d11296148ce31bb8aad40c3c9cd63208a1ea5e4e Author: Andy Nonaka Date: Thu Nov 5 14:39:40 2020 -0800 1/k^2 scaling src_analysis/StructFact.cpp commit 09a1c025a10d36e01c60447a92f2e1dfc0cbbcbc Author: Andy Nonaka Date: Thu Nov 5 14:03:17 2020 -0800 turbulent energy spectra WIP exec/hydro/main_driver.cpp src_analysis/StructFact.cpp commit 93c1432c4a9eadcc8a27b36bd822e15deee5c36a Author: Andy Nonaka Date: Thu Nov 5 10:43:25 2020 -0800 clean up SF class so all arguments are pass by reference added declaration for IntegratekShells() exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit ec5011be1e198800220350e26ec1b3a9482267de Merge: 00f3ff61 3bb6c8ee Author: isriva Date: Thu Nov 5 10:33:33 2020 -0800 Merge branch 'main' into dev_compressible_stag commit 380830575e7f0c7669f59005ac1c001bd4a24b1f Author: Andy Nonaka Date: Thu Nov 5 10:05:21 2020 -0800 verbosity src_analysis/StructFact.cpp commit 3bb6c8eea99fcb850d0bfdf1c24ed8fac72e4743 Author: isriva Date: Thu Nov 5 08:13:49 2020 -0800 changed particle gen to instantiate away from walls. cleaned lj potentials exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/particle_functions_K.H commit 8a7abd4670fe5a53986b51561e16bf0b940e33c2 Author: Andy Nonaka Date: Wed Nov 4 19:11:44 2020 -0800 saving turblent spectra work - WIP exec/hydro/main_driver.cpp commit 71025d0e4310578c9201861a023c0e0157ddebae Author: Andy Nonaka Date: Wed Nov 4 15:27:12 2020 -0800 option to reset structure factor sum will be useful for getting snapshots of spectra src_analysis/StructFact.H src_analysis/StructFact.cpp commit 94cd4c28c39853ff5ab5a24815c5c3c8e5ea21cd Merge: e355246f df8ec810 Author: John Bell Date: Wed Nov 4 14:55:55 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit df8ec81094cbac7224b5d76c58ceae76a0d9e27a Author: Andy Nonaka Date: Wed Nov 4 14:33:56 2020 -0800 implement tracer predictor/corrector exec/hydro/advance.cpp commit 97b3e87c8f6d145cc16c4afb2d705c8af714300f Author: Andy Nonaka Date: Wed Nov 4 13:15:19 2020 -0800 fix KE calc exec/hydro/main_driver.cpp commit 13cb299cc83275507d68801787644692c8b28250 Author: Andy Nonaka Date: Wed Nov 4 13:11:44 2020 -0800 energy dissipation exec/hydro/main_driver.cpp commit de8a7f789e6e8da350b5226cce638c8470f8a859 Author: Andy Nonaka Date: Wed Nov 4 12:47:25 2020 -0800 new routine to compute grad(u) given input face-centered umac and output cell-centered multifab src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit e355246ff8aea3560987adc31ba380f81f80efc6 Merge: 62bddb9a ba2c78ee Author: John Bell Date: Wed Nov 4 12:26:49 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 62bddb9afdaee625806f80611619ca4809265202 Author: John Bell Date: Wed Nov 4 12:26:08 2020 -0800 add stuff for turbulent forcing exec/hydro/advance.cpp exec/hydro/inputs_force commit ba2c78ee3d1cdc5b8615df2012f1924e4e6f71fa Author: Andy Nonaka Date: Wed Nov 4 09:06:46 2020 -0800 weight KE integral by dVol exec/hydro/main_driver.cpp commit e0f535da75847ea8a1f3aa7a965341a365438d95 Author: Andy Nonaka Date: Wed Nov 4 09:03:05 2020 -0800 fix includes src_common/NormInnerProduct.cpp commit 0420a7023d1e75e36912343dcabe628588ecff63 Author: Andy Nonaka Date: Tue Nov 3 16:35:52 2020 -0800 compute kinetic energy (not normalized by domain yet) exec/hydro/main_driver.cpp commit 5169f89200a32742d0b603b04daad51e9fbdeb0f Merge: 51474bb9 0a2e6f77 Author: Andy Nonaka Date: Tue Nov 3 16:24:14 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 51474bb9a41710335bb1758124d0f7d89cdb71a6 Author: Andy Nonaka Date: Tue Nov 3 16:23:55 2020 -0800 move NormInnerProduct.cpp from src_gmres to src_common src_common/Make.package src_common/NormInnerProduct.cpp src_common/common_functions.H src_gmres/Make.package src_gmres/gmres_functions.H commit 0a2e6f77562a1f415ab7cc9e791ae72d41e6f602 Merge: dde28b1e 6b07e657 Author: Daniel Ladiges Date: Tue Nov 3 16:22:34 2020 -0800 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit dde28b1e1851a2f56667355ec8ec8b24a8e505b1 Author: Daniel Ladiges Date: Tue Nov 3 16:18:34 2020 -0800 Updated eo inputs file exec/immersedIons/inputs_eo_test_wet commit 6b07e657fa7f5d34a07a5ddef21cfe3c07813ee4 Author: Andy Nonaka Date: Tue Nov 3 16:14:24 2020 -0800 forgot to add this file src_hydro/Vorticity.cpp commit 30a3924ab1807494c97626b286d2a07250d1f54c Author: Andy Nonaka Date: Tue Nov 3 16:09:59 2020 -0800 magvort routine; added magvort to hydro plotfile exec/hydro/WritePlotFile.cpp src_hydro/Make.package src_hydro/hydro_functions.H commit b19a795c9134f2b3b49f9a055a37cc2ff34f2606 Author: Daniel Ladiges Date: Tue Nov 3 12:48:07 2020 -0800 Additional plotfile output, electro osmosis input file exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/inputs_eo_test_wet commit 001f63162805a29ff00e2cf15ed1e1fdf22cbdcd Author: Daniel Ladiges Date: Mon Nov 2 17:46:20 2020 -0800 Particles per box output no longer rounded exec/immersedIons/main_driver.cpp src_common/species.H commit cd513e9d6c35395872ed93ffb241996148fb9def Merge: 228b6aa1 c0c6ee9b Author: Andy Nonaka Date: Mon Nov 2 08:41:32 2020 -0800 Merge branch 'main' into compressible_mui commit 228b6aa110986bc025fb7d17afa545bfc9af26fa Author: Changho Kim Date: Mon Nov 2 04:50:05 2020 -0800 exec/compressible_mui/test: 8x8x8 with max_grid_size 8x4x4 exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mui exec/compressible_mui/test/cmd exec/compressible_mui/test/in.kmc exec/compressible_mui/test/inputs_fhd_coverage exec/compressible_mui/test/run.sh exec/compressible_mui/test/test_1+1/in.kmc exec/compressible_mui/test/test_1+1/inputs_fhd_coverage exec/compressible_mui/test/test_1+1/run.sh exec/compressible_mui/test/test_4+1_x/in.kmc exec/compressible_mui/test/test_4+1_x/inputs_fhd_coverage exec/compressible_mui/test/test_4+1_x/run.sh exec/compressible_mui/test/test_4+1_y/in.kmc exec/compressible_mui/test/test_4+1_y/inputs_fhd_coverage exec/compressible_mui/test/test_4+1_y/run.sh exec/compressible_mui/test/test_4+1_z/in.kmc exec/compressible_mui/test/test_4+1_z/inputs_fhd_coverage exec/compressible_mui/test/test_4+1_z/run.sh commit 3f983361e56205cc26383fd06dee01cc7d08ae37 Author: Changho Kim Date: Sun Nov 1 23:27:38 2020 -0800 exec/compressible_mui: adding timers exec/compressible_mui/cori/README exec/compressible_mui/cori/submit.sh exec/compressible_mui/cori_coverage/README exec/compressible_mui/cori_coverage/cmd exec/compressible_mui/cori_coverage/cori_slurm.sh exec/compressible_mui/cori_coverage/in.kmc exec/compressible_mui/cori_coverage/inputs_fhd exec/compressible_mui/cori_coverage/mpmd.conf exec/compressible_mui/cori_coverage/submit.sh exec/compressible_mui/main_driver.cpp commit e892a2033194971bdd8890e1a178456712915d33 Author: Daniel Ladiges Date: Fri Oct 30 18:50:31 2020 -0700 Fixed bug causing particles to bunch in centre of domain. exec/immersedIons/main_driver.cpp commit 00f3ff6124f7299cdc79bfed708814ffbe78d925 Author: isriva Date: Thu Oct 29 10:01:25 2020 -0700 added input file for equilibrium 3d test exec/compressible_stag/inputs_equil_3d commit 6270552fd57f9c95703fe01e2ed4d2aefd1cc9fe Author: isriva Date: Thu Oct 29 09:54:42 2020 -0700 some corrections to the stochastic stress tensor src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 2bbb49427734a22b33dce396aee8fe4414cf99d6 Author: Daniel Ladiges Date: Wed Oct 28 18:22:37 2020 -0700 Added density output for species exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_mobility_test exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/collision_functions.F90 commit bac3f3ba3e055f71dc20f393e43ba4480a00d49d Merge: 0817e9a5 c0c6ee9b Author: Daniel Ladiges Date: Wed Oct 28 14:17:05 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 0817e9a5d52f3e0cdc80e72925c6856db1da5dc1 Author: Daniel Ladiges Date: Wed Oct 28 14:16:37 2020 -0700 Electro osmosis input file exec/immersedIons/inputs_eo_test_wet commit c0c6ee9b43002cd6f5b8b4218bab3086d712e100 Merge: 601ea3ad 896ad28a Author: Andy Nonaka Date: Wed Oct 28 12:23:08 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 601ea3ad5d496e96c1a328c081de5edb76ff1f87 Author: Andy Nonaka Date: Wed Oct 28 12:22:58 2020 -0700 comment only src_hydro/StochMomFlux.cpp commit 896ad28a65d8074dfbba2ec64b52a36d1c9dfe4e Merge: 3b5b9618 efc414a4 Author: Daniel Ladiges Date: Tue Oct 27 22:18:53 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 3b5b961877a34380f291ce19d271c7526ad09846 Author: Daniel Ladiges Date: Tue Oct 27 22:18:15 2020 -0700 Removed some debugging messages exec/immersedIons/particleGen.cpp commit efc414a48621a1e7a6f603646bd3e3bf31d454cb Merge: 8f1d908d 986e9a51 Author: Andy Nonaka Date: Tue Oct 27 16:28:14 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 8f1d908dc192b892f0c2cc67dac5cc4d325d2b50 Author: Andy Nonaka Date: Tue Oct 27 16:27:58 2020 -0700 fix OU exec/hydro/TurbForcing.cpp commit 986e9a51b30c72e6ee156cf7701cfcd125de402a Merge: 1f5b9e79 447bccb4 Author: Daniel Ladiges Date: Tue Oct 27 15:04:10 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 1f5b9e791e8b7bb8d93cac9f7cb3a262e2ec3154 Author: Daniel Ladiges Date: Tue Oct 27 14:47:18 2020 -0700 Modifications for measuring potential energy exec/immersedIons/delPlots exec/immersedIons/inputs_density_test exec/immersedIons/inputs_potential_test exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp commit 447bccb49f31b0369d3d76e45fcc807dcf6d490c Author: isriva Date: Tue Oct 27 14:32:36 2020 -0700 added input file tp replicate Jing, Cruz et al JCP 2015 exec/immersedIons/inputs_jing_cruz_jcp exec/immersedIons/main_driver.cpp src_particles/particle_functions_K.H commit 664a4e79721763164e0e8f0910c9fdfad9cfec67 Merge: 8590e214 74c6c5fa Author: John Bell Date: Tue Oct 27 11:27:04 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 8590e214bb4ddc0c9f1a2031dbddd6ee908c6262 Author: John Bell Date: Tue Oct 27 11:25:21 2020 -0700 need to use all of hte U's in forming source exec/hydro/TurbForcing.cpp commit 74c6c5fa6f23d7b03a7aa73b037644a2ad6de990 Author: Andy Nonaka Date: Tue Oct 27 10:49:14 2020 -0700 restart turbForcing exec/hydro/Checkpoint.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit e4c60e7f78e5e6bb6306aa77977be49152e08560 Author: Andy Nonaka Date: Tue Oct 27 10:43:35 2020 -0700 Turbulent forcing persistence exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 11de6a28c3afde79e57b7aa97f689c73479b2b8d Author: Andy Nonaka Date: Tue Oct 27 10:38:06 2020 -0700 adding setters/getters for forcing_U (for future checkpointing) exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp commit 94d932e5b35f05e55378db3e17a58cb703c8a668 Merge: f528dd21 5cdf3360 Author: jbbel Date: Tue Oct 27 10:30:24 2020 -0700 Merge pull request #16 from AMReX-FHD/TurbForceFix increment U, not set U commit 5cdf3360ee9146591e74f6cc538f3f5c23d6824f Author: Andy Nonaka Date: Tue Oct 27 10:21:13 2020 -0700 increment U, not set U exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp commit c0aee065139f6821dd14e8d0517b580f00d656a8 Author: Changho Kim Date: Mon Oct 26 15:17:52 2020 -0700 exec/compressible_mui/cori: cori setting 64x64x64 exec/compressible_mui/cori/cmd exec/compressible_mui/cori/cori_SF.sh exec/compressible_mui/cori/in.kmc_eq exec/compressible_mui/cori/inputs_fhd_SF exec/compressible_mui/cori/mpmd.conf commit f528dd216df99e993e0c8b846a44b2f17cf7bbcd Author: jbb Date: Mon Oct 26 15:00:37 2020 -0700 added forcing inputs exec/hydro/inputs_force commit c47398cc1f6a70bbbed4e1f94961c5ce0df5fc4c Author: Andy Nonaka Date: Fri Oct 23 16:32:20 2020 -0700 implement integral of OU process, and use of a and b from TurbForcing class exec/hydro/TurbForcing.cpp commit 1894ffa42782fd2683b886486091d88874cd3c53 Merge: acc40415 a3549861 Author: Andy Nonaka Date: Fri Oct 23 15:45:29 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit acc40415a7d94fc8012ae60592d62e44d9084d01 Author: Andy Nonaka Date: Fri Oct 23 15:44:59 2020 -0700 add "turb_a" and "turb_b" (default 1.0) to the common namelist fixed a bug in the mode summation exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp exec/hydro/advance.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit a354986119694a22b06a4d52f088d86d45d9e55f Author: Daniel Ladiges Date: Fri Oct 23 13:17:57 2020 -0700 changed timestep ramping back so regressions wont break exec/immersedIons/main_driver.cpp commit 00d4b6a934f81c9cc319bd47259ae7c9f73fc9b9 Merge: d9c1032b 3a833afd Author: Daniel Ladiges Date: Fri Oct 23 13:04:29 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d9c1032b0da719bb6a6d6238da1824de66e548e5 Author: Daniel Ladiges Date: Fri Oct 23 13:04:15 2020 -0700 test inputs file exec/immersedIons/inputs_potential_test commit 9bca216d7af39957f9709f08986206a0219a03ba Author: Daniel Ladiges Date: Fri Oct 23 13:03:37 2020 -0700 Function for outputting potential energy distribution exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 3a833afdd5879c8aebcceca082d6baeed552cccd Author: Andy Nonaka Date: Thu Oct 22 16:03:19 2020 -0700 turblence forcing exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H commit 64c342730c9e3b99e04652704f822b22a8416cce Merge: af5d8ef6 8fb276c4 Author: Andy Nonaka Date: Thu Oct 22 15:06:29 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit af5d8ef66256460cd3f75929b9aa85590a8593db Author: Andy Nonaka Date: Thu Oct 22 15:06:12 2020 -0700 shell of TurbForcing class exec/hydro/Make.package exec/hydro/TurbForcing.H exec/hydro/TurbForcing.cpp commit 8fb276c4aa89449f7c4641454aeaad8946feda56 Merge: e54ccbd6 627337f5 Author: Daniel Ladiges Date: Thu Oct 22 14:25:54 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 627337f587d7d67cb1243923616993050ddaf9d2 Merge: a2715b3f a996cf3a Author: Daniel Ladiges Date: Thu Oct 22 14:25:44 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit a2715b3fcc2f4875d00b49201085e64d872106b7 Author: Daniel Ladiges Date: Thu Oct 22 14:25:23 2020 -0700 Tidied up main driver in immersedIons exec/immersedIons/main_driver.cpp commit e54ccbd6046cd949987ce5a5303c7a8b578bf81d Author: Daniel Ladiges Date: Thu Oct 22 14:25:19 2020 -0700 Added harmonic potential function src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit f42e435eb9e9eaaea7817e5ce45f809d689d4ae9 Author: Daniel Ladiges Date: Thu Oct 22 14:21:09 2020 -0700 Additional channel mobility code src_particles/particle_functions_K.H commit a996cf3a63d711595f9b343d0edc61a6dc37b03b Author: Andy Nonaka Date: Thu Oct 22 08:14:43 2020 -0700 wrote routine to generate X random numbers on one processor and broadcast to all the others exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H commit 962e26e8581d62833a157d1d7bcbb93ec19463e1 Merge: 354d6168 e54f750c Author: Andy Nonaka Date: Wed Oct 21 21:06:57 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 354d6168c2ea708caa4d6cef0df1d254aca57898 Author: Andy Nonaka Date: Wed Oct 21 21:06:43 2020 -0700 more tidying of inertial integrator exec/hydro/advance.cpp commit a5d00f1d86583fdd28dbf73074d6a57a8df8ebc5 Author: Andy Nonaka Date: Wed Oct 21 21:02:32 2020 -0700 tidy inertial back into main advance routine exec/hydro/Make.package exec/hydro/advance.cpp exec/hydro/advanceInertial.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit e54f750c00e7019c5b1dc5ddd27ca39cb1e4f976 Author: isriva Date: Wed Oct 21 20:52:16 2020 -0700 added shited repulsive-only LJ for ion-ion and ion-walls exec/immersedIons/inputs_density_test src_particles/particle_functions_K.H commit 1e6deb84aed663da3b78b0bad51961c773851be7 Author: Andy Nonaka Date: Wed Oct 21 16:07:36 2020 -0700 more cleanup of new inertial incompressible integrator exec/hydro/advance.cpp exec/hydro/advanceInertial.cpp commit 64a491430a51869273cb9d573004866126e4af67 Author: Andy Nonaka Date: Wed Oct 21 15:53:34 2020 -0700 various optimizations; machine level changes exec/hydro/advance.cpp exec/hydro/advanceInertial.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 1b49a6787f7b0cd7901e2934c6e4ed3aa4e0b01f Author: Andy Nonaka Date: Wed Oct 21 14:50:57 2020 -0700 don't reset pressure after solve subsequent solve will speed up if you retain the previous solution as an initial guess exec/hydro/advance.cpp exec/hydro/advanceInertial.cpp commit 382e51136a4c23fc2b54076fba0bd54dff965579 Author: Andy Nonaka Date: Wed Oct 21 14:38:52 2020 -0700 inertial work exec/hydro/Make.package exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 9837a627a4e2e12e58b2b7c68103cf0bf8457ad5 Merge: 461748c8 0853f649 Author: Daniel Ladiges Date: Tue Oct 20 17:00:51 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 461748c808b22b9b70af8f888714f137e3fe5fbf Author: Daniel Ladiges Date: Tue Oct 20 16:59:36 2020 -0700 Added some optimizations for all dry sims (will help with Donev code) src_particles/FhdParticleContainer.cpp commit 0853f649bea04dc05c6cd3ac15148710d69a49fb Author: Andy Nonaka Date: Tue Oct 20 14:59:09 2020 -0700 more charged fluid WIP src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/FluidCharge.cpp src_multispec/multispec_functions.H commit 10a8154e2a76af0b35805e3f12720023b439a5a6 Author: Andy Nonaka Date: Tue Oct 20 14:23:32 2020 -0700 notes on solvability src_electrostatic/electrostatic.cpp commit a642883564fe6e555ee144f5194a30175c24815b Author: Andy Nonaka Date: Tue Oct 20 07:23:02 2020 -0700 charged fluid saving progress src_multispec/ElectroDiffusiveMassFluxdiv.cpp src_multispec/multispec_functions.H commit 96a44a1035073676fdff0517901a38e954efa7c6 Author: Changho Kim Date: Tue Oct 20 04:59:08 2020 -0700 exec/compressible_mui: SF setting 2x exec/compressible_mui/README exec/compressible_mui/in.kmc_eq exec/compressible_mui/inputs_fhd_SF exec/compressible_mui/run_SF.sh commit 46cee89c2a186f1e13aa7eecea07c7dfbef27d5b Author: isriva Date: Mon Oct 19 19:19:45 2020 -0700 output shifted momenta and velocities in plotfiles use shifted momenta and velocities for SFactor cleaned up indents exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit af50c2e831d65778d1c3ca27b833b0a68fdd6109 Author: Daniel Ladiges Date: Mon Oct 19 16:38:09 2020 -0700 Added measured mobility function for test channel src_particles/particle_functions_K.H commit 769a27c1dc6cc976125fda04077f0acaaddd2c3b Merge: 417480f9 7bea1424 Author: Daniel Ladiges Date: Mon Oct 19 12:17:32 2020 -1000 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 417480f941e83f641d13087086e4a7705345d194 Author: Daniel Ladiges Date: Mon Oct 19 12:17:08 2020 -1000 channel mobility measurements exec/notebooks/channel_mobility.nb commit f949389f970d43c487913e8fe19195f23b958b7c Author: Andy Nonaka Date: Mon Oct 19 14:11:39 2020 -0700 start adding shifted mom/vel to plotfile fix SF so it uses shifted mom/vel instead of averaged attempt to select specific variable pairs for SF exec/compressible_stag/main_driver.cpp src_compressible_stag/writePlotFileStag.cpp commit 7bea1424567fa4797407e28c2b569c0c5d3b70e1 Author: Andy Nonaka Date: Mon Oct 19 13:48:56 2020 -0700 more charged stuff src_multispec/ElectroDiffusiveMassFluxdiv.cpp commit 4c88d1969c593c643653e5fa6bc2c551484b9a04 Author: Andy Nonaka Date: Mon Oct 19 13:48:46 2020 -0700 more charged stuff src_multispec/Make.package src_multispec/multispec_functions.H commit dffbec7e04032dba6b7c1c27039ab6d3849026d9 Merge: 754eeecb 696f1857 Author: Daniel Ladiges Date: Mon Oct 19 12:56:49 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 754eeecb042f9dd34776557f38ebc4088d4a7699 Author: Daniel Ladiges Date: Mon Oct 19 12:56:35 2020 -0700 Some notebooks for analysis exec/notebooks/channel_mobility.nb exec/notebooks/densityAnalysis.nb commit 696f185783cb2221cd9d746196bc39e6cc3f031d Author: Andy Nonaka Date: Mon Oct 19 10:14:33 2020 -0700 more charged fluid stuff src_multispec/FluidCharge.cpp commit af463b51ab830d99abd2ce0b405ac5bdbbad89d4 Author: Andy Nonaka Date: Mon Oct 19 09:34:08 2020 -0700 more charged fluid functions src_multispec/FluidCharge.cpp src_multispec/multispec_functions.H commit 8acdf9cf40d190218eefad62aadbf5f534ad1b37 Author: Changho Kim Date: Mon Oct 19 05:09:26 2020 -0700 exec/compressible_mui/cori/cori_SF.sh (error in slurm script), SPPARKS_MUI/MAKE/Makefile.mui_cori: no -g option exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mui_cori exec/compressible_mui/cori/cori_SF.sh commit 0173c2d2dc971dd4af25d15ab385e1ea4fc04379 Author: Andy Nonaka Date: Fri Oct 16 18:09:31 2020 -0700 renname temps src_multispec/multispec_functions.H commit 159882f8b5549db3f6a28530f847a8775c90cede Author: Andy Nonaka Date: Fri Oct 16 18:08:47 2020 -0700 more charged stuff src_multispec/FluidCharge.cpp src_multispec/multispec_functions.H commit c65f808d7a4a81c7d2fdebe2b6b9accac5f6bbd8 Author: Andy Nonaka Date: Fri Oct 16 17:41:55 2020 -0700 bringing some charged fluid stuff over to AMReX src_multispec/FluidCharge.cpp src_multispec/Make.package src_multispec/multispec_functions.H commit 940fb0c2c9a89ea5209baaa7a83adcf4bd4f8101 Author: Andy Nonaka Date: Fri Oct 16 16:40:13 2020 -0700 correction_flux to GPU src_multispec/CorrectionFlux.cpp src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/correction_flux.F90 commit 03d88bb8e1226476437309f8913758745a78dca5 Author: isriva Date: Thu Oct 15 16:14:36 2020 -0700 fix for doing Structure Factors on the host in a CUDA build exec/compressible/GNUmakefile exec/compressible/main_driver.cpp exec/compressible_stag/GNUmakefile exec/compressible_stag/main_driver.cpp exec/hydro/GNUmakefile exec/hydro/main_driver.cpp exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/immersedIons2/GNUmakefile exec/immersedIons2/main_driver.cpp exec/multispec/GNUmakefile exec/multispec/main_driver.cpp exec/tests/RFDanalysis/GNUmakefile exec/tests/RFDanalysis/main_driver.cpp commit e3f967c844fb5c788b8da95302ca2d92d63466ff Merge: c3865621 db9ab21c Author: Andy Nonaka Date: Thu Oct 15 15:42:58 2020 -0700 Merge branch 'main' into compressible_mui commit c386562140e50b3458d1b124ede5bc1af0a724d7 Author: Andy Nonaka Date: Thu Oct 15 15:42:32 2020 -0700 fix for the future so Structure Factors calcs can still be done on the host in a GPU build exec/compressible_mui/GNUmakefile exec/compressible_mui/main_driver.cpp exec/compressible_mui/sav_main_driver/m00.cpp exec/compressible_mui/sav_main_driver/m01-cutemp_jsq.cpp exec/compressible_mui/sav_main_driver/m01.cpp exec/compressible_mui/sav_main_driver/m02.cpp exec/compressible_mui/sav_main_driver/m10.cpp exec/compressible_mui/sav_main_driver/m11.cpp exec/compressible_mui/sav_main_driver/m12.cpp commit c05ba56caed5cfd98f23907ffa0892b18637b38b Merge: abd85608 e7954510 Author: isriva Date: Thu Oct 15 15:25:33 2020 -0700 modified makefile for struct fact on GPU commit abd85608b0b268766585a808cd32256779618261 Author: isriva Date: Thu Oct 15 15:18:18 2020 -0700 modifications to enable structure factor on GPU exec/compressible_stag/GNUmakefile exec/compressible_stag/main_driver.cpp commit e7954510ba3a139a014e64e70506e85f4a650084 Author: Andy Nonaka Date: Thu Oct 15 13:30:21 2020 -0700 cuda logic exec/compressible_stag/GNUmakefile commit af34f919f50b53d2ce7368d899fedff414743ee4 Author: Andy Nonaka Date: Thu Oct 15 13:28:03 2020 -0700 USE_CUDA flag exec/compressible_stag/GNUmakefile commit df8601f60899bb937007cc142b8f11f29239b1d6 Author: isriva Date: Thu Oct 15 13:21:09 2020 -0700 some more modifications to stochastic fluxes and uncomment struct fact src_compressible/compressible_functions.H src_compressible_stag/timeStepStag.cpp commit 037890191c6ff4c1a20ceb5dc2e08d996ba137c9 Author: isriva Date: Thu Oct 15 13:19:19 2020 -0700 some more modifications to stochastoc fluxes exec/compressible_stag/main_driver.cpp commit 0cfe160e95f36bf479e540d2a99c5ff98438446b Author: isriva Date: Tue Oct 13 13:09:50 2020 -0700 updated logic for stochastic fluxes on staggered grid exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit db9ab21cf6c5b0e664a552a1c8097cfb46e4ac5a Author: Daniel Ladiges Date: Mon Oct 12 11:47:43 2020 -0700 Added some code for testing mobility exec/immersedIons/inputs_mobility_test exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 7ab471207b914adf89f9b9453c45deb20ff1ba3a Author: Changho Kim Date: Mon Oct 12 01:08:08 2020 -0700 typo exec/compressible_mui/cori/mpmd.conf commit 2870c1e3a5017a4e57657cfe09bdd30f93990a3d Author: Changho Kim Date: Mon Oct 12 00:54:37 2020 -0700 exec/compressible_mui: cori setup exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mui_cori exec/compressible_mui/cori/README exec/compressible_mui/cori/cori_SF.sh exec/compressible_mui/cori/in.kmc_eq exec/compressible_mui/cori/inputs_fhd_SF exec/compressible_mui/cori/mpmd.conf exec/compressible_mui/cori/submit.sh commit 8a65b3550f065a929b62ad4893f9010a1bc841e2 Author: Daniel Ladiges Date: Sun Oct 11 18:47:55 2020 -0700 Fixed tangential mobility in infinite plane approximation src_particles/particle_functions_K.H commit b4fe9955cbbf9da533b7f882f340e28039aa7f24 Merge: 7b1eddd4 98ddd3bb Author: Changho Kim Date: Sun Oct 11 17:57:35 2020 -0700 Merge branch 'compressible_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_mui commit 7b1eddd47a6a5309df27e3e240f20123255f43c4 Author: Changho Kim Date: Sun Oct 11 17:57:03 2020 -0700 exec/compressible_mui/GNUmakefile exec/compressible_mui/GNUmakefile commit 98ddd3bbfdc41effb4c4f0471275ce911a38dc12 Author: Changho Kim Date: Sun Oct 11 05:32:47 2020 -0700 exec/compressible_mui: forgot to add exec/compressible_mui/scripts/havg.py exec/compressible_mui/scripts/postproc_multi.sh exec/compressible_mui/scripts/rk4_4spec.py commit f15fc931f9d284777a6166de6617582bf2fe95db Author: Changho Kim Date: Sat Oct 10 21:12:59 2020 -0700 exec/compressible_mui: run_SF run_coverage_mult setting exec/compressible_mui/GNUmakefile exec/compressible_mui/in.kmc exec/compressible_mui/in.kmc_eq exec/compressible_mui/inputs_fhd_SF exec/compressible_mui/inputs_fhd_coverage exec/compressible_mui/run_SF.sh exec/compressible_mui/run_coverage.sh exec/compressible_mui/run_coverage_multi.sh exec/compressible_mui/scripts/compressible/inputs_fhd_SF exec/compressible_mui/scripts/compressible/run_SF.sh exec/compressible_mui/scripts/coverage.plt exec/compressible_mui/scripts/coverage_stat.py exec/compressible_mui/scripts/havg_jz.plt exec/compressible_mui/scripts/havg_spec4.plt exec/compressible_mui/scripts/in.kmc_eq exec/compressible_mui/scripts/j_stat.py exec/compressible_mui/scripts/mass_cons.py exec/compressible_mui/scripts/params2.py exec/compressible_mui/scripts/params3.py exec/compressible_mui/scripts/rk4_4spec.py exec/compressible_mui/scripts/stat_cols.py exec/compressible_mui/scripts/vert_stat.py commit c0631b10fd5f882d9c259b843561c36b3ab03a23 Merge: c0aac2d7 fceb19f9 Author: Changho Kim Date: Fri Oct 9 21:59:35 2020 -0700 Merge branch 'main' into compressible_mui commit fceb19f906019e6db2be72778bae3ddcc1cebb9f Author: Daniel Ladiges Date: Thu Oct 8 12:33:06 2020 -0700 test input file exec/immersedIons/inputs_density_test commit 5605f0b8f089ef6e3cec4fde2d0a8df6740dab3f Merge: 05ea71d5 c7f3a65d Author: Daniel Ladiges Date: Thu Oct 8 12:15:58 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 05ea71d53ded26cbd70b08c7b094fe2d88aac782 Author: Daniel Ladiges Date: Thu Oct 8 12:15:31 2020 -0700 Added timestep ramp up to allow higher molarities exec/immersedIons/main_driver.cpp commit c7f3a65d40dd7f000108f06b4c0d12b0f12871e8 Merge: b42aca0a 8e79f8ee Author: Johannes Blaschke Date: Wed Oct 7 21:58:24 2020 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit b42aca0a8c38aeb59024fa09c9599c980aa7c0a4 Author: Johannes Blaschke Date: Wed Oct 7 21:57:45 2020 -0700 extract parameters from package config exec/lib_hydro/demo/CMakeLists.txt commit 8e79f8eea0564e2341adbb7b095717b8b1dbaaa4 Author: Daniel Ladiges Date: Wed Oct 7 20:07:19 2020 -0700 Another wall LJ bugfix src_particles/particle_functions_K.H commit 7ebee44e36113d9cc9d93d68d47d04929d9f9d47 Author: Daniel Ladiges Date: Wed Oct 7 19:27:33 2020 -0700 LJ wall bugfix src_particles/particle_functions_K.H commit a255c534998f1052234fd09460f36a510bc8924b Merge: 30024aca 9080f780 Author: Daniel Ladiges Date: Wed Oct 7 18:42:41 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 30024acacc1183cc721080c9bc063f2918a7748b Author: Daniel Ladiges Date: Wed Oct 7 18:42:00 2020 -0700 Added LJ repulsion to walls plus some modifications to short range calcs exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 8d21c140f24b488012141e80927c8760d60ca8bb Merge: 71fbb3e1 9080f780 Author: isriva Date: Wed Oct 7 17:11:43 2020 -0700 merged with main & updated input files commit 9080f7808ac70ea69c36e96df8294cf2c5dc61a9 Author: Johannes Blaschke Date: Wed Oct 7 13:22:07 2020 -0700 clean up build scripts exec/lib_hydro/cmake/build.fish exec/lib_hydro/cmake/build.macbert.fish exec/lib_hydro/cmake/test/build.fish exec/lib_hydro/cmake/test/build.nmpb.fish exec/lib_hydro/demo/build.fish commit 3939a91a751e56322bd09d9f0ed8d2390ead929a Author: Johannes Blaschke Date: Tue Oct 6 18:15:23 2020 -0700 use improved build script exec/lib_hydro/cmake/test/build.nmpb.fish exec/lib_hydro/demo/build.nmpb.fish commit 9d18adeb398710726ad0fcdd711ec7f2a50446df Author: Johannes Blaschke Date: Tue Oct 6 18:13:12 2020 -0700 update test exec/lib_hydro/cmake/test/CMakeLists.txt commit 59f275b8edc0a1a49610dad60f1086fc1d3cdac3 Author: Johannes Blaschke Date: Tue Oct 6 16:52:20 2020 -0700 implement portable cmake exec/lib_hydro/cmake/CMakeLists.txt commit d6a5bca76aa2e67fb20c5f24319064a8f5fd92b4 Author: Daniel Ladiges Date: Tue Oct 6 11:20:31 2020 -0700 renamed some plotfile output exec/immersedIons/WritePlotFile.cpp commit 5821a56f5b632f52edb2f3a1c7282780b6c9b689 Author: Daniel Ladiges Date: Tue Oct 6 11:10:31 2020 -0700 test input file exec/immersedIons/inputs_density_test commit bcdd7498eadf476b9ccd57de0aeb577cb8765537 Merge: bac9c3a5 82304530 Author: Daniel Ladiges Date: Tue Oct 6 11:02:28 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit bac9c3a59d629cc53001f654100b9242c54d99e3 Author: Daniel Ladiges Date: Tue Oct 6 11:02:16 2020 -0700 Another stats bugfix src_particles/src_F90/collision_functions.F90 commit 82304530b36f883d03add6f47a82b4cb63670ccb Merge: 9bf7760e 97cd1707 Author: Johannes Blaschke Date: Mon Oct 5 18:56:47 2020 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 9bf7760e99309b23ab803239104c5b3b2c1f9564 Author: Johannes Blaschke Date: Mon Oct 5 18:56:42 2020 -0700 update .gitignore .gitignore commit 4847b7a91a8a1a54c82e6166cb50d7897a9b5140 Author: Johannes Blaschke Date: Mon Oct 5 18:54:57 2020 -0700 experiment with buddy parameters exec/immersed_boundary/flagellum/inputs_chlamy.buddy commit b6048389423b25b06747d8f95aa70cc0ea0ffc9b Author: Johannes Blaschke Date: Mon Oct 5 18:54:00 2020 -0700 make verbose exec/lib_hydro/cmake/test/build.fish commit 6e777c458bb852ab0aeac2a02448ba1d9f0263be Author: Johannes Blaschke Date: Mon Oct 5 18:53:26 2020 -0700 start making cmakelists more portable exec/lib_hydro/cmake/CMakeLists.txt commit 38aedb07149c31e1049ca61632833ac00c7efc60 Author: Johannes Blaschke Date: Mon Oct 5 18:52:59 2020 -0700 better build script exec/lib_hydro/cmake/build.nmpb.fish commit 58398433ff5b56c65ce8554bf05113e5c0c545e5 Author: Johannes Blaschke Date: Mon Oct 5 18:52:32 2020 -0700 update inputs to reflect new forcing exec/immersed_boundary/flagellum/inputs_chlamy commit 2846427abf9ab5d34792db102e3395cea68d0392 Author: Johannes Blaschke Date: Mon Oct 5 18:51:16 2020 -0700 track wip exec/immersed_boundary/flagellum/Render Frames.ipynb commit 97cd17074489402a9ef82bfec6cb3a867a7bce67 Author: Andy Nonaka Date: Mon Oct 5 16:38:49 2020 -0700 fix memory leak src_analysis/StructFact.cpp commit 5b9ea2faf2116ceeb3d3adad2a42bc25caa78196 Merge: e68bbbbc 08da967c Author: Daniel Ladiges Date: Mon Oct 5 10:51:44 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit e68bbbbc3ad7af02645e5e7af92224f92b7424fc Author: Daniel Ladiges Date: Mon Oct 5 10:51:24 2020 -0700 Bugfix to stats calc src_particles/src_F90/collision_functions.F90 commit 08da967c4c1394732ffc403f31b33d4f58227277 Author: isriva Date: Mon Oct 5 10:49:38 2020 -0700 modified input file for 4-point peskin kernel exec/immersedIons/inputs_test_fullywet_neutral_noslip_nowca commit dc001baf1bb221972e27f101792bafe1450f1084 Author: Daniel Ladiges Date: Mon Oct 5 09:38:35 2020 -0700 Revised stats routine to track down dead cell bug src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit ae7807142757bdb4d08147f3728160b31933f011 Author: Daniel Ladiges Date: Wed Sep 30 21:13:48 2020 -0700 Explicit stochastic drift calculation for dry part using infinite plane approximation. exec/immersedIons/WritePlotFile.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit f6ffea2cb491cfc5fccbdd259d86c1f95f50837d Author: Daniel Ladiges Date: Wed Sep 30 12:02:07 2020 -0700 Fixed bug causing particle radius to occasionally get zeroed. src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 73bd8854a1d996ebe3504983c1efb541873b4557 Author: Daniel Ladiges Date: Tue Sep 29 12:21:23 2020 -0700 Fixed bug in dry wall mobility src_particles/particle_functions_K.H commit c0aac2d7c0d75628bc403e2c48d1b26e98b497c7 Merge: 65be562c 82c32fb5 Author: Changho Kim Date: Mon Sep 28 14:22:44 2020 -0700 Merge branch 'compressible_mui' of https://github.com/AMReX-FHD/FHDeX into compressible_mui commit 65be562c297aa75f2d2c03a36d232c093491161c Author: Changho Kim Date: Mon Sep 28 14:22:28 2020 -0700 exec/compressible_mui: case_study_2_mom clean up exec/compressible_mui/sav_main_driver/README exec/compressible_mui/sav_main_driver/m01-cutemp_jsq.cpp exec/compressible_mui/scripts/havg_cutemp.py exec/compressible_mui/scripts/j_stat.py exec/compressible_mui/scripts/jsq_stat.py exec/compressible_mui/scripts/jsq_stat2.py commit ccbda4e87501d9e1ff56021cd8c1a3235665ac76 Merge: 72ccc490 fd191ca7 Author: Daniel Ladiges Date: Mon Sep 28 12:37:05 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 72ccc490a0dc21779c68a8681c847d4addf1f01c Author: Daniel Ladiges Date: Mon Sep 28 12:36:28 2020 -0700 Working on dry diff explicit mob calc. exec/immersedIons/GNUmakefile exec/immersedIons/inputs_test_fullywet_neutral_noslip src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 82c32fb5246fd4aac1c9fe3ce0ec15b0da6fff01 Merge: 1da6e7f3 fd191ca7 Author: Andy Nonaka Date: Mon Sep 28 07:29:07 2020 -0700 Merge branch 'main' into compressible_mui commit fd191ca7cccbdd5960535de7652fe925a789a9ce Author: Andy Nonaka Date: Mon Sep 28 07:27:46 2020 -0700 setCGVerbose -> setBottomVerbose src_hydro/MacProj_hydro.cpp commit 1da6e7f33c5ac5480bf75c78e183c0c6998f4cbf Author: Changho Kim Date: Mon Sep 28 04:48:47 2020 -0700 /exec/compressible_mui: output all cu variables for havg exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/sav_main_driver/m00.cpp exec/compressible_mui/sav_main_driver/m01.cpp exec/compressible_mui/scripts/havg.py exec/compressible_mui/scripts/mass_cons.py commit f0fc6f34022410d081510854f5de06c22f080799 Merge: d7ac5242 4400a453 Author: Andy Nonaka Date: Mon Sep 21 15:27:57 2020 -0700 Merge branch 'main' into compressible_mui commit d7ac52423a207361c274d4b3f35fffb9274d262a Author: Changho Kim Date: Mon Sep 21 14:30:49 2020 -0700 maxwell_inflow_sampling (separate code for test) exec/compressible_mui/maxwell_inflow_sampling/a0.cpp exec/compressible_mui/maxwell_inflow_sampling/a1.cpp exec/compressible_mui/maxwell_inflow_sampling/a2.cpp exec/compressible_mui/maxwell_inflow_sampling/a3.cpp exec/compressible_mui/maxwell_inflow_sampling/a4.cpp exec/compressible_mui/maxwell_inflow_sampling/cmd_gnuplot exec/compressible_mui/maxwell_inflow_sampling/hist.py exec/compressible_mui/maxwell_inflow_sampling/hist4.py exec/compressible_mui/maxwell_inflow_sampling/run012.sh exec/compressible_mui/maxwell_inflow_sampling/run3.sh exec/compressible_mui/maxwell_inflow_sampling/run4.sh commit db3b54c424e9167ef6d5819fb6abcf70df54f2be Author: Changho Kim Date: Mon Sep 21 14:19:25 2020 -0700 maxwellian inflow sampling exec/compressible_mui/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/sav_main_driver/README exec/compressible_mui/sav_main_driver/m00.cpp exec/compressible_mui/sav_main_driver/m01.cpp exec/compressible_mui/sav_main_driver/m02.cpp exec/compressible_mui/sav_main_driver/m10.cpp exec/compressible_mui/sav_main_driver/m11.cpp exec/compressible_mui/sav_main_driver/m12.cpp exec/compressible_mui/scripts/postproc.sh commit 5bf7e05742578fbc970c0b2d64d8d5214989d706 Author: Changho Kim Date: Sun Sep 20 21:38:02 2020 -0700 exec/compressible_mui/main_driver.cpp: going back exec/compressible_mui/main_driver.cpp commit 4400a453e48d429ab03313af0f66abd9fa8723af Author: Daniel Ladiges Date: Wed Sep 16 12:33:38 2020 -0700 Still debugging CUDA particle predictor loop ¯\_(ツ)_/¯ exec/immersedIons/inputs_regression_noslip_neumann_det exec/immersedIons/main_driver.cpp src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp commit dad882e85dda906ceb7c71bfe808e93a83d06895 Merge: 62706226 a3ac4c5b Author: Andy Nonaka Date: Wed Sep 16 11:14:01 2020 -0700 Merge branch 'main' into compressible_mui commit 627062260be6ce10d37b49ad6b383e691764cc4c Author: Andy Nonaka Date: Wed Sep 16 11:13:36 2020 -0700 increment a temporary with MUI fetch and add the temporary onto the cu state exec/compressible_mui/main_driver.cpp commit a3ac4c5b9297d221ca87d58cb3c28bf269a2782c Author: Daniel Ladiges Date: Mon Sep 14 17:25:43 2020 -0700 Bufixing some errors that show up running CUDA debug version. exec/immersedIons/GNUmakefile src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit af808a347d338ece42807a39c665cd92132c29e1 Author: Daniel Ladiges Date: Sat Sep 12 18:40:36 2020 -0700 Particle predictor loop now completely GPU. Still fixing a bug in calc of midpoint rejection fraction. src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp commit 71fbb3e1ef5f164bea7850aae420a60dbdbc9f9b Author: isriva Date: Fri Sep 11 13:28:15 2020 -0700 new test input file & some new outputs in main driver exec/compressible_stag/inputs_test_verify exec/compressible_stag/main_driver.cpp commit 0af025b3998a6917714ab9a73823db3bdaa62683 Merge: 9ab42d99 7f0af86b Author: Daniel Ladiges Date: Fri Sep 11 12:50:36 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 9ab42d99308a1d1e2e6cd25903452cbce847535b Author: Daniel Ladiges Date: Fri Sep 11 12:49:52 2020 -0700 Started CUDA conversion of particle move predictor step. exec/immersedIons/main_driver.cpp src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 7f0af86b0892e2edd2ee8e3e672cf091b60fd1aa Author: Andy Nonaka Date: Fri Sep 11 12:48:13 2020 -0700 update species stuff that doesn't matter exec/multispec/inputs_incomp_3d commit d6936e5964069e34ab74faeee3dc7aababd4679c Author: Andy Nonaka Date: Fri Sep 11 12:43:56 2020 -0700 new incompressible setup (2 species, c=0.5 0.5) exec/multispec/inputs_incomp_3d commit 5a364421dca6daf1357487fc4bb24ffb21fd0bf2 Author: Andy Nonaka Date: Fri Sep 11 12:33:56 2020 -0700 update incorrect comments in inputs file exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d exec/multispec/inputs_compare_equil_2d exec/multispec/inputs_compare_equil_3d exec/multispec/inputs_diffusion_2d exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d commit 22bfd6bd5e3b04e673f489b141d6916abd5884a6 Author: jbb Date: Wed Sep 9 17:17:47 2020 -0700 fix differences exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/inputs_det_test exec/compressible_stag/inputs_test_deterministic commit 6287dbce305db3b8ed30314cff6a73359e60a544 Merge: 5908f4b0 b44e5b03 Author: isriva Date: Wed Sep 9 09:37:01 2020 -0700 Merge remote-tracking branch 'origin/main' into main commit 5908f4b0efe2462d28339cbef5829ab3269ac847 Author: isriva Date: Wed Sep 9 09:09:20 2020 -0700 added test input files for noslip. added jupyter notebook for analysis exec/immersedIons/analysis.ipynb exec/immersedIons/inputs_test_fullywet_neutral_noslip exec/immersedIons/inputs_test_fullywet_neutral_noslip_nowca commit b44e5b03e5218c0f5cd9d4f9296d4cab639614fd Author: Andy Nonaka Date: Fri Sep 4 13:20:01 2020 -0700 charged namespace/namelist stuff -> FHDeX multispecies namespace/namelist src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 5a4756be5f0b8f0851ec8591850735cba6de4087 Author: Andy Nonaka Date: Fri Sep 4 12:41:39 2020 -0700 prep for charged fluid code src_common/common_functions.H src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp commit 69316a4d119616bba4b15575d291c63027773aa1 Merge: 66881084 f3660efc Author: isriva Date: Fri Sep 4 10:48:18 2020 -0700 Merge remote-tracking branch 'origin/dev_compressible_stag' into dev_compressible_stag commit 6688108453b5047d3054e4bc07a6d587d4b78385 Author: isriva Date: Fri Sep 4 10:42:51 2020 -0700 added 1D deterministic inputs for unstaggered exec/compressible/inputs_test_deterministic commit f3660efc794b5b7f4d7475d324ef04447008d09f Merge: 941a573d c50f1d1f Author: jbb Date: Fri Sep 4 09:59:04 2020 -0700 Merge branch 'dev_compressible_stag' of https://github.com/AMReX-FHD/FHDeX into dev_compressible_stag commit 941a573dd19aa4880728e8ef6760eacbf950383f Author: jbb Date: Fri Sep 4 09:58:24 2020 -0700 added inputs for sinusoidal density exec/_1d_staggered_comp/inputs_det_test commit ec04c297a6b634f69176e8ab10f8d56a4b080e85 Author: Andy Nonaka Date: Fri Sep 4 09:56:21 2020 -0700 regression for multispecies exec/multispec/inputs_regression_detbubble_2d exec/multispec/inputs_regression_detbubble_3d exec/multispec/inputs_regression_equil_2d exec/multispec/inputs_regression_equil_3d commit c50f1d1f67e519171cf2a94ea0ebe291e46e6ac0 Author: isriva Date: Thu Sep 3 21:46:11 2020 -0700 solved transverse momentum for 1D src_compressible_stag/timeStepStag.cpp commit c00599be7f092d44b95278c4209ef06ad20a17c4 Author: Daniel Ladiges Date: Thu Sep 3 16:12:18 2020 -0700 All particle move functions now C++ src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit bef8bb82d74519e88d64be9282629de0b48a37ac Author: Daniel Ladiges Date: Thu Sep 3 14:06:29 2020 -0700 dry velocity calc now in C++ exec/immersedIons/inputs_regression_noslip_neumann_det src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit e2ef22939823888b22a78d42f09a484d3f68a70b Merge: 71f15027 59b9ba03 Author: jbb Date: Thu Sep 3 13:08:36 2020 -0700 Merge branch 'dev_compressible_stag' of https://github.com/AMReX-FHD/FHDeX into dev_compressible_stag commit 71f15027acfc414839be717a5e003485aa8e86fb Author: jbb Date: Thu Sep 3 13:07:39 2020 -0700 made 1d tests the same exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/driver_old.f exec/compressible_stag/inputs_test_deterministic src_compressible_stag/compressible_functions_stag.cpp commit f0648a84be6500d5eb7f9920515aa3c80daa9641 Author: Daniel Ladiges Date: Thu Sep 3 12:47:50 2020 -0700 C++ of dry mobility function src_particles/particle_functions_K.H commit 59b9ba0322f39d09a91c22a346ea725d2f9c37a1 Author: isriva Date: Thu Sep 3 12:17:45 2020 -0700 fixed FillBoundary issues on fluxes .gitignore exec/compressible/inputs_test_deterministic exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 6cc89cbfc917b87aa7fb26848c7cccd5cb5b5932 Author: Daniel Ladiges Date: Thu Sep 3 10:57:34 2020 -0700 All wet particle motion now in C++ src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp commit f1e734a56db4ee6e4787eaedcb99cb93e375e2dd Author: Daniel Ladiges Date: Wed Sep 2 11:12:12 2020 -0700 More C++ kernels for particle boundary interactions. src_geometry/paramplane_functions_K.H commit 5ff20fead94c1e0666f483e74cdcd84f54badc9c Author: isriva Date: Tue Sep 1 12:30:01 2020 -0700 corrected small errors in RK3 stepping src_compressible_stag/timeStepStag.cpp commit 8155a41463d09a02abbffb063b5e2ebb8d3c1bf3 Author: Changho Kim Date: Tue Sep 1 03:55:19 2020 -0700 exec/compressible_mui: case study 2, 4x4x40 setup exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/run.sh exec/compressible_mui/scripts/havg.py commit 41c5bdad24761dad24ad5d647d4cdbb70d84d7d3 Author: Andy Nonaka Date: Mon Aug 31 21:11:21 2020 -0700 more C++ conversion src_compressible/compressible_functions_F.H src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 10415e575117fb5281c1a3c9410aa2e682cc4ef6 Author: isriva Date: Mon Aug 31 12:22:23 2020 -0700 new dev branch for staggered compressible .gitignore exec/compressible/inputs_test_deterministic exec/compressible_stag/inputs_SFtest exec/compressible_stag/inputs_test_deterministic exec/compressible_stag/main_driver.cpp src_compressible/compressible_functions.cpp src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/fluxStag.cpp commit 7f68f8865d5df938b8fb950a4e49e5a6192a2a70 Author: Changho Kim Date: Sun Aug 30 22:14:57 2020 -0700 exec/compressible_mui: mass final vert setting exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/run.sh exec/compressible_mui/scripts/mass_cons.py exec/compressible_mui/scripts/vert_stat.py commit 36316e574ab3d24dfe94b684d4dff89a44eeb851 Author: Andy Nonaka Date: Fri Aug 28 17:21:55 2020 -0700 evaluate_corrs WIP (C++) restore F90 evaluate_stats (other routines in other programs are calling it) src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit ecf32bb4754bf27d1ae62e09857cd2153eb7dc30 Merge: 03a6baa8 6a345228 Author: Changho Kim Date: Fri Aug 28 14:47:04 2020 -0700 Merge branch 'main' into compressible_mui commit 14ad5fe84a6fd235015255ee4b1e1ef61b490a1c Merge: 7a9b7b27 6a345228 Author: Andy Nonaka Date: Fri Aug 28 09:28:49 2020 -0700 Merge branch 'main' into compressible_stag commit 7a9b7b2760426a3c637b2a98f3faf421e5d9d3c5 Author: Andy Nonaka Date: Fri Aug 28 09:28:09 2020 -0700 synced up with compressible/main_driver.cpp exec/compressible_stag/main_driver.cpp commit 6a3452282b0e77c9bc892b302dc5953b43a590f1 Merge: d2cc24b6 368dcca2 Author: Andy Nonaka Date: Fri Aug 28 09:20:10 2020 -0700 Merge pull request #15 from AMReX-FHD/cpp_stats Cpp stats commit 368dcca2cb3b15465e6df268cac76d965533e6dd Author: Andy Nonaka Date: Fri Aug 28 09:16:30 2020 -0700 convert evaluate_stats to c++ (but not on GPU) added note about how it only works when the lo-x domain face is covered by a single box removed all fortran routines associated with this (including some transport stuff no longer called by fortran) src_compressible/compressible_functions_F.H src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 973239b3b16e9203e378a71804974817617ef039 Merge: 57a51f05 d2cc24b6 Author: Andy Nonaka Date: Wed Aug 26 10:00:40 2020 -0700 Merge branch 'main' into compressible_stag commit 0225575c51a5b79107e7c9fad3759f8ace46e45b Author: Andy Nonaka Date: Wed Aug 26 09:59:32 2020 -0700 stats conversion WIP src_compressible/stats.cpp commit 57a51f05b0740ece7de413564e528f0719b2a8c8 Author: isriva Date: Wed Aug 26 08:48:33 2020 -0700 Added logic for hyperbolic and diffusive fluxes exec/compressible_stag/main_driver.cpp src_compressible_stag/compressible_functions_stag.H src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp commit 03a6baa83f14d49e79a43a697771c02eb514672b Author: Changho Kim Date: Tue Aug 25 18:49:40 2020 -0700 exec/compressible_mui: mass distribution setup exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/scripts/havg.py exec/compressible_mui/scripts/mass_cons.py commit 049e9ad8ac380c55e3aed939bea3e18739dbc6ce Author: Andy Nonaka Date: Mon Aug 24 17:04:33 2020 -0700 stats WIP... still buggy src_compressible/stats.cpp commit f04e496c0fd27f0b0fd41daa43d45b6b9f2de5c3 Author: Andy Nonaka Date: Mon Aug 24 15:59:43 2020 -0700 more C++ conversion progress src_compressible/stats.cpp commit 1b82af0826783366e70ff8993d60a3943459d251 Merge: 7ec94f19 d2cc24b6 Author: Andy Nonaka Date: Mon Aug 24 14:51:02 2020 -0700 Merge branch 'main' into cpp_stats commit a587739218ab860adbd4f470acf21bd1628e19b6 Merge: ebb27e6f d2cc24b6 Author: Andy Nonaka Date: Fri Aug 21 14:09:11 2020 -0700 Merge branch 'main' into compressible_mui commit d2cc24b6bb10a305037a44caaade42fcc458d121 Author: Andy Nonaka Date: Fri Aug 21 14:08:49 2020 -0700 horizontal averages now write to havg text files src_common/ComputeAverages.cpp commit 4c46719537523363dad635b74697fbe4fc735531 Author: Andy Nonaka Date: Fri Aug 21 14:01:23 2020 -0700 clean up horizontal average code src_common/ComputeAverages.cpp commit 4d6a78d5f7c612db4330f99e9dd7624efa451e68 Author: Andy Nonaka Date: Fri Aug 21 13:56:35 2020 -0700 vertical average routine it works; but it writes to standard out (next commit will be writing to ascii text) src_common/ComputeAverages.cpp src_common/common_functions.H commit ebb27e6fdd3f06ea022533b1d476a287e638fc98 Merge: 722b1cd7 c03814b0 Author: Andy Nonaka Date: Fri Aug 21 12:32:55 2020 -0700 Merge branch 'main' into compressible_mui commit c03814b081439adfe72829ddb74dae86d835a08c Author: Andy Nonaka Date: Fri Aug 21 12:32:27 2020 -0700 generalize the MPI communicator for computing the FFT so it works for MUI-coupled codes src_analysis/StructFact.cpp commit 722b1cd786593c29208a641f76ca2f58c76706ef Author: Changho Kim Date: Thu Aug 20 14:26:33 2020 -0700 /exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d commit fdc181f1fdfe81a9fdd2cfe29f5aa2c0000c22fd Author: Andy Nonaka Date: Thu Aug 20 13:40:24 2020 -0700 sync with compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 1049566203096599a1f1821d4e8ba566fef2d47e Merge: 988de351 dc7df443 Author: Andy Nonaka Date: Thu Aug 20 13:34:17 2020 -0700 Merge branch 'main' into compressible_mui commit 988de351eefb117944792fbdcb9a9bb27aa3069f Author: Changho Kim Date: Thu Aug 20 13:39:07 2020 -0700 exec/compressible_mui/inputs_fhd exec/compressible_mui/inputs_fhd commit dc7df44364d7fab7a393356e82c4590b976c9a6f Author: Andy Nonaka Date: Thu Aug 20 13:33:47 2020 -0700 fix runtime error when DEBUG=TRUE and writing SF plotfile src_analysis/StructFact.cpp commit a5fc4bcf9c350595979a612bcd5af9dfc6388c6c Author: Changho Kim Date: Thu Aug 20 13:28:44 2020 -0700 exec/compressible/inputs_equil_3d exec/compressible/inputs_equil_3d commit 3793b772de9df6eb5788658cd0ee3b3ca370f423 Author: isriva Date: Wed Aug 19 11:15:23 2020 -0700 Set up functions and kernels for staggered compressible exec/compressible_stag/GNUmakefile exec/compressible_stag/main_driver.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H src_compressible_stag/compressible_functions_stag.cpp src_compressible_stag/conservedPrimitiveConversionsStag.cpp src_compressible_stag/fluxStag.cpp src_compressible_stag/timeStepStag.cpp src_compressible_stag/writePlotFileStag.cpp commit 4fbf62a9ab5452319e0ff250017b043851964448 Author: Changho Kim Date: Wed Aug 19 01:36:12 2020 -0700 compressible_mui: small changes exec/compressible_mui/README exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/run.sh commit 41e0e465e794a0db50dc69671920d6b6123b153e Author: Changho Kim Date: Wed Aug 19 00:56:52 2020 -0700 exec/compressible_mui: directry and codes cleaned exec/compressible_mui/in.kmc exec/compressible_mui/inputs_fhd exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/scripts/coverage.sh exec/compressible_mui/scripts/coverage_stat.py exec/compressible_mui/scripts/equilibrium_solution.py exec/compressible_mui/scripts/gnuplot_cmd exec/compressible_mui/scripts/params.py exec/compressible_mui/scripts/params2.py exec/compressible_mui/scripts/rk4_4spec.py commit d18a529c2f21c9c3791198f290b1a6b887f7a23c Merge: aa53fb42 8604ca15 Author: Changho Kim Date: Wed Aug 19 00:32:24 2020 -0700 Merge branch 'main' into compressible_mui commit 8604ca15729a0acd1a303b5632bb850aab51009c Merge: ff258744 f0a21827 Author: Johannes Blaschke Date: Fri Aug 14 15:00:09 2020 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit ff258744b8c29c4c79a239a8e1eb468ea84eaec7 Author: Johannes Blaschke Date: Fri Aug 14 15:00:05 2020 -0700 trying a different flaglum forcing method -- this one is less physical, but gives better agreement with experiments exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/advance_midpoint.cpp exec/immersed_boundary/flagellum/advance_stokes.cpp exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit f0a21827a0731640f5dde58ccd48a6b17ee11b71 Author: Andy Nonaka Date: Fri Aug 14 12:44:37 2020 -0700 setup for staggered compressible exec/compressible_stag/GNUmakefile exec/compressible_stag/inputs_SFtest exec/compressible_stag/main_driver.cpp src_compressible_stag/Make.package src_compressible_stag/compressible_functions_stag.H src_compressible_stag/writePlotFileStag.cpp commit 0eb6b418f12f7f43c47960e6b54d0124c9aa1348 Author: Johannes Blaschke Date: Thu Aug 13 11:16:52 2020 -0700 test initial guess for stokes solver exec/lib_hydro/demo/main_driver.cpp commit 112e1322428cd9ae669672ac7f51dd1864f3052c Merge: 05d8d2c9 ddaf284d Author: Johannes Blaschke Date: Thu Aug 13 11:09:36 2020 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 05d8d2c9468126a59e0e6b6e97d694bc32967d9b Author: Johannes Blaschke Date: Thu Aug 13 11:08:07 2020 -0700 initialize flagellum in the correct configuration exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit ddaf284d64f5d70f5cb38c3839b2b1e9528cf60b Merge: c4f7e7f9 356d25e0 Author: Daniel Ladiges Date: Wed Aug 12 23:39:12 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit c4f7e7f92828f4c48ad1995e1512e7e918686a2b Author: Daniel Ladiges Date: Wed Aug 12 23:38:32 2020 -0700 Fixed bug causing leaking particles in c++ boundary detection. exec/immersedIons/particleGen.cpp src_geometry/paramplane_functions_K.H src_geometry/src_F90/paramplane_functions.F90 src_particles/FhdParticleContainer.cpp commit 356d25e03c7a17a536d6e68ff1c480400018e61b Merge: 1184c9c2 ed0f6cf3 Author: Johannes Blaschke Date: Wed Aug 12 10:31:34 2020 -0700 Merge branch 'main' of github.com:AMReX-FHD/FHDeX into main commit 1184c9c21ede733474a9686262cb445153173151 Author: Johannes Blaschke Date: Wed Aug 12 10:31:28 2020 -0700 add pure stokes solver exec/immersed_boundary/flagellum/Make.package exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/advance_midpoint.cpp exec/immersed_boundary/flagellum/advance_stokes.cpp exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit ed0f6cf349767b091cb7ce2384d62fe2ddc07e26 Author: Daniel Ladiges Date: Wed Aug 12 10:03:13 2020 -0700 Temporary fix for leaking particles src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp commit c019f14e0aca0c245ce88accf7d11aef4a20c8d0 Author: Daniel Ladiges Date: Tue Aug 11 14:08:35 2020 -0700 Bug fixes to compile with CUDA=TRUE src_geometry/paramplane_functions_K.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/particle_functions_K.H commit 25a1455148f0d8455327726553da075a56fb3ad6 Author: Johannes Blaschke Date: Tue Aug 11 11:55:02 2020 -0700 updates tracking changes in amrex src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp commit e996f99622a8fec6c19a35fea71249b39a3a4cda Author: Daniel Ladiges Date: Mon Aug 10 11:14:05 2020 -0700 DISCOS boundary intersection detection now C++ src_geometry/paramplane_functions_K.H src_geometry/src_F90/paramplane_functions.F90 src_particles/FhdParticleContainer.cpp commit dd09aabfa7559c2fe1b58c4164c28b5041b8bcdf Author: Daniel Ladiges Date: Thu Aug 6 13:04:50 2020 -0700 Converting kernels for particle move functions. src_geometry/Make.package src_geometry/paramplane_functions_K.H src_particles/FhdParticleContainer.cpp commit aa53fb42a32d28e013781f7390b0929ae5006272 Author: Changho Kim Date: Wed Aug 5 02:14:58 2020 -0700 exec/compressible_mui: case_study_4 exec/compressible_mui/coverage.sh exec/compressible_mui/in.4spec exec/compressible_mui/inputs_equil_3d exec/compressible_mui/params.py exec/compressible_mui/pseudo_fhd/in.4spec exec/compressible_mui/pseudo_fhd/run.sh exec/compressible_mui/run.sh commit 7ec94f19d725008e53dea1ae580b3bf58716eab6 Author: Andy Nonaka Date: Tue Aug 4 16:16:47 2020 -0700 start the C++ conversion src_compressible/stats.cpp commit 8f2cc81a9a93a0b62196566420a0d85a7d0fe614 Author: Daniel Ladiges Date: Tue Aug 4 13:41:03 2020 -0700 test input file exec/immersedIons/inputs_test commit 2810f0d4e10b23756d1cc0f4898cc55c203df6cd Author: Changho Kim Date: Tue Aug 4 01:52:21 2020 -0700 exec/compressible_mui: params for case study 2 exec/compressible_mui/in.4spec exec/compressible_mui/inputs_equil_3d exec/compressible_mui/params.py exec/compressible_mui/params2.py commit 88231cda35c9e8c5437fc8609a48137e287948ab Merge: f0232444 ebc24fe3 Author: Daniel Ladiges Date: Mon Aug 3 22:27:47 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit f023244473a6c17703d0f61ad8672cdfa385977d Author: Daniel Ladiges Date: Mon Aug 3 22:27:09 2020 -0700 Added midpoint rejection to C++ moveIon function. src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp commit 9936e2e7d21bee4ef8943eb5f890c1cc0d87407a Author: Changho Kim Date: Mon Aug 3 15:20:30 2020 -0700 /exec/compressible_mui: params2.py exec/compressible_mui/params.py exec/compressible_mui/params2.py commit ebc24fe389ab4f5e8ef1e80beaddfd7a22107de9 Author: Andy Nonaka Date: Mon Aug 3 12:35:03 2020 -0700 clean up main_driver for compressible exec/compressible/main_driver.cpp commit 80fb3088dc90a64a1b08e639d1db6c4a928b3429 Author: Andy Nonaka Date: Mon Aug 3 12:29:23 2020 -0700 clean up makefile exec/compressible/GNUmakefile commit 20e0e1d3883fd16ea14746fff39524efb7257516 Author: Changho Kim Date: Fri Jul 31 18:40:20 2020 -0700 exec/compressible_mui: seed for fhd exec/compressible_mui/gnuplot_cmd exec/compressible_mui/inputs_equil_3d commit 5e46b4a15eadaff4da5ec7ddff67804c77d252d0 Author: Andy Nonaka Date: Fri Jul 31 18:22:21 2020 -0700 call C++ version of InitConsvar exec/compressible_mui/main_driver.cpp commit b16cc155d5b80a4e35d345ebef56e3e09bea8b1b Author: jbb Date: Fri Jul 31 17:48:47 2020 -0700 removed hack to stop noise after thermalizaton exec/_1d_staggered_comp/driver.f commit 9daa930b9ba0ea3c709a93954ba6294c6332f481 Author: jbb Date: Fri Jul 31 17:45:34 2020 -0700 added random number generator exec/_1d_staggered_comp/stats.c commit bda67667d3cf3046075ec0f86c39672a7d2e59fa Merge: 88cdc275 efed1795 Author: jbb Date: Fri Jul 31 17:44:49 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 88cdc275942d9733d9e08633b5c583f62cf8b5ba Author: jbb Date: Fri Jul 31 17:43:47 2020 -0700 added 1d fluctuating code exec/_1d_staggered_comp/Makefile exec/_1d_staggered_comp/driver.f exec/_1d_staggered_comp/flux.f exec/_1d_staggered_comp/inputs exec/_1d_staggered_comp/inputs.2 commit e723291265d2e49162fba7d6e661afb0ba8bd6a7 Merge: 710f261b efed1795 Author: Andy Nonaka Date: Fri Jul 31 17:12:04 2020 -0700 Merge branch 'main' into compressible_mui commit efed17956aa5ecb15bd5105f1d2619fa38de57cb Author: Andy Nonaka Date: Fri Jul 31 16:40:49 2020 -0700 typo src_compressible/src_F90/stats_funcs.F90 commit cab0e51f67b030f9e31b9f4f65d6471ba2f98154 Merge: d848a36b b5e6c779 Author: Daniel Ladiges Date: Fri Jul 31 15:50:23 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d848a36b5deab22fa7e0f4821839dd04aa52b5e3 Author: Daniel Ladiges Date: Fri Jul 31 15:49:15 2020 -0700 Main branch now using C++ move loop for DISCOS. Kernels still in Fortran and need to add midpoint rejection for particles out of bounds. exec/immersedIons/main_driver.cpp src_geometry/paramPlane.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 710f261b931a5aa4059082a883238a37e4013f79 Merge: fe6cd3b7 b5e6c779 Author: Andy Nonaka Date: Fri Jul 31 13:24:40 2020 -0700 Merge branch 'main' into compressible_mui commit fe6cd3b7b461f54fa110f72489e91f96aa482058 Author: emercado9 Date: Fri Jul 31 11:50:28 2020 -0700 /exec/compressible_mui/: created scripts to calculate equilibrium solution and 4spec rk4 exec/compressible_mui/equilibrium_solution.py exec/compressible_mui/rk4_4spec.py commit a1ed76d377b2a5efa9eaf6cb7fe58301981b294f Author: Changho Kim Date: Fri Jul 31 11:42:13 2020 -0700 FHDeX/exec/compressible_mui: coverage stat exec/compressible_mui/coverage_stat.py exec/compressible_mui/gnuplot_cmd exec/compressible_mui/in.4spec exec/compressible_mui/params.py exec/compressible_mui/pseudo_fhd/in.4spec commit b5e6c7795e6b103c903dc0538ed8541ff55feaae Author: Andy Nonaka Date: Fri Jul 31 10:13:35 2020 -0700 revert std::max/min -> amrex::max/in exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/AdvanceTimestepInertial.cpp src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/transCoeffs.cpp src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp src_hydro/StochMomFlux.cpp src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit 3d7bcf142c17fb9c77de163d244148a960d4ffec Author: Andy Nonaka Date: Fri Jul 31 09:39:57 2020 -0700 ceil -> amrex::Math::ceil floor -> amrex::Math::floor std::abs -> amrex::Math::abs exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC/main_driver.cpp exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/StagExpSolver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/timeStep.cpp exec/brownian/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersedIons2/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_compressible/flux.cpp src_compressible/src_F90/stats_funcs.F90 src_gmres/GMRES.cpp src_gmres/Precon.cpp src_gmres/StagMGSolver.cpp src_hydro/AddMFluctuations.cpp src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit e18f66c83cf9c176f2116a4342657ddec389fc69 Author: Changho Kim Date: Thu Jul 30 23:53:10 2020 -0700 exec/compressible_mui: equilibrium example setup exec/compressible_mui/coverage.sh exec/compressible_mui/in.4spec exec/compressible_mui/inputs_equil_3d exec/compressible_mui/pseudo_fhd/in.4spec commit 29f38b5c40e68de737179e233d8315d21abd7ba0 Author: Changho Kim Date: Thu Jul 30 23:29:43 2020 -0700 exec/compressible_mui/pseudo_fhd exec/compressible_mui/pseudo_fhd/compile.sh exec/compressible_mui/pseudo_fhd/coverage.sh exec/compressible_mui/pseudo_fhd/in.4spec exec/compressible_mui/pseudo_fhd/pseudo_fhd.cpp exec/compressible_mui/pseudo_fhd/run.sh commit e51de291b53aad66ba0c47ce8df7c6b1081b64c7 Author: Daniel Ladiges Date: Thu Jul 30 15:22:59 2020 -0700 Wound back a bugfix to check regressions. exec/immersedIons/main_driver.cpp src_geometry/paramPlane.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit fae5bfc7866616e9c522bd9226aa80246d1fcf2a Author: Changho Kim Date: Thu Jul 30 14:44:19 2020 -0700 exec/compressible_mui/pseudo_kmc/run.sh updated exec/compressible_mui/pseudo_kmc/run.sh commit 2b1017f9d320b375afcaa596594a3f10989c262e Author: Changho Kim Date: Thu Jul 30 14:41:19 2020 -0700 exec/compressible_mui: params.py organized and updated exec/compressible_mui/params.py commit 008d123670a9b9619e20ba493d131c72ad4f9c1e Author: Daniel Ladiges Date: Thu Jul 30 10:38:24 2020 -0700 Main particle move loop completed in C++, still need to convert kernels. src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 52a68a820c0b6fca9d1bf3f6329df47091622c8c Merge: 7977ab47 31832910 Author: Daniel Ladiges Date: Tue Jul 28 17:59:18 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 7977ab4715119d9227c22977f0d9b776e1aadbed Author: Daniel Ladiges Date: Tue Jul 28 17:58:24 2020 -0700 Predictor step and dry part of move loop converted to c++ src_geometry/paramPlane.cpp src_geometry/src_F90/paramplane_functions.F90 src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 0fd114c74c11f33b128799f55ec50fe03d81a354 Author: emercado9 Date: Tue Jul 28 13:02:44 2020 -0700 exec/compressible_mui/: updated input scripts to include 4 species ads/des exec/compressible_mui/in.4spec exec/compressible_mui/inputs_equil_3d exec/compressible_mui/params.py commit 318329101ee9c58d19ef5acc2f8bd8019039ae65 Author: Johannes Blaschke Date: Mon Jul 27 21:11:23 2020 -0700 fix implicit type inference src_immersed-boundary/MFUtil.H commit db131016d22609e9e4a6b8ccf27910c65fa36bdf Author: Johannes Blaschke Date: Mon Jul 27 17:39:39 2020 -0700 speed up demo exec/lib_hydro/demo/main_driver.cpp commit 5a0db80e80483b0f070ec9747bfad625b752e78b Author: Johannes Blaschke Date: Mon Jul 27 15:59:08 2020 -0700 deposit force data on RHS exec/lib_hydro/demo/main_driver.cpp commit 3355489c521d9350de2919f1f7680b694fae4b75 Author: Johannes Blaschke Date: Mon Jul 27 12:09:25 2020 -0700 add stokes solver to demo exec/lib_hydro/demo/CMakeLists.txt exec/lib_hydro/demo/WritePlotFile.cpp exec/lib_hydro/demo/main.cpp exec/lib_hydro/demo/main_driver.H exec/lib_hydro/demo/main_driver.cpp exec/lib_hydro/demo/main_driver_F.H commit e3d2d6771566a5bf28f646cec2304d4e412751c8 Author: Johannes Blaschke Date: Mon Jul 27 08:35:55 2020 -0700 clean up exec/lib_hydro/demo/build.nmpb.fish commit 6d1a0bf81be28578ac977cba557c1d7723fe0054 Author: Johannes Blaschke Date: Mon Jul 27 08:35:23 2020 -0700 clean up exec/lib_hydro/cmake/build.nmpb.fish commit acc79a304fc7e82153777730e2181d2157e89ba0 Author: Changho Kim Date: Fri Jul 24 15:56:09 2020 -0700 exec/compressible_mui: README updated exec/compressible_mui/README commit ad78f0b29aa79e5e55282253a6bab842c17a2299 Author: Changho Kim Date: Wed Jul 22 01:43:14 2020 -0700 exec/compressible_mui/README exec/compressible_mui/README commit f5c8570c17ee4e591549a74bd657ef65a6238742 Author: Changho Kim Date: Wed Jul 22 01:39:16 2020 -0700 FHDeX/exec/compressible_mui: kmc+fhd setup exec/compressible_mui/in.4spec exec/compressible_mui/inputs_equil_3d exec/compressible_mui/params.py exec/compressible_mui/pseudo_kmc/compile.sh exec/compressible_mui/pseudo_kmc/run.sh exec/compressible_mui/run.sh commit 9fcbcd3b4cf902c42d8148d79257369884ff74ec Author: Changho Kim Date: Wed Jul 22 00:31:21 2020 -0700 exec/compressible_mui/SPPARKS_MUI/create_sites.cpp: #define EPSILON 1.e-10 exec/compressible_mui/SPPARKS_MUI/create_sites.cpp commit 2e9176e099538804bd2e956ff5157427e51a00d6 Author: Changho Kim Date: Tue Jul 21 23:54:17 2020 -0700 exec/compressible_mui/pseudo_kmc.bin: should not have been included exec/compressible_mui/pseudo_kmc.bin commit 90f434d8feb266aa46725cc3725559ba05e2da30 Author: Changho Kim Date: Tue Jul 21 23:50:00 2020 -0700 exec/compressible_mui/pseudo_kmc exec/compressible_mui/inputs_equil_3d exec/compressible_mui/pseudo_kmc/compile.sh exec/compressible_mui/pseudo_kmc/inputs_equil_3d exec/compressible_mui/pseudo_kmc/pseudo_kmc.cpp exec/compressible_mui/pseudo_kmc/run.sh exec/compressible_mui/run.sh exec/compressible_mui/src_pseudo_kmc/compile.sh commit f4c1912d4f93bd6124795104536cceb01c6b029e Author: Changho Kim Date: Tue Jul 21 23:25:44 2020 -0700 exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp and .h: mui_kmc_lattice_offset implemented exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h commit 54093c7a4732a3a29106c0d495cd5e8ec09ab665 Author: Daniel Ladiges Date: Tue Jul 21 16:46:13 2020 -0700 Framework of C++ particle move function moved into main branch. exec/immersedIons/precheck.F90 src_geometry/src_F90/paramplane_type.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 0072a3e703ec01ff3595ac84c4ad34a5ec068128 Author: Daniel Ladiges Date: Tue Jul 21 16:31:46 2020 -0700 ditto src_geometry/src_F90/paramplane_functions.F90 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 2904da44330e2dd20fb74274fb76a1f6043b9720 Author: Daniel Ladiges Date: Tue Jul 21 14:48:18 2020 -0700 Bringing over geometry functions from cplusplus branch src_geometry/paramplane_functions_F.H commit 834bc7eaf154a99583fb9406b45796eb40745687 Author: Daniel Ladiges Date: Tue Jul 21 14:39:04 2020 -0700 as above src_particles/FhdParticleContainer.H commit caef12c09a3ab73939c2208d0e797375eca8cd43 Author: Daniel Ladiges Date: Tue Jul 21 14:35:31 2020 -0700 Adding c interfaces for some elementary fortran functions. src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H commit 42aff42f38233ddee46ffc5e479efa7d86d00187 Author: Daniel Ladiges Date: Tue Jul 21 14:07:05 2020 -0700 Started adding C++ particle move function. src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 3b91667ea0848f2032a3722512ff8f2f168dd9e9 Author: Daniel Ladiges Date: Tue Jul 21 10:57:10 2020 -0700 Previous bugfix uncovered another bug in the calculation of force from neighbourlist images. Fixed. src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 675d5b7b52efdbe72ee7a9015f81fdbcb64a17c2 Author: Daniel Ladiges Date: Mon Jul 20 23:06:38 2020 -0700 Cleaned up debugging code src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 6815424415b8dc65485d2f9023acb6d22cbf690c Merge: 59056021 1348b23e Author: Daniel Ladiges Date: Mon Jul 20 23:01:43 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 590560216ea78649694fdf76c72fa4514a602310 Author: Daniel Ladiges Date: Mon Jul 20 23:00:48 2020 -0700 Fixed error in c++ code incorrectly detecting particle near boundary for image charge calc. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 1348b23e4c8cbd705a4f09e1a66db9694c329ae9 Author: Johannes Blaschke Date: Mon Jul 20 21:49:28 2020 -0700 add immersed boundaries to libhydro exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/cmake/build.macbert.fish commit c7bafdc353cedc72cb07128fcffa5b1d43904b93 Merge: f23acb54 bfa348ba Author: Johannes Blaschke Date: Mon Jul 20 10:08:38 2020 -0700 Merge branch 'main' commit f23acb543a0bd02f522a4e757442f0c7ea9251b0 Author: Johannes Blaschke Date: Mon Jul 20 10:08:06 2020 -0700 debug git exec/lib_hydro/demo/CMakeLists.txt exec/lib_hydro/demo/build.fish exec/lib_hydro/demo/inputs_3d_test exec/lib_hydro/demo/main.cpp exec/lib_hydro/demo/main_driver.H exec/lib_hydro/demo/main_driver.cpp exec/lib_hydro/demo/main_driver_F.H commit 6f9292b07c2fc0880da0d5fc47c8d7821e814878 Author: Johannes Blaschke Date: Mon Jul 20 10:07:08 2020 -0700 debug git exec/lib_hydro/asdf/CMakeLists.txt exec/lib_hydro/asdf/build.fish exec/lib_hydro/asdf/inputs_3d_test exec/lib_hydro/asdf/main.cpp exec/lib_hydro/asdf/main_driver.H exec/lib_hydro/asdf/main_driver.cpp exec/lib_hydro/asdf/main_driver_F.H commit bfa348ba48893cbfc6e5b34e9be1edcf12e56cdf Merge: 4e2039b8 a7cbde31 Author: Andy Nonaka Date: Thu Jul 16 19:32:53 2020 -0700 Merge branch 'gpu_initconsvar' into main commit a7cbde315a776304bfb25e2148522711e5179fba Author: Andy Nonaka Date: Thu Jul 16 19:32:28 2020 -0700 gpu init_consvar src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/init_consvar.F90 commit c03f4afc16fcfe2ffae51fb7bfcfe19c266d71be Author: Andy Nonaka Date: Thu Jul 16 18:00:03 2020 -0700 more GPU progress on init_consvar src_compressible/compressible_functions.cpp commit c5004075ad5358006f40e7956c97ecab8ebd045f Author: Andy Nonaka Date: Thu Jul 16 14:59:41 2020 -0700 WIP src_compressible/compressible_functions.cpp commit 4e2039b85f9f092146bb3a61dede540709b5af2b Merge: c660e3a7 3743d7b2 Author: Daniel Ladiges Date: Thu Jul 16 13:57:13 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit c660e3a751f3f1d648e3abbc9bf882f4ddeb79d5 Author: Daniel Ladiges Date: Thu Jul 16 13:56:46 2020 -0700 SpreadIons function in main branch now C++/CUDA exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 88706961310c013c4cb9a174d91abcc863da1c82 Author: Daniel Ladiges Date: Thu Jul 16 13:42:04 2020 -0700 Added gpu version of E-field interpolation exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 18f61d969e09ca2718afd865369d298593c41bf0 Author: Andy Nonaka Date: Thu Jul 16 11:23:23 2020 -0700 work on GPU init_consvar src_compressible/compressible_functions.cpp commit 3743d7b21930577543ba699f8370065a8dea7533 Author: Andy Nonaka Date: Thu Jul 16 09:59:00 2020 -0700 set up for more gpu exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp commit 94112ee3b56366fb828ae41ccb88d183ac5cb2ce Merge: 719e99e7 535e990f Author: Andy Nonaka Date: Thu Jul 16 08:50:16 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 719e99e7b6beaa0d3b78d31173dbcc7aeabc5162 Author: Andy Nonaka Date: Thu Jul 16 08:50:04 2020 -0700 killing fortran src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/transCoeffs.cpp commit 535e990f807b2834e5189b0835d0d6f734b35379 Author: Daniel Ladiges Date: Wed Jul 15 22:41:23 2020 -0700 Continuing conversion of SpreadIons to C++/CUDA src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 29ce5c93db7d79696f169424fd60ea5059087c90 Merge: 172b6dda 5665a81d Author: Daniel Ladiges Date: Wed Jul 15 13:13:50 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 172b6dda2d2f93bd8d761712711efc53461db1b0 Author: Daniel Ladiges Date: Wed Jul 15 13:12:55 2020 -0700 Finished adding of C++/CUDA short range forces into main branch exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit b2fec4215d35943ef6d75ab091c1ccc35c8e0b8e Author: Daniel Ladiges Date: Wed Jul 15 11:22:05 2020 -0700 Still trying to track down fortran/C++ precision mismatch src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 5665a81d07c125ea44a111a7f0c23c8f3b042ab6 Author: Andy Nonaka Date: Wed Jul 15 07:20:32 2020 -0700 put in Na and Cl diffusion coefficients for sodium and chloride ions in water in the infinite dilution limit exec/immersedIons/inputs_paper_eo commit 070dd7e995abcfc03c5f9afbc62e8063b2c83b2a Author: Andy Nonaka Date: Wed Jul 15 06:32:20 2020 -0700 tidy up run directory exec/immersedIons/inputs_paper1/inputs_paper_cond10 exec/immersedIons/inputs_paper1/inputs_paper_cond11 exec/immersedIons/inputs_paper1/inputs_paper_cond12 exec/immersedIons/inputs_paper1/inputs_paper_cond12a exec/immersedIons/inputs_paper1/inputs_paper_cond12b exec/immersedIons/inputs_paper1/inputs_paper_cond12c exec/immersedIons/inputs_paper1/inputs_paper_cond4 exec/immersedIons/inputs_paper1/inputs_paper_cond5 exec/immersedIons/inputs_paper1/inputs_paper_cond6 exec/immersedIons/inputs_paper1/inputs_paper_cond7 exec/immersedIons/inputs_paper1/inputs_paper_cond8 exec/immersedIons/inputs_paper1/inputs_paper_cond9 exec/immersedIons/inputs_paper1/inputs_paper_cond9a exec/immersedIons/inputs_paper1/inputs_paper_cond9b exec/immersedIons/inputs_paper1/inputs_paper_cond9c exec/immersedIons/inputs_paper1/inputs_paper_gr1 exec/immersedIons/inputs_paper1/inputs_paper_gr2 exec/immersedIons/inputs_paper1/inputs_paper_gr3 exec/immersedIons/inputs_paper1/inputs_paper_gr4 commit 56f2ca383d2e31f7d36825371064c7745734b39f Author: Daniel Ladiges Date: Tue Jul 14 21:51:04 2020 -0700 bugfix in interpolation of p3m table. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit f209debc2f043ac22f1f822fee7e2d94cab0549b Merge: 5d1ec3cf 55758e61 Author: Andy Nonaka Date: Tue Jul 14 15:14:24 2020 -0700 Merge branch 'main' into gpu_flux commit 5d1ec3cf4e80b1a8d3ac6a0c7cc0d0b7329f640f Author: Andy Nonaka Date: Tue Jul 14 15:14:09 2020 -0700 z stochastic fluxes src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit fa2633f39dd6236669924a48af03e70778748e9e Author: Andy Nonaka Date: Tue Jul 14 14:59:01 2020 -0700 stoch y fluxes completed src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit a0e56453a39162a4041b0521612f300e1da40069 Author: Andy Nonaka Date: Tue Jul 14 14:10:21 2020 -0700 index bug fix on eta switch ij ordering on Dij read stoch x fluxes now match src_compressible/flux.cpp commit 32b6b19977219e5ed1c19b68c3b6bb330d0bbc54 Author: Andy Nonaka Date: Tue Jul 14 07:04:42 2020 -0700 loop bugfix src_compressible/compressible_functions.H commit 8efc777c7ef66bbbfcf04dfd891acc99af9eadfb Author: Daniel Ladiges Date: Mon Jul 13 12:54:41 2020 -0700 Tracking down error in gpu version of p3m correction. exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/particle_functions_K.H src_particles/src_F90/particle_functions.F90 commit 843a1380311e26371400bccbf51e443a8a43f62d Author: Johannes Blaschke Date: Mon Jul 13 09:46:59 2020 -0700 enable cross-platform + add demo exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/demo/CMakeLists.txt exec/lib_hydro/demo/build.fish exec/lib_hydro/demo/inputs_3d_test exec/lib_hydro/demo/main.cpp exec/lib_hydro/demo/main_driver.H exec/lib_hydro/demo/main_driver.cpp exec/lib_hydro/demo/main_driver_F.H commit 55758e612f2f1c71c794989791910c06de3ff0ac Merge: 502b9a24 47ae020d Author: Andy Nonaka Date: Mon Jul 13 07:16:05 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 502b9a244b1a3830414ddfe5564a4d0acecc4862 Merge: 16d88df3 8b57a6eb Author: Andy Nonaka Date: Mon Jul 13 07:15:14 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX into main commit 8b57a6eba8353812cf343b79a03e3786857a66aa Author: Johannes Blaschke Date: Sun Jul 12 22:29:04 2020 -0700 forgot about rng fortran components exec/lib_hydro/cmake/CMakeLists.txt commit 68882cb05e6c3d62fcb57ea7fabd2715f03894ca Author: Johannes Blaschke Date: Sun Jul 12 21:50:11 2020 -0700 don't need a redundant copy of modules exec/lib_hydro/cmake/CMakeLists.txt commit fe7c368ceb9e8f84c2407ecb88c580f120f5d2ec Merge: cf22b026 381819dd Author: Johannes Blaschke Date: Sun Jul 12 21:49:16 2020 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit cf22b02686f15ac4064187b0fb6c548b529c123e Author: Johannes Blaschke Date: Sun Jul 12 21:49:11 2020 -0700 first stab at building a fhdex library exec/lib_hydro/cmake/CMakeLists.txt exec/lib_hydro/cmake/build.fish exec/lib_hydro/cmake/test/CMakeLists.txt exec/lib_hydro/cmake/test/build.fish exec/lib_hydro/cmake/test/hello.cpp exec/lib_hydro/gnumake/Makefile commit 47ae020d1916e6b44f9fb9c6c69866ee26d70cbe Author: Daniel Ladiges Date: Sat Jul 11 12:01:40 2020 -0700 Now compiles with CUDA=TRUE src_common/common_functions.H src_common/common_functions.cpp commit 7426f85d614ac31f086a83fac6f4e811faa06709 Author: Daniel Ladiges Date: Sat Jul 11 11:45:13 2020 -0700 Fixing some namespace declarations for CUDA src_common/common_namespace.H src_common/common_namespace_declarations.H commit 1f7780c4e36baec6ded1aae4e237588dc0eca516 Author: Daniel Ladiges Date: Sat Jul 11 11:33:23 2020 -0700 Trying to fix bugs preventing code from compiling in CUDA mode... exec/immersedIons/GNUmakefile src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 20338d72cc8d125214d2bafce1ab4225f6748897 Merge: d19ec40f 6056120e Author: Daniel Ladiges Date: Fri Jul 10 23:11:27 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit d19ec40fb5dccfec9c8b12c0759ba922aa86c239 Author: Daniel Ladiges Date: Fri Jul 10 23:10:29 2020 -0700 Merged GPU short range interaction into main. P3M correction giving big diffs for some reason. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 6056120eb02edc4e269eeb0e9ef4811da39bc47d Merge: 1be7aa67 16d88df3 Author: John Bell Date: Fri Jul 10 16:38:25 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit 1be7aa6756e499d8cf7a3dde5e7820082b7a96e6 Author: John Bell Date: Fri Jul 10 16:36:32 2020 -0700 correct inputs for temp grad exec/compressible/inputs_temp_grad commit 16d88df3c20c66babe63a092bb547c3338201ddd Merge: ab698aa0 043e376a Author: jbb Date: Fri Jul 10 16:13:34 2020 -0700 Merge branch 'main' of https://github.com/AMReX-FHD/FHDeX into main commit ab698aa045e4a0285d6848bdb355a9e4568ddd36 Merge: e4b05716 381819dd Author: jbb Date: Fri Jul 10 16:12:45 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX into main commit e4b05716f934c03500029ccdad164e033ceed5af Author: jbb Date: Fri Jul 10 16:09:47 2020 -0700 made constants real doubles src_compressible/src_F90/stats_funcs.F90 commit b58fa5ff0dea66a2db85b9a4277cbf24805df73e Author: Daniel Ladiges Date: Fri Jul 10 14:54:03 2020 -0700 Porting particle force calculation to main branch src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit 043e376a60f8c52b630f3b5de52f48d862335eaa Author: Daniel Ladiges Date: Fri Jul 10 14:01:43 2020 -0700 test push exec/immersedIons/main_driver.cpp commit 381819ddf1c5631144b4380e196a8490646e3e7d Author: Andy Nonaka Date: Fri Jul 10 13:22:00 2020 -0700 shorten name exec/immersedIons/inputs_regression_slip_dirichlet_det commit e84d7b5708f43800a3dd9e8dbe7f341c269c4d7c Author: Daniel Ladiges Date: Fri Jul 10 13:11:22 2020 -0700 Deterministic reg test input file exec/immersedIons/inputs_regression_slip_dirichlet_deterministic exec/tests/RFDanalysis/main_driver.cpp commit eee38dba6623736dd3c42d5608a7633564e60d06 Merge: a06e9396 f5fa79f5 Author: Andy Nonaka Date: Fri Jul 10 12:32:14 2020 -0700 Merge branch 'master' into gpu_flux commit f5fa79f5ec92f19b8c5524e2475475c4c7f40eea Author: Daniel Ladiges Date: Fri Jul 10 11:19:06 2020 -0700 Now using collectFieldsGPU in master branch. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_K.H commit bb36dccae8e8fb45601f3446a7eb0e0481cda33e Author: Daniel Ladiges Date: Fri Jul 10 10:59:52 2020 -0700 Merging collectfields.... src_particles/FhdParticleContainer.cpp src_particles/Make.package src_particles/particle_functions_K.H commit fa6cf150e4c24e54e0d26217a63ac4c7bcfc7361 Author: Daniel Ladiges Date: Fri Jul 10 10:48:42 2020 -0700 Started merging collect_fields GPU version into master src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit a06e939673680fc529b97ca5a9ef4c283051d487 Author: Andy Nonaka Date: Thu Jul 9 17:37:44 2020 -0700 for loop typo src_compressible/flux.cpp commit 79f364bf97443fdd26c12854f71fc768b03b3d3e Author: Andy Nonaka Date: Thu Jul 9 10:04:50 2020 -0700 x stoch flux coded; needs debugging src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 581655a9ce87828222bce79cb94beb3783d2cc44 Author: Andy Nonaka Date: Thu Jul 9 09:15:51 2020 -0700 add some n_cell_z tests from the original code src_compressible/flux.cpp commit 66b0f71a84b8f4ecbd8e78cc7bec82c93315d92f Author: Andy Nonaka Date: Thu Jul 9 08:45:36 2020 -0700 more stochastic flux src_compressible/compressible_functions.H src_compressible/flux.cpp src_compressible/src_F90/multispec_funcs.F90 commit 072f9e9e8e00e93801af3dfea1404bae5db7986d Author: Andy Nonaka Date: Wed Jul 8 13:26:44 2020 -0700 diffusive fluxes on GPU src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 9f42b3aeb5df1e3c66cab33ead48dafffeec0737 Author: Andy Nonaka Date: Wed Jul 8 13:03:59 2020 -0700 nodal flux loop src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 87b01392493585d55655e6146597f9f843756c3e Author: Andy Nonaka Date: Wed Jul 8 12:29:22 2020 -0700 use dx_gpu for kernels src_compressible/flux.cpp commit 747f845a29781d55047d8ab7712c8b57f9fc99fc Author: Andy Nonaka Date: Wed Jul 8 11:45:58 2020 -0700 cleanup - still segfaults on GPU src_compressible/flux.cpp commit e6a11432010373c6a95f7b12083e8b4497d2dc12 Author: Andy Nonaka Date: Wed Jul 8 07:55:35 2020 -0700 diffusive flux fixes... one index fix, and swapping the order of the Dij components src_compressible/flux.cpp commit 128027e5fd679f9167feadd61975d298532b6577 Author: Andy Nonaka Date: Tue Jul 7 15:21:02 2020 -0700 index bugfix src_compressible/flux.cpp commit a5c7a270374352531b3425801eb85e32728044bc Author: Andy Nonaka Date: Tue Jul 7 15:10:21 2020 -0700 diffusive fluxes WIP src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 4042778b204478912652273151ff771f13077ed4 Author: Andy Nonaka Date: Tue Jul 7 14:31:06 2020 -0700 gpu updates WIP src_compressible/flux.cpp commit b6264359ec24b6c89cf37f77b7fd545c7a7b0300 Author: Andy Nonaka Date: Tue Jul 7 12:41:58 2020 -0700 diffusive flux WIP src_compressible/compressible_functions.H src_compressible/flux.cpp commit 5a0041261acde1181d284e883ca4cda730b7c0c5 Author: Andy Nonaka Date: Tue Jul 7 11:12:07 2020 -0700 begin setup for diffusive fluxes on gpu src_compressible/flux.cpp commit 6155ad9823817db2bf154bdeb3811e400b338a16 Author: Andy Nonaka Date: Tue Jul 7 07:39:49 2020 -0700 new regression test exec/compressible/inputs_regression_temp_grad commit 8445a76d335ca49a3110ce1d6debdd280d68c06b Author: Andy Nonaka Date: Tue Jul 7 07:30:46 2020 -0700 index bugfix in fluxes src_compressible/flux.cpp commit ba2c01b6b3cc2fe4c096b28dcc6b7b0d00fd2678 Author: Andy Nonaka Date: Tue Jul 7 06:48:55 2020 -0700 fixed dimensioning of temporaries src_compressible/flux.cpp commit 4ec71d451b2d1019f2d3622eb04f8ac8c49ae450 Merge: 765d8280 a03c6897 Author: Andy Nonaka Date: Tue Jul 7 05:21:39 2020 -0700 Merge branch 'master' into gpu_flux commit 21ce4b5fa5516909991d782fc849ff40c22e1a19 Author: Changho Kim Date: Tue Jul 7 03:38:39 2020 -0700 exec/compressible_mui/SPPARKS_MUI: SPPARKS_MUI source codes included exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.blackrose exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.chama exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.cygwin exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.flamer.gnu exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.g++ exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.linux exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mac exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mac_debug exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mac_mpi exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mpi exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.mui exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.redsky exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.serial exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.serial_debug exec/compressible_mui/SPPARKS_MUI/MAKE/Makefile.xt5 exec/compressible_mui/SPPARKS_MUI/Make.sh exec/compressible_mui/SPPARKS_MUI/Makefile exec/compressible_mui/SPPARKS_MUI/Makefile.lib exec/compressible_mui/SPPARKS_MUI/Makefile.shlib exec/compressible_mui/SPPARKS_MUI/Package.csh exec/compressible_mui/SPPARKS_MUI/am_ellipsoid.h exec/compressible_mui/SPPARKS_MUI/am_raster.h exec/compressible_mui/SPPARKS_MUI/app.cpp exec/compressible_mui/SPPARKS_MUI/app.h exec/compressible_mui/SPPARKS_MUI/app_chemistry.cpp exec/compressible_mui/SPPARKS_MUI/app_chemistry.h exec/compressible_mui/SPPARKS_MUI/app_diffusion.cpp exec/compressible_mui/SPPARKS_MUI/app_diffusion.h exec/compressible_mui/SPPARKS_MUI/app_erbium.cpp exec/compressible_mui/SPPARKS_MUI/app_erbium.h exec/compressible_mui/SPPARKS_MUI/app_ising.cpp exec/compressible_mui/SPPARKS_MUI/app_ising.h exec/compressible_mui/SPPARKS_MUI/app_ising_single.cpp exec/compressible_mui/SPPARKS_MUI/app_ising_single.h exec/compressible_mui/SPPARKS_MUI/app_lattice.cpp exec/compressible_mui/SPPARKS_MUI/app_lattice.h exec/compressible_mui/SPPARKS_MUI/app_membrane.cpp exec/compressible_mui/SPPARKS_MUI/app_membrane.h exec/compressible_mui/SPPARKS_MUI/app_off_lattice.cpp exec/compressible_mui/SPPARKS_MUI/app_off_lattice.h exec/compressible_mui/SPPARKS_MUI/app_potts.cpp exec/compressible_mui/SPPARKS_MUI/app_potts.h exec/compressible_mui/SPPARKS_MUI/app_potts_additive.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_additive.h exec/compressible_mui/SPPARKS_MUI/app_potts_grad.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_grad.h exec/compressible_mui/SPPARKS_MUI/app_potts_neigh.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_neigh.h exec/compressible_mui/SPPARKS_MUI/app_potts_neighonly.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_neighonly.h exec/compressible_mui/SPPARKS_MUI/app_potts_phasefield.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_phasefield.h exec/compressible_mui/SPPARKS_MUI/app_potts_pin.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_pin.h exec/compressible_mui/SPPARKS_MUI/app_potts_strain.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_strain.h exec/compressible_mui/SPPARKS_MUI/app_potts_strain_pin.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_strain_pin.h exec/compressible_mui/SPPARKS_MUI/app_potts_weld.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_weld.h exec/compressible_mui/SPPARKS_MUI/app_potts_weld_jom.cpp exec/compressible_mui/SPPARKS_MUI/app_potts_weld_jom.h exec/compressible_mui/SPPARKS_MUI/app_relax.cpp exec/compressible_mui/SPPARKS_MUI/app_relax.h exec/compressible_mui/SPPARKS_MUI/app_sinter.cpp exec/compressible_mui/SPPARKS_MUI/app_sinter.h exec/compressible_mui/SPPARKS_MUI/app_sos.cpp exec/compressible_mui/SPPARKS_MUI/app_sos.h exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/app_surfchemtest.h exec/compressible_mui/SPPARKS_MUI/app_test_group.cpp exec/compressible_mui/SPPARKS_MUI/app_test_group.h exec/compressible_mui/SPPARKS_MUI/cluster.cpp exec/compressible_mui/SPPARKS_MUI/cluster.h exec/compressible_mui/SPPARKS_MUI/comm_lattice.cpp exec/compressible_mui/SPPARKS_MUI/comm_lattice.h exec/compressible_mui/SPPARKS_MUI/comm_off_lattice.cpp exec/compressible_mui/SPPARKS_MUI/comm_off_lattice.h exec/compressible_mui/SPPARKS_MUI/create_box.cpp exec/compressible_mui/SPPARKS_MUI/create_box.h exec/compressible_mui/SPPARKS_MUI/create_sites.cpp exec/compressible_mui/SPPARKS_MUI/create_sites.h exec/compressible_mui/SPPARKS_MUI/diag.cpp exec/compressible_mui/SPPARKS_MUI/diag.h exec/compressible_mui/SPPARKS_MUI/diag_array.cpp exec/compressible_mui/SPPARKS_MUI/diag_array.h exec/compressible_mui/SPPARKS_MUI/diag_cluster.cpp exec/compressible_mui/SPPARKS_MUI/diag_cluster.h exec/compressible_mui/SPPARKS_MUI/diag_diffusion.cpp exec/compressible_mui/SPPARKS_MUI/diag_diffusion.h exec/compressible_mui/SPPARKS_MUI/diag_energy.cpp exec/compressible_mui/SPPARKS_MUI/diag_energy.h exec/compressible_mui/SPPARKS_MUI/diag_erbium.cpp exec/compressible_mui/SPPARKS_MUI/diag_erbium.h exec/compressible_mui/SPPARKS_MUI/diag_propensity.cpp exec/compressible_mui/SPPARKS_MUI/diag_propensity.h exec/compressible_mui/SPPARKS_MUI/diag_sinter_density.cpp exec/compressible_mui/SPPARKS_MUI/diag_sinter_density.h exec/compressible_mui/SPPARKS_MUI/diag_sinter_free_energy.cpp exec/compressible_mui/SPPARKS_MUI/diag_sinter_free_energy.h exec/compressible_mui/SPPARKS_MUI/diag_sinter_free_energy_pore.cpp exec/compressible_mui/SPPARKS_MUI/diag_sinter_free_energy_pore.h exec/compressible_mui/SPPARKS_MUI/diag_surfchemtest.cpp exec/compressible_mui/SPPARKS_MUI/diag_surfchemtest.h exec/compressible_mui/SPPARKS_MUI/domain.cpp exec/compressible_mui/SPPARKS_MUI/domain.h exec/compressible_mui/SPPARKS_MUI/dump.cpp exec/compressible_mui/SPPARKS_MUI/dump.h exec/compressible_mui/SPPARKS_MUI/dump_image.cpp exec/compressible_mui/SPPARKS_MUI/dump_image.h exec/compressible_mui/SPPARKS_MUI/dump_sites.cpp exec/compressible_mui/SPPARKS_MUI/dump_sites.h exec/compressible_mui/SPPARKS_MUI/dump_text.cpp exec/compressible_mui/SPPARKS_MUI/dump_text.h exec/compressible_mui/SPPARKS_MUI/dump_vtk.cpp exec/compressible_mui/SPPARKS_MUI/dump_vtk.h exec/compressible_mui/SPPARKS_MUI/error.cpp exec/compressible_mui/SPPARKS_MUI/error.h exec/compressible_mui/SPPARKS_MUI/finish.cpp exec/compressible_mui/SPPARKS_MUI/finish.h exec/compressible_mui/SPPARKS_MUI/groups.cpp exec/compressible_mui/SPPARKS_MUI/groups.h exec/compressible_mui/SPPARKS_MUI/image.cpp exec/compressible_mui/SPPARKS_MUI/image.h exec/compressible_mui/SPPARKS_MUI/input.cpp exec/compressible_mui/SPPARKS_MUI/input.h exec/compressible_mui/SPPARKS_MUI/irregular.cpp exec/compressible_mui/SPPARKS_MUI/irregular.h exec/compressible_mui/SPPARKS_MUI/lattice.cpp exec/compressible_mui/SPPARKS_MUI/lattice.h exec/compressible_mui/SPPARKS_MUI/lattice.py exec/compressible_mui/SPPARKS_MUI/library.cpp exec/compressible_mui/SPPARKS_MUI/library.h exec/compressible_mui/SPPARKS_MUI/main.cpp exec/compressible_mui/SPPARKS_MUI/math_const.h exec/compressible_mui/SPPARKS_MUI/math_extra.cpp exec/compressible_mui/SPPARKS_MUI/math_extra.h exec/compressible_mui/SPPARKS_MUI/memory.cpp exec/compressible_mui/SPPARKS_MUI/memory.h exec/compressible_mui/SPPARKS_MUI/output.cpp exec/compressible_mui/SPPARKS_MUI/output.h exec/compressible_mui/SPPARKS_MUI/pair.cpp exec/compressible_mui/SPPARKS_MUI/pair.h exec/compressible_mui/SPPARKS_MUI/pair_lj_cut.cpp exec/compressible_mui/SPPARKS_MUI/pair_lj_cut.h exec/compressible_mui/SPPARKS_MUI/pointers.h exec/compressible_mui/SPPARKS_MUI/pool_shape.h exec/compressible_mui/SPPARKS_MUI/potential.cpp exec/compressible_mui/SPPARKS_MUI/potential.h exec/compressible_mui/SPPARKS_MUI/random_mars.cpp exec/compressible_mui/SPPARKS_MUI/random_mars.h exec/compressible_mui/SPPARKS_MUI/random_park.cpp exec/compressible_mui/SPPARKS_MUI/random_park.h exec/compressible_mui/SPPARKS_MUI/read_sites.cpp exec/compressible_mui/SPPARKS_MUI/read_sites.h exec/compressible_mui/SPPARKS_MUI/region.cpp exec/compressible_mui/SPPARKS_MUI/region.h exec/compressible_mui/SPPARKS_MUI/region_block.cpp exec/compressible_mui/SPPARKS_MUI/region_block.h exec/compressible_mui/SPPARKS_MUI/region_cylinder.cpp exec/compressible_mui/SPPARKS_MUI/region_cylinder.h exec/compressible_mui/SPPARKS_MUI/region_intersect.cpp exec/compressible_mui/SPPARKS_MUI/region_intersect.h exec/compressible_mui/SPPARKS_MUI/region_sphere.cpp exec/compressible_mui/SPPARKS_MUI/region_sphere.h exec/compressible_mui/SPPARKS_MUI/region_union.cpp exec/compressible_mui/SPPARKS_MUI/region_union.h exec/compressible_mui/SPPARKS_MUI/set.cpp exec/compressible_mui/SPPARKS_MUI/set.h exec/compressible_mui/SPPARKS_MUI/shell.cpp exec/compressible_mui/SPPARKS_MUI/shell.h exec/compressible_mui/SPPARKS_MUI/solve.cpp exec/compressible_mui/SPPARKS_MUI/solve.h exec/compressible_mui/SPPARKS_MUI/solve_group.cpp exec/compressible_mui/SPPARKS_MUI/solve_group.h exec/compressible_mui/SPPARKS_MUI/solve_linear.cpp exec/compressible_mui/SPPARKS_MUI/solve_linear.h exec/compressible_mui/SPPARKS_MUI/solve_tree.cpp exec/compressible_mui/SPPARKS_MUI/solve_tree.h exec/compressible_mui/SPPARKS_MUI/spktype.h exec/compressible_mui/SPPARKS_MUI/spparks.cpp exec/compressible_mui/SPPARKS_MUI/spparks.h exec/compressible_mui/SPPARKS_MUI/style_app.h exec/compressible_mui/SPPARKS_MUI/style_command.h exec/compressible_mui/SPPARKS_MUI/style_diag.h exec/compressible_mui/SPPARKS_MUI/style_dump.h exec/compressible_mui/SPPARKS_MUI/style_pair.h exec/compressible_mui/SPPARKS_MUI/style_region.h exec/compressible_mui/SPPARKS_MUI/style_solve.h exec/compressible_mui/SPPARKS_MUI/teardrop.h exec/compressible_mui/SPPARKS_MUI/timer.cpp exec/compressible_mui/SPPARKS_MUI/timer.h exec/compressible_mui/SPPARKS_MUI/universe.cpp exec/compressible_mui/SPPARKS_MUI/universe.h exec/compressible_mui/SPPARKS_MUI/variable.cpp exec/compressible_mui/SPPARKS_MUI/variable.h exec/compressible_mui/SPPARKS_MUI/version.h exec/compressible_mui/SPPARKS_MUI/viz.py exec/compressible_mui/SPPARKS_MUI/weld_geometry.h commit a03c6897664869b21887a39f809f29d7f25d92a0 Author: Daniel Ladiges Date: Mon Jul 6 22:50:39 2020 -0700 Fixed several stats bugs exec/compressible/inputs_temp_grad src_compressible/src_F90/stats_funcs.F90 commit 765d828099138b9d3716c7879ed024bded2256bd Author: Andy Nonaka Date: Mon Jul 6 14:19:47 2020 -0700 remove unused variable src_compressible/flux.cpp commit 1b082ea49fc0e1e62b7b568021a1091e47d0553b Author: Andy Nonaka Date: Mon Jul 6 13:49:56 2020 -0700 flux conversion WIP src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 40b092a644add10bbc214ea2e06da7955d32a719 Author: Andy Nonaka Date: Mon Jul 6 12:30:23 2020 -0700 hyp_flux_cons progress src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 859492ced4811d338a5cacb428df47188cfea8a7 Merge: 1805dcba 4f6ed3a6 Author: Johannes Blaschke Date: Fri Jul 3 09:27:34 2020 -0700 Merge branch 'flagellum_compile' commit 4f6ed3a612cf2c2a579b9fe311bd061d3066937a Author: Johannes Blaschke Date: Fri Jul 3 09:25:55 2020 -0700 use common Kernel Functions exec/immersed_boundary/flagellum/GNUmakefile src_immersed-boundary/IBParticleContainer.cpp src_particles/MakeKernels.package commit 5db480580c62e69bf9778b7dabc5271949ccfad7 Author: Changho Kim Date: Thu Jul 2 14:10:53 2020 -0700 exec/compressible_mui/MUI: MUI source codes included exec/compressible_mui/GNUmakefile exec/compressible_mui/MUI/Doxyfile exec/compressible_mui/MUI/LICENSE-Apache-v2 exec/compressible_mui/MUI/LICENSE-GPL-v3 exec/compressible_mui/MUI/README.md exec/compressible_mui/MUI/bin.h exec/compressible_mui/MUI/chrono_sampler_exact.h exec/compressible_mui/MUI/chrono_sampler_gauss.h exec/compressible_mui/MUI/chrono_sampler_mean.h exec/compressible_mui/MUI/chrono_sampler_null.h exec/compressible_mui/MUI/chrono_sampler_sum.h exec/compressible_mui/MUI/comm.h exec/compressible_mui/MUI/comm_factory.h exec/compressible_mui/MUI/comm_mpi.h exec/compressible_mui/MUI/comm_mpi_nxn.h exec/compressible_mui/MUI/comm_mpi_smart.h exec/compressible_mui/MUI/comm_tcp.h exec/compressible_mui/MUI/config.h exec/compressible_mui/MUI/dim.h exec/compressible_mui/MUI/dynstorage.h exec/compressible_mui/MUI/exception.h exec/compressible_mui/MUI/geometry.h exec/compressible_mui/MUI/lib_dispatcher.h exec/compressible_mui/MUI/lib_factory.h exec/compressible_mui/MUI/lib_mpi_hepler.h exec/compressible_mui/MUI/lib_mpi_multidomain.h exec/compressible_mui/MUI/lib_mpi_split.h exec/compressible_mui/MUI/lib_singleton.h exec/compressible_mui/MUI/lib_uri.h exec/compressible_mui/MUI/message.h exec/compressible_mui/MUI/mui.h exec/compressible_mui/MUI/point.h exec/compressible_mui/MUI/reader.h exec/compressible_mui/MUI/reader_variable.h exec/compressible_mui/MUI/sampler.h exec/compressible_mui/MUI/sampler_exact.h exec/compressible_mui/MUI/sampler_gauss.h exec/compressible_mui/MUI/sampler_kmc_fhd.h exec/compressible_mui/MUI/sampler_mov_avg.h exec/compressible_mui/MUI/sampler_nn.h exec/compressible_mui/MUI/sampler_null.h exec/compressible_mui/MUI/sampler_pseudo_n2_linear.h exec/compressible_mui/MUI/sampler_pseudo_nn.h exec/compressible_mui/MUI/sampler_shepard_quintic.h exec/compressible_mui/MUI/sampler_sph_quintic.h exec/compressible_mui/MUI/sampler_sum_quintic.h exec/compressible_mui/MUI/span.h exec/compressible_mui/MUI/spatial_storage.h exec/compressible_mui/MUI/stream.h exec/compressible_mui/MUI/stream_ordered.h exec/compressible_mui/MUI/stream_string.h exec/compressible_mui/MUI/stream_tuple.h exec/compressible_mui/MUI/stream_unordered.h exec/compressible_mui/MUI/stream_vector.h exec/compressible_mui/MUI/uniface.h exec/compressible_mui/MUI/util.h exec/compressible_mui/MUI/virtual_container.h exec/compressible_mui/MUI/wrapper_c/Makefile exec/compressible_mui/MUI/wrapper_c/mui_3d.cpp exec/compressible_mui/MUI/wrapper_c/mui_3d.h exec/compressible_mui/MUI/wrapper_c/mui_3d.o exec/compressible_mui/MUI/wrapper_c/unit_test.c exec/compressible_mui/MUI/wrapper_c/unit_test.o exec/compressible_mui/MUI/wrapper_f/Makefile exec/compressible_mui/MUI/wrapper_f/TODO exec/compressible_mui/MUI/wrapper_f/mui.F90 exec/compressible_mui/MUI/wrapper_f/mui_3df.cpp exec/compressible_mui/MUI/wrapper_f/unit_test.f90 commit 1805dcbae92cd302704a2f3441c3bb6655a78867 Author: Andy Nonaka Date: Thu Jul 2 13:44:12 2020 -0700 sync up with compressible_mui exec/compressible/main_driver.cpp commit 284c2ff88bc5cfb7ba90ff6b4fac604cc1ad546f Author: Andy Nonaka Date: Thu Jul 2 13:43:05 2020 -0700 sync up mui compressible main_driver exec/compressible/main_driver.cpp exec/compressible_mui/main_driver.cpp commit 62433ff53930d74ed635e72887fad084aeac953a Merge: a7ab4abf 6ecde8cf Author: Andy Nonaka Date: Thu Jul 2 13:14:51 2020 -0700 Merge branch 'master' into compressible_mui commit a7ab4abf8a5fea2abb77784fa73f583340355e4a Author: Changho Kim Date: Thu Jul 2 05:26:03 2020 -0700 compressible_mui: sign errors exec/compressible_mui/main_driver.cpp commit 6ecde8cfc186f1c8e9949364d589753543497cb9 Merge: e56b7f56 1dd765a5 Author: Daniel Ladiges Date: Thu Jul 2 00:03:08 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e56b7f56cd958b14cddac00c47076787906b663f Author: Daniel Ladiges Date: Thu Jul 2 00:02:40 2020 -0700 moved kernel definitions to ibmarkercontaineri src_immersed-boundary/kernel_functions_K.H commit 282ccc9eced058a80c59d063acdb4d6a4d775423 Author: Changho Kim Date: Wed Jul 1 13:11:42 2020 -0700 compressible_mui: velocity sampling and state update implemented exec/compressible_mui/main_driver.cpp commit d73c75c6e51692072d5e8a1cf8d08a3329eedfcc Author: Andy Nonaka Date: Wed Jul 1 10:39:36 2020 -0700 trying to get this to compile again exec/immersed_boundary/flagellum/GNUmakefile src_particles/Make.package commit 1dd765a5aeacb7369adc0684b8adbdae98878584 Author: Andy Nonaka Date: Wed Jul 1 08:36:01 2020 -0700 clean up make system and include dependencies exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/multispec/GNUmakefile src_hydro/MacProj_hydro.cpp commit d27a5654ac21b0a104f0ca6ff0c1c4611e250168 Author: Changho Kim Date: Wed Jul 1 04:34:02 2020 -0700 compressible_mui: mui_fetch and mui_push use prim exec/compressible_mui/main_driver.cpp exec/compressible_mui/pseudo_kmc.bin exec/compressible_mui/src_pseudo_kmc/pseudo_kmc.cpp commit ab1ef2afe3ad04bb460fafd19eda95a4ea792906 Author: Changho Kim Date: Wed Jul 1 02:11:01 2020 -0700 compressible_mui: mui_fetch mui_push separated exec/compressible_mui/inputs_equil_3d exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/src_pseudo_kmc/pseudo_kmc.cpp commit 00840fdbb79b6c0bfb7437157d630a3590acb013 Author: Andy Nonaka Date: Tue Jun 30 09:54:54 2020 -0700 removing fortran for transport coefficient related stuff (now called by C++ lambda) src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/matrix.f src_compressible/src_F90/matrixnp.f src_compressible/src_F90/multispec_funcs.F90 src_compressible/transCoeffs.cpp commit cb06f114d40c30ce58b7c0468e3813a232349337 Author: Daniel Ladiges Date: Mon Jun 29 16:21:57 2020 -0700 Master branch now using C++/GPU RFD version. exec/compressible/inputs_temp_grad exec/immersedIons/main_driver.cpp exec/tests/RFDanalysis/GNUmakefile exec/tests/RFDanalysis/INS_functions.H exec/tests/RFDanalysis/Make.package exec/tests/RFDanalysis/WritePlotFile.cpp exec/tests/RFDanalysis/WritePlotFileHydro.cpp exec/tests/RFDanalysis/delPlots exec/tests/RFDanalysis/inputs_3d exec/tests/RFDanalysis/main_driver.cpp exec/tests/RFDanalysis/particleGen.cpp commit 550015491335092e296569aaf6cd5d20033cb51f Author: Daniel Ladiges Date: Mon Jun 29 12:37:24 2020 -0700 Bug fixes for stat collection. Addded new stats to restart files. exec/compressible/inputs_temp_grad exec/compressible/main_driver.cpp src_compressible/checkpoint.cpp src_compressible/compressible_functions.H src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 869ee1964b7d1fcb55059851ce4a6d0306a4676e Author: Daniel Ladiges Date: Sun Jun 28 11:41:11 2020 -0700 Merged C++/GPU kernel functions from C++ to master src_particles/kernel_functions_K.H commit b88f4feb76cebd480a0768726d75bb902380d790 Author: Daniel Ladiges Date: Sun Jun 28 11:38:19 2020 -0700 Merging IBMarkerContainerBase class from branch cplusplus back into master src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit fa33f93916c13ae81939e81f7e55a8fce261075f Author: Daniel Ladiges Date: Sat Jun 27 00:35:15 2020 -0700 Updated versions of stats calcs. exec/compressible/main_driver.cpp src_compressible/src_F90/stats_funcs.F90 commit 657fbe9497660aecee13dc1a2981552f8a137f58 Merge: 5a3a45fd 3facf1d4 Author: Daniel Ladiges Date: Fri Jun 26 11:10:03 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5a3a45fdc720ccff069b2b09b47c6f4fe3ab411e Author: Daniel Ladiges Date: Fri Jun 26 11:09:44 2020 -0700 changes to stats calculations exec/compressible/inputs_temp_grad src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp commit 3facf1d45689c0270615aa969fd76234b983bc1b Author: Andy Nonaka Date: Wed Jun 24 15:26:53 2020 -0700 index C++/F90 fix in transport turned back on random numbers on GPU src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp src_rng/MultiFabFillRandom.cpp commit d0ca08022924069cc0d0166e87d512d92c63a563 Author: Andy Nonaka Date: Wed Jun 24 08:25:04 2020 -0700 fixed 2 GPU bugs in calculateTransportCoeffs (the F90 is still enabled) src_compressible/compressible_functions.H commit 75e088ee149d67498995408b2b0e094105e0c8ad Merge: 3f157918 2fb702af Author: Daniel Ladiges Date: Tue Jun 23 19:42:28 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3f157918329d1e1763842b7386306b3f091e708a Author: Daniel Ladiges Date: Tue Jun 23 19:42:09 2020 -0700 Started remaking stats calcs exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 1a59b9beb21ab3da4b158cb422f1da708758f683 Author: Changho Kim Date: Tue Jun 23 16:54:14 2020 -0700 exec/compressible_mui: inputs_equil_3d main_driver.cpp exec/compressible_mui/inputs_equil_3d exec/compressible_mui/main_driver.cpp commit 2fb702af565b5febf9fe1e18e8378da8edb325dc Author: Andy Nonaka Date: Tue Jun 23 04:17:07 2020 -0700 revert back to f90 for now src_compressible/transCoeffs.cpp commit ceb13dcd187dc3dab10715a86a2cbe2fee6b1d57 Merge: 179a4a3e 8764d3fc Author: jbb Date: Mon Jun 22 14:44:02 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 179a4a3eaeaa163d46f07dc9f48d329d8a87b102 Author: jbb Date: Mon Jun 22 14:39:05 2020 -0700 put in real constants src_compressible/src_F90/flux_funcs.F90 commit 8764d3fc025c6b2eb05e94f2347957db6e49f0dd Author: John Date: Mon Jun 22 14:39:02 2020 -0700 added inputs for temperature gradient test exec/compressible/inputs_temp_grad commit 6d3ebc1c87f70372566076964997078bf1c6bda4 Author: Andy Nonaka Date: Mon Jun 22 13:39:20 2020 -0700 tiling bug in sumstag src_gmres/NormInnerProduct.cpp commit 350a6737e00e993d10e20260d8756b63e893d1d1 Author: Daniel Ladiges Date: Fri Jun 19 21:41:30 2020 -0700 Bugchecking single particle forcing causing no GMRES convergence exec/immersedIons2/GNUmakefile exec/immersedIons2/main_driver.cpp exec/immersedIons2/particleGen.cpp src_hydro/advance.cpp src_particles/src_F90/particle_functions.F90 commit 83230c98e054a2040da328f331f4ce0778311d0a Author: Daniel Ladiges Date: Fri Jun 19 21:39:58 2020 -0700 Fixed call to corretion table build in main_driver exec/immersedIons/main_driver.cpp commit 307b035ef205ec0186750772699fffd46caac88a Merge: e8660d3c 2c2a356f Author: Daniel Ladiges Date: Thu Jun 18 17:40:45 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2c2a356fc9305c07a6008a7ce1739f0eeeb2f6f3 Author: Daniel Ladiges Date: Thu Jun 18 17:39:48 2020 -0700 Test framework for periodic diffusion effects exec/immersedIons2/Checkpoint.cpp exec/immersedIons2/Eanalysis.nb exec/immersedIons2/GNUmakefile exec/immersedIons2/INS_functions.H exec/immersedIons2/Make.package exec/immersedIons2/Make_debug.package exec/immersedIons2/Make_precheck.package exec/immersedIons2/WritePlotFile.cpp exec/immersedIons2/WritePlotFileHydro.cpp exec/immersedIons2/channel_mobility.nb exec/immersedIons2/delPlots exec/immersedIons2/init_funcs.F90 exec/immersedIons2/inputs_3d exec/immersedIons2/main_driver.cpp exec/immersedIons2/particleGen.cpp exec/immersedIons2/precheck.F90 commit 8727d953ef880048d9c5cdd3d4fe211d120d236a Merge: 4bb8cbf5 d1a89aa1 Author: Daniel Ladiges Date: Thu Jun 18 15:51:25 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4bb8cbf56b655d6703186c12f96a96ccae836b3d Author: Daniel Ladiges Date: Thu Jun 18 15:49:02 2020 -0700 I dont' actually remember, but synching work I did on my laptop a week ago. exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_hydro/advance.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit d1a89aa1e4ccb2fc451cd0ab2515bfd8ad15bdaa Author: Johannes Blaschke Date: Sun Jun 14 14:15:03 2020 -0700 remove unused code (due to updates in AMReX) src_immersed-boundary/IBMarkerContainer.cpp commit 6ef8b6d34f9f902c3763676ea8907d9276f9ae17 Author: Andy Nonaka Date: Fri Jun 12 16:24:56 2020 -0700 switch to GPU-enabled version of calculateTransportCoefficients old code is still there for now ifdef's out in transCoeffs.cpp the old code will be removed in another commit src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit e5f712ca0fd61460810bb246af05eb781cff6ab2 Author: Andy Nonaka Date: Fri Jun 12 13:14:38 2020 -0700 fix pass-by-reference/value mistakes src_compressible/compressible_functions.H commit 269ead40ea877f5bd9cc1a784d5bf0dd0a1362c6 Author: Andy Nonaka Date: Fri Jun 12 09:54:59 2020 -0700 index bugfix src_compressible/compressible_functions.H commit 29fe44798f5b43c5394d7cfd1bdbd7ef5614ff28 Author: Andy Nonaka Date: Fri Jun 12 08:33:22 2020 -0700 index bugs src_compressible/compressible_functions.H commit 0a25c7a1c8d5a79f098b77b69e643ce2553c23c4 Author: Andy Nonaka Date: Fri Jun 12 08:17:53 2020 -0700 fix compilation errors src_compressible/compressible_functions.H commit aeaa808425d4d4ac77ac9dcd25cd6695d33c61e0 Author: Andy Nonaka Date: Fri Jun 12 08:14:56 2020 -0700 LambdaLin to GPU src_compressible/compressible_functions.H commit dc8bd6c31fd8c2af34836c0039254d3f63f2fb8a Author: Andy Nonaka Date: Fri Jun 12 07:48:34 2020 -0700 solvenp and decompnp on GPU src_compressible/compressible_functions.H src_compressible/src_F90/matrixnp.f commit ba6489690c31355f46f3b5cbb20732cd01c04338 Author: Andy Nonaka Date: Fri Jun 12 07:23:00 2020 -0700 GPU ThermalDiff (excetp for decompnp and solvenp) src_compressible/compressible_functions.H commit 2fccf629e8e8eb72a3489c08c5ce27178beb7123 Author: Andy Nonaka Date: Fri Jun 12 07:10:39 2020 -0700 convert D_GIOVANGIGLI to GPU src_compressible/compressible_functions.H commit 1ac2e62a5f5744afeb90588795578bd213f24cda Author: Andy Nonaka Date: Thu Jun 11 15:11:10 2020 -0700 first attempt at c++ lambda version of Solve() src_compressible/compressible_functions.H commit a9f461795764562d5cdc1d88bbdec2347c99d1d8 Author: Andy Nonaka Date: Thu Jun 11 15:02:09 2020 -0700 bugfix in 2d array access first attempt at C++ lambda Decomp src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit 6eb1812298605f33828b54d375e0039eb07891db Author: Andy Nonaka Date: Thu Jun 11 14:42:27 2020 -0700 add commented-out zero-based array routines for easier conversion to c++ src_compressible/src_F90/matrix.f commit cfd2a36655c7513f4298f6513ee2817ebe73164a Author: Andy Nonaka Date: Thu Jun 11 07:53:07 2020 -0700 ViscLin GPU src_compressible/compressible_functions.H commit 2aac700aa316b80b8342d53855cf6426dc9a6e57 Author: Andy Nonaka Date: Thu Jun 11 07:20:21 2020 -0700 GPU progress src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit b9213fe88af4bff0f3673c1fd535ffaaeb904681 Author: Andy Nonaka Date: Thu Jun 11 06:56:17 2020 -0700 cleanup GPU implementation thus far src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/transCoeffs.cpp commit c2ead236af7291ddd30e3b66248db35f5194bed5 Merge: 8819b7b9 d384c855 Author: Andy Nonaka Date: Wed Jun 10 17:12:02 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8819b7b94c9292499b2cb49a2cbb60e9353afdbe Author: Andy Nonaka Date: Wed Jun 10 17:09:32 2020 -0700 consolidate the definitions of MAX_SPECIES to only appear in src_common change value of MAX_SPECIES to 4, and abort if nspecies>MAX_SPECIES src_common/common_functions.H src_common/src_F90/common_namelist.F90 src_compressible/compressible_functions.H src_compressible/src_F90/compressible_namelist.F90 src_multispec/multispec_functions.H commit ef6cda356cb03637234509c02c49f4898a3fd431 Author: Andy Nonaka Date: Wed Jun 10 16:57:03 2020 -0700 more gpu comments, examples src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp commit b0c217dbed5c341d20eb837f5bdc4e10bbd7e838 Author: Andy Nonaka Date: Wed Jun 10 15:45:38 2020 -0700 comments src_compressible/conservedPrimitiveConversions.cpp commit 0c9c5a1a4e968497e866bebdd1519c03f5ab9489 Author: Andy Nonaka Date: Wed Jun 10 15:06:21 2020 -0700 gpuarray molmass src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp commit d384c855226c480a16fa3d706c4450e671f49920 Merge: c65f64a5 542678c4 Author: Johannes Blaschke Date: Wed Jun 10 10:32:36 2020 -0700 Merge branch 'master' into jpb/fix-neighbor commit c65f64a5cd89c85209fc262ef158329a3a8dbc76 Author: Johannes Blaschke Date: Wed Jun 10 10:31:47 2020 -0700 fix flagellum app to track latest changes in FHDeX proper/AMReX exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/ib_md.cpp commit 542678c467a6d8935c9ab448116cd5be6de5a0af Author: Andy Nonaka Date: Wed Jun 10 09:25:56 2020 -0700 more temporary memory cleanup src_compressible/src_F90/multispec_funcs.F90 commit f05dc72d38e1439a220d3447233443252014200d Author: Andy Nonaka Date: Wed Jun 10 08:07:34 2020 -0700 cleanup temporary memory usage src_compressible/src_F90/multispec_funcs.F90 commit 5d76b2f7fb896921acab394c3dbfcb5025c02210 Author: Andy Nonaka Date: Wed Jun 10 07:39:08 2020 -0700 rewrite F77 code to F90 style src_compressible/src_F90/matrix.f src_compressible/src_F90/matrixnp.f commit 74112c2bc32f2cd5e2f0b186060cf73525ba4a36 Author: Andy Nonaka Date: Tue Jun 9 15:59:43 2020 -0700 gpu progress src_compressible/compressible_functions.H src_compressible/transCoeffs.cpp commit 255ea839875a43a9db70e1c0c3edc8704d27451c Author: Andy Nonaka Date: Tue Jun 9 08:34:52 2020 -0700 structure factor index bug fix; was trying to copy from an invalid memory address (but later overwriting so the results are ok; just prone to segfaults depending on the compiler/system) exec/compressible/main_driver.cpp commit c82a32a363a33b7e29822c5bbb22dafb931ea8fd Author: Johannes Blaschke Date: Mon Jun 8 17:48:58 2020 -0700 must clear neighbors _before_ redistributing exec/immersed_boundary/channel_dumbbell/advance.cpp commit 0e03994c2d34ea59672dc850dede65000913825b Author: Johannes Blaschke Date: Mon Jun 8 10:40:47 2020 -0700 fix non-constant neighbor particle iterator: exec/immersed_boundary/channel_dumbbell/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/Make.package commit 849a300b11fe7d79668214d7a9b9d86e57a2a8df Author: Andy Nonaka Date: Sun Jun 7 09:10:46 2020 -0700 added multifab memory usage output at end of each time step exec/compressible/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/multispec/main_driver.cpp commit 299a4908c06930f00f434ffad6f1635eeb92ac4a Author: Andy Nonaka Date: Sun Jun 7 08:30:33 2020 -0700 fix dx exec/compressible/inputs_SFtest commit cc2671763df7644e034bc90a0bf90cd43adc655c Merge: 9284ed91 70de6f22 Author: Andy Nonaka Date: Fri Jun 5 06:28:24 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9284ed91477801756ba1374b0599ab51908c7bfb Author: Andy Nonaka Date: Fri Jun 5 06:28:07 2020 -0700 trying to match the Kaushik SF compressible test setup exec/compressible/inputs_SFtest commit 70de6f220cfdd4664df4d9d8dc575db221e2a474 Author: jbb Date: Thu Jun 4 10:21:14 2020 -0700 fix conservative src_compressible/src_F90/flux_funcs.F90 commit da96231518fc5984f1a2ebde861d3c0dec366ba2 Author: jbb Date: Thu Jun 4 10:20:08 2020 -0700 fixed 1/12 in flux src_compressible/conservedPrimitiveConversions.cpp src_compressible/src_F90/flux_funcs.F90 commit 5662afabfb6641528f2321bf67bd89a0cce497a1 Merge: f5942cc8 c31617e2 Author: jbb Date: Wed Jun 3 12:58:57 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f5942cc87f41f6bf2008cc03e3c7453e54f00da6 Author: jbb Date: Wed Jun 3 12:58:29 2020 -0700 minor tweak to format and noting something wrong src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 commit c31617e23b30a582740c79aa708ac8dc2bb7cf02 Merge: 2de9745c e8c4b3ac Author: Andy Nonaka Date: Wed Jun 3 07:45:53 2020 -0700 Merge pull request #12 from AMReX-FHD/gpu_constoprim Put cons_to_prim on GPU commit e8c4b3ac587ef723e3455fc60ad5e9b1e4fc28c5 Author: Andy Nonaka Date: Wed Jun 3 07:42:08 2020 -0700 finished GPU conversion of cons_to_prim had to compute hcv and hcp on the host (wasn't being done) exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/src_F90/conv_funcs.F90 commit 7697549acc54aaa1367934413a767e790ffaff5c Author: Andy Nonaka Date: Wed Jun 3 06:48:23 2020 -0700 conservedPrimitiveConversions compiles now, still generates NaNs src_compressible/conservedPrimitiveConversions.cpp commit a7e07985d8c0147fe035a7068701e383a8ee5b8c Author: Andy Nonaka Date: Wed Jun 3 06:44:07 2020 -0700 GPU WIP src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp commit f57e098624b0e7639f7e635c8338366b74f2c6cb Author: Andy Nonaka Date: Tue Jun 2 16:59:27 2020 -0700 more Weiqun suggestions src_compressible/compressible_functions.H commit 459be241b3f1c80678679201c340cd69255236c8 Author: Andy Nonaka Date: Tue Jun 2 16:58:20 2020 -0700 WIP (doesn't compile) but has Weiqun's fixes commented in src_compressible/conservedPrimitiveConversions.cpp commit 1e06b2ec7df7f2efc3c56f08c135b0f3d38e9375 Author: Andy Nonaka Date: Tue Jun 2 16:08:15 2020 -0700 attempting gpu conversion of conservedToPrimitive. WIP src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_rng/MultiFabFillRandom.cpp commit 2de9745c9582ca9ccae3e075b0172427a7d96944 Author: Andy Nonaka Date: Mon Jun 1 17:01:43 2020 -0700 profilers exec/compressible/main_driver.cpp src_compressible/boundary.cpp src_compressible/checkpoint.cpp src_compressible/compressible_functions.cpp src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/membrane.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp src_compressible/writePlotFile.cpp commit 310a35d468d1d6847edd7b8d3dd149dee825d54d Author: Andy Nonaka Date: Fri May 29 08:53:24 2020 -0700 conservative pair structure factors exec/compressible/main_driver.cpp commit a5ff29384c362c81d405a9fcd3daa25aa6b55f8c Author: Andy Nonaka Date: Thu May 28 06:08:07 2020 -0700 structure factor test for primitive variables (conserved still need to be done) exec/compressible/inputs_SFtest exec/compressible/main_driver.cpp commit 22bdeac27225642a2c70c5c49f5108147b5dc463 Author: Andy Nonaka Date: Tue May 26 14:24:55 2020 -0700 abs -> std::abs for integer cases exec/DiffuisonTest/StagExpSolver.cpp exec/immersedIons/main_driver.cpp src_gmres/Precon.cpp src_gmres/StagMGSolver.cpp src_immersed-boundary/IBGMRES.cpp commit e3a9dadf8ffd0c95aff03f3ec9af28702b3004c6 Author: Andy Nonaka Date: Tue May 26 14:18:37 2020 -0700 abs -> std::abs for double cases exec/DSMC-LDT/particleGen.cpp src_particles/FhdParticleContainer.cpp commit 7f800f6c1183faf07a756f0f06a0ac902083ff5b Author: Andy Nonaka Date: Fri May 22 14:07:34 2020 -0700 implement structure factors for hydro example exec/hydro/main_driver.cpp commit 2bc6226116de6c6e884da1946b962c9266025bfd Author: Andy Nonaka Date: Thu May 21 14:48:32 2020 -0700 make MacProj a class - eliminats having to rebuild the linear operator (time savings) each Precon application src_gmres/GMRES.cpp src_gmres/MacProj.H src_gmres/MacProj.cpp src_gmres/Make.package src_gmres/Precon.H src_gmres/Precon.cpp src_gmres/Utility.cpp src_gmres/gmres_functions.H src_immersed-boundary/IBGMRES.cpp src_multispec/InitialProjection.cpp commit fe6ab7d95ff33ab7f512c33d6a189c5929e443fe Author: Andy Nonaka Date: Tue May 19 09:42:07 2020 -0700 precond settings src_gmres/MacProj.cpp src_gmres/src_F90/gmres_namelist.F90 commit 0283a9d706ff0ba4ae1cd2810a3510e33c4b84f6 Author: Andy Nonaka Date: Tue May 19 09:39:27 2020 -0700 typo src_gmres/MacProj.cpp commit 120706d4ee9d24cc1eaa0a86d10bb6df88c8f5d1 Author: Andy Nonaka Date: Tue May 19 09:22:16 2020 -0700 can set the number of v-cycles, nsmooths_down/up/bottom for the Preconditioner Poisson solve via the inputs file now exec/DSMC/inputs_2d exec/DSMCstatcheck/inputs_2d exec/brownian/inputs_2d exec/immersedIons/inputs_2d src_gmres/MacProj.cpp src_gmres/src_F90/gmres_namelist.F90 commit 3dbe8f67e05bb1224ab55aaf0753ce6572106d97 Author: Andy Nonaka Date: Fri May 15 12:53:36 2020 -0700 forgot to add this src_gmres/GMRES.H commit 369f807e4ee337daca3048e76a3152cd3974b3a2 Author: Andy Nonaka Date: Fri May 15 12:40:20 2020 -0700 "class"-ify GMRES exec/hydro/advance.cpp exec/multispec/AdvanceTimestepInertial.cpp src_gmres/GMRES.cpp src_gmres/Make.package src_gmres/Precon.H src_gmres/Precon.cpp src_gmres/StagMGSolver.H src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_hydro/advance.cpp commit 5f6e107e5651ba2067c35dfe7ee8bd10a361b6d6 Author: Andy Nonaka Date: Fri May 15 11:35:28 2020 -0700 more eliminaton of memory transfers. subtractWeightedGradP now takes in the gradp as an input src_gmres/MacProj.cpp src_gmres/Precon.H src_gmres/Precon.cpp src_gmres/gmres_functions.H src_immersed-boundary/IBGMRES.cpp src_multispec/InitialProjection.cpp commit 6c7890c3f6cfd42b38bc9cfa1be73c949760b570 Author: Andy Nonaka Date: Fri May 15 11:23:16 2020 -0700 make the preconditioner its own class to remove Host/Device gpu memory transfers src_gmres/GMRES.cpp src_gmres/Make.package src_gmres/Precon.H src_gmres/Precon.cpp src_gmres/StagMGSolver.H src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 585e0f5008f44b75c1b6cb84fe2bc1d0802ebc15 Author: Andy Nonaka Date: Fri May 15 10:53:33 2020 -0700 typo fix in header guard src_gmres/StagMGSolver.H commit 600b32058c4cccfda57122fc4b936369a4000db9 Author: Andy Nonaka Date: Fri May 15 06:17:40 2020 -0700 0.1M Weak E, 22% 11% and 6% wet runs exec/immersedIons/inputs_paper_cond12a exec/immersedIons/inputs_paper_cond12b exec/immersedIons/inputs_paper_cond12c commit bbb2f83888f17d61002a9728613b40968a1b61c8 Author: Andy Nonaka Date: Fri May 15 06:00:02 2020 -0700 0.1M Strong E, 22% 11% and 6% wet runs exec/immersedIons/inputs_paper_cond9a exec/immersedIons/inputs_paper_cond9b exec/immersedIons/inputs_paper_cond9c commit f7e482b34ea6d33e50ecf7cc5b0887ab9b48be38 Author: Andy Nonaka Date: Wed May 13 17:23:11 2020 -0700 more multifab movement restructure src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/gmres_functions.H commit 36a0a3689addf5fe1680d7d778f38a05f9863c06 Author: Andy Nonaka Date: Wed May 13 17:10:21 2020 -0700 fix comment src_gmres/MacProj.cpp commit cef580760912354811ad956b2700735bcb644f5a Author: Andy Nonaka Date: Wed May 13 17:05:25 2020 -0700 remove temporary allocation of multifab src_gmres/GMRES.cpp src_gmres/NormInnerProduct.cpp src_gmres/gmres_functions.H commit a29e79c82ad25fdc40c1f02eca76337f49acc952 Author: Andy Nonaka Date: Wed May 13 12:41:50 2020 -0700 rennamed/rewrote CCApplyOp -> CCApplyNegLap so it's more clear this is simply computing the negative laplacian removed more temporary multifabs because of this change src_gmres/ApplyPrecon.cpp src_gmres/MacProj.cpp src_gmres/gmres_functions.H src_immersed-boundary/IBGMRES.cpp commit 6f7464c04f2b91540ea16eee5df5f4b64a601698 Author: Andy Nonaka Date: Wed May 13 12:01:02 2020 -0700 remove unneeded MultiFabs src_gmres/ApplyPrecon.cpp commit d5236f7825a84b1e7d954e809650445da8180a2d Author: Andy Nonaka Date: Wed May 13 11:50:47 2020 -0700 remove unneeded temporary multifab src_gmres/ApplyMatrix.cpp commit 3016d8f7101fc1df8e68d9d29b81ae3b5f11ffcc Author: Andy Nonaka Date: Wed May 13 11:50:33 2020 -0700 added option to increment gradient rather than set gradient src_common/ComputeDivAndGrad.cpp src_common/common_functions.H commit 7b6c7240c2ade414ba87c7347e0db7b7d4f73d1b Author: Andy Nonaka Date: Wed May 13 10:12:38 2020 -0700 add BL_Timers with correct names src_gmres/StagMGSolver.cpp commit 9f907ca064ed93139f55401f8ad4db75be30f310 Merge: 8ac83503 4b0b3697 Author: Andy Nonaka Date: Wed May 13 10:07:48 2020 -0700 Merge pull request #11 from AMReX-FHD/StagMGSolver_class Stag mg solver class commit 4b0b369766213939de22e6aa7082b9cf6813739b Author: Andy Nonaka Date: Wed May 13 10:05:46 2020 -0700 create the StagMGSolver at the GMRES level. should reduce HtoD/DtoH copies of multifabs used in this algorithm by an order of magnitude or so src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/gmres_functions.H commit b9cb687c9284e59f4a0e0b9de77644676c008076 Author: Andy Nonaka Date: Wed May 13 09:56:58 2020 -0700 made StagMGSolver a class When calling the solver in ApplyPrecon, I create the StagMGSolver object then immediately destroy it. This will be changed so the object is declared in GMRES (or perhaps higher) in a future commit src_gmres/ApplyPrecon.cpp src_gmres/Make.package src_gmres/StagMGSolver.H src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 8ac835039b6464f0477de779843772ee05d2a316 Merge: 95c150a5 f079eb8c Author: Andy Nonaka Date: Fri May 1 12:08:21 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 95c150a58eb610cfbecc9589c95fdc2e8b93e272 Author: Andy Nonaka Date: Fri May 1 12:07:38 2020 -0700 3d structure factor test exec/multispec/inputs_compare_equil_3d commit f079eb8c91d8644a85c8fb35c94aa71f952847b9 Author: Oscar Antepara Date: Thu Apr 30 14:45:09 2020 -0700 Fixing computation of temp var src_compressible/src_F90/stats_funcs.F90 commit 9ea5b986e2ccdfca063c56dfaf35aca617ffe78b Author: Andy Nonaka Date: Wed Apr 29 14:42:40 2020 -0700 turn on structure factor for all pairs including rho, Vel, Temp exec/compressible/main_driver.cpp commit d8943db4c7adfa4db6fa19190db3e3e16f5ab3b7 Author: Andy Nonaka Date: Mon Apr 27 13:28:18 2020 -0400 128^3 single grid configuration, no plotfile exec/hydro/inputs_profiling_3d commit e8660d3c2840e49ef84ce0a52d53cd50b56485e7 Merge: f128a8dc cf47e117 Author: Daniel Ladiges Date: Mon Apr 27 08:09:24 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f128a8dcc82ebc98b1618c8424b0353d3f5816af Author: Daniel Ladiges Date: Mon Apr 27 08:09:08 2020 -0700 rfd stuff exec/compressible/inputs_equil_3d_mem exec/immersedIons/delPlots exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_gr1 exec/immersedIons/old_inputs_files/README exec/immersedIons/old_inputs_files/inputs_paper_cond1 exec/immersedIons/old_inputs_files/inputs_paper_cond10 exec/immersedIons/old_inputs_files/inputs_paper_cond11 exec/immersedIons/old_inputs_files/inputs_paper_cond12 exec/immersedIons/old_inputs_files/inputs_paper_cond2 exec/immersedIons/old_inputs_files/inputs_paper_cond3 exec/immersedIons/old_inputs_files/inputs_paper_cond4 exec/immersedIons/old_inputs_files/inputs_paper_cond5 exec/immersedIons/old_inputs_files/inputs_paper_cond6 exec/immersedIons/old_inputs_files/inputs_paper_cond7 exec/immersedIons/old_inputs_files/inputs_paper_cond8 exec/immersedIons/old_inputs_files/inputs_paper_cond9 src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 10fdf9bb7be260184ae2d101f66e798bd94ebb62 Merge: 15bab090 cf47e117 Author: Johannes Blaschke Date: Sun Apr 26 17:16:40 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 15bab090a604ca221c411d75560bec2985d32dd5 Author: Johannes Blaschke Date: Sun Apr 26 17:16:23 2020 -0700 start moving the IBMarkerContainer API in line with the recent changes to AMReX particles exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/flagellum/ib_md.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit cf47e117e7de94cb562bf91c617bc5a8902b30c0 Merge: 42bd9edf 336db2c4 Author: Andy Nonaka Date: Fri Apr 24 14:31:21 2020 -0700 Merge pull request #10 from AMReX-FHD/atmyers/consolidation Update neighbor particle stuff to use the new C++-ready style. commit 42bd9edf971f4303310b59392181de0cddaab667 Author: Andy Nonaka Date: Fri Apr 24 08:41:34 2020 -0700 fix timers, add timers src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/InitialProjection.cpp src_multispec/MkDiffusiveMFluxdiv.cpp src_multispec/RhoUtil.cpp src_multispec/StochMassFlux.cpp src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_mobility.cpp commit 477235b18556ea416a26f1e726343602662daa3c Author: Andy Nonaka Date: Fri Apr 24 07:57:36 2020 -0700 MultiFAB -> MultiFab src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_compressible/timeStep.cpp src_electrostatic/electrostatic.cpp src_hydro/AddMFluctuations.cpp src_hydro/StochMomFlux.cpp src_multispec/StochMassFlux.cpp src_rng/Make.package src_rng/MultiFabFillRandom.cpp src_rng/rng_functions.H commit 1b08eaf11e3ba53bd88aaf838131fc1e4db7cde4 Author: Andy Nonaka Date: Fri Apr 24 07:49:28 2020 -0700 more timers renname MkAdvSFluxdiv -> MkAdvSFluxdiv_cc for version that takes cell-centered "s_in" as input exec/channel/advance.cpp exec/exercises/incompressible/advance.cpp exec/hydro/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_soft/advance.cpp src_gmres/MacProj.cpp src_gmres/StagMGSolver.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.cpp src_hydro/advance.cpp src_hydro/hydro_functions.H commit 666a5512abcedb0c553aa227d0cfdf82357ce175 Author: Andy Nonaka Date: Fri Apr 24 07:36:11 2020 -0700 timers src_common/BCPhysToMath.cpp src_common/ComputeBasicStats.cpp src_common/MultiFabPhysBC.cpp src_hydro/AddMFluctuations.cpp src_hydro/ConvertMToUmac.cpp src_hydro/HydroBCs.cpp src_hydro/MacProj_hydro.cpp commit 6c2f1cfd6622e1082160de7787bd35f632bdd068 Author: Andy Nonaka Date: Fri Apr 24 07:24:40 2020 -0700 ifdef structure factor stuff so gpu compiles exec/compressible/GNUmakefile exec/compressible/main_driver.cpp commit ae4e68bf6d663207c6f4347266be8a972fa35a80 Author: Andy Nonaka Date: Fri Apr 24 07:01:31 2020 -0700 don't compile in AMReX particle source exec/hydro/GNUmakefile commit 3b1f992569e941769867869d457448f4d2d7d094 Author: Andy Nonaka Date: Fri Apr 24 09:15:22 2020 -0400 revert one print statement exec/immersedIons/main_driver.cpp commit c89f21f17bddea9e0d6a85d232f0c212ff7c14c7 Author: Andy Nonaka Date: Fri Apr 24 09:13:33 2020 -0400 remove print statements exec/immersedIons/main_driver.cpp commit 336db2c43ca96357cd736ed4e020875b07204462 Author: atmyers Date: Thu Apr 23 19:46:19 2020 -0700 set variance_coef_mom back to 0 in the inputs file exec/immersedIons/inputs_regression_cond commit 7e26df46ce3d82ad8c2716b13829465792c96221 Author: Andy Nonaka Date: Thu Apr 23 15:22:58 2020 -0700 ifdef's out structure factor code for gpu builds exec/hydro/GNUmakefile exec/hydro/main_driver.cpp exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/multispec/GNUmakefile exec/multispec/main_driver.cpp commit 3ff16b4e5495e99f88b9e71206788cf504fef78f Author: atmyers Date: Thu Apr 23 13:51:00 2020 -0700 clear neighbors before we redistribute exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit fe8168c3a2d80ae5c967d545f78afc17976d74c5 Author: atmyers Date: Thu Apr 23 13:49:07 2020 -0700 a few more size -> numParticles() src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBParticleContainer.H commit ff175d16aec65e52ef69daaaab89e4ba52e90dd8 Author: Andy Nonaka Date: Thu Apr 23 09:07:17 2020 -0700 changes to checkPair struct src_particles/DsmcParticleContainer.H commit ed345c6bf4903c930149316630495ac71e1a491e Author: Andy Nonaka Date: Thu Apr 23 07:16:57 2020 -0700 gpu fix; namelist stuff into temporaries src_multispec/RhoUtil.cpp commit f861c5d7177efae55b8eb83c1bd2ddeaf852eb67 Author: Andy Nonaka Date: Thu Apr 23 08:53:32 2020 -0400 changes to checkPair struct and array/vector declaration to make this compile on gpu src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit db484f0060c04319c5ef66c4f14bf8d8b60b71bd Author: Andy Nonaka Date: Wed Apr 22 14:43:39 2020 -0700 Changed the thing storing particle cell lists (in DSMCParticleContainer) from a multifab of intvects to a vector of intvects. made necessary changes to indexing. src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp commit d77c21a9d1dd14807782767a794bd33356e54b17 Author: Daniel Ladiges Date: Wed Apr 22 12:05:39 2020 -0700 Changed the thing storing particle cell lists (in FHDParticleContainer) from a multifab of intvects to a vector of intvects. made necessary changes to indexing. Note the samething will have to be done for DSMCParticleContainer. src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit d1e313394f144d3ab50f5f70b60522a8fae126eb Author: Andy Nonaka Date: Wed Apr 22 09:50:21 2020 -0400 disable structure factor and fft stuff exec/compressible/GNUmakefile exec/compressible/main_driver.cpp exec/immersedIons/GNUmakefile commit bcc45164f148a656b2434e56ac58c8b19222d5a1 Author: Andrew Nonaka Date: Wed Apr 22 09:49:19 2020 -0400 gpu fixes src_compressible/timeStep.cpp commit f87e3c3f334188e710e592a658b732ec22eff92c Merge: 8170604f 97ee3386 Author: Andy Nonaka Date: Wed Apr 22 06:34:05 2020 -0700 Merge pull request #9 from AMReX-FHD/renname_surfaces renname surface(s) -> paramPlane(s) commit 97ee3386d42e0b801676d853565873c5605b2958 Author: Andy Nonaka Date: Wed Apr 22 06:11:24 2020 -0700 renname surface(s)s -> paramPlane(s) comment out structure factor code in immersedIons trying to get this to build on corigpu and ascent exec/DSMC-LDT/GNUmakefile exec/DSMC-LDT/INS_functions.H exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/paramPlane.nb exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/precheck.F90 exec/DSMC-LDT/thermostat.F90 exec/DSMC/GNUmakefile exec/DSMC/main_driver.cpp exec/DSMC/paramPlane.nb exec/DSMC/precheck.F90 exec/DSMCstatcheck/GNUmakefile exec/DSMCstatcheck/main_driver.cpp exec/DSMCstatcheck/paramPlane.nb exec/DSMCstatcheck/precheck.F90 exec/brownian/GNUmakefile exec/brownian/Make_paramPlane.package exec/brownian/Make_surface.package exec/brownian/main_driver.cpp exec/brownian/precheck.F90 exec/brownian/surfaces.cpp exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp exec/immersedIons/precheck.F90 exec/tests/RFDanalysis/GNUmakefile exec/tests/RFDanalysis/main_driver.cpp exec/tests/RFDanalysis/precheck.F90 src_geometry/Make.package src_geometry/paramPlane.H src_geometry/paramPlane.cpp src_geometry/src_F90/Make.package src_geometry/src_F90/paramplane_functions.F90 src_geometry/src_F90/paramplane_type.F90 src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 src_surfaces/Make.package src_surfaces/src_F90/Make.package src_surfaces/surfaces.cpp commit 8170604fbd43212b3368bd2c5a391b2163838da3 Author: Andy Nonaka Date: Tue Apr 21 15:25:31 2020 -0700 gpu compiler error fixes src_common/MultiFabPhysBC.cpp commit a454c0b071b2d09326f7182e10d426ce2b05eb8d Author: Andy Nonaka Date: Tue Apr 21 10:39:38 2020 -0700 comparison to old code SF doesn't work for multiples grids right now exec/multispec/inputs_compare_equil_2d commit af9c0f9ffc2ef2d8c68379b19bea9d0e1d034349 Author: Andy Nonaka Date: Tue Apr 21 07:40:40 2020 -0700 a few bugfixes in Lonsager calc src_multispec/src_F90/mass_flux_utilities.F90 commit e7669e643edb775c7a3918985a937a0ed1536b7c Author: Andy Nonaka Date: Tue Apr 21 06:46:55 2020 -0700 add stoch mass flux internal boundary syncs src_multispec/StochMassFlux.cpp commit 31b2cd83193f24c9a8e1e7ceafa1ba247388be8d Merge: 1618fd52 a8128efd Author: Andy Nonaka Date: Tue Apr 21 06:07:29 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a8128efdbb75c76d8571a61cb938490e4af49558 Author: Oscar Antepara Date: Mon Apr 20 18:52:48 2020 -0700 Adding BC regression tests for compressible code exec/compressible/inputs_regression_noslip_reservoir_isothermal exec/compressible/inputs_regression_slip_wall_adiabatic commit 1618fd5216a7398ca99c45b497170690ad08b394 Author: Andy Nonaka Date: Mon Apr 20 15:24:56 2020 -0700 bug fix in number of components in stoch_mass_flux exec/multispec/main_driver.cpp commit 930a7f2ae70899d2056af91c9d92f79773be8bcb Author: Andy Nonaka Date: Mon Apr 20 11:37:30 2020 -0700 remove print statement src_multispec/MassFluxUtil.cpp commit 3f5e60353137b7d7d4feca335d02654bdededb13 Author: Andy Nonaka Date: Mon Apr 20 11:37:18 2020 -0700 attempt at equil fluct setup exec/multispec/inputs_compare_equil_2d src_multispec/MassFluxUtil.cpp commit ce3fcedfcc81e8dad44127e3a4961cb9930f7441 Author: Andy Nonaka Date: Mon Apr 20 11:37:08 2020 -0700 fortran interface bugfixes src_multispec/src_F90/mass_flux_utilities.F90 commit 062fddb162a9fb2308f931971548b3c6524952cb Author: Andy Nonaka Date: Mon Apr 20 11:30:13 2020 -0700 bugfix in weighted stoch mass flux calculation src_multispec/StochMassFlux.cpp commit cd302c2f0d18c31ba5bf139b4d9085d453b435dd Author: Andy Nonaka Date: Mon Apr 20 10:42:52 2020 -0700 no slip and slip walls check out exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d commit 9eb3ced3eee0e03afca12b9bf66071cbfb0cee57 Author: Andy Nonaka Date: Mon Apr 20 09:32:40 2020 -0700 bugfix in 3d matvec_mul src_multispec/src_F90/matvec_mul.F90 commit 5a0890186e04b9b921fc9809753800d6f5a53dfb Author: Andy Nonaka Date: Mon Apr 20 08:54:45 2020 -0700 testing inputs files for code comparison exec/multispec/inputs_compare_detbubble_2d exec/multispec/inputs_compare_detbubble_3d commit b28416d6ed08f5b638af5838d94f1bac19739f34 Author: Andy Nonaka Date: Fri Apr 17 13:31:40 2020 -0700 bugfix in setting bc's src_common/src_F90/common_namelist.F90 commit 6f3bac36d994076b5c377b8c17952e053659f66d Author: Andy Nonaka Date: Fri Apr 17 13:22:34 2020 -0700 another plotfile bug exec/multispec/WritePlotFile.cpp commit be674487ce1d46756a15ecbef3f45741c5e8a883 Author: Andy Nonaka Date: Fri Apr 17 13:11:12 2020 -0700 fix plotfile error exec/multispec/WritePlotFile.cpp commit 4cfbbd6187b53499106f8dc27d9925c816510e7b Author: Andy Nonaka Date: Fri Apr 17 13:06:41 2020 -0700 more plotfile variables exec/multispec/WritePlotFile.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit 38468f0153262f47564b8e4c918942181c5ee2ec Author: Andy Nonaka Date: Fri Apr 17 10:46:09 2020 -0700 first cut at inertial integrator complete exec/multispec/AdvanceTimestepInertial.cpp commit 68221909ab8b4afee642ae586a3258f3e8ddf5cc Author: Andy Nonaka Date: Fri Apr 17 07:09:16 2020 -0700 code cleanup exec/hydro/main_driver.cpp exec/multispec/main_driver.cpp src_hydro/AddMFluctuations.cpp src_hydro/ConvertMToUmac.cpp src_hydro/Make.package src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp src_hydro/hydro_functions.H src_multispec/Make.package src_multispec/MkDiffusiveMFluxdiv.cpp src_multispec/multispec_functions.H commit f8b2b1370c859a210710410bfcf8859ba3dce389 Author: Andy Nonaka Date: Fri Apr 17 06:27:13 2020 -0700 inertial integrator progress exec/multispec/AdvanceTimestepInertial.cpp commit 7bd59f275ac89a13ddfcf52fc39bc7f663bff305 Author: Andy Nonaka Date: Thu Apr 16 16:00:05 2020 -0700 implemented physical boundary-away ComputeGrad exec/channel/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/multispec/AdvanceTimestepInertial.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp src_gmres/MacProj.cpp src_multispec/DiffusiveMassFluxdiv.cpp commit fb46cd19c5bf0198ae72592a7ba792a0775bda62 Author: Andy Nonaka Date: Thu Apr 16 15:37:34 2020 -0700 more inertial integrator exec/multispec/AdvanceTimestepInertial.cpp commit ca79a89e4d7fffe0970e51d45f7e086909641b7a Author: Andy Nonaka Date: Thu Apr 16 15:37:14 2020 -0700 more inertial integrator exec/multispec/AdvanceTimestepInertial.cpp src_common/MultiFabPhysBC.cpp commit a092f26b1c20936f4837e88c5c8dd47795185115 Author: Andy Nonaka Date: Thu Apr 16 15:01:55 2020 -0700 add ZeroEdgevalPhysical routine exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_multispec/InitialProjection.cpp commit d406f433a461e73eec4569a196dff431f0c59a0f Author: Andy Nonaka Date: Thu Apr 16 13:35:27 2020 -0700 All instances of StochM are now StochMom to not be confused with StochMass exec/brownian/main_driver.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp commit 79208f74b859788d6d07913f9fce20fb436d9321 Author: Andy Nonaka Date: Thu Apr 16 11:41:42 2020 -0700 more inertial integrator work exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H src_multispec/multispec_functions.H commit d699983e922d14e57e105250fdfba7db6bd21f62 Author: Andy Nonaka Date: Wed Apr 15 15:14:50 2020 -0700 diffusive momentum fluxdiv routine exec/multispec/AdvanceTimestepInertial.cpp src_hydro/Make.package src_hydro/MkDiffusiveMFluxdiv.cpp src_hydro/hydro_functions.H commit 3faefcaa30e9c79501cb2ed33e9779ce29ee4610 Author: Andy Nonaka Date: Fri Apr 10 15:02:31 2020 -0700 more routines for FHD multispec integrator exec/multispec/AdvanceTimestepInertial.cpp src_hydro/ConvertMToUmac.cpp src_hydro/Make.package src_hydro/StochMomFlux.cpp src_hydro/hydro_functions.H commit ac4ece6ffc1c8fe218d6aad377d09c557a81d9a5 Author: Andy Nonaka Date: Fri Apr 10 15:01:59 2020 -0700 bugfix in MkAdvMFluxdiv src_hydro/MkAdvMFluxdiv.cpp commit 74505252be16e5c7c790ce9bba04211315fbfaa5 Author: Andy Nonaka Date: Fri Apr 10 14:15:02 2020 -0700 add #if (AMREX_SPACEDIM==3) for 3d only code src_common/ConvertStag.cpp commit e4b581ff15c662c6937d01c98c512a8727b695c2 Author: Andy Nonaka Date: Fri Apr 10 14:13:33 2020 -0700 gpu bc-aware AverageCCToFace routine src_common/ConvertStag.cpp commit 7c659e4ef338b603cfa238179513fc4c5e31e73a Author: Andy Nonaka Date: Fri Apr 10 13:57:21 2020 -0700 change interface to AverageCCToFace to support boundary conditions in the future exec/exercises/incompressible/advance.cpp exec/multispec/AdvanceTimestepInertial.cpp src_chem/AmrCoreAdv.cpp src_common/ConvertStag.cpp src_common/common_functions.H src_hydro/MacProj_hydro.cpp src_hydro/StochMomFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/InitialProjection.cpp commit 6bc1ce5d7a81fd3fae5cf391f18cf579947b5878 Author: Andy Nonaka Date: Thu Apr 9 11:11:40 2020 -0700 more general MkAdvSFluxdiv interface exec/channel/advance.cpp exec/exercises/incompressible/advance.cpp exec/hydro/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/multispec/AdvanceTimestepInertial.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/advance.cpp src_hydro/hydro_functions.H commit 405cf0a244e6f4bfc1a3b8c67895437705f567ed Author: Andy Nonaka Date: Thu Apr 9 10:58:28 2020 -0700 add version of MkAdvSFluxdiv that takes in face-centered s src_hydro/MkAdvSFluxdiv.cpp src_hydro/hydro_functions.H commit c38c71e61beaf9b411fc90c80e48974846d6965d Author: Andy Nonaka Date: Wed Apr 8 10:42:48 2020 -0700 tweak bubble problem exec/multispec/inputs_bubble_2d commit 9d6b746f34de661a9299ba44c60255a4b873077f Author: Andy Nonaka Date: Wed Apr 8 10:30:13 2020 -0700 finish initial projection routine src_multispec/InitialProjection.cpp commit f6520aab694399cd2789e74295a4cb3bf54d9650 Author: Andy Nonaka Date: Wed Apr 8 10:30:07 2020 -0700 remove Abort statements src_multispec/RhoUtil.cpp commit f1305603c33997fd9f8105d804d0a1a05bd65306 Author: Andy Nonaka Date: Wed Apr 8 09:09:47 2020 -0700 make distrinction between 2 different mac project routines in different source directories. one takes in umac, the other doesn't. in the latter you have to manually subtract grad(phi). the latter was built that way since it works better in the gmres framework need to combine these somehow exec/channel/main_driver.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_hydro/MacProj_hydro.cpp src_hydro/hydro_functions.H commit aff6372db7845cbc49c5fb4375caf31b021d1a59 Author: Andy Nonaka Date: Tue Apr 7 15:44:01 2020 -0700 prep for initial projection src_multispec/ComputeMassFluxdiv.cpp src_multispec/InitialProjection.cpp src_multispec/multispec_functions.H commit a4280829176c576fa511f9b250d8dbbad47b0657 Author: Andy Nonaka Date: Tue Apr 7 10:43:09 2020 -0700 ported compute_sqrtLonsager_fc into AMReX src_multispec/CorrectionFlux.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/compute_mixture_properties.F90 src_multispec/src_F90/mass_flux_utilities.F90 commit 5605b611ffe53eef0991ca0b82cab07f9fa94762 Author: Andy Nonaka Date: Tue Apr 7 09:09:10 2020 -0700 more amrex and gpu prep src_multispec/ComputeMixtureProperties.cpp src_multispec/CorrectionFlux.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions_F.H src_multispec/src_F90/compute_mixture_properties.F90 src_multispec/src_F90/correction_flux.F90 src_multispec/src_F90/mass_flux_utilities.F90 commit 610c9207e04b9258b2af65390536fdac73cab547 Author: Andy Nonaka Date: Tue Apr 7 08:56:03 2020 -0700 code cleanup - AMReX port and GPU prep src_multispec/ComputeMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/mass_flux_utilities.F90 commit c8ca65dd104900d7f2fe7e1e6abb476d9db27b72 Author: Andy Nonaka Date: Fri Apr 3 14:20:08 2020 -0700 more progress on diffusive mass flux routines - fixing up bugs, tidying up src_common/common_functions.H src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/DiffusiveMassFluxdiv.cpp commit 260b81a39e4550b85fca92067143084bf681771f Author: Andy Nonaka Date: Fri Apr 3 13:46:40 2020 -0700 ComputeMolconcMolmtot, ComputeGamma, ComputeRhoWChi now include ghost cells src_multispec/ComputeMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp commit 710d07b1e216cdc6f5d0420b809ef94a51b5b82d Author: Andy Nonaka Date: Fri Apr 3 13:36:11 2020 -0700 more code porting work exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/main_driver.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/InitialProjection.cpp src_multispec/multispec_functions.H commit 756b9997788ee64dbf891b2351e69a992ae2dadc Author: Andy Nonaka Date: Wed Apr 1 22:01:37 2020 -0700 cleanup; working on initial projection exec/exercises/incompressible/init_funcs.F90 exec/multispec/init_funcs.F90 src_multispec/InitialProjection.cpp src_multispec/Make.package src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 2619983cd4fd46955802d9591db253e43fb84289 Author: Andy Nonaka Date: Wed Apr 1 21:44:58 2020 -0700 clean up include statements src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/MatvecMul.cpp commit 7c3c26899404fb66fd743146d6fa7d5c0704de1b Author: Andy Nonaka Date: Wed Apr 1 16:14:07 2020 -0700 clean up interface for AverageCCToFace exec/exercises/incompressible/advance.cpp src_chem/AmrCoreAdv.cpp src_common/ConvertStag.cpp src_common/common_functions.H src_hydro/MacProj_hydro.cpp src_hydro/StochMomFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp commit f671cd605a5edd7746cf215cbde3c245bcd5b2ab Author: Andy Nonaka Date: Wed Apr 1 16:07:21 2020 -0700 advance timestep inertial setup exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/multispec_test_functions.H commit 162cfded8f5bb87e30f8233a178dc85ecb58b6db Author: Andy Nonaka Date: Wed Apr 1 15:41:01 2020 -0700 setting up inertial function exec/multispec/AdvanceTimestepInertial.cpp exec/multispec/Make.package exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit bda314844d57785bce055a8fa3e0239c3ac2d2f6 Author: Andy Nonaka Date: Wed Apr 1 14:45:47 2020 -0700 tidy up main_driver exec/multispec/main_driver.cpp commit 0361d12d3e93b964a3649a7d7ba1b5ab0794b030 Author: Andy Nonaka Date: Wed Apr 1 13:51:25 2020 -0700 write rho, r, rhotot ghost cell fill routines for low mach mixing model src_common/BCPhysToMath.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit ac48dfece9ffe122bd8473ecdb1575b2380f2284 Author: Andy Nonaka Date: Wed Apr 1 12:25:27 2020 -0700 generalize MultiFabPhysBC to multiple components exec/channel/advance.cpp exec/channel/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit 599bf05313e44a1f3a057616bdeceb2761f37d94 Author: Andy Nonaka Date: Wed Apr 1 11:57:40 2020 -0700 homogeneous Dirichlet BC's implemented for all scalar types src_common/MultiFabPhysBC.cpp commit 7d98467c32eb6c7bafbaea20fa057a12635662ad Author: Andy Nonaka Date: Wed Apr 1 11:37:10 2020 -0700 converted MultiFabPhysBCPres to the more flexible MultiFabPhysBC that will be used for pressure, densities, temperature, electrostatics (for the pure hydro-FHD code) supports only homogeneous Neumann conditions at the moment. exec/channel/advance.cpp exec/channel/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp commit 8a0d2b3c4c520e8a7ed42b9f2909ed07649d0536 Author: Andy Nonaka Date: Wed Apr 1 10:27:04 2020 -0700 boundary bugfix src_common/MultiFabPhysBC.cpp commit 52974c9ac57b5285dfbc7e89c95cf943747bc8fa Author: Andy Nonaka Date: Wed Apr 1 10:25:23 2020 -0700 bugfix in MultiFabPhysBCPres stencils and starting to morph this routine into the more flexible MultiFabPhysBC routine src_common/MultiFabPhysBC.cpp commit 332353c6827e10234fb363e40d22308c95f846c8 Author: Andy Nonaka Date: Wed Apr 1 10:13:45 2020 -0700 MultiFABPhysBC -> MultiFabPhysBC exec/channel/advance.cpp exec/channel/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/main_driver.cpp src_common/Make.package src_common/MultiFabPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_hydro/MacProj_hydro.cpp src_hydro/StochMomFlux.cpp src_hydro/advance.cpp src_particles/FhdParticleContainer.cpp commit 0421487cbece97e5a619c661550be6a70d01e119 Author: Andy Nonaka Date: Wed Apr 1 09:37:14 2020 -0700 added support for pressure to use MultiFABPhysBC via BCPhysToMath interface src_common/BCPhysToMath.cpp commit b43197bf918eee54b364ce3600db88ede6b7b674 Author: Andy Nonaka Date: Wed Apr 1 09:34:48 2020 -0700 more multispecies rho routines src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit 5bdb62bf0660767d7d126dda0d61f23e47a21a72 Author: Andy Nonaka Date: Wed Apr 1 07:46:34 2020 -0700 code cleanup exec/immersedIons/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_hydro/advance.cpp commit 643f506c0626d349bb31637dbfebe5672878f4e6 Author: Andy Nonaka Date: Tue Mar 31 16:23:29 2020 -0700 more Multispecies work exec/multispec/main_driver.cpp src_multispec/Make.package src_multispec/MassFluxUtil.cpp src_multispec/RhoUtil.cpp src_multispec/multispec_functions.H commit e269d4c33958090a60f021fdfad290619b2d5045 Author: Andy Nonaka Date: Tue Mar 31 09:36:27 2020 -0700 Wrote AverageCCToEdge for GPU and Host src_common/ConvertStag.cpp commit 7de9e0f53884a01d093cbf147a3220f19bda1848 Author: Andy Nonaka Date: Tue Mar 31 08:59:54 2020 -0700 some error checking make sure AverageCCToFace fills ghost faces started interface for AverageCCToEdge src_common/ConvertStag.cpp src_common/common_functions.H commit 518c9c90a83a8f5ef818882b131347000b6e45d9 Author: Andy Nonaka Date: Mon Mar 30 13:43:20 2020 -0700 wrote bc-aware AverageCCToNode on GPU src_common/ConvertStag.cpp src_common/common_functions.H commit ba85fb62cd9ec284e2e55f8f881f038cddde0c9f Author: Andy Nonaka Date: Mon Mar 30 08:44:54 2020 -0700 Helper routine "BCPhysToMath()" This is loosely analogous to what "define_bc_tower" used to do in pure fortran codes. It converts "physical" boundary descriptions to "mathematical" descriptions used to fill ghost cells in PhysBC routines src_common/BCPhysToMath.cpp src_common/Make.package src_common/common_functions.H commit edff80ef1185d09defb06dc0c644489994a4057a Author: Andy Nonaka Date: Mon Mar 30 08:44:05 2020 -0700 comment src_common/MultiFABPhysBC.cpp commit 821964319cba503c00453e070558c9eb00d246aa Author: Andy Nonaka Date: Mon Mar 30 07:22:55 2020 -0700 wrote ZeroEdgevalWalls (host and GPU versions) src_common/MultiFABPhysBC.cpp src_common/common_functions.H commit d4edf5118688d0edc513ef296be116bcdd883376 Author: Andy Nonaka Date: Fri Mar 27 12:55:33 2020 -0700 remove multifab_physbc_mod.F90 src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/multifab_physbc_mod.F90 commit 824bf5c4c06175f29ebe1c46426af2ea1fe75d37 Author: Andy Nonaka Date: Fri Mar 27 11:07:25 2020 -0700 port PhysBCMacStress to GPU src_common/MultiFABPhysBC.cpp src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 151ece533a6a651be55cf8c7cabc1c3c5a8b885d Author: Andy Nonaka Date: Fri Mar 27 11:03:53 2020 -0700 index bugfix src_common/src_F90/multifab_physbc_mod.F90 commit 60f95efdae93be5e9c90d0f80a5df73cd7c3bbc0 Author: Andy Nonaka Date: Fri Mar 27 08:20:17 2020 -0700 port MultiFABDomainStress to GPU src_common/MultiFABPhysBC.cpp src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 461a5baa5cb220ad6f9abac6dd47d2e784f84148 Author: Andy Nonaka Date: Fri Mar 27 07:34:03 2020 -0700 fix 3d slip wall domainstress implementation (inputs_regression_slip_dirichlet answer will change) src_common/src_F90/multifab_physbc_mod.F90 commit 4c95f6ae642ac77d24580ceeac1891a1a1ff2677 Author: Andy Nonaka Date: Thu Mar 26 16:11:30 2020 -0700 gpu port prep src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 20de92c790ef0dd3ac64b5d24d9aefa4a2a7a50f Author: Andy Nonaka Date: Thu Mar 26 11:49:24 2020 -0700 port MultiFABPhysBCCharge to GPU This was particularly tricky as the action is performed on interior cells, not ghost cells However for wall-wall cases you must fold ghost charges into the transverse ghost regions so the corner charges properly make it into the domain I'm about 99% sure this is the correct thing to do for 3D also removed f90 code for bc routines I've been porting over the last week src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 5557f75c44d530ed5aad98bd1cb85e99a7785b38 Author: Andy Nonaka Date: Wed Mar 25 14:58:16 2020 -0700 port MultiFABPhysBCPotential_solver to GPU src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 2f9f07c25e2f9b0f594f9b9a52adb13fe222d4ed Merge: 334e9806 1990463f Author: Andy Nonaka Date: Wed Mar 25 14:35:32 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 334e9806a1be84815a920dfeb549e03a60d9356d Author: Andy Nonaka Date: Wed Mar 25 14:34:19 2020 -0700 ported MultiFABPhysBCPotential to GPU src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 1990463fa19fe893f330b261836153924f7a51ef Author: Oscar Antepara Date: Wed Mar 25 14:33:09 2020 -0700 Inputs file that blows up exec/compressible/inputs_equil_3d_mem src_compressible/flux.cpp commit ae2e74a3d1c71ca146d692037892b6f4ee2f25a5 Author: Andy Nonaka Date: Tue Mar 24 09:22:43 2020 -0700 instructions for how to run hydro examples on corigpu exec/hydro/README.CONVERGENCE exec/hydro/README.CORIGPU commit b32a9e0c61e6802eff77701b5bc54b264eabc13a Author: Andy Nonaka Date: Tue Mar 24 08:19:53 2020 -0700 ported electricBC to GPU and fixed a bug where corner ghost cells weren't being filled correctly src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp commit 9256bd5830495853fc3f466a3c1065e871cf2851 Author: Andy Nonaka Date: Mon Mar 23 15:35:17 2020 -0700 GPU modernize MultiFABPhysBCPres src_common/Make.package src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp commit ccfd0e35bff9bc0b348604f035b90dc7c3c25644 Author: Andy Nonaka Date: Mon Mar 23 15:02:42 2020 -0700 clean up bc's to not use grown domain boxes anymore (consistent with other routines) src_common/MultiFABPhysBC.cpp commit b3943e17774af404c0903159a10f774aeea0fa91 Author: Andy Nonaka Date: Mon Mar 23 10:01:19 2020 -0700 ParallelFor implementation of MultiFABPhysBCMacVel src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp commit 1b24ddee6afb87c840c5f1b8131afdeba8df396b Author: Andy Nonaka Date: Mon Mar 23 09:27:02 2020 -0700 amrex::ParallelFor-ize PhysBCDomainVel src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp commit 035cc55b7b8b18ea8e05ccdeaca980de8aaf3eed Author: Andy Nonaka Date: Mon Mar 23 09:03:06 2020 -0700 convert kernels to ParallelFor-ready implementation src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp commit 2c23717c053a8b9d862b1a495eb858c8da777a4b Author: Andy Nonaka Date: Mon Mar 23 08:45:10 2020 -0700 regression tests with slip and no slip walls, dirichlet and neumann phi exec/immersedIons/inputs_regression_noslip_neumann exec/immersedIons/inputs_regression_slip_dirichlet commit a66621948fd7eed8d3bdeaab7fbae5dd2be96b7d Author: Andy Nonaka Date: Mon Mar 23 08:04:22 2020 -0700 more bc cleanup src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp commit 55954d4e7b5d65ebe28e6d76012b111d4bf5ed9b Author: Andy Nonaka Date: Mon Mar 23 06:41:38 2020 -0700 more bc gpu prep work src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp src_common/common_functions.H commit a5fdae01cd6ba20db80dda14f64cbbc14fb62603 Author: Andy Nonaka Date: Fri Mar 20 16:29:22 2020 -0700 PhysBCDomainVel cleanup src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp src_common/common_functions.H commit bb5eba5ef192aed4eb482f372336fceb0510e528 Merge: e15c8c48 af6b3597 Author: Andy Nonaka Date: Fri Mar 20 15:59:06 2020 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e15c8c48eb23d764354f8f71ec92803ed9950faf Author: Andy Nonaka Date: Fri Mar 20 15:58:21 2020 -0700 begin cleanup of PhysBC functions src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_gmres/ApplyMatrix.cpp commit af6b35975f5d3cfbb81cf4063977fd672dd19421 Author: Oscar Antepara Date: Fri Mar 20 15:56:59 2020 -0700 Adding write/read checkpoint files exec/compressible/inputs_equil_3d_mem exec/compressible/main_driver.cpp src_compressible/Make.package src_compressible/checkpoint.cpp src_compressible/compressible_functions.H commit 5ff12b10d135cf8eed4584d6e9b88db26dc1c11a Author: Oscar Antepara Date: Fri Mar 20 15:23:17 2020 -0700 Adding back correlations computation exec/compressible/GNUmakefile exec/compressible/inputs_equil_3d_mem exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_compressible/writePlotFile.cpp commit 9def04a81a4e5e5ed878460aa0968758f75c6673 Author: Andy Nonaka Date: Fri Mar 20 07:50:09 2020 -0700 cleaning up regression tests exec/compressible/inputs_regression_RT_3d exec/hydro/inputs_regression_equil_2d exec/hydro/inputs_regression_equil_3d exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d exec/structFactTest/inputs_regression_3d commit 786a8a62ff0d002d9a5747328b0a19791818ba14 Author: Andy Nonaka Date: Thu Mar 19 17:13:18 2020 -0700 regression testing - EO with *walls* exec/immersedIons/inputs_regression_eo commit 94167d77fe8d7dfa4e8ef404e87d835c7cc7e110 Author: Andy Nonaka Date: Thu Mar 19 16:25:51 2020 -0700 modernize gpu implementation where possible src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit 900f1a9829f755670fdbd9323c26639ceb90783a Author: Andy Nonaka Date: Thu Mar 19 07:18:59 2020 -0700 more GPU modernization src_gmres/StagApplyOp.cpp src_hydro/StochMomFlux.cpp commit 714db4491485b2225a50d0c725249c50a7c3ad79 Author: Andy Nonaka Date: Thu Mar 19 06:51:38 2020 -0700 modernize the GPU code exec/structFactTest/main_driver.cpp src_compressible/timeStep.cpp src_hydro/MacProj_hydro.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.cpp src_multispec/StochMassFlux.cpp src_rng/MultiFABFillRandom.cpp commit edb2416911f6957f6dac11c114b70e72cc77c3ad Author: Andy Nonaka Date: Wed Mar 18 16:48:49 2020 -0700 renname plotfiles exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d commit 32e5ad630fb47a178a9cc60c8e00691ee03e5ae5 Author: Andy Nonaka Date: Wed Mar 18 16:48:08 2020 -0700 new deterministic vortex spindown problems for testing slip and no slip walls exec/hydro/inputs_regression_vortex_2d exec/hydro/inputs_regression_vortex_3d commit 3e0ae3bbbbbfb37717b8f753441ad45d0aa94cf5 Author: Andy Nonaka Date: Wed Mar 18 16:31:49 2020 -0700 modernize GPU implementation - eliminate nasty lambda code src_common/ConvertStag.cpp src_common/SqrtMF.cpp commit 76d2c201037a95fbf59c9d35d787e3ae0c8cf504 Author: Andy Nonaka Date: Wed Mar 18 16:21:44 2020 -0700 modernize the GPU implementation of all functions in ComputeDivAndGrad.cpp - eliminated so much yucky lambda function code!!! src_common/ComputeDivAndGrad.cpp commit 0e6d223032a222476449284e66d5b193cf2dad52 Author: Andy Nonaka Date: Wed Mar 18 13:13:48 2020 -0700 minor exec/multispec/main_driver.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H commit b54894af164a038ef08eeb088b2da35c81c38775 Author: Andrew Myers Date: Tue Mar 17 14:39:49 2020 -0700 toggle test parameter exec/immersedIons/inputs_regression_cond commit 801bbf3066f45ad4f352921a589a78c6e129dd35 Author: Andrew Myers Date: Fri Mar 13 11:15:36 2020 -0700 changes to track with upstream modifications to amrex exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/flagellum/ib_md.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_particles/FhdParticleContainer.cpp commit b8dce2e64408f852340a4ceed537887a7e49318b Author: Andy Nonaka Date: Thu Mar 5 16:36:57 2020 -0800 main driver progress exec/multispec/main_driver.cpp commit 4ef00c7bdb0e9c95976f69915afe5d56b6e37bc3 Author: Andy Nonaka Date: Thu Mar 5 15:33:24 2020 -0800 more LM multispecies driver updates exec/multispec/main_driver.cpp commit 322c7d4ee8414c8d9c2a9859a4807724b20fcf34 Author: Andy Nonaka Date: Thu Mar 5 12:22:09 2020 -0800 clean up rng header files exec/DSMC-LDT/main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMCstatcheck/main_driver.cpp exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/main_driver.cpp exec/_GL_alt_1D/timeStep.cpp exec/brownian/main_driver.cpp exec/channel/main_driver.cpp exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp exec/exercises/incompressible/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/low_density/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_compressible/timeStep.cpp src_hydro/StochMomFlux.H src_immersed-boundary/IBMarkerContainerBaseI.H src_low-density/timeStep.cpp src_particles/DsmcParticleContainer.H src_particles/FhdParticleContainer.H src_rng/MultiFABFillRandom.cpp src_rng/rng_functions.H commit 5a374932e34dfd2e62208637d8f4285cf3a6bb25 Author: Andy Nonaka Date: Thu Mar 5 12:05:19 2020 -0800 tidy up compressible Headers exec/_GL_alt/main_driver.cpp exec/_GL_alt_1D/main_driver.cpp exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp exec/exercises/compressible/writePlotFile.cpp exec/low_density/main_driver.cpp src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/membrane.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp src_compressible/writePlotFile.cpp src_low-density/boundary.cpp src_low-density/flux.cpp src_low-density/stats.cpp src_low-density/timeStep.cpp commit 7768a97529f80c89552404dfd6d2cf420f5d82eb Author: Andy Nonaka Date: Thu Mar 5 12:00:23 2020 -0800 move #include "multispec_namespace.H" and "multispec_functions_F.H" and using namespace multispec to multispec_functions.H exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/MatvecMul.cpp src_multispec/StochMassFlux.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp commit 17312d79e14d3084abbd54aeafa35bd9f65a5458 Author: Andy Nonaka Date: Thu Mar 5 11:52:18 2020 -0800 move #include "hydro_functions_F.H" into hydro_functions.H exec/_GL_alt/main_driver.cpp exec/_GL_alt_1D/main_driver.cpp exec/brownian/advance.cpp exec/brownian/main_driver.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_hydro/HydroBCs.cpp src_hydro/MacProj_hydro.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.cpp src_hydro/advance.cpp src_hydro/hydro_functions.H commit 0aaee0a9bfaab9e734569693a7a7d34a369551cd Author: Andy Nonaka Date: Thu Mar 5 11:49:54 2020 -0800 move "use common namespace" and #include "common_namespace.H" into common_functions.H exec/DSMC-LDT/main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/WritePlotFile.cpp exec/DiffuisonTest/main_driver.cpp exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/main_driver.cpp exec/_GL_alt_1D/timeStep.cpp exec/brownian/WritePlotFileHydro.cpp exec/brownian/advance.cpp exec/brownian/main_driver.cpp exec/channel/WritePlotFile.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp exec/exercises/compressible/writePlotFile.cpp exec/exercises/incompressible/WritePlotFile.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/Checkpoint.cpp exec/hydro/WritePlotFile.cpp exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/WritePlotFile.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/low_density/main_driver.cpp exec/low_density/writePlotFile.cpp exec/multispec/WritePlotFile.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/WritePlotFile.cpp exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp exec/structFactTest/main_driver.cpp exec/tests/RFDanalysis/WritePlotFileHydro.cpp exec/tests/RFDanalysis/main_driver.cpp exec/tests/RFDanalysis/particleGen.cpp src_analysis/StructFact.H src_common/ComputeAverages.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/common_namespace.H src_compressible/flux.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/writePlotFile.cpp src_electrostatic/electrostatic.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_hydro/MacProj_hydro.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMomFlux.H src_hydro/advance.cpp src_immersed-boundary/IBCore.H src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_low-density/flux.cpp src_low-density/stats.cpp src_low-density/timeStep.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/MatvecMul.cpp src_multispec/StochMassFlux.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_rng/MultiFABFillRandom.cpp src_surfaces/surfaces.cpp commit e95e8931181007178e080986828a3ab56efcc7df Author: Andy Nonaka Date: Thu Mar 5 11:39:41 2020 -0800 more #include "common_functions_F.H" to common_functions.H exec/DSMC-LDT/TimeStep.cpp exec/DSMC-LDT/main_driver.cpp exec/DSMC/TimeStep.cpp exec/DSMC/main_driver.cpp exec/DSMCstatcheck/TimeStep.cpp exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/main_driver.cpp exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/main_driver.cpp exec/_GL_alt_1D/timeStep.cpp exec/brownian/TimeStep.cpp exec/brownian/advance.cpp exec/brownian/main_driver.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp exec/compressible/main_driver.cpp exec/exercises/compressible/main_driver.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/low_density/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp exec/structFactTest/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_common/ComputeAverages.cpp src_common/ComputeBasicStats.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/Debug.cpp src_common/FindCoords.cpp src_common/FindNodalValues.cpp src_common/MultiFABPhysBC.cpp src_common/SqrtMF.cpp src_common/common_functions.H src_common/common_functions.cpp src_compressible/timeStep.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/StagApplyOp.cpp src_hydro/MacProj_hydro.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/advance.cpp src_immersed-boundary/IBGMRES.cpp src_low-density/timeStep.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/MatvecMul.cpp src_rng/MultiFABFillRandom.cpp commit a5ed1a3401d422cb3a4f60c84fffe21334fbc2ab Author: Andy Nonaka Date: Thu Mar 5 09:52:45 2020 -0800 move #include gmres_namespace.H and "using namespace gmres" to only appear in gmres_functions.H exec/DSMC-LDT/main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/main_driver.cpp exec/brownian/advance.cpp exec/brownian/main_driver.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/NormInnerProduct.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions.cpp src_hydro/MacProj_hydro.cpp src_hydro/advance.cpp src_immersed-boundary/IBGMRES.cpp commit ceea77aaeba8d2095f79f2a32ec6d88d908ef67f Author: Andy Nonaka Date: Thu Mar 5 09:41:40 2020 -0800 code cleanup - move #include "gmres_function_F.H" into gmres_functions.H so we don't have to keep including the former in every file more to come exec/DSMC-LDT/main_driver.cpp exec/DSMC/main_driver.cpp exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/main_driver.cpp exec/brownian/advance.cpp exec/brownian/main_driver.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/advance_timestep_inertial.cpp exec/multispec/main_driver.cpp exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/NormInnerProduct.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions.cpp src_hydro/advance.cpp src_immersed-boundary/IBGMRES.cpp commit 3d70f41ff153debc3500f6898959419ad27fa193 Merge: be4e331c cd03f8b0 Author: Andy Nonaka Date: Wed Mar 4 17:55:05 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit be4e331cda1d2cc3bd26ccca9fdf68260b1beab1 Author: Andy Nonaka Date: Wed Mar 4 17:54:48 2020 -0800 writing the low mach multispecies driver exec/multispec/Make.package exec/multispec/advance_timestep_inertial.cpp exec/multispec/init_funcs.F90 exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H exec/multispec/multispec_test_functions_F.H commit cd03f8b0f405b26ee2101bae023949af0316c8ce Merge: 941a997e 8175418a Author: Daniel Ladiges Date: Wed Mar 4 16:11:14 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 941a997e5a7a129ff61c7f7b415700d8b7569d7a Author: Daniel Ladiges Date: Wed Mar 4 16:10:11 2020 -0800 Various fixes for cases where extrememly large forces result from particles being in bad initial state. exec/immersedIons/inputs_3d exec/tests/boundarySpreading/Data.ipynb exec/tests/boundarySpreading/GNUmakefile exec/tests/boundarySpreading/INS_functions.H exec/tests/boundarySpreading/Make.package exec/tests/boundarySpreading/Make_precheck.package exec/tests/boundarySpreading/README exec/tests/boundarySpreading/WritePlotFile.cpp exec/tests/boundarySpreading/WritePlotFileHydro.cpp exec/tests/boundarySpreading/amrex_to_vtp.py exec/tests/boundarySpreading/convertSeries exec/tests/boundarySpreading/delPlots exec/tests/boundarySpreading/inputs_3d_dirichlet_noslip exec/tests/boundarySpreading/inputs_3d_dirichlet_slip exec/tests/boundarySpreading/main_driver.cpp exec/tests/boundarySpreading/particleGen.cpp exec/tests/boundarySpreading/precheck.F90 exec/tests/boundarySpreading/write_pview_file.py exec/tests/boundarySpreading/write_pview_file.pyc exec/tests/electroPeriodic/Data.ipynb exec/tests/electroPeriodic/GNUmakefile exec/tests/electroPeriodic/INS_functions.H exec/tests/electroPeriodic/Make.package exec/tests/electroPeriodic/Make_precheck.package exec/tests/electroPeriodic/README exec/tests/electroPeriodic/WritePlotFile.cpp exec/tests/electroPeriodic/WritePlotFileHydro.cpp exec/tests/electroPeriodic/amrex_to_vtp.py exec/tests/electroPeriodic/analysis.nb exec/tests/electroPeriodic/convertSeries exec/tests/electroPeriodic/delPlots exec/tests/electroPeriodic/inputs_3d exec/tests/electroPeriodic/main_driver.cpp exec/tests/electroPeriodic/particleGen.cpp exec/tests/electroPeriodic/precheck.F90 exec/tests/electroPeriodic/write_pview_file.py exec/tests/electroPeriodic/write_pview_file.pyc exec/tests/electroTwoWall/Data.ipynb exec/tests/electroTwoWall/GNUmakefile exec/tests/electroTwoWall/INS_functions.H exec/tests/electroTwoWall/Make.package exec/tests/electroTwoWall/Make_precheck.package exec/tests/electroTwoWall/README exec/tests/electroTwoWall/WritePlotFile.cpp exec/tests/electroTwoWall/WritePlotFileHydro.cpp exec/tests/electroTwoWall/amrex_to_vtp.py exec/tests/electroTwoWall/analysis.nb exec/tests/electroTwoWall/convertSeries exec/tests/electroTwoWall/delPlots exec/tests/electroTwoWall/inputs_3d exec/tests/electroTwoWall/main_driver.cpp exec/tests/electroTwoWall/particleGen.cpp exec/tests/electroTwoWall/precheck.F90 exec/tests/electroTwoWall/write_pview_file.py exec/tests/electroTwoWall/write_pview_file.pyc src_particles/src_F90/particle_functions.F90 src_surfaces/surfaces.cpp commit 8175418aef4875bdaaf7a5f60430a43e3c2ebc9d Author: Andy Nonaka Date: Wed Mar 4 16:05:07 2020 -0800 dusting off multispecies - setting up bubble problem again much work to do exec/multispec/Make.package exec/multispec/WritePlotFile.cpp exec/multispec/advance.cpp exec/multispec/init_funcs.F90 exec/multispec/init_s_funcs.F90 exec/multispec/inputs_bubble_2d exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit a2620cf211dffa6126cade9e47695503e76c6f58 Author: Daniel Ladiges Date: Tue Feb 25 18:31:33 2020 -0800 Fix to calculation of diffusion coefficients when all_dry=1 exec/immersedIons/main_driver.cpp commit 109c350fe555d9c76b006de1cacbacc745a8ee4c Merge: 048e0647 b78fd28c Author: Daniel Ladiges Date: Tue Feb 25 17:50:22 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 048e06479625b4fd88f48e8d3b0224a603d9fef0 Author: Daniel Ladiges Date: Tue Feb 25 17:49:54 2020 -0800 thin channel mobility func src_particles/src_F90/particle_functions.F90 commit b78fd28cccd3c07a7895415ca8e6218c6b23363f Author: Oscar Antepara Date: Tue Feb 25 16:46:40 2020 -0800 setting zero flux at the membrane in the stochBC exec/compressible/inputs_equil_3d_mem src_compressible/flux.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp commit 13129481e579a73f48972451631841407dda980f Author: Andy Nonaka Date: Wed Feb 12 18:02:01 2020 -0800 first cut at complete stochastic mass flux class it compiles but is not tested yet because other functions that provide inputs to the routines need to be written src_multispec/StochMassFlux.H src_multispec/StochMassFlux.cpp commit 9dde63b41955e3999716521f7dfe70c98ab98bd2 Author: Andy Nonaka Date: Wed Feb 12 17:41:59 2020 -0800 simplify some code src_hydro/StochMomFlux.cpp commit c21f589397b128e22e1a55c46809b8cb67327eba Author: Andy Nonaka Date: Wed Feb 12 16:29:51 2020 -0800 implemented stochastic mass flux boundary conditions src_multispec/StochMassFlux.H src_multispec/StochMassFlux.cpp commit bc38bdfee4b5d4c05b3ca3c75b2b777ca0077a97 Author: Andy Nonaka Date: Wed Feb 12 16:29:35 2020 -0800 turned on error checking, fixed timers src_hydro/StochMomFlux.cpp commit c178d13567286d8f3b01415b57143ac6a0c2f144 Author: Andy Nonaka Date: Wed Feb 12 16:01:35 2020 -0800 fix erroneous comments src_hydro/StochMomFlux.cpp commit a08febf37f55e39e9d86eaab98b78057caf9a445 Author: Andy Nonaka Date: Wed Feb 12 15:33:12 2020 -0800 starting setup for stochastic mass flux class src_multispec/Make.package src_multispec/StochMassFlux.H src_multispec/StochMassFlux.cpp commit 7ab8359dff6e4c72bcfc4456d836ac2f79483d69 Author: Andy Nonaka Date: Wed Feb 12 15:10:12 2020 -0800 comments and code tidying only src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp commit ac6ba41aa2b61751807b82b4431a3dd4f98f0f4c Author: Andy Nonaka Date: Wed Feb 12 12:11:24 2020 -0800 changed all instances of "StochMFlux" with "StochMomFlux" this is prep for the new "StochMassFlux" class exec/_GL_alt/main_driver.cpp exec/_GL_alt_1D/main_driver.cpp exec/brownian/main_driver.cpp exec/channel/main_driver.cpp exec/exercises/incompressible/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp exec/tests/RFDanalysis/main_driver.cpp exec/tests/boundarySpreading/main_driver.cpp exec/tests/electroPeriodic/main_driver.cpp exec/tests/electroTwoWall/main_driver.cpp src_hydro/Make.package src_hydro/StochMomFlux.H src_hydro/StochMomFlux.cpp commit f8058684b8a743bade0a5d31bafe136016127dd7 Author: Daniel Ladiges Date: Wed Feb 12 10:16:04 2020 -0800 changed crange default src_common/src_F90/common_namelist.F90 commit 515f369662b8c055a701659f91746941e24e58d9 Author: Daniel Ladiges Date: Wed Feb 12 10:10:11 2020 -0800 Added some default values to namelist src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit e78635a61aca9a64402dc97c37e54ea866fd7e39 Author: Daniel Ladiges Date: Mon Feb 10 14:03:38 2020 -0800 Bug fix on rfd magnitude src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit 478677ea0fae3f0c52e2839743fbb60318acd05d Author: Daniel Ladiges Date: Mon Feb 10 12:06:54 2020 -0800 variance_coef_mom now modifes rdf magnitude, as well as wet and dry fluctuations. src_particles/src_F90/particle_functions.F90 commit 932f7f119fbbac0a84c0fee0ce7c736f6e6b38be Merge: c9847971 75638d7d Author: Daniel Ladiges Date: Mon Feb 10 10:44:48 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c9847971e0e1c02ef73beb2cd9b7a8de19d19125 Author: Daniel Ladiges Date: Mon Feb 10 10:44:19 2020 -0800 Added input option for RFD delta src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit 75638d7dfa7a0e68a8d489243966aacd60228ea9 Author: Oscar Antepara Date: Fri Feb 7 15:45:01 2020 -0800 Pushing membrane functions into src_compressible exec/compressible/GNUmakefile exec/compressible/inputs_equil_3d_mem src_compressible/flux.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/timeStep.cpp commit 1241a9f79b3b4125b212cbf95328edfc95afef48 Merge: 6761729f 19df0d7d Author: Daniel Ladiges Date: Thu Feb 6 12:45:14 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6761729f99b357e4b414a540ccb4b7ebe29f7ebe Author: Daniel Ladiges Date: Thu Feb 6 12:44:47 2020 -0800 Changed pushUp to pushUpAdd src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 19df0d7d201ca5c754b844a03012ba7eab364ecd Author: Andy Nonaka Date: Thu Feb 6 12:05:42 2020 -0800 change max_grid_size back to haswell config exec/immersedIons/inputs_paper_eo commit 0431920827694d52678d0aa72bab5ce86f15bd17 Merge: 860bf7ea 6777c2b5 Author: Daniel Ladiges Date: Thu Feb 6 12:03:37 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 860bf7ea43cd94eb71a510a0b58708e1bc7784cc Author: Daniel Ladiges Date: Thu Feb 6 12:03:18 2020 -0800 Fixed particle gen bug exec/immersedIons/Make.package exec/immersedIons/inputs_3d exec/immersedIons/inputs_paper_eo exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/src_F90/particle_functions.F90 commit 6777c2b56d00ec1390f57a29f442761b20ebd8fe Author: Andy Nonaka Date: Thu Feb 6 07:53:23 2020 -0800 fix compilation on NERSC exec/immersedIons/GNUmakefile exec/structFactTest/GNUmakefile commit 800ed7d2ff0c329a379c8c09cc55e805ff0918fd Author: Daniel Ladiges Date: Wed Feb 5 19:05:36 2020 -0800 another mobility mod! exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit b75ccbd7ea30cb57491af7981dcf024f7f102a43 Author: Daniel Ladiges Date: Wed Feb 5 17:20:24 2020 -0800 Some changes to move Donev specific code into a seperate repo. exec/fluctuatingMembrane/DEBUG.F90 exec/fluctuatingMembrane/Data.ipynb exec/fluctuatingMembrane/GNUmakefile exec/fluctuatingMembrane/INS_functions.H exec/fluctuatingMembrane/Make.package exec/fluctuatingMembrane/Make_debug.package exec/fluctuatingMembrane/Make_precheck.package exec/fluctuatingMembrane/TimeStep.cpp exec/fluctuatingMembrane/WritePlotFile.cpp exec/fluctuatingMembrane/WritePlotFileHydro.cpp exec/fluctuatingMembrane/advance.cpp exec/fluctuatingMembrane/amrex_to_vtp.py exec/fluctuatingMembrane/convertSeries exec/fluctuatingMembrane/debug_functions_F.H exec/fluctuatingMembrane/delPlots exec/fluctuatingMembrane/hydro_test_functions.H exec/fluctuatingMembrane/hydro_test_functions_F.H exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane.dat exec/fluctuatingMembrane/membrane_forces.F90 exec/fluctuatingMembrane/particleGen.cpp exec/fluctuatingMembrane/precheck.F90 exec/fluctuatingMembrane/write_pview_file.py exec/fluctuatingMembrane/write_pview_file.pyc exec/immersedIons/channel_mobility.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 5c783236dd97ff97e21ea24a3e510c83ad37fc45 Author: Daniel Ladiges Date: Wed Jan 29 16:52:40 2020 -0800 Updates to efield calculation and mobility calculation near boundaries. Difference to slit channel flow appears to be fairly small. exec/immersedIons/main_driver.cpp exec/tests/electroTwoWall/inputs_3d src_common/ComputeBasicStats.cpp src_electrostatic/electrostatic.cpp src_particles/src_F90/particle_functions.F90 commit 5ac76535cc4680eb7eedd1fe1d5085c98823f487 Author: Daniel Ladiges Date: Mon Jan 27 15:48:54 2020 -0800 Fixed time calculation in membrane forces. exec/fluctuatingMembrane/membrane_forces.F90 commit 55769306b07e68a7ee8e5f185669f21c83c12320 Author: Daniel Ladiges Date: Mon Jan 27 13:12:16 2020 -0800 updated inputs file again exec/fluctuatingMembrane/inputs_3d commit 64a5cb0ad33fd26cbee83366826bc0a5809b4217 Merge: 469a728f 9078e4f0 Author: Daniel Ladiges Date: Mon Jan 27 13:05:29 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 469a728faa48af89d7b80a0772dc3e5fa5d8f041 Author: Daniel Ladiges Date: Mon Jan 27 13:04:57 2020 -0800 Added some fields to input file for fluctMembrane exec/fluctuatingMembrane/inputs_3d commit 9078e4f00fcb899048c66924311169408f0dbfb7 Author: Aleks Donev Date: Mon Jan 27 15:34:36 2020 -0500 Added missing backslash in Makefile exec/fluctuatingMembrane/GNUmakefile commit 81e40c1defc712c9bf415fc720a5aa2fda653b29 Author: Johannes Blaschke Date: Sun Jan 26 22:22:19 2020 -0800 fix broken header gards src_hydro/StochMFlux.H src_hydro/hydro_functions.H commit 7ad31d9f5f5eb91e8a0f7318b39a20b997e21d84 Author: Daniel Ladiges Date: Wed Jan 22 15:09:35 2020 -0800 Fixed typo in last. Commented out section in immersedions makefile which was written to compile on nersc. exec/immersedIons/GNUmakefile src_common/ComputeBasicStats.cpp src_common/common_functions.H commit 6e3c686ad2dde6af0d3ade6b89f1146ac5f04c8d Merge: 0737007e ae6686a8 Author: Daniel Ladiges Date: Wed Jan 22 14:55:58 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0737007e551887a27a416a9bfbfd68f6a612705b Author: Daniel Ladiges Date: Wed Jan 22 14:54:35 2020 -0800 Added OutputVolumeMean(...) function which outputs the total volume density at each step of a specified multifab to a specified file. exec/immersedIons/Electrolyte_Data.xlsx exec/immersedIons/channel_mobility.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_common/ComputeBasicStats.cpp src_common/common_functions.H src_common/src_F90/compute_averages.F90 src_particles/src_F90/particle_functions.F90 commit ae6686a830accc9b3282a68ac687a85d898a2c9b Author: Oscar Antepara Date: Tue Jan 21 10:51:32 2020 -0800 Converting spread_markers and spread_kernel from fortran to cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit dabd5cfda874ece3b20edb9ef4c93530780f5265 Merge: db90d6fa 23511c8d Author: Johannes Blaschke Date: Thu Jan 16 11:16:12 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit db90d6fa44f51328cc8faa6fce106791de5cd4ed Author: Johannes Blaschke Date: Thu Jan 16 11:15:47 2020 -0800 use compiler wrapper on NERSC, maybe check with Weiqun about a better way to do this exec/immersedIons/GNUmakefile commit 23511c8d26529d7cb5a3d9ea42306198548f0fc7 Author: Andy Nonaka Date: Thu Jan 16 07:44:19 2020 -0800 remove -lfftw3_omp from GNUmakefile exec/_GL_alt/GNUmakefile exec/_GL_alt_1D/GNUmakefile exec/brownian/GNUmakefile exec/channel/GNUmakefile exec/compressible/GNUmakefile exec/exercises/compressible/GNUmakefile exec/exercises/incompressible/GNUmakefile exec/fluctuatingMembrane/GNUmakefile exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/flagellum/GNUmakefile exec/low_density/GNUmakefile exec/multispec/GNUmakefile exec/overdamped/GNUmakefile exec/structFactTest/GNUmakefile exec/tests/RFDanalysis/GNUmakefile exec/tests/boundarySpreading/GNUmakefile exec/tests/electroPeriodic/GNUmakefile exec/tests/electroTwoWall/GNUmakefile commit a455c01455256529e426f1163c2b58aec66e07ae Merge: 4d0ea511 848be844 Author: Daniel Ladiges Date: Wed Jan 15 15:21:45 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4d0ea511b3d3fd95f4917158865ed5b07e01bab6 Author: Daniel Ladiges Date: Wed Jan 15 15:20:59 2020 -0800 Added mobility functions for channel. Note this is for the specific channel being used in EO tests. exec/immersedIons/channel_mobility.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/p3mcalc.nb exec/immersedIons/plots.nb exec/immersedIons/poissonTest.nb exec/immersedIons/stokesPlots.nb exec/immersedIons/varAnalysis.nb exec/immersedIons/velAnalysis.nb src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 848be844a89134da2f8f0f30276a35ec24d96aa1 Author: Andy Nonaka Date: Tue Jan 14 17:42:10 2020 -0800 remove time_step_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 commit 17b1b9313477692e39231e36a552d174d9e07a94 Author: Andy Nonaka Date: Tue Jan 14 17:30:19 2020 -0800 put timeStep.cpp on GPU; fixed bug in energy evolution in RK3. Was doing rho^2 u g instead of rho u g src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit b67fcba627d2ed15fb50439de0ed4a00cef3c26b Merge: e88a509b bfd611f7 Author: Daniel Ladiges Date: Mon Jan 13 17:28:21 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e88a509b0e9663a9492c564adf5aa9795fcaf8e3 Author: Daniel Ladiges Date: Mon Jan 13 17:27:53 2020 -0800 Some changes to dry mobility calc with walls, still working on this. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit bfd611f7bc7125fe86554c2b901eef25dad443ef Author: Andy Nonaka Date: Mon Jan 13 17:03:49 2020 -0800 updated EO problem exec/immersedIons/inputs_paper_eo commit e26104ce4b7c5fa4e0cdf26b6bd1c2c74ce56eb3 Merge: ae2f72cc 02158dba Author: Daniel Ladiges Date: Mon Jan 13 16:13:13 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ae2f72ccb5e22989c134d248d1dc7a85be842f89 Author: Daniel Ladiges Date: Mon Jan 13 16:12:52 2020 -0800 Testing git channel on new slack exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/tests/electroTwoWall/analysis.nb src_particles/FhdParticleContainer.cpp commit 02158dba4e8a68b04bab3124cfc07e1f0d43ca10 Author: Andy Nonaka Date: Mon Jan 13 11:04:07 2020 -0800 the actual runs for conductivity - tests 7 through 12 exec/immersedIons/inputs_paper_cond10 exec/immersedIons/inputs_paper_cond11 exec/immersedIons/inputs_paper_cond12 exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 commit eba03aa02a69cc7436c3b6c51a4482334f198887 Merge: e8343eb3 ccf5bff3 Author: Daniel Ladiges Date: Fri Jan 10 17:47:10 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e8343eb352975d0ae67104ad13842bf41a84a2a0 Author: Daniel Ladiges Date: Fri Jan 10 17:46:37 2020 -0800 Added direct calculation of dry mobility rather than using grid. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d exec/immersedIons/inputs_paper_eo exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit ccf5bff3d78f04de5ea26e91fefb00137935335b Author: Oscar Antepara Date: Fri Jan 10 13:09:02 2020 -0800 Fix compiling bug src_common/src_F90/multifab_physbc_mod.F90 commit bb416176f223c1f22e184553574da31f464ce591 Author: Daniel Ladiges Date: Thu Jan 9 14:58:22 2020 -0800 Fixed particle restart bug. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/tests/electroTwoWall/inputs_3d src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 460169e19921d429fba07858d949991dbe9e6750 Author: Daniel Ladiges Date: Thu Jan 9 13:31:06 2020 -0800 Fixed particle id reset for when boxes != mpi ranks. exec/immersedIons/inputs_3d exec/immersedIons/particleGen.cpp exec/tests/electroTwoWall/inputs_3d exec/tests/electroTwoWall/main_driver.cpp exec/tests/electroTwoWall/particleGen.cpp commit cdf83d41f209b074b1b72c318a8a508fd8b4eb08 Author: Daniel Ladiges Date: Wed Jan 8 18:35:27 2020 -0800 Setup some testing for individual grid refinement. exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/tests/boundarySpreading/GNUmakefile exec/tests/boundarySpreading/WritePlotFileHydro.cpp exec/tests/boundarySpreading/main_driver.cpp exec/tests/electroTwoWall/GNUmakefile exec/tests/electroTwoWall/INS_functions.H exec/tests/electroTwoWall/Make.package exec/tests/electroTwoWall/WritePlotFile.cpp exec/tests/electroTwoWall/WritePlotFileHydro.cpp exec/tests/electroTwoWall/inputs_3d exec/tests/electroTwoWall/main_driver.cpp exec/tests/electroTwoWall/particleGen.cpp commit e668bb70273b17284a3a799f6d1d626c68098c91 Author: Daniel Ladiges Date: Wed Jan 8 15:00:42 2020 -0800 Particle restart now works with refined/coarsened grid exec/immersedIons/Checkpoint.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_immersed-boundary/IBMarkerContainerBaseI.H commit 0410286ba7ff72b84ef9008d6bd8ddf9b35beb49 Author: Daniel Ladiges Date: Tue Jan 7 18:38:55 2020 -0800 Particle restart on refined/coarsened grid implemented but not tested. exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H commit a44a73416d2be051ea8f075a7cd1f387bb1444ae Author: Daniel Ladiges Date: Tue Jan 7 16:25:16 2020 -0800 Working on particle restart from different grid. exec/immersedIons/Checkpoint.cpp exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.cpp commit 319b1232fc4bd9ca34ced2ede250eb1c808a6dbe Merge: 99dd43d6 f5ca56f4 Author: Daniel Ladiges Date: Mon Jan 6 18:08:52 2020 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f5ca56f4c2d5f5d500d80e4575d4492bdea8ca0c Author: jbb Date: Mon Jan 6 14:24:13 2020 -0800 removed fboxlib exec/compressible/GNUmakefile commit 343432ad731b4555875e2b1d28a744c00cf8a0f1 Author: Andy Nonaka Date: Fri Dec 20 09:56:19 2019 -0800 add checkpointing (verified it works bitwise perfectly on my workstation) exec/immersedIons/inputs_paper_eo commit 0c6b349d80fbb272e8bb34237dd7b7febf86ae3e Author: Andy Nonaka Date: Fri Dec 20 09:53:11 2019 -0800 fix plotfile logic for negative n_steps_skip... need to write when (istep+1)%plot_int==0 so the average stats aren't reset exec/immersedIons/main_driver.cpp commit 17df1d980c00f31915d8d88c673b238f1d8ccc5d Author: Andy Nonaka Date: Fri Dec 20 09:23:04 2019 -0800 write out particles to cplt files don't write out pplt files (these are checkpoints already contained within chk files) exec/immersedIons/WritePlotFile.cpp commit 6be1010ce27efed5dc454009709308d849ccd749 Author: Andy Nonaka Date: Thu Dec 19 16:58:24 2019 -0800 added mean and variance of charge and potential to plotfile (and also made sure checkpoint works for them) exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/main_driver.cpp commit 1a94ef935d9eb71b49138de4632a22c1fedb833e Author: Andy Nonaka Date: Thu Dec 19 08:03:14 2019 -0800 implement inhomogeneous Neumann bc's for filling electric potential AFTER the solver src_common/MultiFABPhysBC.cpp src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 3dc63190d365181df9be3c85cc0acdd920148692 Author: Andy Nonaka Date: Tue Dec 17 18:41:06 2019 -0800 comments exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_poisson exec/immersedIons/inputs_3d_reflect exec/immersedIons/inputs_paper_cond10 exec/immersedIons/inputs_paper_cond4 exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_cond6 exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 exec/immersedIons/inputs_paper_eo exec/immersedIons/inputs_regression_cond src_common/common_namespace.H commit 95534649bd76987025c5a09c4d2d41e4e8e331b0 Author: Andy Nonaka Date: Tue Dec 17 18:35:14 2019 -0800 protect against using inhomogeneous Neumann until multifabPotentialBC is fixed src_common/src_F90/multifab_physbc_mod.F90 commit 41a15e16ce4bd98b2f1179dd49628efdf63defba Author: Andy Nonaka Date: Tue Dec 17 18:35:05 2019 -0800 EO with inhomogeneous Neumann - needs more testing exec/immersedIons/inputs_paper_eo commit 1f290087fa761610875ca99cdbd8a79d85accac0 Author: Andy Nonaka Date: Tue Dec 17 18:22:27 2019 -0800 finish implementing inhomogeneous bc; Dirichlet and Neumann; for Poisson solve src_electrostatic/electrostatic.cpp commit 68ca9d3026ebd60ec36f7b12b681c7c65ee85f01 Author: Andy Nonaka Date: Tue Dec 17 17:47:40 2019 -0800 called wrong ghost cell filling routine src_common/MultiFABPhysBC.cpp commit 8612e282c025d51e05543bcd798d98498bdc24da Author: Andy Nonaka Date: Tue Dec 17 17:45:39 2019 -0800 support for electrostatic solver inhomogeneous Dirichlet and inhomogeneous Neumann - WIP src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit 26ed681554e59e155e1d4070eff10ea5e2d411a1 Author: Andy Nonaka Date: Tue Dec 17 13:21:28 2019 -0800 0.1M, weak E, 88% wet exec/immersedIons/README exec/immersedIons/inputs_paper_cond10 commit 25dda8c0027146b2b003ac58be99cacb8900f39b Author: Andy Nonaka Date: Tue Dec 17 13:12:27 2019 -0800 add 0 field, 0.1M runs exec/immersedIons/README exec/immersedIons/inputs_paper_cond4 exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_cond6 commit 6d5ed020528bfe267ec533c3a80930841a3452a7 Author: Andy Nonaka Date: Tue Dec 17 13:04:32 2019 -0800 add strong E field tests exec/immersedIons/README exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 commit a603ee8dbfb9687a47b970560daf561e5a146d4a Author: Andy Nonaka Date: Tue Dec 17 12:58:11 2019 -0800 move old inputs files out of the way exec/immersedIons/README exec/immersedIons/old_inputs_files/README exec/immersedIons/old_inputs_files/inputs_paper_cond1 exec/immersedIons/old_inputs_files/inputs_paper_cond10 exec/immersedIons/old_inputs_files/inputs_paper_cond11 exec/immersedIons/old_inputs_files/inputs_paper_cond12 exec/immersedIons/old_inputs_files/inputs_paper_cond2 exec/immersedIons/old_inputs_files/inputs_paper_cond3 exec/immersedIons/old_inputs_files/inputs_paper_cond4 exec/immersedIons/old_inputs_files/inputs_paper_cond5 exec/immersedIons/old_inputs_files/inputs_paper_cond6 exec/immersedIons/old_inputs_files/inputs_paper_cond7 exec/immersedIons/old_inputs_files/inputs_paper_cond8 exec/immersedIons/old_inputs_files/inputs_paper_cond9 commit 15455898855ca1ac8ec9275813bc048570968dce Merge: 6d134ba4 f6ec5993 Author: Changho Kim Date: Mon Dec 16 13:58:33 2019 -0800 Merge branch 'master' into compressible_mui commit f6ec5993a5e799bbe989923616301f053c87aaf7 Author: Andy Nonaka Date: Mon Dec 16 11:50:48 2019 -0800 allow c++ random number seed control via "seed" exec/compressible/main_driver.cpp commit 6d134ba47e60370712a233ad83b0329ebf7d9351 Author: Changho Kim Date: Mon Dec 9 16:28:00 2019 -0800 exec/compressible_mui: now working with pseudo_kmc exec/compressible_mui/inputs_equil_3d exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh exec/compressible_mui/src_pseudo_kmc/compile.sh exec/compressible_mui/src_pseudo_kmc/pseudo_kmc.cpp commit 153ea6f220eb6349ea601d67b595402e56e1b2dd Author: Andy Nonaka Date: Wed Dec 4 16:41:57 2019 -0800 updated spreadsheet exec/immersedIons/Electrolyte_Data.xlsx commit 99dd43d6f31fa3def94ab8033745ba0c24380d9a Merge: 05270094 153ea6f2 Author: Daniel Ladiges Date: Wed Dec 4 16:41:05 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 05270094ea38f2d4f78965678d3824d9b5f92c04 Author: Daniel Ladiges Date: Wed Dec 4 16:39:18 2019 -0800 Some testing changes exec/tests/RFDanalysis/analysis.nb exec/tests/RFDanalysis/inputs_3d src_particles/FhdParticleContainer.cpp commit fabe13af303b479792bda9057e1a389b2b67e663 Author: Andy Nonaka Date: Wed Dec 4 16:19:50 2019 -0800 write out velocity structure factors exec/immersedIons/main_driver.cpp commit 95a64e28ecb80690172dc1be8156ef425d9103a0 Author: Andy Nonaka Date: Wed Dec 4 10:01:25 2019 -0800 cleanup structure factor stuff - prep to add vel-vel SF exec/immersedIons/main_driver.cpp commit 067cc4a5f40a6e65b49cf36cf5779c8a64a284c5 Merge: 35ba65ca 5432d561 Author: Changho Kim Date: Mon Dec 2 16:20:44 2019 -0800 Merge branch 'master' into compressible_mui commit 35ba65ca3f3017d0902451f9b054524f64eae16a Author: Changho Kim Date: Mon Dec 2 16:17:58 2019 -0800 exec/compressible_mui/main_driver.cpp: MFIter in exchange_mui() exec/compressible_mui/main_driver.cpp commit e8b96df9786fd66cea9f7fddfe5cf4367dcd2924 Author: Changho Kim Date: Mon Dec 2 12:42:12 2019 -0800 exec/compressible_mui directory created exec/compressible_mui/GNUmakefile exec/compressible_mui/inputs_equil_3d exec/compressible_mui/main.cpp exec/compressible_mui/main_driver.cpp exec/compressible_mui/run.sh commit 5432d56148ad20c9492c262214eea05af383d134 Author: Andy Nonaka Date: Wed Nov 27 16:11:53 2019 -0800 write out plot_int-1 plotfile for now (for time averages) exec/immersedIons/main_driver.cpp commit 47059dea6407b7b482960f21f617d298953b906d Author: Andy Nonaka Date: Wed Nov 27 16:04:13 2019 -0800 comments exec/immersedIons/main_driver.cpp commit 816bcd623e9e8a42aa9e42b1bbbc1015d1264ffe Author: Andy Nonaka Date: Wed Nov 27 14:20:44 2019 -0800 revert exec/immersedIons/inputs_paper_cond2 commit 58be494fbfdaf517567ae17e086b566d015a7af2 Author: Andy Nonaka Date: Wed Nov 27 13:08:54 2019 -0800 code to output running average of a list of numbers exec/immersedIons/inputs_paper_cond2 exec/immersedIons/postprocessing/running_avg.f90 commit 5337466da8e4979203f318a4d4e6358d1848364a Merge: 221df120 a090eb57 Author: Daniel Ladiges Date: Wed Nov 27 10:58:58 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a090eb5776f7296abb672e3e3450b7fc6f57df7f Author: Andy Nonaka Date: Tue Nov 26 16:41:54 2019 -0800 fine tune EO example exec/immersedIons/inputs_paper_eo commit bebcf53aa9c44fb64aa98d9ef62ee6f098617520 Author: Andy Nonaka Date: Tue Nov 26 08:45:45 2019 -0800 had to cut the time step for cond7 exec/immersedIons/inputs_paper_cond7 commit 66b26be3810d05b5caf28d8cde4dfd16f6f9b7e5 Author: Andy Nonaka Date: Mon Nov 25 16:19:45 2019 -0800 no longer always using random seeds. use "seed = X" in the inputs file changed RT regression test to use a fixed seed bugfix in primitive variable output - we weren't calling conservedtoprimitive at the end of each time step removed call to conservedtoprimitive at the beginning of the time step added call to conservedtoprimitive ghost cell fills at the beginning of simulation exec/compressible/inputs_regression_RT_3d exec/compressible/main_driver.cpp src_compressible/timeStep.cpp commit 9d87e7aa6533102c806cd62f9efe9493ae277a88 Author: Andy Nonaka Date: Sat Nov 23 17:43:52 2019 -0800 change the particle means code to use an MFIter instea of an FhdParIter so the means always get evaluated (it wasn't entering this loop when the grid had no particles) note: the evaluate_corrs still won't work for low particle counts for the same reason src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit c27a9bd75e2605144b5d10111ae228cac8126dec Author: Andy Nonaka Date: Fri Nov 22 13:40:31 2019 -0800 bugfix: computation of current when some grids have no particles now works correctly src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit b45bb6b780517c2f4c6cbe744b72eba96b1ece89 Author: Andy Nonaka Date: Fri Nov 22 10:44:37 2019 -0800 bugfix in conductivity measurement when there are no particles on a particular grid src_particles/FhdParticleContainer.cpp commit 483cf2ea8e0715d8f85f3057bc06a2e8a2807d9b Author: Andy Nonaka Date: Thu Nov 21 16:19:55 2019 -0800 new seed exec/immersedIons/inputs_paper_cond1 exec/immersedIons/inputs_paper_cond10 exec/immersedIons/inputs_paper_cond11 exec/immersedIons/inputs_paper_cond12 exec/immersedIons/inputs_paper_cond2 exec/immersedIons/inputs_paper_cond3 exec/immersedIons/inputs_paper_cond4 exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_cond6 exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 commit 70e60704db0a89f463cae76aae7b90960b61c8d8 Author: Andy Nonaka Date: Thu Nov 21 15:26:14 2019 -0800 updated workstation-sized conductivity runs exec/immersedIons/README exec/immersedIons/inputs_paper_cond1 exec/immersedIons/inputs_paper_cond10 exec/immersedIons/inputs_paper_cond11 exec/immersedIons/inputs_paper_cond12 exec/immersedIons/inputs_paper_cond2 exec/immersedIons/inputs_paper_cond3 exec/immersedIons/inputs_paper_cond4 exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_cond6 exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 commit 43debd110b3d28fb9a800c6f0cf680f2f4724a53 Author: Andy Nonaka Date: Thu Nov 21 14:50:11 2019 -0800 starting config on conductivity runs - not ready yet exec/immersedIons/inputs_paper_cond1 exec/immersedIons/inputs_paper_cond10 exec/immersedIons/inputs_paper_cond11 exec/immersedIons/inputs_paper_cond12 exec/immersedIons/inputs_paper_cond2 exec/immersedIons/inputs_paper_cond3 exec/immersedIons/inputs_paper_cond4 exec/immersedIons/inputs_paper_cond5 exec/immersedIons/inputs_paper_cond6 exec/immersedIons/inputs_paper_cond7 exec/immersedIons/inputs_paper_cond8 exec/immersedIons/inputs_paper_cond9 commit 5b50f160b9b52893800a0befa0bfea4c139550cd Author: Andy Nonaka Date: Wed Nov 20 13:38:07 2019 -0800 typo exec/immersedIons/README commit d0df9e6643bfcdc1701d72335d353441a0b99bdd Author: Andy Nonaka Date: Tue Nov 19 15:06:35 2019 -0800 structure factor now works correctly for negative n_steps_skip... although it never resets. It just uses |n_steps_skip| to indicate where to start taking snapshots, but won't reset at intervals (for now) exec/immersedIons/main_driver.cpp commit dbeef4b05a6ea1a60c0cc37688bb846ae08751be Author: Andy Nonaka Date: Tue Nov 19 13:08:19 2019 -0800 neutral g(r) exec/immersedIons/README exec/immersedIons/inputs_paper_gr4 commit cde1a53da711315b80b21f19015223851bd9aa32 Author: Andy Nonaka Date: Tue Nov 19 12:53:48 2019 -0800 "finalized" run setups (each runs in ~8 hours on a workstation) for the 3 g(r) tests binsize is now 1/4th what we used to run and searchDist is limited to an outer radius that makes sense given our parameters inputs_paper_gr1 - 0.1M, 14% wet inputs_paper_gr2 - 1.0M, 14% wet inputs_paper_gr3 - 1.0M, 55% wet exec/immersedIons/README exec/immersedIons/inputs_paper_gr1 exec/immersedIons/inputs_paper_gr2 exec/immersedIons/inputs_paper_gr3 commit 5505d54d8e3e7c172d09f06d1e213181a68fadc7 Author: Andy Nonaka Date: Mon Nov 18 17:21:23 2019 -0800 save memory: don't allocate storage for pair correlation functions unless you are computing it. src_particles/FhdParticleContainer.cpp commit 6cfe0c5920f9a0bb0e15e1ef81a5763242792347 Author: Andy Nonaka Date: Mon Nov 18 16:50:35 2019 -0800 you now MUST specify binsize and searchdist in the inputs file if you are computing g(r) (radialdist_int or cartdist_int is positive) exec/immersedIons/inputs_paper_gr src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 9182d7589db7e7ee318ca2a0f343c378d9c120a0 Author: Andy Nonaka Date: Mon Nov 18 12:56:35 2019 -0800 write out standard error exec/immersedIons/postprocessing/std.f90 commit a5c94442baf91661535d15cbe649d767e66e4323 Author: Andy Nonaka Date: Mon Nov 18 11:19:10 2019 -0800 compilation error exec/immersedIons/postprocessing/std.f90 commit 698065197a563a5d2e4e2da4f33c47907742d6bd Author: Andy Nonaka Date: Mon Nov 18 11:18:20 2019 -0800 print mean and error bar exec/immersedIons/postprocessing/std.f90 commit a148209434ffa59c74a5bf6ea6f9ea1a9f1879bc Author: Andy Nonaka Date: Mon Nov 18 10:56:39 2019 -0800 standard deviation calculator exec/immersedIons/postprocessing/std.f90 commit 173ed64e9aa3005147a40d59aef652982e2d5eb1 Merge: ffc13f4b 72f48f38 Author: Andy Nonaka Date: Mon Nov 18 10:14:09 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ffc13f4b8fc34104ecd4bc59869bd70934ee0ac6 Author: Andy Nonaka Date: Mon Nov 18 10:13:53 2019 -0800 code for combining gr outputs exec/immersedIons/postprocessing/read_gr.f90 commit 72f48f38f1b1eeeca5c10cdefa4b6854f7a95037 Merge: 1f58faff eba48c24 Author: Johannes Blaschke Date: Sat Nov 16 10:28:50 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 1f58faffa9b95a309b59da4a1ada6dd2ebd35ca0 Author: Johannes Blaschke Date: Sat Nov 16 10:28:25 2019 -0800 added more debug data exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit eba48c244be0c5fa79b42adc12b3f10eb4a8e483 Author: Andy Nonaka Date: Fri Nov 15 17:28:37 2019 -0800 fix output interval exec/immersedIons/inputs_paper_gr commit 600103c18e34ec169f0b94ece12effd3bc8e2b35 Author: Andy Nonaka Date: Fri Nov 15 16:59:29 2019 -0800 updated paper runs exec/immersedIons/inputs_paper_cond exec/immersedIons/inputs_paper_gr commit 686e25d1916db69243cdac92dcc97c7f3da089c7 Author: Andy Nonaka Date: Fri Nov 15 16:54:11 2019 -0800 error in radialdist_int and cartdist_int logic exec/immersedIons/main_driver.cpp commit 514c29a1c333a8d4392af91e799bd3d1380e2584 Author: Andy Nonaka Date: Thu Nov 14 14:02:33 2019 -0800 process current exec/immersedIons/postprocessing/read_curr.f90 commit f45733fb6cbee324ae531127c3a7f3f1189c59ca Author: Johannes Blaschke Date: Wed Nov 13 22:01:49 2019 -0800 spread forces over multi-blob markers exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit 35b05df6fdaceeb9f731a8368a9eb25a703751a2 Author: Johannes Blaschke Date: Wed Nov 13 21:15:13 2019 -0800 cleanup src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit f78aa97d2ecc7446347abeb34e64ac3080d52bc2 Author: Johannes Blaschke Date: Wed Nov 13 21:11:09 2019 -0800 fix problem double-counting neighbor multi-blobs exec/immersed_boundary/channel_multiblob/advance.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit f3af526e8ce9bbdb83a75b700f01889080c87726 Author: Johannes Blaschke Date: Wed Nov 13 15:48:57 2019 -0800 once again, accumulated in the inner loop! src_immersed-boundary/IBMultiBlobContainer.cpp commit b830da72a283c01df7d7c027622c1fd525cbcedc Author: Johannes Blaschke Date: Wed Nov 13 15:47:45 2019 -0800 update plot file name exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres commit 09f8818944ac02670d7255bf0e3584ab690e95f3 Author: Johannes Blaschke Date: Wed Nov 13 15:44:54 2019 -0800 accumulation in the wrong place src_immersed-boundary/IBMultiBlobContainer.cpp commit 06b2e3ec3998babfb95b7c5bba918f382b0ad3c9 Author: Johannes Blaschke Date: Wed Nov 13 15:41:05 2019 -0800 add debug print statements, and debug intermittent compiler error src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/src_F90/Make.package src_immersed-boundary/src_F90/param_mod.F90 commit 243e8f93618de8e4f58ae6dd39f80451a391ca21 Author: Andy Nonaka Date: Fri Nov 8 14:17:06 2019 -0800 fix mistake in inputs exec/immersedIons/inputs_paper_cond commit 26ce2f307d2540263b84dcb3780359c89af1a0e0 Author: Andy Nonaka Date: Fri Nov 8 14:15:15 2019 -0800 conductivity update exec/immersedIons/inputs_paper_cond commit e6a063955fde666765bca08812d8462b8eb7b359 Author: Johannes Blaschke Date: Thu Nov 7 16:04:04 2019 -0800 blob-move operation works now except for sign error exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/inputs_3d_grav.highres exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit b8e72602294ecc2fc83271e228cd342cd5dad45b Merge: c6beda34 0af93999 Author: Johannes Blaschke Date: Thu Nov 7 12:38:42 2019 -0800 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit c6beda34630b72604d26d26a1ef4d660db212ecb Author: Johannes Blaschke Date: Thu Nov 7 12:38:24 2019 -0800 couple forces between multi-blob and markers src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 0af93999651c5209417420d61fafbcf9dc4cd06f Author: Johannes Blaschke Date: Thu Nov 7 10:53:19 2019 -0800 add cori parameter file exec/immersed_boundary/flagellum/inputs_chlamy.cori commit 32bf60230d3e40b2d6dae158d6695b92e8da34b4 Author: Johannes Blaschke Date: Thu Nov 7 09:40:23 2019 -0800 move marker (and predictor) now are aware of multi-blob COM exec/immersed_boundary/channel_multiblob/advance.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit 1a0d8d0d69662df41aade6d76d337834eacfc4ab Author: Andy Nonaka Date: Thu Nov 7 08:20:16 2019 -0800 write out current mean and variance to file currentEst. This also has the same "n_steps_skip" logic, where positive resets the stats once, negative reset the stats at that interval src_particles/FhdParticleContainer.cpp commit 2ca2ac313545763c74c508ea62f8cd818b09a601 Merge: c33b7548 d8951822 Author: Johannes Blaschke Date: Wed Nov 6 16:19:23 2019 -0800 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit c33b7548aad8c67bd4d74b26bd66da2bce629e2b Author: Johannes Blaschke Date: Wed Nov 6 16:19:21 2019 -0800 add move-blob function exec/immersed_boundary/channel_multiblob/inputs_3d_test.highres src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit d8951822a778dd947cffe1dccd3e2c2ae0955f2d Author: Andy Nonaka Date: Wed Nov 6 14:19:19 2019 -0800 modify postprocessing exec/immersedIons/postprocessing/read_cond.f90 commit 2dea951c6b75308610c72cdd70532e5efb0e6ad3 Author: Andy Nonaka Date: Wed Nov 6 11:11:08 2019 -0800 postprocessing program to read in conductivity data to get the overall average conductivity (if n_steps_skip<0). Allows you to throw out an arbitrary number of data points at the beginning/equilibration exec/immersedIons/postprocessing/read_cond.f90 commit 954a9eb96d107f78910aaf08889cb0bc12539664 Author: Andy Nonaka Date: Wed Nov 6 10:34:11 2019 -0800 allow diffusion/conductivity n_steps_skip to work for negative intervals (reset every |n_steps_skip|) exec/immersedIons/main_driver.cpp commit f951728cdd879875da3463a94a5cf6e28431473f Author: Andy Nonaka Date: Wed Nov 6 10:01:43 2019 -0800 sync up Daniel's conductivity test with inputs_paper_cond exec/immersedIons/inputs_conductivity exec/immersedIons/inputs_paper_cond commit 29675bbbc01dad314ea00e351ec55ba2e082f005 Author: Andy Nonaka Date: Wed Nov 6 09:45:18 2019 -0800 premitivitty -> permittivity exec/fluctuatingMembrane/inputs_3d exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_poisson exec/immersedIons/inputs_3d_reflect exec/immersedIons/inputs_conductivity exec/immersedIons/inputs_paper_cond exec/immersedIons/inputs_paper_diffusion exec/immersedIons/inputs_paper_eo exec/immersedIons/inputs_paper_gr exec/immersedIons/inputs_paper_sf exec/immersedIons/inputs_regression_cond exec/tests/RFDanalysis/inputs_3d exec/tests/boundarySpreading/inputs_3d_dirichlet_noslip exec/tests/boundarySpreading/inputs_3d_dirichlet_slip exec/tests/electroPeriodic/inputs_3d exec/tests/electroTwoWall/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 57456e739f19da3457da38c876669bb1825bcbfe Author: Andy Nonaka Date: Wed Nov 6 09:38:43 2019 -0800 4 point kernel needs crange 5 (6 point needs crange 7) exec/immersedIons/inputs_conductivity exec/immersedIons/inputs_paper_cond exec/immersedIons/inputs_paper_gr commit 221df1201a3de0a5a3c52406ddf134c9dff01d75 Merge: e48cad01 6267a53c Author: Daniel Ladiges Date: Tue Nov 5 18:08:13 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e48cad01b1a637868cb6697ecc6087f36acde765 Author: Daniel Ladiges Date: Tue Nov 5 18:07:49 2019 -0800 Setup for EH conductivity test. exec/immersedIons/inputs_conductivity exec/immersedIons/main_driver.cpp exec/tests/electroPeriodic/inputs_3d commit 6267a53c2ea468439b8acb9cbeb67e94c6f75856 Author: Andy Nonaka Date: Tue Nov 5 17:37:05 2019 -0800 reset the stats for g(r), g(x/y/z) if n_steps_skip<0 AFTER you write out the g(r) src_particles/FhdParticleContainer.cpp commit 5d2e071ccfa02bf7b5cb7d64f3ee892f3461ef11 Author: Andy Nonaka Date: Tue Nov 5 17:27:33 2019 -0800 12 hour g(r) calc on a single core with random seed exec/immersedIons/inputs_paper_gr commit 9e0c5cd8ed925e38c10875d4802219b316902848 Merge: 8305807f f28e600d Author: Daniel Ladiges Date: Tue Nov 5 16:50:38 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8305807f49230bf17786e83461e3461dfdb40943 Author: Daniel Ladiges Date: Tue Nov 5 16:50:25 2019 -0800 Testing of p3m for 4pt exec/tests/RFDanalysis/particleGen.cpp exec/tests/boundarySpreading/particleGen.cpp exec/tests/electroPeriodic/GNUmakefile exec/tests/electroPeriodic/WritePlotFileHydro.cpp exec/tests/electroPeriodic/main_driver.cpp exec/tests/electroPeriodic/particleGen.cpp exec/tests/electroTwoWall/particleGen.cpp commit f28e600d04d204fb8be6d1ac50d932a8aeaf2f7a Author: Andy Nonaka Date: Tue Nov 5 16:28:34 2019 -0800 fix cartesian version of g(x/y/z) to work in parallel. added ++, +-, -- diagnostics to cartesian g(x/y/z) exec/immersedIons/inputs_paper_gr src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit af2c94e8e0ed4130d7b61e15e5225c44719a59aa Merge: ad57ffad e17afa28 Author: Daniel Ladiges Date: Tue Nov 5 16:23:59 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ad57ffad431b63c5a3cdcd16d2fc806bbff158e8 Author: Daniel Ladiges Date: Tue Nov 5 16:23:18 2019 -0800 Added functions for calculating 3pm correction tables. Started implementing for 4 pt kernel. exec/immersedIons/inputs_3d exec/immersedIons/inputs_conductivity exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit e17afa285cd67dcb428aae0d8dba9928e5100828 Author: Johannes Blaschke Date: Tue Nov 5 16:02:21 2019 -0800 specify a different number of ghost cells for the blobs and markers exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 2deb5b959d3af09b9bbe0454c21fcc96f59f9c8c Merge: d73d6e3d ca303ac7 Author: Johannes Blaschke Date: Tue Nov 5 15:50:16 2019 -0800 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit ca303ac7acaf8b78cdb61023d0cd150a21be7c24 Merge: 6fa88c1d 90b1c47b Author: Andy Nonaka Date: Tue Nov 5 15:52:19 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6fa88c1d24b69486b544a0f087158eceb20c0883 Author: Andy Nonaka Date: Tue Nov 5 15:52:11 2019 -0800 g(r) inputs exec/immersedIons/inputs_paper_gr commit 32f63b23ccecae63da6305d755b3a10d19dea958 Author: Andy Nonaka Date: Tue Nov 5 15:51:30 2019 -0800 add g(r) for pairs ++, +-, -+, --, of ions src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 83df35adb52624216e1d4e813ef4bf68d31e2a02 Author: Andy Nonaka Date: Tue Nov 5 15:51:16 2019 -0800 PullDown / PushUp now work assuming 1-based particle ID src_immersed-boundary/IBMarkerContainerBaseI.H commit d73d6e3d93fc6e9ec4a7843cd8828a7970c0f182 Author: Johannes Blaschke Date: Tue Nov 5 15:50:11 2019 -0800 find minimal number of ghost cells exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit 90b1c47b3cec8f0f65cfe28cf0e6372a365daadb Author: Johannes Blaschke Date: Tue Nov 5 15:33:12 2019 -0800 ensure that face_coords has enough ghost cells exec/immersed_boundary/channel_multiblob/main_driver.cpp src_common/src_F90/find_coords.F90 src_immersed-boundary/IBMarkerContainerBaseI.H commit 5fc376b62083b3e957aca01cf8a0227a756a6baf Merge: 1cd317a3 8271051d Author: Johannes Blaschke Date: Tue Nov 5 15:10:45 2019 -0800 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 1cd317a35f6c41a337a3bcdef2d65e0301161866 Author: Johannes Blaschke Date: Tue Nov 5 15:10:42 2019 -0800 fix issue with fillNeighbors exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit 8271051dad85de7f5bcf57ef021702fba10cc401 Author: Andy Nonaka Date: Tue Nov 5 14:45:42 2019 -0800 revert: put particles IDs back to 1, 2, 3, ... (1-based, not 0-based) exec/immersedIons/particleGen.cpp commit 631f7a218554b215cb390ec1e1ba81c0c41144cc Author: Andy Nonaka Date: Tue Nov 5 14:16:14 2019 -0800 oops.. want particleID's to start at 0. (not 2) exec/immersedIons/particleGen.cpp commit b939287700cddcc1a770e386adc872ee432c5368 Author: Andy Nonaka Date: Tue Nov 5 11:30:17 2019 -0800 print out wet/dry % for each species; also abort if "use_dry=1 && fluid_tog != 0" exec/immersedIons/main_driver.cpp commit abcb54619a7090364e97976487fb3a1762ac50fe Author: Daniel Ladiges Date: Mon Nov 4 19:15:46 2019 -0800 Some adjustments co conductivity calc exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.cpp commit aa8db311a1f26fc1e56370b15913fca888cfedde Merge: 4e79ebce 83b54092 Author: Daniel Ladiges Date: Mon Nov 4 18:10:51 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4e79ebce302e1584c8cebbc64ad499fa33b956b9 Author: Daniel Ladiges Date: Mon Nov 4 18:09:13 2019 -0800 Finished mean square disp function for diffusion and conductivity. Acting a bit weird, not sure if its correct or not. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 83b54092a287b4a96817bd2ee31208dc5a901af6 Merge: 78d9d8c7 e4ddcc25 Author: Johannes Blaschke Date: Mon Nov 4 16:48:27 2019 -0800 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 78d9d8c76d475220980fb90a7cee749eebf5c958 Author: Johannes Blaschke Date: Mon Nov 4 16:48:21 2019 -0800 debug for andrew exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit e4ddcc250af8af5ef2e40fc59040efb941ed058f Author: Daniel Ladiges Date: Mon Nov 4 14:38:08 2019 -0800 Left out a semicolon exec/immersedIons/main_driver.cpp commit 92fb8b401b1896f48784f3de6f302bed0cad2f9d Merge: b3108529 43f6e1ff Author: Daniel Ladiges Date: Mon Nov 4 14:37:07 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b3108529b29cb5b9ecfed8ba1092241db4076f4b Author: Daniel Ladiges Date: Mon Nov 4 14:35:12 2019 -0800 Started means sqr calc for conductivity exec/immersedIons/inputs_paper_cond exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 43f6e1ff7ec9ee347fa5aa549522a96bd34aa5e4 Author: Andy Nonaka Date: Mon Nov 4 13:00:32 2019 -0800 immersedIons: start particle ID at 1 instead of 0 exec/immersedIons/particleGen.cpp commit 7d1426acf64774b120969ed9d6119bd6702621a5 Author: Johannes Blaschke Date: Fri Nov 1 17:55:20 2019 -0700 debugging exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.cpp commit 48cadb87aa804d21531a85cfae7ae99425416b1e Author: Johannes Blaschke Date: Fri Nov 1 17:11:04 2019 -0700 add force accumulation function src_immersed-boundary/IBMultiBlobContainer.cpp commit a0db8f33a4a46e8e9f2767e4d4ae015662b4621d Author: Johannes Blaschke Date: Fri Nov 1 17:00:34 2019 -0700 build multi-blob hash table src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 6062ae76145b45abcd95d128000026d0f5a9d803 Author: Johannes Blaschke Date: Fri Nov 1 15:42:10 2019 -0700 cleanup advance exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance_CN.cpp commit 655d33c18547989bd092bac5718c5cc80c55287f Author: Andy Nonaka Date: Fri Nov 1 12:39:34 2019 -0700 g(x/y/z) working. fixed bug in g(r) code if Lx, Ly, and Lz aren't the same exec/immersedIons/inputs_paper_gr src_particles/FhdParticleContainer.cpp commit cae25d09f0fa5ea38070e10750cd714b7a90eab2 Author: Andy Nonaka Date: Fri Nov 1 10:39:29 2019 -0700 clean up post_restart src_particles/FhdParticleContainer.cpp commit 5e5603d8e439558edde9cc56db34547497c50deb Author: Andy Nonaka Date: Fri Nov 1 06:38:23 2019 -0700 addition to previous commit - forgot to add modified main_driver.cpp exec/immersedIons/main_driver.cpp commit 7ab05168d9cdb76f689ca10c27942639f414528a Author: Andy Nonaka Date: Fri Nov 1 06:36:25 2019 -0700 separate toggle for computing g(r) and g(x/y/z) so it doesn't use struct_fact_int (now uses radialdist_int, cartdist_int). also similar to the structure factor stuff, the control over whether you add a snapshot is done at the main.cpp level, rather than within the analysis code itself. src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp commit 473153d43cf91295ff0e35cd5a4f2edaa522e26a Merge: bff9b7d2 1e5d68bc Author: Johannes Blaschke Date: Thu Oct 31 22:32:30 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bff9b7d2128a00016c64cb19042d03fbfed5cdaa Author: Johannes Blaschke Date: Thu Oct 31 22:32:23 2019 -0700 store anchoring spring constants in IBBlob/IBMB exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 1e5d68bc646b9bf5c3a2c5f9b3683f41c99ebd60 Author: Andy Nonaka Date: Thu Oct 31 16:16:34 2019 -0700 progress toward g(x) g(y). still buggy exec/immersedIons/delPlots exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit a8a90257c624de100fa0b5fd298c11811ff9a18b Author: Andy Nonaka Date: Thu Oct 31 12:10:20 2019 -0700 particle position only restart now works use e.g., "particle_restart = 5" note that if you use regular restart and a particle restart with different values, the simulation will restart as normal except now the particles will be restarted from particle_restart exec/immersedIons/Checkpoint.cpp exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp commit 16fdcabd79c769e73c4862162097e54221a984b9 Author: Andy Nonaka Date: Thu Oct 31 11:14:41 2019 -0700 cleanup only src_common/src_F90/common_namelist.F90 commit 2aafa11c7cfe22d38ae4c5501167dfc293fb3786 Author: Andy Nonaka Date: Thu Oct 31 11:06:28 2019 -0700 remove "perm" from the common namelist (we already have "permittivity") exec/DSMC-LDT/inputs_3d exec/DSMC/inputs_3d exec/DSMCstatcheck/inputs_3d exec/brownian/inputs_3d exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_poisson exec/immersedIons/inputs_3d_reflect exec/immersedIons/inputs_paper_cond exec/immersedIons/inputs_paper_diffusion exec/immersedIons/inputs_paper_eo exec/immersedIons/inputs_paper_gr exec/immersedIons/inputs_paper_sf exec/immersedIons/inputs_regression_cond exec/tests/RFDanalysis/inputs_3d exec/tests/boundarySpreading/inputs_3d_dirichlet_noslip exec/tests/boundarySpreading/inputs_3d_dirichlet_slip exec/tests/electroPeriodic/inputs_3d exec/tests/electroTwoWall/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit a5d57affbd6162265ab3db983f867d9b387c4b10 Author: Andy Nonaka Date: Thu Oct 31 10:57:00 2019 -0700 added "all_dry" to common namelist; allows you to force the dry diffusion coefficient to be equal to diff exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 800aca89b362b188b123233bc48a54f72e279eff Merge: 22f84292 d9fb0477 Author: Andy Nonaka Date: Thu Oct 31 09:39:02 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 22f84292564fb99677590f9adc5cb3ebc4237c17 Author: Andy Nonaka Date: Thu Oct 31 09:38:25 2019 -0700 restore 6 point kernel wet radius to the new value exec/immersedIons/main_driver.cpp commit d9fb0477a414297892d13ffba1be89ba88b26cda Author: Andy Nonaka Date: Wed Oct 30 18:45:07 2019 -0700 reduce the periodic search size by figuring out in advance which periodic images could contain the closest charge. 2x speedup also fixed a potential bug when Lx != Ly != Lz in not computing the correct images - now the search radius minimum is the min over Lx, Ly, Lz src_particles/FhdParticleContainer.cpp commit 433ea063104fc8222038a57861f22393fbd8fe7b Author: Johannes Blaschke Date: Tue Oct 29 18:59:57 2019 -0700 read colloid properties form inputs file exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 1d7e472832503536fe917040337512dcdb784350 Merge: 36f6400c b2f509a2 Author: Johannes Blaschke Date: Tue Oct 29 18:08:40 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 36f6400c8e1fb9445a70a711a9bba2620076bc77 Author: Johannes Blaschke Date: Tue Oct 29 18:08:33 2019 -0700 expand namespace to contains colloid parameters exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/ib_functions.H src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit b2f509a2d5e1113d65010babcadf353735280e06 Author: Andy Nonaka Date: Tue Oct 29 16:07:27 2019 -0700 comment up g(r) code. fix up inputs file to test g(r). made one functional change: normalized g(r) so the tail has a value of 1 exec/immersedIons/inputs_paper_gr src_particles/FhdParticleContainer.cpp commit fb6ab947c5abfee350df5f1b6fc46bb52d9f34a7 Author: Johannes Blaschke Date: Tue Oct 29 15:46:50 2019 -0700 make cleanup to make consistent exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp exec/immersed_boundary/channel_multiblob/inputs_3d_test exec/immersed_boundary/channel_multiblob/main_driver.H commit 2a4420613cf488a57a609b805e41f7ee8a8fc85c Author: Johannes Blaschke Date: Tue Oct 29 09:34:01 2019 -0700 add high-res simulation exec/immersed_boundary/channel_multiblob/inputs_3d_test.highres exec/immersed_boundary/channel_multiblob/main_driver.cpp commit dacab2c51c88c4a189bb8a68696ec6a300a70897 Author: Johannes Blaschke Date: Mon Oct 28 17:30:11 2019 -0700 increase number of markers for better solution. IBPartilceContainer is deprecated now exec/immersed_boundary/channel_multiblob/main_driver.cpp commit 557fc49d16581e3f58445b8df666662abcc451bb Author: Johannes Blaschke Date: Mon Oct 28 17:27:52 2019 -0700 fix parallelized initialization src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit d50b46911dce16780307c4e5f55f46180e9f1fde Merge: a32fc5b4 2f282187 Author: Johannes Blaschke Date: Mon Oct 28 16:31:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a32fc5b47e0d931c516d05267d8799f44f9dc270 Author: Johannes Blaschke Date: Mon Oct 28 16:31:32 2019 -0700 couple MultiBlob to fluid exec/immersed_boundary/channel_multiblob/advance.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 41ccd390f2b4f0401ea86bf1900ce94fe1651418 Author: Johannes Blaschke Date: Mon Oct 28 16:31:14 2019 -0700 add imputs file for testing exec/immersed_boundary/channel_multiblob/inputs_3d_test commit 2f2821873160b40dccd5184d8fa3857f07590370 Merge: b294d1c8 9c7f4f0c Author: Andy Nonaka Date: Mon Oct 28 16:19:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b294d1c8315590f3022776d0710d9e97560465f3 Author: Andy Nonaka Date: Mon Oct 28 16:19:26 2019 -0700 sync scaling up with LowMachFHD version exec/structFactTest/main_driver.cpp src_analysis/StructFact.cpp commit 9c7f4f0c4e2ac4f1b3bca23a2a87ba1b4b5d9719 Author: Johannes Blaschke Date: Mon Oct 28 16:04:32 2019 -0700 add reference-preserving move-markers src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 67148b3249cbb4ac5a092f6a105f49c83f346ae6 Author: Johannes Blaschke Date: Mon Oct 28 15:48:30 2019 -0700 accumulate pred_pos[x,y,z], instead of overwriting src_immersed-boundary/IBMarkerContainerBaseI.H commit 1cb9e6f8c10133a750210effb186360050ccd8bb Author: Johannes Blaschke Date: Mon Oct 28 15:20:18 2019 -0700 start implementing linear force modle in multiblob, and move MarkerListIndex to base class exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit e9ca32d3f28fe98ffcaebc368f7fa0d6b15d78fc Author: Johannes Blaschke Date: Mon Oct 28 14:51:59 2019 -0700 save marker data as additional particle data exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 23c93e60bf29fa038ded43c998b35feae7d4750c Author: Johannes Blaschke Date: Mon Oct 28 14:40:11 2019 -0700 fix writing to plotfile exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 481cc9507ff3dfec05b91a985cd3bd07bac019eb Merge: 636848e8 da0a4b40 Author: Johannes Blaschke Date: Mon Oct 28 13:58:21 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 636848e8824f49b39d7711313d4e0952fe41f044 Author: Johannes Blaschke Date: Mon Oct 28 13:58:18 2019 -0700 expanded multiblob to model chlamy cell body exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/main_driver.H exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/MakeBase.package commit da0a4b407b60adb30038e96a25191dc9a7324fa9 Author: Andy Nonaka Date: Mon Oct 28 12:20:03 2019 -0700 print out current mean and variance over all simulation, not on a tile by tile basis. also, the current variance on tiles isn't working properly - it works on multiple grids but gives different answers on multiple tiles src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit 657218056c92b9209f42c2bb7963dd13d1277e2a Author: Andy Nonaka Date: Mon Oct 28 11:21:27 2019 -0700 write out move_ions_fhd diagnostics on a GLOBAL basis (not grid-by-grid) src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 4c7373a7ccbe6f735398dd7ffe838b92f9f2afc8 Author: Daniel Ladiges Date: Fri Oct 25 16:29:45 2019 -0700 Mathematica file for stability criteria exec/compressible/mathematica/stability.nb commit 89f961e5c90169729eddfcb4520a286f9148b860 Author: Daniel Ladiges Date: Fri Oct 25 16:27:17 2019 -0700 Tracking plotfile.cpp for examples. exec/exercises/compressible/writePlotFile.cpp commit eb392b4c3217a28d67d1309c33c8212847573af4 Author: Andy Nonaka Date: Thu Oct 24 18:15:10 2019 -0700 add function exec/structFactTest/main_driver.cpp commit 31f52197441f9d86afcb034b64790909979912ba Author: Andy Nonaka Date: Thu Oct 24 18:03:07 2019 -0700 FHDeX struct fact test setup exec/structFactTest/GNUmakefile exec/structFactTest/inputs_3d exec/structFactTest/main_driver.cpp commit a4e12c51d8b01545ff4bc3cded974ed6b2f2cc16 Author: Daniel Ladiges Date: Thu Oct 24 17:22:41 2019 -0700 Print out sensible error for negative density or energy in compressible. exec/exercises/compressible/inputs_temperature_3d src_compressible/src_F90/time_step_funcs.F90 commit bb4f3fe3365e844f0bb7ffa979c001dba8ae709d Author: Daniel Ladiges Date: Thu Oct 24 17:02:00 2019 -0700 Added another input file for Berlin exercises exec/exercises/compressible/inputs_temperature_deterministic_3d commit 70b5f35199b90629022b65a0e34a6938a569fc03 Author: Daniel Ladiges Date: Thu Oct 24 16:52:54 2019 -0700 More stuff for Berlin exercises. exec/exercises/compressible/inputs_equilibrium_3d exec/exercises/compressible/inputs_temperature_3d exec/exercises/compressible/main_driver.cpp exec/exercises/compressibleMS/GNUmakefile exec/exercises/compressibleMS/delPLots exec/exercises/compressibleMS/inputs_3dy exec/exercises/compressibleMS/inputs_3dz exec/exercises/compressibleMS/inputs_RT_3d exec/exercises/compressibleMS/inputs_equil_3d exec/exercises/compressibleMS/inputs_giantfluct_3d exec/exercises/compressibleMS/inputs_regression_RT_3d exec/exercises/compressibleMS/main_driver.cpp exec/exercises/incompressible/init_funcs.F90 exec/exercises/incompressible/inputs_diffusion_2d exec/exercises/incompressible/main_driver.cpp exec/multispec/inputs_bubble_2d src_common/ComputeBasicStats.cpp src_compressible/src_F90/init_consvar.F90 src_compressible/src_F90/stats_funcs.F90 commit 3fc24c2b613bee89daa6eff1eca6b6415955f130 Merge: 9c943bf4 c3851e98 Author: Andy Nonaka Date: Thu Oct 24 11:02:57 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9c943bf48b24b74e066c91f523b6260a2551b3bc Author: Andy Nonaka Date: Thu Oct 24 11:02:31 2019 -0700 print out how long g(r) computation takes exec/immersedIons/main_driver.cpp commit c3851e98a184e24f1292b8ff88c85844289d5194 Author: Daniel Ladiges Date: Wed Oct 23 16:59:12 2019 -0700 Compressible multispecies exercise exec/exercises/compressibleMS/GNUmakefile exec/exercises/compressibleMS/delPLots exec/exercises/compressibleMS/inputs_3dy exec/exercises/compressibleMS/inputs_3dz exec/exercises/compressibleMS/inputs_RT_3d exec/exercises/compressibleMS/inputs_equil_3d exec/exercises/compressibleMS/inputs_giantfluct_3d exec/exercises/compressibleMS/inputs_regression_RT_3d exec/exercises/compressibleMS/inputs_test_3d exec/exercises/compressibleMS/main_driver.cpp commit bee330b0f0c76c7e2432abf98ed6774d1819a9a6 Author: Daniel Ladiges Date: Wed Oct 23 14:20:50 2019 -0700 input file for checking exec/exercises/incompressible/inputs_diffusion_2d commit 6cd6fbbf182b37f0bca7afa5f099453872cfc84d Author: Andy Nonaka Date: Wed Oct 23 12:21:51 2019 -0700 immersed ion spreadsheet exec/immersedIons/Electrolyte_Data.xlsx commit f26eadf1b634b564861e5ed343a85f92b1b54ec3 Author: Andy Nonaka Date: Wed Oct 23 11:18:31 2019 -0700 proper implementation of writing out radialDistribution on plot_int exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit 9cd18e2987489b8873bd8f48da6b58b11d7ffbd2 Author: Andy Nonaka Date: Wed Oct 23 11:15:57 2019 -0700 only write out radialDistribution on plot_int exec/immersedIons/main_driver.cpp commit 48b34b25168c404615df9cdb5265bb4c1211de58 Author: Andy Nonaka Date: Tue Oct 22 17:45:46 2019 -0700 dust off structure factor code exec/immersedIons/inputs_paper_gr exec/immersedIons/inputs_paper_sf exec/immersedIons/main_driver.cpp commit 88eb3c045e624b32c961d6e2faf57cce02e93c48 Author: Andy Nonaka Date: Tue Oct 22 16:58:09 2019 -0700 temporary periodic bc fill fixes exec/exercises/incompressible/advance.cpp src_multispec/ComputeMassFluxdiv.cpp commit f5489b119072d21375b090b7c74fdddba55d2f84 Merge: 01e0d674 55ba8716 Author: Daniel Ladiges Date: Tue Oct 22 16:35:58 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 01e0d67404fa5f80556ec9a85ecf9a3a9ab77a1c Author: Daniel Ladiges Date: Tue Oct 22 16:35:46 2019 -0700 Latest Berlin stuff exec/exercises/incompressible/inputs_diffusion_2d exec/exercises/incompressible/main_driver.cpp src_common/ComputeBasicStats.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_basic_stats.F90 commit 55ba871661cb36bcac1d4706d721eac018760439 Author: Johannes Blaschke Date: Tue Oct 22 08:37:50 2019 -0700 fix MPI deadlock exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 1025b417b2cfd8605dced77b4144e0eb9d262923 Author: Andy Nonaka Date: Mon Oct 21 16:01:03 2019 -0700 updated wet radius computation - 3 point and 4 point match Donev exec/immersedIons/main_driver.cpp commit c669deaf98355b04e644173fc004e6f9fd2999a4 Author: Andy Nonaka Date: Mon Oct 21 15:05:56 2019 -0700 move exec/tutorials/AdvDiff_StructFact/README exec/tutorials/AdvDiff_StructFact/main.cpp commit 7a91536bd7e27ceae4481f295f756a9c4846711a Author: Andy Nonaka Date: Mon Oct 21 15:00:52 2019 -0700 test 1d adv-diff structure factor code exec/tutorial/AdvDiff_StructFact/README exec/tutorial/AdvDiff_StructFact/main.cpp commit 9a735cbee60396b64d386d4d016218a111cc65da Author: Daniel Ladiges Date: Mon Oct 21 13:12:46 2019 -0700 Pushing some inputs with parameters for Berlin exercises exec/exercises/compressible/inputs_temperature_3d exec/exercises/incompressible/inputs_diffusion_2d src_common/src_F90/compute_basic_stats.F90 commit 5656f0bc162dabe487bda610f683f7b94beb0476 Merge: b1dd3d74 23f35b21 Author: Daniel Ladiges Date: Fri Oct 18 16:44:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b1dd3d741919a01bc9ca7bb682a74745bfda31a7 Author: Daniel Ladiges Date: Fri Oct 18 16:43:50 2019 -0700 Started adding cell centered spreading to IB base. exec/exercises/compressible/inputs_temperature_3d exec/exercises/compressible/main_driver.cpp exec/exercises/incompressible/inputs_diffusion_2d src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/trans_funcs.F90 src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 23f35b21072b4a5048b56537cc0b3aad89578870 Author: Johannes Blaschke Date: Fri Oct 18 13:48:17 2019 -0700 that should be a 7 exec/hydro/Checkpoint.cpp commit 6ec5ee148069660654ced0ddb2b9052d10276ba3 Author: Johannes Blaschke Date: Fri Oct 18 13:41:22 2019 -0700 fix restart exec/hydro/Checkpoint.cpp commit 2800186eb455f2fc536fb8310b08913744749bcf Author: Andy Nonaka Date: Thu Oct 17 15:08:55 2019 -0700 fix domain size exec/immersedIons/inputs_paper_diffusion commit 4c63be38a62cd3017238bfa714bfe0123c61ba2e Merge: 32aa5a51 fcf4b9f2 Author: Daniel Ladiges Date: Thu Oct 17 15:02:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 32aa5a5197bd3f4cfd3e5ca2284dee951bf2b080 Author: Daniel Ladiges Date: Thu Oct 17 15:02:22 2019 -0700 Some more setup of Berlin exercises. exec/exercises/compressible/inputs_temperature_3d exec/exercises/incompressible/WritePlotFile.cpp exec/exercises/incompressible/inputs_diffusion_2d exec/exercises/incompressible/main_driver.cpp exec/exercises/incompressible/multispec_test_functions.H src_common/src_F90/compute_basic_stats.F90 commit fcf4b9f22dde4c3932edc642d52890c58c4e425a Author: Andy Nonaka Date: Thu Oct 17 15:00:23 2019 -0700 0 seed exec/immersedIons/inputs_paper_diffusion commit 3d15be868fd4ed1b4c7d2cb658a249c21314e382 Merge: ba68fb0e 3fdb22cb Author: Andy Nonaka Date: Thu Oct 17 14:35:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ba68fb0ed6843af7581bafeb04dd09eb9111c027 Author: Andy Nonaka Date: Thu Oct 17 14:35:31 2019 -0700 update diffusion test exec/immersedIons/inputs_paper_diffusion commit 04cfdaa5414c4d02784e9022933d403124dbb223 Merge: a7e54e0f 8afa10ef Author: Daniel Ladiges Date: Thu Oct 17 12:40:29 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a7e54e0f5ab2e37c33c52635b75b1c235727457b Author: Daniel Ladiges Date: Thu Oct 17 12:40:00 2019 -0700 Added some analysis functions for Berlin. exec/exercises/compressible/GNUmakefile exec/exercises/compressible/inputs_temperature_3d exec/exercises/compressible/main_driver.cpp exec/exercises/incompressible/GNUmakefile src_common/ComputeBasicStats.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_basic_stats.F90 src_compressible/flux.cpp commit 3fdb22cbca4b65d1b55f690a678698952d5a6369 Merge: 3a2c0a5b 2f6a73fa Author: Johannes Blaschke Date: Thu Oct 17 12:38:44 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 2f6a73facbf317d9643f18a689f95a17ec12c1ba Merge: cbff12b7 04cfdaa5 Author: Johannes Blaschke Date: Thu Oct 17 12:42:48 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3a2c0a5b7a3fd30cdeabb91c0677fa8051f6952b Author: Johannes Blaschke Date: Thu Oct 17 12:38:42 2019 -0700 fiddle with parameters to speed up exec exec/immersed_boundary/flagellum/inputs_chlamy.large-thin commit cbff12b7df5d4062cdab1dd1c57e19af194afccf Author: Johannes Blaschke Date: Thu Oct 17 11:04:31 2019 -0700 implement handoff to particle-container member-class src_immersed-boundary/IBMultiBlobContainer.cpp commit 8afa10ef28a37120890edf040d058c9635d99200 Merge: e675d504 f337024f Author: Johannes Blaschke Date: Thu Oct 17 10:56:31 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e675d504a68d804fb238d031e72e92412afef9df Author: Johannes Blaschke Date: Thu Oct 17 10:54:16 2019 -0700 remove unused reference lists src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit f337024f32d3a24839aaa9acf4aa4e4e5843e340 Merge: b1cd45e7 af341289 Author: Andy Nonaka Date: Thu Oct 17 10:44:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit af341289a737e83266abc597c11f9c52c03d7793 Merge: 7a30b73e 9c60cdc9 Author: Johannes Blaschke Date: Thu Oct 17 10:44:03 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b1cd45e74ef310e5079a169f7e29d7ba1994493b Author: Andy Nonaka Date: Thu Oct 17 10:44:03 2019 -0700 playing around with diffusion test exec/immersedIons/inputs_paper_diffusion commit 7a30b73e6a98955291cda5a2262849c274a16c2e Author: Johannes Blaschke Date: Thu Oct 17 10:43:58 2019 -0700 update the way we initialize multiblobs exec/immersed_boundary/channel_multiblob/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 0822e36adea020327a3bede9339f6a77d27ac44a Author: Andy Nonaka Date: Thu Oct 17 10:29:39 2019 -0700 misspelling src_particles/src_F90/particle_functions.F90 commit 9c60cdc9b5a2a6588112914816bac100109cdfcb Merge: d1790984 da1f83a8 Author: Daniel Ladiges Date: Thu Oct 17 09:54:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d1790984d25f5a6b795c3a9a2836403763e5121d Author: Daniel Ladiges Date: Thu Oct 17 09:53:49 2019 -0700 Added directories for Berlin examples. exec/exercises/compressible/GNUmakefile exec/exercises/compressible/delPLots exec/exercises/compressible/inputs_temperature_3d exec/exercises/compressible/main_driver.cpp exec/exercises/incompressible/GNUmakefile exec/exercises/incompressible/Make.package exec/exercises/incompressible/WritePlotFile.cpp exec/exercises/incompressible/advance.cpp exec/exercises/incompressible/delPLots exec/exercises/incompressible/init_funcs.F90 exec/exercises/incompressible/init_s_funcs.F90 exec/exercises/incompressible/inputs_diffusion_2d exec/exercises/incompressible/main_driver.cpp exec/exercises/incompressible/multispec_test_functions.H exec/exercises/incompressible/multispec_test_functions_F.H commit da1f83a82ddaccf4381c248193897ac86ca75e2f Author: Johannes Blaschke Date: Thu Oct 17 09:05:20 2019 -0700 add multiblob exec exec/immersed_boundary/channel_multiblob/GNUmakefile exec/immersed_boundary/channel_multiblob/Make.package exec/immersed_boundary/channel_multiblob/WritePlotFile.cpp exec/immersed_boundary/channel_multiblob/advance.cpp exec/immersed_boundary/channel_multiblob/init_funcs.F90 exec/immersed_boundary/channel_multiblob/init_s_funcs.F90 exec/immersed_boundary/channel_multiblob/main_driver.H exec/immersed_boundary/channel_multiblob/main_driver.cpp exec/immersed_boundary/channel_multiblob/main_driver_F.H commit bd2014b11ecf2545b1b82bf41caf60e0bbd40272 Merge: ab7daf35 e76af47e Author: Johannes Blaschke Date: Thu Oct 17 08:54:55 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit e76af47e9ead0182fb68d781aed5b8181ec87123 Merge: 5412e9a0 2de45d19 Author: Daniel Ladiges Date: Wed Oct 16 18:56:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5412e9a0fc4bd81950238fff4eb55ba880c305a4 Author: Daniel Ladiges Date: Wed Oct 16 18:55:56 2019 -0700 Various modifications for Berlin demo. exec/compressible/GNUmakefile exec/compressible/inputs_test_3d exec/compressible/main_driver.cpp exec/multispec/GNUmakefile exec/multispec/init_funcs.F90 exec/multispec/inputs_bubble_2d exec/multispec/inputs_diffusion_2d src_compressible/flux.cpp src_compressible/src_F90/init_consvar.F90 commit ab7daf35dc1e29aad94bbf2416f37c6fed8318c4 Author: Johannes Blaschke Date: Wed Oct 16 16:40:09 2019 -0700 add new parameter file exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy.large-thin commit e4ccc7fa00972ba4cfb14c4f65ce5137a6d176e9 Merge: fc3e55e2 2de45d19 Author: Johannes Blaschke Date: Wed Oct 16 12:58:32 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit fc3e55e270ad2fd9d9adb8ac3db3f64698651edf Author: Johannes Blaschke Date: Wed Oct 16 12:58:28 2019 -0700 update render script exec/immersed_boundary/flagellum/Render Frames.ipynb commit 2de45d1952c0f9987c3b64c88d6c0f08e46a2f87 Author: Andy Nonaka Date: Tue Oct 15 17:04:05 2019 -0700 poisson tolerance to 1.d-8y exec/immersedIons/inputs_paper_cond commit 49905d7fbc75a6f80cc94868f9a0a9d2491a7a23 Merge: 54325d08 eb2164d7 Author: Daniel Ladiges Date: Tue Oct 15 16:33:53 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 54325d087c72c2cb11c2a3a6cd626965bbaf4aec Author: Daniel Ladiges Date: Tue Oct 15 16:33:38 2019 -0700 Added output of current variance exec/compressible/GNUmakefile exec/compressible/inputs_giantfluct_3d exec/immersedIons/inputs_3d src_particles/src_F90/collision_functions.F90 commit eb2164d792d7f04760a1a870f0e15ffa085af831 Author: Andy Nonaka Date: Tue Oct 15 16:08:30 2019 -0700 checkpoint pressure stochastic restart with particles and multiple grids now works with 4 processors (with at least the test I'm using on my workstation) exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp commit d8359ba09b09ac771427f5d6972c9269b89d8827 Author: Andy Nonaka Date: Tue Oct 15 15:02:47 2019 -0700 checkpointing electric potential (used as initial guess for ES solve in next time step) exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp commit 37af5cb30fe8ea45c102c7a1ce67d64f9d5905dc Author: Andy Nonaka Date: Tue Oct 15 11:12:11 2019 -0700 restart now works for particle mean and variances note that it even works when the particle grid has a different refinement than the fluid grid exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp commit 73557a4733ffb6e3813b113c5b12794dee7085de Author: Andy Nonaka Date: Tue Oct 15 09:14:43 2019 -0700 add call to UpdateCellVectors after restarting particles. simulation runs but results don't match...? exec/immersedIons/Checkpoint.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 1ea158165c9bfb0d40fd898adfa6c7aecadca37e Merge: 05ec259a 19ae3fe5 Author: Daniel Ladiges Date: Mon Oct 14 18:58:28 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 05ec259a7450f46a2e2d756eb981e5c86df51227 Author: Daniel Ladiges Date: Mon Oct 14 18:57:37 2019 -0700 Finished distributed g(r) calculation and output. Except still have to add correct normalization. exec/immersedIons/delPlots exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/Debug.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 19ae3fe55fc09c66c79a233f0af19a2beaf53faf Author: Andy Nonaka Date: Mon Oct 14 17:09:20 2019 -0700 gmres_rel_tol to 1d-10 from 1d-12 exec/immersedIons/inputs_paper_cond exec/immersedIons/inputs_paper_eo exec/immersedIons/inputs_paper_gr commit 5cc70623e57b38e7e52c83fe84c7838903c276f6 Author: Andy Nonaka Date: Mon Oct 14 16:42:27 2019 -0700 fix parallel particle init bug exec/immersedIons/particleGen.cpp commit 468d5249d1fcfc3f89e8ebf21d15e3d7ef9ec768 Author: Andy Nonaka Date: Mon Oct 14 14:42:06 2019 -0700 make parameters for Na Cl exec/immersedIons/inputs_paper_cond commit 45c83c4bc8bf37188d1b6815eb83fb13987e7aab Author: Andy Nonaka Date: Fri Oct 11 18:35:09 2019 -0700 checkpoint/restart umac mean and variance stats working single processor exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp commit 0595d928f4da123f2c1c7b5f99bf8875995eb2f6 Author: Andy Nonaka Date: Fri Oct 11 18:11:38 2019 -0700 immersedIon checkpoint/restart with 1 processor is now working up to solver tolerances exec/immersedIons/Checkpoint.cpp commit a13e0a7cc5b9b79f38698c2f052fda31079fa7f1 Author: Andy Nonaka Date: Fri Oct 11 16:11:35 2019 -0700 fix timer name exec/immersedIons/Checkpoint.cpp commit fc38f87bb7e9bd935bd3267c1b8c884cbcd80e29 Author: Andy Nonaka Date: Fri Oct 11 15:21:26 2019 -0700 rng engine restart fixes exec/immersedIons/Checkpoint.cpp src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 commit 2db56244115986e8b861ead0b8ecbb4e500595d5 Author: Andy Nonaka Date: Thu Oct 10 18:29:51 2019 -0700 calling checkpoint and restart now for hydro, rng, and particles... not working yet exec/hydro/Checkpoint.cpp exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 commit 1d4714592d52703f37f146df18f03eff990ebc92 Author: Andy Nonaka Date: Thu Oct 10 16:56:42 2019 -0700 more code cleanup/prep for checkpoint/restart exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp commit 497e90a8c7323d9631c09f2de5c097185437fd6d Author: Andy Nonaka Date: Thu Oct 10 15:48:56 2019 -0700 checkpoint updates exec/immersedIons/Checkpoint.cpp commit 986d1c079678e3e9f03338d9e0809fe6da270edc Author: Andy Nonaka Date: Thu Oct 10 14:59:00 2019 -0700 checkpoint progress exec/immersedIons/Checkpoint.cpp exec/immersedIons/INS_functions.H exec/immersedIons/delPlots exec/immersedIons/main_driver.cpp commit 2815511c82c81c08bfb63228cd72f985933e2664 Author: Andy Nonaka Date: Thu Oct 10 14:35:25 2019 -0700 more code tidying exec/immersedIons/main_driver.cpp commit e356415d0ac9bf88bdb4475a298c44d15200eaff Merge: 62bdeb4a a35578ad Author: Andy Nonaka Date: Thu Oct 10 14:07:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 62bdeb4a87c41677e875d0f8ca88f181d4d81d22 Author: Andy Nonaka Date: Thu Oct 10 14:07:02 2019 -0700 clean out unused code starta adding some checkpointing stuff in exec/immersedIons/Checkpoint.cpp exec/immersedIons/DEBUG.F90 exec/immersedIons/GNUmakefile exec/immersedIons/INS_functions.H exec/immersedIons/Make.package exec/immersedIons/TimeStep.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/debug_functions_F.H exec/immersedIons/hydro_test_functions.H exec/immersedIons/hydro_test_functions_F.H exec/immersedIons/init_s_funcs.F90 exec/immersedIons/main_driver.cpp exec/immersedIons/main_driver_OLD.cpp exec/immersedIons/particleGen.cpp commit a35578ada70c01eb7265744a026fa977a73ee141 Merge: ad2317dd 92cae877 Author: Johannes Blaschke Date: Thu Oct 10 10:51:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ad2317dd553c113e19ae822b90b3cc45c070499d Author: Johannes Blaschke Date: Thu Oct 10 10:51:34 2019 -0700 this seems to fix the mpi error exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/inputs_chlamy.highres-thin exec/immersed_boundary/flagellum/inputs_chlamy.large commit 92cae8773eda20b1051c0c7129cc99c4e62c47bf Author: Andy Nonaka Date: Thu Oct 10 09:42:46 2019 -0700 more cleanup; also fixed the logic on the seeds so none overlap. this will change regression (when battra comes alive) exec/immersedIons/main_driver.cpp commit 44d42104bc1249d09afda537d7695ee15821891a Merge: c78151ad 68294aa1 Author: Andy Nonaka Date: Thu Oct 10 08:57:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c78151ad7ecc79f0874d4dd7b21ebcd87f997f94 Author: Andy Nonaka Date: Thu Oct 10 08:56:45 2019 -0700 cleaning up main driver... no functional changes. tidying up so I can put the restart capability in a bit easier... exec/immersedIons/main_driver.cpp commit 68294aa1d3db91360ab6fcd532ef26619c946faa Author: Johannes Blaschke Date: Wed Oct 9 22:40:03 2019 -0700 crap! forgot these files exec/immersed_boundary/flagellum/advance_CN.cpp exec/immersed_boundary/flagellum/ib_md.cpp commit 91d79b690f558e8858d1ae334e46c85e3cb7ef98 Author: Johannes Blaschke Date: Wed Oct 9 18:59:08 2019 -0700 save force (spread to fluid) in plot files exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit 9f62d92956d4cba34d388a19e89d8741c3e925cd Author: Johannes Blaschke Date: Wed Oct 9 18:44:42 2019 -0700 seperate out the different functions in advance.cpp exec/immersed_boundary/flagellum/Make.package exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H commit ce02effa67a9397895e448e7d5d4764565b9a449 Author: Johannes Blaschke Date: Wed Oct 9 18:21:52 2019 -0700 tidy up and suggest improvement src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit e2853e5ea589b794f08fe33563f682314bc70c23 Author: Johannes Blaschke Date: Wed Oct 9 17:46:33 2019 -0700 clean up unused projects exec/immersed_boundary/channel_dumbbell_sol/Explore Data MP.ipynb exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/GNUmakefile exec/immersed_boundary/channel_dumbbell_sol/Make.package exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/compute_convfact_2.sh exec/immersed_boundary/channel_dumbbell_sol/init_funcs.F90 exec/immersed_boundary/channel_dumbbell_sol/init_s_funcs.F90 exec/immersed_boundary/channel_dumbbell_sol/inputs_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell_sol/main_driver.H exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver_F.H exec/immersed_boundary/channel_dumbbell_sol/run_conv_tests_2.sh exec/immersed_boundary/flagellum_chlamy/Explore Data MP.ipynb exec/immersed_boundary/flagellum_chlamy/Explore Data.ipynb exec/immersed_boundary/flagellum_chlamy/GNUmakefile exec/immersed_boundary/flagellum_chlamy/Make.package exec/immersed_boundary/flagellum_chlamy/Render Frames.ipynb exec/immersed_boundary/flagellum_chlamy/WritePlotFile.cpp exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/compute_convfact_2.sh exec/immersed_boundary/flagellum_chlamy/init_funcs.F90 exec/immersed_boundary/flagellum_chlamy/init_s_funcs.F90 exec/immersed_boundary/flagellum_chlamy/inputs_2d exec/immersed_boundary/flagellum_chlamy/inputs_3d exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum_chlamy/main_driver.H exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/main_driver_F.H exec/immersed_boundary/flagellum_chlamy/run_conv_tests_2.sh commit 3c8f3f6a9ec7fa16593bed843cea57de6d673237 Author: Johannes Blaschke Date: Wed Oct 9 17:43:11 2019 -0700 fix the stuff I broke, again exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.H commit ee602955e4ce1f2152c4b9f5bf10af8f51539e3b Author: Johannes Blaschke Date: Wed Oct 9 17:33:34 2019 -0700 update neighbor list algorithm exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit b60d2e15d233311e6171cda402a4165020bcc735 Author: Johannes Blaschke Date: Wed Oct 9 14:38:02 2019 -0700 fix the stuff I broke exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp commit 3b0026628e2b34a6fc96619745af25e584c18427 Author: Johannes Blaschke Date: Wed Oct 9 14:26:36 2019 -0700 replace cumbersome names exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 08144a905d279e4d5e610aa1fa3ba79ec5c25208 Author: Johannes Blaschke Date: Wed Oct 9 11:41:44 2019 -0700 update neighbor list API exec/immersed_boundary/flagellum/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit fae285236ac009a1623067f7bab8fa4fc0c46533 Merge: 6d63e477 5c61e1dd Author: Daniel Ladiges Date: Tue Oct 8 17:04:40 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6d63e47797d83ca7bc1bfff004b96e554960a7da Author: Daniel Ladiges Date: Tue Oct 8 17:03:45 2019 -0700 Added pulldown and pushup functions to IB base for sharing particle info between MPI ranks. Started radial dist function. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 5c61e1dd0f6a118848c4d6503c8b7286ca8edfd4 Author: Johannes Blaschke Date: Tue Oct 8 15:52:40 2019 -0700 Don't use and MFIter in a ParIter Other changes: 1. make static that which should be static 2. iterate over staggered stencil with proper bounds exec/immersed_boundary/flagellum/Render Frames.ipynb src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9b284f9ad962ae139b3fc75db3df78e43da1a2a7 Author: Johannes Blaschke Date: Tue Oct 8 12:24:14 2019 -0700 fix instability while time stepping exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp commit a5df77410dcb98fc70d9959ca80e8922d07b57ac Author: Johannes Blaschke Date: Tue Oct 8 10:27:58 2019 -0700 some things should be static src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 267cb7e67ad7f94aa01f9be4a6e01b4bb1ab1a6f Author: Johannes Blaschke Date: Tue Oct 8 09:55:55 2019 -0700 fix formatting src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 1dec4e4b01984cb038624809a28be4e7511173e0 Merge: 43cc20dd fb8db0c2 Author: Andy Nonaka Date: Mon Oct 7 18:15:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 43cc20dd8a3aba0d75f5ed8648c9b68d25bc9d5a Author: Andy Nonaka Date: Mon Oct 7 18:15:26 2019 -0700 conductivity test exec/immersedIons/inputs_paper_cond commit c419f7045bb4eb3fc682cafcf12f8c6e07c0dd55 Author: Andy Nonaka Date: Mon Oct 7 17:31:24 2019 -0700 remove debugging statement exec/immersedIons/main_driver.cpp commit 09ff183951fcda5002637e986d6800da20a492a7 Author: Andy Nonaka Date: Mon Oct 7 17:28:41 2019 -0700 turn on statistics by time interval exec/immersedIons/inputs_paper_eo commit fb8db0c2fab88f426e6972d4fc6f13af00357148 Author: Daniel Ladiges Date: Mon Oct 7 16:03:46 2019 -0700 Boundary spreading test case. exec/tests/boundarySpreading/Data.ipynb exec/tests/boundarySpreading/GNUmakefile exec/tests/boundarySpreading/INS_functions.H exec/tests/boundarySpreading/Make.package exec/tests/boundarySpreading/Make_precheck.package exec/tests/boundarySpreading/README exec/tests/boundarySpreading/WritePlotFile.cpp exec/tests/boundarySpreading/WritePlotFileHydro.cpp exec/tests/boundarySpreading/amrex_to_vtp.py exec/tests/boundarySpreading/convertSeries exec/tests/boundarySpreading/delPlots exec/tests/boundarySpreading/inputs_3d_dirichlet_noslip exec/tests/boundarySpreading/inputs_3d_dirichlet_slip exec/tests/boundarySpreading/main_driver.cpp exec/tests/boundarySpreading/particleGen.cpp exec/tests/boundarySpreading/precheck.F90 exec/tests/boundarySpreading/write_pview_file.py exec/tests/boundarySpreading/write_pview_file.pyc src_particles/src_F90/particle_functions.F90 commit 4e6e1dbcf69afd37bddd93c77083ae57f5851366 Merge: 0188d161 ddd1fd6c Author: Andy Nonaka Date: Mon Oct 7 15:50:02 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0188d16171c5fce53e4597279609b9cdf88f5838 Author: Andy Nonaka Date: Mon Oct 7 15:49:36 2019 -0700 turn of external field, set molarity to ~0.01 exec/immersedIons/inputs_paper_gr commit d91ecc8a73d1479f1c358246cd54cf106e45f47d Author: Andy Nonaka Date: Mon Oct 7 15:48:48 2019 -0700 if n_steps_skip is negative, now we reset the time averaging every -n_steps_skip time steps (useful for profiles that change slowly over time) exec/immersedIons/inputs_paper_eo exec/immersedIons/main_driver.cpp commit ddd1fd6ce3c966755490093417d9976976a2b7c2 Merge: 602b432e 398edb44 Author: Daniel Ladiges Date: Mon Oct 7 15:19:30 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 602b432edef9396a073260dbc29251054c3bf728 Author: Daniel Ladiges Date: Mon Oct 7 15:19:06 2019 -0700 Removed explicit application of electric field bc. src_electrostatic/electrostatic.cpp commit 398edb4428f3b3f27c8eb09a4e9cadb9ee0b467d Author: Andy Nonaka Date: Mon Oct 7 15:03:53 2019 -0700 tighten GMRES tolerance by 6 orders of magnitude for the production run... they were pretty loose and the flow field wasn't particularly divergence-free exec/immersedIons/inputs_paper_eo exec/immersedIons/inputs_paper_gr commit d926467f7e58182b4b87283c467092eb5801caeb Author: Andy Nonaka Date: Mon Oct 7 14:55:02 2019 -0700 giving the inputs file the "_paper_" string... getting serious now... exec/immersedIons/inputs_paper_eo commit d1c6a7445a7f1abc89afaa0283216e026efb83ab Author: Andy Nonaka Date: Mon Oct 7 14:52:00 2019 -0700 starting point for comparison to FHD EO. Doing fake Na+ Na-... needs to be fixed along with other parameters exec/immersedIons/inputs_eo commit 08efacad822da7569338aa1ed282a241af8e96b1 Author: Johannes Blaschke Date: Fri Oct 4 10:06:57 2019 -0700 tweak anchoring exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.cpp commit 879e7fa7fc72bc420eb443f69f298819396d01bd Author: Johannes Blaschke Date: Thu Oct 3 18:56:12 2019 -0700 fix more things broken by new bcs exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/flagellum/main_driver.cpp src_hydro/StochMFlux.cpp src_rng/MultiFABFillRandom.cpp commit 64be93b47fd5fc3252306029461543df36be2732 Author: Johannes Blaschke Date: Thu Oct 3 17:24:40 2019 -0700 fix new BCs exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/flagellum/Render Frames.ipynb src_common/MultiFABPhysBC.cpp src_hydro/MacProj_hydro.cpp src_hydro/StochMFlux.cpp commit 8b430e438721b444a07fba87dcf13f1e1e4cd974 Author: Johannes Blaschke Date: Thu Oct 3 16:45:07 2019 -0700 fix linker error exec/immersed_boundary/channel_dumbbell/main_driver.H commit 8a9858a2f4ff0b0037a956da94035c3fae90c2fb Merge: d52a881a 90f726ef Author: Johannes Blaschke Date: Thu Oct 3 16:18:17 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 90f726ef498d23c913901b03e151d25846ea327e Author: Daniel Ladiges Date: Thu Oct 3 16:07:34 2019 -0700 Charge spread order fix exec/tests/electroTwoWall/README src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.cpp commit d52a881a08298c43870250e0d9762fac960d7907 Merge: 6f3f9cb3 779882a0 Author: Johannes Blaschke Date: Thu Oct 3 15:53:17 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 6f3f9cb396b3422b8a0536f1ba78836dfe14193b Author: Johannes Blaschke Date: Thu Oct 3 15:53:00 2019 -0700 fix problem where we a putting the flagellum too close to a confining wall exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy.large commit 779882a051cd03e69391d5d89ec784b670b2380c Merge: d7a9f343 632da78c Author: Daniel Ladiges Date: Thu Oct 3 15:17:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d7a9f343640dfc04f90eaa193d4dec92f2732ae6 Author: Daniel Ladiges Date: Thu Oct 3 15:16:55 2019 -0700 Fixed bug in domainStressBC src_common/src_F90/multifab_physbc_mod.F90 commit 632da78cdddb0b46f3bc0713960589db20f81685 Author: Andy Nonaka Date: Thu Oct 3 14:56:32 2019 -0700 Abort if you try to call the direction-by-direction PhysBCMacVel or PhysBCDomainVel Lots of routines still need fixing; Abort at runtime indicating what to do src_common/MultiFABPhysBC.cpp src_gmres/ApplyMatrix.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit 7d9d38303a3e0307432971999240836d5b0b813b Author: Andy Nonaka Date: Thu Oct 3 14:53:13 2019 -0700 consolidate the umac ghost cell fill routines, and call the version that fills all the components at once (the dir-by-dir one doesn't work correctly with certain bc combinations) src_hydro/advance.cpp commit 099a689e60e55cd69a1d8d721e09b82834898a68 Author: Daniel Ladiges Date: Thu Oct 3 14:18:04 2019 -0700 slip bc kernel folding bug fix src_common/src_F90/multifab_physbc_mod.F90 commit 22d91b0ab1a5ba032a120b779a6b68c083ddc7c9 Author: Daniel Ladiges Date: Thu Oct 3 12:37:19 2019 -0700 Forgot to track new advance.cpp src_hydro/advance.cpp commit 3b99d0f9fd89bd5a7bfb9621b78b8be2a8918308 Author: Daniel Ladiges Date: Thu Oct 3 12:31:56 2019 -0700 Moved advance.cpp to src_hydro exec/immersedIons/INS_functions.H exec/immersedIons/advance.cpp exec/tests/RFDanalysis/INS_functions.H exec/tests/RFDanalysis/advance.cpp exec/tests/electroPeriodic/INS_functions.H exec/tests/electroPeriodic/advance.cpp exec/tests/electroTwoWall/INS_functions.H exec/tests/electroTwoWall/advance.cpp src_hydro/Make.package src_hydro/hydro_functions.H commit 2327aec9d6bafb65398a485956226dc453bbe231 Merge: 9350d86f c035eb93 Author: Daniel Ladiges Date: Thu Oct 3 12:12:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c035eb935ec0c9d9dc8cee345d15ccd79cb8abd8 Author: Andy Nonaka Date: Thu Oct 3 12:10:58 2019 -0700 bugfix; swap the order of sum boundary and fluid force kernal folding exec/immersedIons/advance.cpp commit 9350d86fd110f8c31e2b7672ddd72cac64037c6e Merge: 81f4c660 f0febb3d Author: Daniel Ladiges Date: Thu Oct 3 12:09:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f0febb3d16229ea4144d30fcdb71384ae0bcfb6e Author: Andy Nonaka Date: Thu Oct 3 12:09:17 2019 -0700 bugfix; swap the order of sum boundary and fluid force kernal folding src_common/MultiFABPhysBC.cpp src_particles/FhdParticleContainer.cpp commit 81f4c660f3c44050cf087a5f70b3daff507b36a8 Author: Daniel Ladiges Date: Thu Oct 3 11:23:41 2019 -0700 More unit test stuff src_common/src_F90/multifab_physbc_mod.F90 src_immersed-boundary/IBMarkerContainerBaseI.H commit ca2a345e933681a0fdc86d760f4b336cc756d7f3 Author: Andy Nonaka Date: Thu Oct 3 10:58:42 2019 -0700 abort message if you try to call the sequential macstress or domainstress kernal folding routines src_common/MultiFABPhysBC.cpp commit 421fa732abcbf0df79b94bf599ab0f7d87be1fa6 Author: Johannes Blaschke Date: Wed Oct 2 21:37:54 2019 -0700 find first and second markers exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/src_analysis/data_model.py commit bd18e79fca7b642767927fdb619077a39f64f8c4 Merge: 7d08e79d 1720a368 Author: Johannes Blaschke Date: Wed Oct 2 21:13:11 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 7d08e79d25f36686020b5c31876458ba1f00a588 Author: Johannes Blaschke Date: Wed Oct 2 21:12:55 2019 -0700 don't use indices, use p.id instead. also fix self.contains_id exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/src_analysis/data_model.py commit 1720a3688e1f8b487062c4950167c3ca12e42b09 Merge: 57e9fd65 e3f3a687 Author: Daniel Ladiges Date: Wed Oct 2 16:20:58 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 57e9fd65b18d6a1732876357f65d79544d0a1965 Author: Daniel Ladiges Date: Wed Oct 2 16:20:09 2019 -0700 Added slip to kernel fluid bcs. Added a multfab sum function for debugging. src_common/ComputeBasicStats.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_basic_stats.F90 src_common/src_F90/debug_mod.F90 src_common/src_F90/multifab_physbc_mod.F90 src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit e3f3a6878a80bc9920b599294e55c6ccb0e80781 Author: Johannes Blaschke Date: Wed Oct 2 15:52:01 2019 -0700 fix python weak reference, and play with parameters exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/src_analysis/visualize.py src_common/FindCoords.cpp commit b288f7901a37fc43023b949d1ff34158c98c5f27 Author: KKlymko Date: Wed Oct 2 14:12:06 2019 -0700 fixed fc_alpha and IBInit exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp commit 8c3226081d7215dad92875aca4ccb03b500ea500 Author: Johannes Blaschke Date: Tue Oct 1 16:32:54 2019 -0700 remove overloading src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 22a715504fc1d4d289a050576c5bc30ae3b75b57 Author: Johannes Blaschke Date: Tue Oct 1 16:21:25 2019 -0700 fix ghost flag in spreading src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/IBParticleContainer.cpp commit 0968e28373bc5037f562f9a3615d907430525e15 Merge: 35d774a4 8ea65b48 Author: Johannes Blaschke Date: Tue Oct 1 15:05:13 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 35d774a4b42cf4172a83f44873d1f8f54cef410f Author: Johannes Blaschke Date: Tue Oct 1 15:05:07 2019 -0700 move frame rendering to python backend exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/src_analysis/data_model.py exec/immersed_boundary/src_analysis/visualize.py commit 8ea65b481dd0f1606c006ec96bf9f6780829ded5 Merge: cfc00723 877e6b57 Author: jbb Date: Tue Oct 1 14:00:34 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 877e6b574307588d4953dc6a14f783b8a3e7b6da Merge: a75fbc6d 35c419d2 Author: Andy Nonaka Date: Tue Oct 1 13:41:30 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a75fbc6d2fcccbcbb7d06cd2fd4bf08c731e1d1b Author: Andy Nonaka Date: Tue Oct 1 13:41:15 2019 -0700 revert inputs_eo exec/immersedIons/inputs_eo commit 35c419d22eb526608df764b34651c29dd8412a4c Merge: 7d13cbbe 8e344a14 Author: Daniel Ladiges Date: Tue Oct 1 13:39:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7d13cbbebc63a969aa492a0437c1edcac79b2b25 Author: Daniel Ladiges Date: Tue Oct 1 13:38:45 2019 -0700 Added unit tests for electrostatic with dirichlet boundary. exec/tests/electroPeriodic/analysis.nb exec/tests/electroPeriodic/main_driver.cpp exec/tests/electroTwoWall/Data.ipynb exec/tests/electroTwoWall/GNUmakefile exec/tests/electroTwoWall/INS_functions.H exec/tests/electroTwoWall/Make.package exec/tests/electroTwoWall/Make_precheck.package exec/tests/electroTwoWall/README exec/tests/electroTwoWall/WritePlotFile.cpp exec/tests/electroTwoWall/WritePlotFileHydro.cpp exec/tests/electroTwoWall/advance.cpp exec/tests/electroTwoWall/amrex_to_vtp.py exec/tests/electroTwoWall/analysis.nb exec/tests/electroTwoWall/convertSeries exec/tests/electroTwoWall/delPlots exec/tests/electroTwoWall/inputs_3d exec/tests/electroTwoWall/main_driver.cpp exec/tests/electroTwoWall/particleGen.cpp exec/tests/electroTwoWall/precheck.F90 exec/tests/electroTwoWall/write_pview_file.py exec/tests/electroTwoWall/write_pview_file.pyc src_particles/FhdParticleContainer.cpp commit 8e344a148d1abb6e07c381ca9bafb5aced3562e7 Author: Andy Nonaka Date: Tue Oct 1 13:37:56 2019 -0700 don't write out means and variances to plotfile unless plot_means=1 or plot_vars=1 (0 by default) exec/compressible/inputs_regression_RT_3d src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/compressible_namelist.F90 src_compressible/writePlotFile.cpp commit cfc0072378d303cdeddb26593395462d4c8db40a Merge: 12b73b25 e20befc6 Author: jbb Date: Tue Oct 1 12:59:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 12b73b25d72e2a451cae8f18db09f3a080bf902e Author: jbb Date: Tue Oct 1 12:58:40 2019 -0700 fixed error in primitive variable flux and set up taylor green src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/init_consvar.F90 commit e20befc61f038fed6c06f963006dc4ad4be3e936 Author: Johannes Blaschke Date: Tue Oct 1 10:29:57 2019 -0700 start moving contents from notebooks to python backend exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy.large exec/immersed_boundary/src_analysis/data_model.py commit c26e5388243bad98f17cf79ab56a90b49cd27d99 Author: Daniel Ladiges Date: Mon Sep 30 17:07:40 2019 -0700 Added README to electrostatic tests. exec/tests/electroPeriodic/README commit 6194f2c096af38fc02185f703deb72e976829c1e Author: Daniel Ladiges Date: Mon Sep 30 17:05:31 2019 -0700 Added another periodic electrostatic test exec/immersedIons/inputs_eo exec/tests/electroPeriodic/inputs_3d exec/tests/electroPeriodic/main_driver.cpp commit 30c6497351c42fc20e5cd3015b00c95368bb5d45 Merge: f3f1cbee 187e5910 Author: Daniel Ladiges Date: Mon Sep 30 16:42:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f3f1cbee8ca40fc988d62e34e63ebf6f46edc432 Author: Daniel Ladiges Date: Mon Sep 30 16:41:14 2019 -0700 Added some functions to FHDparticleContainer which print modify particle info for debugging. Set up some directories with unit tests. exec/tests/RFDanalysis/Data.ipynb exec/tests/RFDanalysis/GNUmakefile exec/tests/RFDanalysis/INS_functions.H exec/tests/RFDanalysis/Make.package exec/tests/RFDanalysis/Make_precheck.package exec/tests/RFDanalysis/WritePlotFile.cpp exec/tests/RFDanalysis/WritePlotFileHydro.cpp exec/tests/RFDanalysis/advance.cpp exec/tests/RFDanalysis/amrex_to_vtp.py exec/tests/RFDanalysis/analysis.nb exec/tests/RFDanalysis/convertSeries exec/tests/RFDanalysis/delPlots exec/tests/RFDanalysis/inputs_3d exec/tests/RFDanalysis/main_driver.cpp exec/tests/RFDanalysis/particleGen.cpp exec/tests/RFDanalysis/precheck.F90 exec/tests/RFDanalysis/write_pview_file.py exec/tests/RFDanalysis/write_pview_file.pyc exec/tests/electroPeriodic/Data.ipynb exec/tests/electroPeriodic/GNUmakefile exec/tests/electroPeriodic/INS_functions.H exec/tests/electroPeriodic/Make.package exec/tests/electroPeriodic/Make_precheck.package exec/tests/electroPeriodic/WritePlotFile.cpp exec/tests/electroPeriodic/WritePlotFileHydro.cpp exec/tests/electroPeriodic/advance.cpp exec/tests/electroPeriodic/amrex_to_vtp.py exec/tests/electroPeriodic/analysis.nb exec/tests/electroPeriodic/convertSeries exec/tests/electroPeriodic/delPlots exec/tests/electroPeriodic/inputs_3d exec/tests/electroPeriodic/main_driver.cpp exec/tests/electroPeriodic/particleGen.cpp exec/tests/electroPeriodic/precheck.F90 exec/tests/electroPeriodic/write_pview_file.py exec/tests/electroPeriodic/write_pview_file.pyc src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 187e5910ab6dbe2b98cee2d5c87182d3e1f1d94d Author: Andy Nonaka Date: Mon Sep 30 09:36:51 2019 -0700 9 digit number strings for hydro to match the other plotfiles exec/immersedIons/WritePlotFileHydro.cpp commit fcdd46e019b1552b04bd1bc4a904e828c8e9b215 Author: Daniel Ladiges Date: Fri Sep 27 16:41:20 2019 -0700 Version of RFD in IB base now running and tested. exec/RFDanalysis/analysis.nb exec/RFDanalysis/inputs_3d exec/immersedIons/inputs_3d src_common/ComputeDivAndGrad.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit ab7b8c6b932610c5e3b47c9705b7f0f0b8c64f98 Merge: 762fc55b 263f0059 Author: Daniel Ladiges Date: Fri Sep 27 16:31:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 762fc55b4963ee6a56705ff3f34beeb8df3b8494 Author: Daniel Ladiges Date: Fri Sep 27 16:29:08 2019 -0700 Zero all fields in particle init for immersedIons exec/immersedIons/particleGen.cpp commit 263f005925bf6edbcebe42e9d4118e7fa5b6a0b1 Author: Johannes Blaschke Date: Fri Sep 27 13:07:54 2019 -0700 Merge Andy's changes and fix new FPEs exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy.large src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp commit 530caf08ee8a6d20dc4634624fb2939766efe50e Author: Andy Nonaka Date: Thu Sep 26 17:12:02 2019 -0700 bugfix in preconditioner logic for singular problems src_gmres/ApplyPrecon.cpp commit e7ed234a0593e7b3601f3583a48ba288efef069d Author: Andy Nonaka Date: Thu Sep 26 11:16:39 2019 -0700 add subroutine get_uniform() back in src_rng/src_F90/rng_functions.F90 commit 9ea70a76030308e89bcb6c17d2d86d1191fdb81a Author: Andy Nonaka Date: Thu Sep 26 09:58:28 2019 -0700 StagApplyOp now enforces physical boundary conditions (probably redundantly if the ghost cells were filled correctly, but the original code does this) touched a LOT of files - everything that calls StagApplyOp now needs a Geometry object input exec/DSMC-LDT/TimeStep.cpp exec/DSMC/TimeStep.cpp exec/DSMCstatcheck/TimeStep.cpp exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/main_driver.cpp exec/RFDanalysis/advance.cpp exec/brownian/TimeStep.cpp exec/channel/advance.cpp exec/fluctuatingMembrane/TimeStep.cpp exec/fluctuatingMembrane/advance.cpp exec/hydro/advance.cpp exec/immersedIons/TimeStep.cpp exec/immersedIons/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/multispec/advance.cpp src_gmres/ApplyMatrix.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_immersed-boundary/IBGMRES.cpp commit 94bfd579fb698bf4fe7f971d9f597d1d2abf9cd3 Author: Andy Nonaka Date: Wed Sep 25 17:19:31 2019 -0700 don't call stokes solver before low mach solver if fluid_tog==2 exec/immersedIons/main_driver.cpp commit 019b96fdf7261b21fb61f4577b341b84341ffaea Author: Andy Nonaka Date: Wed Sep 25 16:41:59 2019 -0700 rng restart first attempt... buggy WIP exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 commit 06458564ccc2cd3ae4e8e2898ef335f244882575 Merge: 6eb0ba5d 15ce3c1b Author: Andy Nonaka Date: Wed Sep 25 16:13:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6eb0ba5d701d843428858e6668d42b5495b4db53 Author: Andy Nonaka Date: Wed Sep 25 16:12:50 2019 -0700 writing out random number engine states to checkpoint exec/hydro/Checkpoint.cpp src_rng/rng_functions_F.H src_rng/src_F90/bl_random.F90 src_rng/src_F90/rng_functions.F90 commit 15ce3c1b8dab415a8885d84a75c154d14988f3e4 Merge: 171a835d e24549a8 Author: Daniel Ladiges Date: Wed Sep 25 15:19:01 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 171a835d2599fed4854609dd9c3d01a85dcc4ffc Author: Daniel Ladiges Date: Wed Sep 25 15:17:51 2019 -0700 Minor fix to midpoint stepping near boundaries. This is almost certainly unrelated to bunching behaviour exec/RFDanalysis/GNUmakefile exec/RFDanalysis/analysis.nb exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit e24549a879812e4ac9d71fde14db4ab987961d02 Author: Andy Nonaka Date: Wed Sep 25 11:06:07 2019 -0700 progress toward random number restart src_rng/bl_random_c.H src_rng/bl_random_c.cpp src_rng/src_F90/bl_random.F90 commit 01d7a56b636dbb06a1ae39a5118887601c9548d5 Author: Andy Nonaka Date: Tue Sep 24 15:03:42 2019 -0700 hydro restart works exec/hydro/Checkpoint.cpp exec/hydro/main_driver.cpp commit 85cc56d3d85d24a72006f3205dfc9ee8b5541c88 Author: Andy Nonaka Date: Tue Sep 24 14:13:53 2019 -0700 restart routines for the hydro/ example grid data exec/hydro/Checkpoint.cpp exec/hydro/Make.package exec/hydro/WritePlotFile.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit 2928b99722aec3f5686a4507bb8748ba4a753bab Author: Andy Nonaka Date: Tue Sep 24 10:57:25 2019 -0700 fix gpu version of random number fill to be normal, not uniform src_rng/MultiFABFillRandom.cpp commit 10e66c170947bd60032d1e7fe9f59aa986719100 Author: Daniel Ladiges Date: Tue Sep 24 08:20:12 2019 -0700 Fixed bug in calculation of force for image charges src_particles/src_F90/particle_functions.F90 commit 9375e858e852f43b65c982ddf8505d02fc1a5b00 Author: Andy Nonaka Date: Mon Sep 23 14:58:31 2019 -0700 set particleMeans and particleVars to zero at beginning of simulation exec/immersedIons/main_driver.cpp commit caa0befedafb53009ea4764a96df81c217146d17 Merge: 4f4f1d52 3edd825e Author: Andy Nonaka Date: Mon Sep 23 11:23:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4f4f1d52c9ec65f18efbb5a299f0d1f6230c9dde Author: Andy Nonaka Date: Mon Sep 23 11:23:19 2019 -0700 electro-osmosis setup exec/immersedIons/inputs_eo commit 3edd825e2e9513ee5c666f576e1896add1d92fdd Author: Johannes Blaschke Date: Fri Sep 20 22:14:19 2019 -0700 Merge exec/immersed_boundary/flagellum/Render Frames.ipynb src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 60d639feae4950014758de05fa6a04194bc7f9b9 Merge: 0d61ea47 da2665c1 Author: Johannes Blaschke Date: Fri Sep 20 22:08:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0d61ea470fb5575d78d272fded4c128201a1e8e4 Author: Johannes Blaschke Date: Fri Sep 20 22:08:06 2019 -0700 do not normalize t! exec/immersed_boundary/src_models/IBMarkerMD.cpp commit da2665c17b851c8cffa1b14f7924a971613e86a9 Author: Andy Nonaka Date: Fri Sep 20 18:12:46 2019 -0700 add timer (wallclock time per time step) exec/immersedIons/main_driver.cpp commit 40f392675dcb71dd2e43cf9064b5ac4b4aae4b52 Author: Andy Nonaka Date: Fri Sep 20 17:45:43 2019 -0700 electroosmosis setup exec/immersedIons/inputs_eo commit aaa5a8f14eaec3e85fd86f68dce0ed15beaf2a66 Author: Andy Nonaka Date: Fri Sep 20 16:31:25 2019 -0700 conductivity regression test exec/immersedIons/inputs_regression_cond commit efddb8284cd6eee3cd1feab0631d4e7a69e52829 Merge: 64252440 63d4c287 Author: Daniel Ladiges Date: Fri Sep 20 15:18:32 2019 -0700 Merge conflict because SOMEONE keeps fixing formatting on functions I'm actively working on. Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 64252440c95297f0136ea5b64461a5a1136867a3 Author: Daniel Ladiges Date: Fri Sep 20 15:13:42 2019 -0700 Some debugging code for RFD exec/RFDanalysis/analysis.nb exec/RFDanalysis/inputs_3d src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/src_F90/particle_functions.F90 commit 09fd1263eb8fe745cf611527097329099838e5d9 Author: Daniel Ladiges Date: Fri Sep 20 15:10:19 2019 -0700 Some updates to for Andy to play with. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit 63d4c2875d50d7f0b6eaa8cf6f67a8dedffd7eee Author: Andy Nonaka Date: Fri Sep 20 09:34:21 2019 -0700 Update README.md README.md commit e66e999a55ad760ba2c9d7b3374593d1fb40221f Author: Daniel Ladiges Date: Thu Sep 19 11:10:55 2019 -0700 Ditto again. exec/RFDanalysis/GNUmakefile src_particles/src_F90/particle_functions.F90 commit d17d55f4039b4fafd50570c4976ad748a51371f4 Merge: 6772b520 e66e999a Author: Johannes Blaschke Date: Thu Sep 19 11:09:11 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 6772b52076cea5b471ea89d08bdc462bd97a66ca Author: Johannes Blaschke Date: Thu Sep 19 11:09:05 2019 -0700 make const inputs const src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit ac5d95cb1ce2beba237b5ed9e43557fed46d1611 Author: Daniel Ladiges Date: Thu Sep 19 11:07:57 2019 -0700 Ditto src_particles/src_F90/particle_functions.F90 commit efd5c4de498131fbb0d94d0de00d29826d75e921 Merge: 0456d2f4 3fc60c28 Author: Daniel Ladiges Date: Thu Sep 19 11:06:31 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0456d2f428689859709ec02e7a7818504a7f1801 Author: Daniel Ladiges Date: Thu Sep 19 11:03:51 2019 -0700 Turned off boundary intersection check for midpoint step - not necessary and fixes small bug. exec/RFDanalysis/analysis.nb exec/RFDanalysis/inputs_3d exec/RFDanalysis/main_driver.cpp exec/fluctuatingMembrane/GNUmakefile exec/fluctuatingMembrane/particleGen.cpp exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 3fc60c28be3e84409cfc0c9c0c895f7c0b1ddd62 Author: Johannes Blaschke Date: Thu Sep 19 11:02:24 2019 -0700 fix missing coord inputs exec/immersed_boundary/flagellum/Render Frames.ipynb src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit ea5f966604046582383d9e4f09b438a69ab2ba32 Merge: cf71c823 64a952b7 Author: Johannes Blaschke Date: Thu Sep 19 09:38:18 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit cf71c8232631c86c590f8a0f60d1c73490a43c07 Author: Johannes Blaschke Date: Thu Sep 19 09:38:11 2019 -0700 checking for finite size effects exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.large commit c7420433db298189503744e207702bc043f8adf9 Author: Johannes Blaschke Date: Wed Sep 18 17:34:55 2019 -0700 solve some more nans exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.highres exec/immersed_boundary/src_models/IBMarkerMD.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp commit 64a952b7a44fa3acf45cd79c6352305ae1907dbb Author: Daniel Ladiges Date: Wed Sep 18 12:53:06 2019 -0700 Undid some debugging code that was stopping force spreading. exec/RFDanalysis/analysis.nb exec/RFDanalysis/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit 7605638d2ccf0288b49c7a161a773c4355d75aca Merge: 85d70327 527748d6 Author: Daniel Ladiges Date: Tue Sep 17 19:24:51 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 85d703276da91f0afe278b5bc4288a906255aeae Author: Daniel Ladiges Date: Tue Sep 17 19:21:49 2019 -0700 Added passing of correct coordinates to RFD function. Still a bug somewhere. exec/RFDanalysis/GNUmakefile exec/RFDanalysis/inputs_3d exec/RFDanalysis/main_driver.cpp src_electrostatic/electrostatic.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/src_F90/particle_functions.F90 commit 527748d619c239c5ce623054f9c63a0b9dd30bbc Author: Johannes Blaschke Date: Tue Sep 17 18:33:29 2019 -0700 make the buffered immersed boundary umac also adhere to boundary conditioms exec/immersed_boundary/flagellum/advance.cpp commit 20234d97acb3989d8b2403a5f4bd0bdf698270c1 Merge: 93fec08f a72b7d80 Author: Johannes Blaschke Date: Tue Sep 17 18:28:01 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 93fec08f15eb2991df50849ee5808124bd5e3b1c Author: Johannes Blaschke Date: Tue Sep 17 18:27:55 2019 -0700 finally found the nan exec/hydro/advance.cpp exec/immersed_boundary/flagellum/advance.cpp src_immersed-boundary/IBMarkerContainerBaseI.H commit a72b7d80e589c8547550880210dc9f518f3cf549 Merge: 8fc3764e 11d6b924 Author: Daniel Ladiges Date: Tue Sep 17 16:59:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8fc3764ec28c9bed16d35f61ac73e9875ca247ac Author: Daniel Ladiges Date: Tue Sep 17 16:49:50 2019 -0700 Kernel spread/inerp bounds in ib_fort_util functions now set according to pkernel_fluid. Fixes seg fault for 3pt kernel, still a bug in RFD somewhere though. exec/RFDanalysis/GNUmakefile exec/RFDanalysis/analysis.nb exec/RFDanalysis/inputs_3d exec/immersedIons/inputs_3d src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit f56e944803101e70b9f0c92eb7e98315150122f5 Author: Johannes Blaschke Date: Tue Sep 17 15:54:20 2019 -0700 fix bug where macro returns 2D case instead of 3D exec/immersed_boundary/src_models/IBMarkerMD.cpp commit cdecccc187c849d66dc6844e85644d74f4ebb028 Author: Johannes Blaschke Date: Tue Sep 17 15:54:14 2019 -0700 fix bug where macro returns 2D case instead of 3D exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 11d6b9240a27e78ffac2fe816c0c292fa0d59145 Merge: 037eea25 2e0ad330 Author: Johannes Blaschke Date: Mon Sep 16 17:01:50 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 037eea253413b35e768dc498570ded9f0450351b Author: Johannes Blaschke Date: Mon Sep 16 17:01:46 2019 -0700 fix some bits exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 2e0ad330d739c2d16c92396ff6979b855afc4d0c Author: Andy Nonaka Date: Mon Sep 16 15:52:58 2019 -0700 consolidate use statements src_particles/src_F90/particle_functions.F90 commit e02797022344d3a35aa0a6460a11b68427d53fe5 Author: Andy Nonaka Date: Mon Sep 16 15:40:33 2019 -0700 some cleanup of particle_functions module... WIP src_particles/src_F90/particle_functions.F90 commit 35b6e155da66b76c925d2431045a0e41c977d48e Author: Andy Nonaka Date: Mon Sep 16 15:13:33 2019 -0700 move everything into particle_functions_module src_particles/src_F90/particle_functions.F90 commit 8c0d44dfb9376a1aaa24e5a75a4d79c678b20590 Author: Johannes Blaschke Date: Mon Sep 16 13:38:55 2019 -0700 clean up some hacks exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.cpp commit 587dcd006c42fefc5289928a0600b3c5cd76e896 Author: Johannes Blaschke Date: Sun Sep 15 15:58:12 2019 -0700 fiddle with some parameters exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy.highres commit 10c5b977b666680950b9d377cd783096588b8f6d Author: Johannes Blaschke Date: Sun Sep 15 11:33:18 2019 -0700 fix issue where positions are initialized accross periodic boundaries exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/main_driver.cpp commit 0bba0aaac74b0d9b332ce32dc5d26d4e4c502a6e Author: Johannes Blaschke Date: Sun Sep 15 11:03:46 2019 -0700 chlamy motion is working now exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/main_driver.cpp commit c205b412928917e241cd4e8803a5326367dd7293 Author: Johannes Blaschke Date: Sun Sep 15 11:03:19 2019 -0700 properly renormalize the bond lenght exec/immersed_boundary/src_models/IBMarkerMD.cpp commit bba248fbed17903fa835e1c5aa55fb68c38b9bc0 Author: Johannes Blaschke Date: Fri Sep 13 21:24:18 2019 -0700 chlamy test run: no time dependence exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_chlamy commit d9c7cfd54620ed9b5b93e61c5393523bdee901f9 Author: Johannes Blaschke Date: Fri Sep 13 19:18:53 2019 -0700 prepare to use fourier modes in advance exec/immersed_boundary/flagellum/advance.cpp commit 3f06ee774510b0a7eb1c18c82549976fa4ba4eb2 Merge: b40fdc7e 0ffb3d19 Author: Johannes Blaschke Date: Fri Sep 13 16:43:02 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b40fdc7ed79e1d6a47a98ca1774a1c0d1bdafaf8 Author: Johannes Blaschke Date: Fri Sep 13 16:42:56 2019 -0700 add node-dependent N exec/immersed_boundary/flagellum/inputs_chlamy_data src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 0ffb3d19f0fb5a058a235595e1ff6e85007832d4 Author: Daniel Ladiges Date: Fri Sep 13 16:18:44 2019 -0700 Restored change to F90 spreading function to use function pointer for kernel. exec/RFDanalysis/inputs_3d src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 6e43d55b0c9cf92f9d90471825d2a834e6c96def Merge: b03902e5 67fa6a0b Author: Daniel Ladiges Date: Fri Sep 13 16:15:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b03902e5d94ccfdd82921c928a3392b481b67e8d Author: Daniel Ladiges Date: Fri Sep 13 16:13:45 2019 -0700 Overloaded spreading operators to allow passing of cell size variable. Added directory in exec with test framework for RFD. Revert "ib base spread and interpolations now have 6pt and 3pt options - set with pkernel_fluid, default is 6." This reverts commit 701fcdba4e1a075efc4cdce560ac063f974a2c36. exec/RFDanalysis/Data.ipynb exec/RFDanalysis/GNUmakefile exec/RFDanalysis/INS_functions.H exec/RFDanalysis/Make.package exec/RFDanalysis/Make_precheck.package exec/RFDanalysis/WritePlotFile.cpp exec/RFDanalysis/WritePlotFileHydro.cpp exec/RFDanalysis/advance.cpp exec/RFDanalysis/amrex_to_vtp.py exec/RFDanalysis/analysis.nb exec/RFDanalysis/convertSeries exec/RFDanalysis/delPlots exec/RFDanalysis/inputs_3d exec/RFDanalysis/main_driver.cpp exec/RFDanalysis/particleGen.cpp exec/RFDanalysis/precheck.F90 exec/RFDanalysis/write_pview_file.py exec/RFDanalysis/write_pview_file.pyc exec/fluctuatingMembrane/main_driver.cpp exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 67fa6a0ba030d0da51b89294a03911b1031848c0 Author: Johannes Blaschke Date: Fri Sep 13 14:47:56 2019 -0700 copy fourier data to c-land src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 1a91daf74220b78898759b5990ecf01c99ba807c Author: Johannes Blaschke Date: Thu Sep 12 21:19:33 2019 -0700 clean up and add make kernel functions pure: src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 701fcdba4e1a075efc4cdce560ac063f974a2c36 Author: Daniel Ladiges Date: Thu Sep 12 16:45:34 2019 -0700 ib base spread and interpolations now have 6pt and 3pt options - set with pkernel_fluid, default is 6. src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 80ec785067fbea63dc87090c6c519d34f909f991 Merge: 2a088ce4 e7a90975 Author: Daniel Ladiges Date: Thu Sep 12 15:56:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e7a909754037d3c92add743fde8a179684952f22 Author: Johannes Blaschke Date: Thu Sep 12 15:56:48 2019 -0700 start builiding the interface that will move the fourier coefficients src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 2a088ce49a573cddc498c0625631db78a6e9867a Author: Daniel Ladiges Date: Thu Sep 12 15:56:07 2019 -0700 Started adding different kernels to ib base class exec/immersedIons/advance.cpp exec/immersedIons/analysis.nb src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/src_F90/particle_functions.F90 commit 91eef62d2cbcec263f8eb6bd523ff7907e6a1aec Author: Johannes Blaschke Date: Thu Sep 12 15:45:26 2019 -0700 successfully read fourier coefficients into fortran exec/immersed_boundary/flagellum/inputs_chlamy_data src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 2824a0b1ac75ded974db0643f11ddfa98e5ba1dc Author: Johannes Blaschke Date: Thu Sep 12 14:33:22 2019 -0700 expan immbdy namespace exec/immersed_boundary/flagellum/inputs_chlamy src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit f0316c8de28b5066e7b267f9aa95d84e337ad429 Author: Johannes Blaschke Date: Thu Sep 12 13:34:36 2019 -0700 add clarifying comment src_immersed-boundary/IBMarkerContainerBaseI.H commit 28ac69ff2112900bb2383ced5a3701a7348b9804 Merge: b2ed4b2e df2765bb Author: Johannes Blaschke Date: Thu Sep 12 13:28:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b2ed4b2efba2f56166ae30dd653a4d4c73ccf30a Author: Johannes Blaschke Date: Thu Sep 12 13:26:38 2019 -0700 fix really annoying segfault src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit df2765bb07ebf393a4120d2a19d50a41b13b0182 Author: Daniel Ladiges Date: Thu Sep 12 13:19:16 2019 -0700 Added option to zero the net force on fluid for grmes solve. exec/fluctuatingMembrane/advance.cpp exec/fluctuatingMembrane/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit c0fc92f3cc91bbb1dd0b735e95deaee959a542d0 Author: Daniel Ladiges Date: Thu Sep 12 13:04:51 2019 -0700 Fixed bug in new version of RFD iin IB base class. src_immersed-boundary/IBMarkerContainerBaseI.H commit 7e09c6408958a8791d64512f1e2cd9a3e0ad4465 Author: Daniel Ladiges Date: Thu Sep 12 12:21:38 2019 -0700 Simplified plot output for fluctuatingMembrane exec/fluctuatingMembrane/WritePlotFile.cpp exec/fluctuatingMembrane/inputs_3d exec/immersedIons/WritePlotFile.cpp commit a1cb5a901f7975f12dfdf4dfaad47f6aa6535ebc Author: Johannes Blaschke Date: Wed Sep 11 15:38:06 2019 -0700 this way we can (finally) pass a fourier parameter file name exec/immersed_boundary/flagellum/inputs_chlamy exec/immersed_boundary/flagellum/inputs_chlamy_data src_immersed-boundary/src_F90/immbdy_namelist.F90 commit d062bc70addb1afa6aeef036fc7ca6039d6451df Author: Johannes Blaschke Date: Wed Sep 11 14:01:19 2019 -0700 exampand input file parser to include chlamy data src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit a36783faf2451c24e1ce5b50c011ffadd7fec57e Author: KKlymko Date: Tue Sep 10 14:31:41 2019 -0700 fixed reverse comments exec/_GL_alt_1D/backward_1d exec/_GL_alt_1D/inputs_1d commit a2e8245be1675a1d93f157907748923a31fd47d0 Author: Andy Nonaka Date: Mon Sep 9 13:21:36 2019 -0700 code cleanup src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/membrane.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp commit cdd3ab0efc1022b8413c4121ac77cf7e4026d2c5 Author: Andy Nonaka Date: Mon Sep 9 12:56:49 2019 -0700 more code cleanup src_compressible/src_F90/init_consvar.F90 src_compressible/src_F90/trans_funcs.F90 commit 87bac58f2dd80058641443c5191b417edfb40aa9 Author: Andy Nonaka Date: Mon Sep 9 12:43:24 2019 -0700 comments src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit 8eb24c82fdd93b3caae5e50c619759728f9b6a45 Author: Andy Nonaka Date: Mon Sep 9 12:30:19 2019 -0700 comments exec/compressible/main_driver.cpp src_compressible/src_F90/bound_funcs.F90 commit 14306f4bab1a1fb36a3883fece42e5a7271afcc6 Author: Andy Nonaka Date: Mon Sep 9 11:45:10 2019 -0700 compressible code cleanup exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/src_F90/stats_funcs.F90 src_compressible/writePlotFile.cpp commit 17c91f08e4da858d98401a38fc008a420a43675e Author: Andy Nonaka Date: Fri Sep 6 18:32:35 2019 -0700 comments src_common/MultiFABPhysBC.cpp commit 90a3babbc65802d7d767c42cd551f9ab2a4bcddc Author: Andy Nonaka Date: Fri Sep 6 18:17:02 2019 -0700 implement slip wall support for physbc_domainvel and physbc_macvel src_common/MultiFABPhysBC.H commit 4c32232f42fd4de6199a397880e5bbcf07fc99c7 Author: Andy Nonaka Date: Thu Sep 5 18:28:52 2019 -0700 fixed a bug in MultiFABPhysBCMacVel where were were operating on tileboxes grown only in the dir direction (not the other 2 directions) moved GPU kernels for PhysBC routines to a separate file added some comments exec/channel/GNUmakefile src_common/Make.package src_common/MultiFABPhysBC.H src_common/MultiFABPhysBC.cpp commit a656f48d48106f004f3ad53fb9247793be3a25ba Author: Andy Nonaka Date: Thu Sep 5 15:28:31 2019 -0700 comments only exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.cpp commit d15dda59040a65e546a9316e6e24bc2a6e99f5c4 Author: Andy Nonaka Date: Thu Sep 5 08:16:10 2019 -0700 implement 'plot_stag' in the common namelist/namespace. plots out the staggered velocities in a separate plotfile (default value 0) exec/DiffuisonTest/WritePlotFile.cpp exec/brownian/WritePlotFileHydro.cpp exec/channel/WritePlotFile.cpp exec/fluctuatingMembrane/WritePlotFileHydro.cpp exec/hydro/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_rigid/WritePlotFile.cpp exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum_chlamy/WritePlotFile.cpp exec/multispec/WritePlotFile.cpp exec/overdamped/WritePlotFile.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit e88fbcfb130ce31f6526e0ab4dc404bbe3d828ef Author: Andy Nonaka Date: Thu Sep 5 08:03:50 2019 -0700 get this compiling again exec/multispec/advance.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H commit 20bfa9d8dab515d2ad02461c9b0ae8a271d22f72 Merge: 0ef4db12 b6ef74c3 Author: Andy Nonaka Date: Wed Sep 4 16:19:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0ef4db12b723e2cbd703905a126c6109f4d2db5d Author: Andy Nonaka Date: Wed Sep 4 16:18:55 2019 -0700 remove outdated/unused example exec/immersedParticles/GNUmakefile exec/immersedParticles/INS_functions.H exec/immersedParticles/Make.package exec/immersedParticles/Make_precheck.package exec/immersedParticles/Make_surface.package exec/immersedParticles/TimeStep.cpp exec/immersedParticles/WritePlotFile.cpp exec/immersedParticles/WritePlotFileHydro.cpp exec/immersedParticles/advance.cpp exec/immersedParticles/hydro_test_functions.H exec/immersedParticles/hydro_test_functions_F.H exec/immersedParticles/inputs_2d exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp exec/immersedParticles/precheck.F90 exec/immersedParticles/surfaces.cpp commit b6ef74c359b8ea1290bce6eba91fc1a563a32ba5 Author: Johannes Blaschke Date: Wed Sep 4 09:07:00 2019 -0700 added components to macvel filling src_common/MultiFABPhysBC.cpp commit c8c04c8fe6e6d9be8e5fa51fe5afbd649c071d03 Author: Johannes Blaschke Date: Tue Sep 3 18:27:35 2019 -0700 iterate over ncomp for domainvel src_common/MultiFABPhysBC.cpp commit 5ecf1a4f34d2d82800cc5336ed00f9a5bf44a6ac Author: Johannes Blaschke Date: Tue Sep 3 18:19:00 2019 -0700 start itterating over components in bcs src_common/MultiFABPhysBC.cpp src_common/common_functions.H commit 18e3705ef6ab488ffe4723d210333977541e30a3 Merge: 00c7c53c 2349f91f Author: Johannes Blaschke Date: Fri Aug 30 17:10:53 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit 00c7c53cb44c2b24d2a9e7463d9aa83e03818521 Author: Johannes Blaschke Date: Fri Aug 30 17:10:29 2019 -0700 add for consistency src_common/MultiFABPhysBC.cpp commit fd9bc6087bd08316b62fa849ce9232817bf83e95 Author: Johannes Blaschke Date: Fri Aug 30 17:03:37 2019 -0700 ha! fixed it! src_common/MultiFABPhysBC.cpp commit 639e567b7e41b61eee5ad03d350b0da51e672497 Author: Johannes Blaschke Date: Fri Aug 30 16:58:41 2019 -0700 work on fixing indexing error src_common/MultiFABPhysBC.cpp commit 2349f91f13f1332e1401c641930955b7185d02b9 Author: Daniel Ladiges Date: Fri Aug 30 16:51:25 2019 -0700 immersed ions now uses Max_particle_tile_size feature exec/immersedIons/inputs_3d commit 82dae30fbac10c6967ef75b87c9164b1f795c1c3 Author: Johannes Blaschke Date: Fri Aug 30 16:33:09 2019 -0700 finished add dim flags src_common/MultiFABPhysBC.cpp commit 8ff2d28bf80d99ffb09a422857578db5d70f5c74 Merge: f5718872 377dc7e6 Author: Daniel Ladiges Date: Fri Aug 30 16:28:01 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f5718872ee410281f59718b1b4c33db4cdef59fd Author: Daniel Ladiges Date: Fri Aug 30 16:26:50 2019 -0700 Added max_particle_tile_size to namelist. This sets particle tile size for building neighbourlists exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 4d2346be60eceaf575feef33ab851b11e85d3534 Author: Johannes Blaschke Date: Fri Aug 30 16:18:40 2019 -0700 include dim flag src_common/MultiFABPhysBC.cpp commit be008f086b02e595f565d022cab06aa8f47d982a Author: Johannes Blaschke Date: Fri Aug 30 16:13:36 2019 -0700 don't go into these loops if they we're not touching the boundary exec/channel/inputs_3d_test src_common/MultiFABPhysBC.cpp commit 76e6220fa43cf47da11875013708b161a8bc1b6b Author: Daniel Ladiges Date: Fri Aug 30 15:02:37 2019 -0700 immersedIons now uses IB base class RFD function. Seems to work. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 1134aa3725f50f405f1e4f32951a4a9f9625dec9 Author: Daniel Ladiges Date: Fri Aug 30 14:50:11 2019 -0700 Made C++ version of RFD function in IBmarker base class. src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 377dc7e61bc21385ea3aa0df29d5d2c5c05bc266 Author: Johannes Blaschke Date: Fri Aug 30 13:42:19 2019 -0700 add mavel bcs src_common/MultiFABPhysBC.cpp src_common/src_F90/multifab_physbc_mod.F90 commit 325e20ad767be9e9534321c8b9b9b7899f9c2fe4 Merge: 4cc7b4df ef0dc90d Author: Johannes Blaschke Date: Fri Aug 30 11:17:47 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit ef0dc90dec96504fda4b5a0abd36c89cb3bdd493 Author: Andy Nonaka Date: Fri Aug 30 11:15:06 2019 -0700 move bc_mass_lo/hi and bc_therm_lo/hi from compressible to common namespace/namelist exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/flux_funcs.F90 commit 4cc7b4df2aed7fe8e11743e7996b49c98d2ff460 Author: Johannes Blaschke Date: Fri Aug 30 11:13:51 2019 -0700 added domainvel bcs src_common/MultiFABPhysBC.cpp commit 27b04b16e4aa0ff9c565e8ff8897635249cf03f4 Author: Andy Nonaka Date: Fri Aug 30 10:23:03 2019 -0700 update a comment src_common/common_namespace.H commit e3ccd7574cc1479aed4677e215df28949d54088e Author: Andy Nonaka Date: Fri Aug 30 10:21:02 2019 -0700 update a comment src_common/src_F90/common_namelist.F90 commit c0b63c132bd36fea392a9bdda02031124a10bfaf Author: Andy Nonaka Date: Thu Aug 29 19:45:58 2019 -0700 bc_lo/hi -> bc_vel_lo/hi exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC/inputs_2d exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMCstatcheck/inputs_2d exec/DSMCstatcheck/inputs_3d exec/DSMCstatcheck/main_driver.cpp exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/inputs_debug_multigrid_2d exec/DiffuisonTest/main_driver.cpp exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt_1D/inputs_1d exec/_GL_alt_1D/main_driver.cpp exec/brownian/inputs_2d exec/brownian/inputs_3d exec/brownian/main_driver.cpp exec/channel/inputs_2d exec/channel/inputs_3d exec/channel/inputs_3d_test exec/channel/inputs_3d_test.2 exec/channel/inputs_incomp_equil_fluct_2d exec/channel/inputs_incomp_equil_fluct_3d exec/channel/main_driver.cpp exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/inputs_regression_2d exec/hydro/inputs_regression_3d exec/hydro/main_driver.cpp exec/immersedIons/inputs_2d exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_poisson exec/immersedIons/inputs_3d_reflect exec/immersedIons/main_driver.cpp exec/immersedIons/main_driver_OLD.cpp exec/immersedParticles/inputs_2d exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_rigid/inputs_2d exec/immersed_boundary/channel_rigid/inputs_3d exec/immersed_boundary/channel_rigid/inputs_3d_test exec/immersed_boundary/channel_rigid/inputs_3d_test.2 exec/immersed_boundary/channel_rigid/inputs_3d_test.3 exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/inputs_2d exec/immersed_boundary/channel_soft/inputs_3d exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/inputs_3d_test.2 exec/immersed_boundary/channel_soft/inputs_3d_test.3 exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/inputs_2d exec/immersed_boundary/flagellum/inputs_3d exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/inputs_2d exec/immersed_boundary/flagellum_chlamy/inputs_3d exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/low_density/inputs_3d exec/low_density/main_driver.cpp exec/multispec/inputs_2d exec/multispec/inputs_3d exec/multispec/inputs_bubble_2d exec/multispec/main_driver.cpp exec/overdamped/inputs_incomp_equil_fluct_2d exec/overdamped/inputs_incomp_equil_fluct_3d exec/overdamped/main_driver.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_common/src_F90/multifab_physbc_mod.F90 src_hydro/StochMFlux.cpp src_hydro/src_F90/hydro_bounds_mod.F90 src_low-density/src_F90/bound_funcs.F90 src_low-density/src_F90/flux_funcs.F90 src_low-density/src_F90/stats_funcs.F90 src_particles/src_F90/particle_functions.F90 src_surfaces/surfaces.cpp commit f9cb6db2cc510bbb37f7acc76ac631d99b600e41 Merge: 2e64f84c d10f3321 Author: Johannes Blaschke Date: Thu Aug 29 18:51:55 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit d10f33217b6dc543ea9d55b288071f6ea006ff69 Author: Andy Nonaka Date: Thu Aug 29 18:49:53 2019 -0700 temporary hack to make tracers work (without usings NaN's in calculations) until physical ghost cell routine is implemented exec/hydro/advance.cpp exec/hydro/main_driver.cpp commit 2e64f84c2f4f6b981e226345bc57bcd0ab26d60d Author: Johannes Blaschke Date: Thu Aug 29 18:48:08 2019 -0700 add domainvel kernel src_common/MultiFABPhysBC.cpp commit 03fe6c7c84a42a56c87e7d8cc4f7dd8f990ee60c Author: Andy Nonaka Date: Thu Aug 29 18:38:56 2019 -0700 renname MultiFABPhysBC -> MultiFABPhysBCPres renname MultiFABChargeBC -> MultiFABPhysBCCharge exec/channel/advance.cpp exec/channel/main_driver.cpp exec/fluctuatingMembrane/advance.cpp exec/immersedIons/advance.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_electrostatic/electrostatic.cpp src_gmres/ApplyMatrix.cpp commit f6a1e26b8fa5b9ee385cb0f3f3994295f72c760f Author: Daniel Ladiges Date: Thu Aug 29 17:48:39 2019 -0700 Default seed set to zero (ie set off clock) src_common/src_F90/common_namelist.F90 commit cab32a9ad89fada73aaf177d444e776b8144cce1 Author: Daniel Ladiges Date: Thu Aug 29 17:46:22 2019 -0700 ions, membrane, & DSMC now use 'seed' input variable for rngs exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit c654e6b84732c813f0b3c3929a1b55c1b07c1196 Author: Johannes Blaschke Date: Thu Aug 29 17:22:55 2019 -0700 remove n components exec/channel/GNUmakefile src_common/MultiFABPhysBC.cpp commit b90dff7c34fd6080219b5c447c317ea60df21ef9 Author: Daniel Ladiges Date: Thu Aug 29 16:39:58 2019 -0700 Default tile size is now box size in ibmarkercontainerbase src_immersed-boundary/IBMarkerContainerBaseI.H commit 14dd7651cf6c165e90bf23a23ffdccdda21ec2e5 Merge: 97df1dec 587486d3 Author: Daniel Ladiges Date: Thu Aug 29 16:35:00 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 97df1dec055c1fe023b82fc40fc25d22226a869c Author: Daniel Ladiges Date: Thu Aug 29 16:34:14 2019 -0700 Removed unecessary functions from dsmc particle container class exec/DSMC/GNUmakefile exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_particles/DsmcParticleContainer.cpp commit e3b6a16b56abe9115ffcc13e37716e3a87e4b48f Author: Daniel Ladiges Date: Thu Aug 29 16:20:12 2019 -0700 Disentangled DSMC from FHD particles - Now in a seperate particle class exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_particles/DsmcParticleContainer.H src_particles/DsmcParticleContainer.cpp src_particles/FhdParticleContainer.H src_particles/Make.package src_particles/MakeDSMC.package src_particles/src_F90/membrane_forces.F90 src_particles/src_F90/particle_type.F90 commit 587486d3e43c3dcc42052fab20a134f52cf6b530 Merge: 407c28db 710ea65f Author: Johannes Blaschke Date: Thu Aug 29 16:03:51 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 407c28db32a93e2a612b45e2affea80f8c07a765 Author: Johannes Blaschke Date: Thu Aug 29 16:03:46 2019 -0700 ramp up fluctuations exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres commit 710ea65fad0e03290671801917f72415222b8a00 Author: Andy Nonaka Date: Thu Aug 29 11:29:32 2019 -0700 fix boundary condition treatment for walls in StagMGSolver added/moved several calls to physbcdomainvel and physbcmacvel. note physbc itself should have never been used because that's for cell-centered pressure src_gmres/StagMGSolver.cpp commit fba04516f7d526929fe1b1f0b28eccd39b0ff497 Author: Andy Nonaka Date: Thu Aug 29 11:05:10 2019 -0700 clean up initial momentum noise code. no ghost cells required; removed erroneous calls to MultiFABPhysBC. fixed a bug: abs() -> std::abs() in C++ for real numbers src_hydro/StochMFlux.cpp commit f488719c8b373553f4b5a2559850d9631db0bcec Author: Andy Nonaka Date: Thu Aug 29 09:34:11 2019 -0700 fix bc specification inputs exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d commit 0c3cfd3a6858f22df7bdd65f3f5e285d7abf4a45 Merge: dc84695b 3f2613a5 Author: Johannes Blaschke Date: Thu Aug 29 05:08:20 2019 +0000 :Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit dc84695b9bc03d40eeba9d8d68a92af6f3f04279 Author: Johannes Blaschke Date: Thu Aug 29 05:08:11 2019 +0000 remove swfft for this example (for now) exec/channel/GNUmakefile commit 3f2613a53ffead3a543b88a642782b1071213e53 Author: Andy Nonaka Date: Wed Aug 28 18:44:39 2019 -0700 renname variable so it won't get in the way of the upcoming bc_lo -> bc_vel_lo replacement src_chem/AmrCoreAdv.cpp commit 574263b8575dab6ece1fc9b275d7910f9b339b84 Author: Johannes Blaschke Date: Thu Aug 29 01:28:51 2019 +0000 fix pass-by-value src_common/MultiFABPhysBC.cpp commit 355cf279a1f4e160acfca759a9753d25cbe79513 Merge: 6e3a92b5 a5e01463 Author: Andy Nonaka Date: Wed Aug 28 17:55:12 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6e3a92b554704fc64ecd5e145bf886686af21afc Author: Andy Nonaka Date: Wed Aug 28 17:53:58 2019 -0700 changed how boundary conditions work in the compressible code bc_lo and bc_hi are no longer used at all instead you set bc_vel_lo/hi, bc_mass_lo/hi, and bc_therm_lo/hi as noted in the inputs files: ! NOTE: setting bc_vel to periodic sets all the other bc's to periodic) ! bc_vel: -1 = periodic ! 1 = slip wall ! 2 = no-slip wall ! bc_mass: -1 = periodic ! 1 = wall ! 2 = reservoir (set bc_Yk or bc_Xk in compressible namelist) ! bc_therm: -1 = periodic ! 1 = adiabatic ! 2 = isothermal (set with t_lo/hi in common namelist) exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d exec/compressible/main_driver.cpp src_compressible/compressible_functions.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/init_consvar.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/src_F90/stats_funcs.F90 commit a5e01463aa814daab0af1194c1afe2f3af9ad438 Merge: d8d33db9 c939a054 Author: Daniel Ladiges Date: Wed Aug 28 17:22:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d8d33db977df1785285ba50f68b22eb1acb3f16e Author: Daniel Ladiges Date: Wed Aug 28 17:21:15 2019 -0700 Fluctuating membrane now works with new base class exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/particleGen.cpp src_immersed-boundary/MakeBase.package commit c939a05464e29f3b6e2e3d0a59eeeebf80ad9796 Merge: 6afbe4d7 38e21110 Author: Johannes Blaschke Date: Wed Aug 28 17:07:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6afbe4d7f92e7efc08938b612a786b1ed7732717 Author: Johannes Blaschke Date: Wed Aug 28 17:07:40 2019 -0700 fix includes exec/channel/GNUmakefile exec/channel/main_driver.cpp commit 38e21110b4d4e531b0bc5572d9c787b83682c2c9 Author: Andy Nonaka Date: Wed Aug 28 17:06:11 2019 -0700 a few more naming conventions exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d commit ca316f43a447b1035b7fbe06891928b0b9ca1cc6 Author: Daniel Ladiges Date: Wed Aug 28 17:03:52 2019 -0700 Immersed ions converted to use ib container base class. exec/fluctuatingMembrane/GNUmakefile exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/Make.package commit 30dd700d317770532295bd1884e088e97c636e8a Author: Andy Nonaka Date: Wed Aug 28 17:03:10 2019 -0700 naming convention exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d src_compressible/src_F90/compressible_namelist.F90 commit b037a1be30efcb37e6e4d68625edddd4f7d8b53f Merge: 6f556034 693b9de5 Author: Daniel Ladiges Date: Wed Aug 28 16:49:13 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9110d589d4d7c3c6c4d7c395cc94f230e9293167 Author: Andy Nonaka Date: Wed Aug 28 16:15:19 2019 -0700 rennaming variables only to be more consistent with the other applications src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/init_consvar.F90 commit f8a9ef0291f48ba13f4ab7d3c8e03434cd54bc47 Merge: b570d80f 693b9de5 Author: Andy Nonaka Date: Wed Aug 28 16:04:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b570d80f297510e07bb484910826adf3570e5104 Author: Andy Nonaka Date: Wed Aug 28 16:04:02 2019 -0700 rennaming of lobc and hibc objects to be more illustrative of the fact that they are temporaries used to define solvers src_electrostatic/electrostatic.cpp src_gmres/MacProj.cpp src_hydro/MacProj_hydro.cpp commit 6f55603419f108c88b761cb20ae922f810abe4bf Author: Daniel Ladiges Date: Wed Aug 28 13:49:18 2019 -0700 Put membrane forces stub in particles f90 dir so non membrane codes will compile. Partway through migration to immersed boundary base class exec/fluctuatingMembrane/INS_functions_F.H exec/immersedIons/GNUmakefile exec/immersedIons/Make.package exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/MakeBase.package src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/Make.package src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/membrane_forces.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 693b9de5b520db4f5d959cd856a71a2c9b4e860f Merge: d424d0d7 0c9aa7ee Author: Johannes Blaschke Date: Wed Aug 28 11:43:41 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit 0c9aa7ee85e89a0af3c66bb402aeac02db44e8b5 Author: Andy Nonaka Date: Wed Aug 28 11:29:34 2019 -0700 remmove unused fortran interfaces src_gmres/gmres_functions_F.H commit f1502fb78a9bba00d517bea88db2d165543a18bb Author: Andy Nonaka Date: Wed Aug 28 11:28:29 2019 -0700 remove unnused fortran interfaces src_hydro/hydro_functions_F.H commit f0a2210f807acdbbe68dedddc41aba096e82c4b1 Author: Andy Nonaka Date: Wed Aug 28 10:27:33 2019 -0700 put SqrtMF on GPU src_common/SqrtMF.cpp src_common/src_F90/Make.package src_common/src_F90/sqrt_mf.F90 commit 4d62fd4481ba1c21e3f320d94e4747ba87f93a34 Author: Andy Nonaka Date: Wed Aug 28 10:16:03 2019 -0700 add some timers src_common/ComputeAverages.cpp src_common/ComputeBasicStats.cpp src_common/ComputeDivAndGrad.cpp src_common/Debug.cpp src_common/FindCoords.cpp src_common/FindNodalValues.cpp src_common/Make.package src_common/SqrtMF.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/outputAscii.cpp src_particles/FhdParticleContainer.cpp commit d424d0d764327031a2894b231f64b71febd481e1 Merge: aa14c766 a8760fac Author: Johannes Blaschke Date: Tue Aug 27 13:24:37 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit aa14c76636724206f5ddd5040d5775d92dedb6ee Author: Johannes Blaschke Date: Tue Aug 27 13:24:13 2019 -0700 move bc type to GPU src_common/ComputeDivAndGrad.cpp src_common/MultiFABPhysBC.cpp commit de7bbb34acd9e851b21d18e096e9b5ce750b89dd Author: Andy Nonaka Date: Tue Aug 27 13:23:55 2019 -0700 for compressible code, change behavior of output when project_dir >=0. It now outputs the structure factors for the full dataset AND the vertically-averaged dataset exec/compressible/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit a8760face80542f440cb87acfdfbe6d9e4010262 Author: Andy Nonaka Date: Tue Aug 27 13:02:10 2019 -0700 structure factor plot file now takes in a require plotfile prefix exec/channel/main_driver.cpp exec/compressible/main_driver.cpp exec/fluctuatingMembrane/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersedIons/main_driver_OLD.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit e1619e65ac24d696ee5fc112be78412efded312c Author: Andy Nonaka Date: Tue Aug 27 12:40:45 2019 -0700 another change to function of project_dir... 0/1/2 means x/y/z. Negative means don't do it and analyze the entire grid exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_regression_RT_3d exec/compressible/main_driver.cpp src_common/src_F90/common_namelist.F90 commit a053bfa75ca58acf77caa76c914cf6aad25c5bb9 Author: Andy Nonaka Date: Tue Aug 27 12:28:13 2019 -0700 re-arrange input file exec/compressible/inputs_giantfluct_3d commit ab10a8ad48b816ae5a0c3b42612f51b02cd5ef18 Author: Andy Nonaka Date: Tue Aug 27 12:26:52 2019 -0700 minor cleanups. set project_dir default to zero for structure factor calculation. positive value of project_dir will vertically average down onto a DIM-1 dataset to do the analysis (not fully implemented yet) exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_regression_RT_3d exec/compressible/main_driver.cpp src_analysis/StructFact.cpp src_common/ComputeAverages.cpp src_common/src_F90/common_namelist.F90 commit 5829ddfad17b83af91927e6b8a92a2dc825bf540 Author: Andy Nonaka Date: Tue Aug 27 09:41:07 2019 -0700 more code cleanup, comments exec/compressible/inputs_equil_3d exec/compressible/main_driver.cpp src_analysis/StructFact.cpp src_compressible/compressible_functions.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp commit 1a946592cc71b19661aa3177b155903f1de2c44a Merge: f5ef9924 9bfabdb6 Author: Andy Nonaka Date: Mon Aug 26 18:44:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f5ef992445aab5508e09c844684fbad824b9e1de Author: Andy Nonaka Date: Mon Aug 26 18:44:20 2019 -0700 code cleanup, comments exec/compressible/main_driver.cpp src_compressible/src_F90/init_consvar.F90 src_compressible/timeStep.cpp commit 9bfabdb6567292bcf38be659ebc3ab1a44e59f44 Merge: d0796888 d2addfe3 Author: Johannes Blaschke Date: Mon Aug 26 18:06:17 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit d07968883291dc775f02bdac634d0f4ee0498284 Author: Johannes Blaschke Date: Mon Aug 26 18:05:58 2019 -0700 fix time stepping exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres commit d2addfe3616d18e328a9e953e2bd232b41bd599b Author: Andy Nonaka Date: Mon Aug 26 17:35:34 2019 -0700 re-org exec/compressible/mathematica/interpAnalysis.nb exec/compressible/mathematica/stressTensor.nb commit e91a972554b7d7837d3ab5bbc670612317b8834b Author: Andy Nonaka Date: Mon Aug 26 17:28:12 2019 -0700 begin cleanup of compressible code exec/compressible/GNUmakefile exec/compressible/Make.package exec/compressible/compressible_test_functions_F.H exec/compressible/exec_functions.H exec/compressible/main_driver.cpp src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/init_consvar.F90 src_compressible/writePlotFile.cpp commit 8880aa2f304c2fdb7fa56fb6aa174bccc218982d Author: Andy Nonaka Date: Mon Aug 26 16:09:40 2019 -0700 tiling src_gmres/StagMGSolver.cpp commit e691927712708fc4249549acd60325706ef3ebb4 Merge: 720a7e10 7b8bd55a Author: Andy Nonaka Date: Mon Aug 26 16:01:15 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 720a7e10a49303e74e9cc904b96cf191a7b46c53 Author: Andy Nonaka Date: Mon Aug 26 16:00:49 2019 -0700 various cleanup and OpenMP tiling implementations src_gmres/StagMGSolver.cpp src_hydro/MacProj_hydro.cpp src_hydro/MkAdvMFluxdiv.cpp commit 7b8bd55afbf426a242cfd645e325ed24eb768743 Author: Johannes Blaschke Date: Mon Aug 26 15:06:40 2019 -0700 add parameter file exec/immersed_boundary/flagellum/inputs_3d_test.scaled.highres commit 41690c5e4e714c038be6843ca90e238e0ab1592a Merge: 6a8bdb72 900f54aa Author: Johannes Blaschke Date: Mon Aug 26 14:58:58 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6a8bdb721ef8f995ca9b99ab16e281185c8d1b2b Merge: 5548aa82 6d27fdaa Author: Johannes Blaschke Date: Mon Aug 26 14:52:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5548aa82298862bd751038c272d13f82dbcb86e9 Author: Johannes Blaschke Date: Mon Aug 26 14:52:21 2019 -0700 put predictor-corrector back in exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit 900f54aa2b3c33c8c93f0768a499b3345d6bec2b Merge: 5ff7b8ec 6d27fdaa Author: Johannes Blaschke Date: Mon Aug 26 14:49:24 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 6d27fdaa5007935106c0e66cb2d6a83bee0bfd7a Author: Andy Nonaka Date: Mon Aug 26 14:08:00 2019 -0700 more openMP tiling src_common/SqrtMF.cpp src_gmres/NormInnerProduct.cpp src_gmres/StagApplyOp.cpp commit f5532494bc9acfc6506eddc64b7dcd6c8ce82e77 Author: Andy Nonaka Date: Mon Aug 26 13:57:19 2019 -0700 implement OMP if not using GPU src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp commit 540e8ce9000d1b1711b6ad435554ac750f3d7c89 Merge: c6af93ef 0fb8af43 Author: Andy Nonaka Date: Mon Aug 26 12:06:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c6af93ef32adcd7ca6d7d700fa58d5e28e56d118 Author: Andy Nonaka Date: Mon Aug 26 12:06:11 2019 -0700 crude attempt at generating RNGs on GPU src_rng/MultiFABFillRandom.cpp commit 0fb8af43bc6e8afabbf4d15fb72d53c8bfef44b9 Author: Johannes Blaschke Date: Mon Aug 26 11:20:25 2019 -0700 remove tracers exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit 5ff7b8eced6840b9fd029dba103ac278388884d8 Merge: 2e67047e 8ff5cf38 Author: Johannes Blaschke Date: Mon Aug 26 08:52:55 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 2e67047e7e2896c2930658e15a4b96ac004d2f4e Author: Johannes Blaschke Date: Mon Aug 26 08:52:52 2019 -0700 debugging drift exec/immersed_boundary/flagellum/Render Frames.ipynb commit 8ff5cf38e5a5f2b8ca775c9d4a1612802ad6f517 Author: Johannes Blaschke Date: Fri Aug 23 16:30:55 2019 -0700 clean up debug code exec/channel/GNUmakefile src_common/MultiFABPhysBC.cpp commit 2591105c6a899cbe9130d927c2c28d57db69fa33 Author: Johannes Blaschke Date: Fri Aug 23 16:02:13 2019 -0700 found the nan exec/channel/GNUmakefile exec/channel/main_driver.cpp src_common/MultiFABPhysBC.cpp src_gmres/NormInnerProduct.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/StochMFlux.cpp commit f0442e1e688ce30ec3c69d513f9e19edef7ae620 Merge: ca05abb5 19031d86 Author: Johannes Blaschke Date: Fri Aug 23 10:57:41 2019 -0700 Merge branch 'master' into jpb/gpu-bc commit ca05abb57f5ea780cb571f5b9995ff5e5e3e1fe5 Author: Johannes Blaschke Date: Fri Aug 23 10:57:07 2019 -0700 debugging exec/channel/advance.cpp exec/channel/hydro_test_functions.H exec/channel/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/MultiFABPhysBC.cpp src_common/src_F90/multifab_physbc_mod.F90 commit 19031d8647b3933b4679f8edc850fc2b4940b33d Author: Andy Nonaka Date: Fri Aug 23 10:14:12 2019 -0700 port mult_by_sqrt_temp_eta to GPU src_hydro/StochMFlux.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/stoch_m_force.F90 commit 0e53ac36e146608920206884d68f0a1bb4efb509 Author: Andy Nonaka Date: Fri Aug 23 09:07:23 2019 -0700 stoch_m_fluxdiv on gpu src_hydro/StochMFlux.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/stoch_m_force.F90 commit b0ba6863178877cb2ff8b06ee27fff83e86db962 Merge: 3a6fbffc b1f857c8 Author: Andy Nonaka Date: Fri Aug 23 08:39:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3a6fbffc126193ce6144241b2d57234cc9fdbaaa Author: Andy Nonaka Date: Fri Aug 23 08:38:56 2019 -0700 mk_advective_m_fluxdiv on GPU src_hydro/MkAdvMFluxdiv.cpp src_hydro/src_F90/Make.package src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit b1f857c853e775543124be0d020ba1c791525db4 Author: Johannes Blaschke Date: Thu Aug 22 18:24:53 2019 -0700 add average (int time) v exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit b141a1fa1fcccb1820acede4e95ab5513c9a8497 Merge: dcbbbe51 574ab60e Author: Johannes Blaschke Date: Thu Aug 22 18:15:51 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit dcbbbe51000dad343f671ec78104bf4e3bad7c52 Author: Johannes Blaschke Date: Thu Aug 22 18:15:47 2019 -0700 add average (int time) v exec/immersed_boundary/flagellum/Render Frames.ipynb commit 574ab60e25a37fdb135591a8102e58ecbf7b45ee Author: Andy Nonaka Date: Thu Aug 22 16:29:20 2019 -0700 save some flops src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit d6602e8c33094dea614c595e1f1c7c70a21f9377 Author: Andy Nonaka Date: Thu Aug 22 16:15:46 2019 -0700 GPU-friendly version of fortran kernal for momentum advective fluxes when ported, there will be no data movement onto GPU, no temporary storage on GPU src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit 86d075c318f84d9404a1ab69bb4c22912645895d Author: Andy Nonaka Date: Thu Aug 22 15:23:04 2019 -0700 2d bc support for stochastic momentum fluxes fixed a few bugs in the 3d version as well src_hydro/StochMFlux.cpp commit 62b8166af8cc5d8c846bcd479a7c41f8083fca10 Merge: 7f5ed16e f0a42915 Author: Johannes Blaschke Date: Thu Aug 22 14:04:12 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 7f5ed16ed05c7a708d7dc1e642240ca60ec832ea Author: Johannes Blaschke Date: Thu Aug 22 14:04:10 2019 -0700 find some interesting parameters exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_3d_test.scaled commit f0a429159b9d531fcd9769a9e80650bdb400d49e Merge: e3d3de03 c5691e17 Author: Andy Nonaka Date: Thu Aug 22 12:41:56 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e3d3de0367c50703d276c579f04025a7fbc0eeba Author: Andy Nonaka Date: Thu Aug 22 12:41:27 2019 -0700 implemented stochastic momentum flux physical boundary conditions (host and GPU versions) src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp commit c5691e1791fc8b4d83accbd1bc2bd17d450742ec Author: Daniel Ladiges Date: Wed Aug 21 16:34:46 2019 -0700 Added missing header to ib_functions.cpp src_immersed-boundary/ib_functions.cpp commit 3e7271358c075ee1bf5acfa7c1c389b21737964a Merge: 03e32169 73d1776b Author: Daniel Ladiges Date: Wed Aug 21 15:53:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 03e32169a51a30e71f114d900474af02f8e43f77 Author: Daniel Ladiges Date: Wed Aug 21 15:52:26 2019 -0700 Started merge of fhdParticleContainer and IBmarkerContainer exec/immersedIons/GNUmakefile exec/immersedIons/Make.package exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H commit 73d1776b9e3baa831e1840da3ad85d33bc7fa985 Author: Andy Nonaka Date: Wed Aug 21 14:57:30 2019 -0700 changed the function signature for stochMforce to include an "increment" option to either increment or overwrite the force also changed the name of stochMforce to StochMFluxDiv to match the old code and be more illustrative exec/brownian/main_driver.cpp exec/channel/main_driver.cpp exec/fluctuatingMembrane/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersedIons/main_driver_OLD.cpp exec/immersedParticles/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp commit d342479f474db19d553c48f436dbbd59ff490054 Author: Andy Nonaka Date: Wed Aug 21 14:10:38 2019 -0700 bugfix in computing stochastic momentum flux variance for values other than 0 or 1 various cleanup to match original code's handling of ghost cell fill calls src_hydro/StochMFlux.cpp commit 11b020618a29dcc15af5e72939165dc515737d14 Author: Andy Nonaka Date: Wed Aug 21 13:11:01 2019 -0700 remove geom as an argument to addMFluctuations (geom is already part of the StochMFlux class) various tidies to StochMFlux - WIP exec/brownian/main_driver.cpp exec/channel/main_driver.cpp exec/fluctuatingMembrane/main_driver.cpp exec/hydro/main_driver.cpp exec/immersedIons/main_driver.cpp exec/immersedIons/main_driver_OLD.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/multispec/main_driver.cpp exec/overdamped/main_driver.cpp src_common/common_namespace.H src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp commit 5d717441bdf8c0eb73ba0cad91b41040ef172b71 Merge: 2c9cd228 c2588606 Author: Andy Nonaka Date: Tue Aug 20 10:56:28 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2c9cd2281237a2b3bbb44902781b355390c9cab8 Author: Andy Nonaka Date: Tue Aug 20 10:55:26 2019 -0700 fixed bug in SumStag; wasn't resetting the sum when moving onto the next directional component src_gmres/NormInnerProduct.cpp commit c2588606ed4e3fbb7c271233933feae0c8658bd5 Author: Aleksandar Donev Date: Mon Aug 19 19:37:30 2019 -0400 Added namelist HydroGrid to inputs_3d exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 commit 2f906d7fb6be445a7bba644bf266139060ce077c Author: Daniel Ladiges Date: Mon Aug 19 14:30:55 2019 -0700 Added untracked file exec/fluctuatingMembrane/INS_functions_F.H commit e6561854df3e1111d6fa5cdb03d4688c8bcca33d Author: Daniel Ladiges Date: Mon Aug 19 14:26:02 2019 -0700 -All particles are now passed to user_force_calc, sorted by species. Input file being passed to user_force_calc_init exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane_forces.F90 exec/fluctuatingMembrane/particleGen.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 64c92e512a28b97d4aa634cd14adcbf86c453a68 Merge: 14250cf6 1a535132 Author: Daniel Ladiges Date: Mon Aug 19 13:33:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 14250cf6cf045d4d3e752162345b1f92e9b92f22 Author: Daniel Ladiges Date: Mon Aug 19 13:33:27 2019 -0700 Added step number for user_force_calc exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane_forces.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H commit 1a535132b9048baef6708dce365e397723b706d1 Merge: 34f6df51 7e83b6d5 Author: Aleksandar Donev Date: Mon Aug 19 16:32:11 2019 -0400 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 34f6df510ee7aba074581efe8f75a8c0c1861e49 Author: Aleksandar Donev Date: Mon Aug 19 16:32:05 2019 -0400 Added namelist FluctuatingMembrane to inputs_3d exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 commit 7e83b6d5e378c9fa31c2c837daa060061d2963b2 Author: Daniel Ladiges Date: Mon Aug 19 13:17:09 2019 -0700 Fixed 'double debug' exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane_forces.F90 commit f5d43a75c89441282ab24a9f29550f61a88ea128 Merge: 34ac6084 0029ef5f Author: Daniel Ladiges Date: Mon Aug 19 13:13:21 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 34ac60849975cf0ba5f54b0f7383a8e219c73e61 Author: Daniel Ladiges Date: Mon Aug 19 13:12:47 2019 -0700 Added namelist input and cleanup for membrane force calc. exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane_forces.F90 commit 0029ef5fe23db98a44bc4b4b6eec472f4d030882 Author: Aleksandar Donev Date: Mon Aug 19 16:06:35 2019 -0400 membrane_forces now calls HydroGrid exec/fluctuatingMembrane/membrane_forces.F90 commit 24f7b1f00836d60f90769d0ae1f947862ebfbf6f Merge: 1606f77d 49aac382 Author: Aleksandar Donev Date: Mon Aug 19 15:54:57 2019 -0400 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 1606f77da3b6102f7b09afa53e051ce6f993de3a Author: Aleksandar Donev Date: Mon Aug 19 15:54:43 2019 -0400 membrane_forces now uses HydroGrid exec/fluctuatingMembrane/GNUmakefile exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 commit 49aac382d8e48df32362c309b25e523b8b33e2b6 Merge: 9abc0b85 56ce2893 Author: Daniel Ladiges Date: Mon Aug 19 12:52:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9abc0b85f7fa3e8444d5e276ff5a5a2e8f807af3 Author: Daniel Ladiges Date: Mon Aug 19 12:51:19 2019 -0700 Added offset to right hand side of GMRES. Still not converging for high accuracy. exec/fluctuatingMembrane/advance.cpp exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 exec/immersedIons/advance.cpp commit 56ce2893395bcec04b2e7863cf4f27343896675d Author: Aleksandar Donev Date: Mon Aug 19 15:39:35 2019 -0400 Tried using HydroGrid exec/fluctuatingMembrane/membrane_forces.F90 commit 0cc40085c155acd3e13180a1addaeb1926ad5dcf Merge: 65b82301 0e3bddef Author: Daniel Ladiges Date: Mon Aug 19 11:57:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 65b823017e817366fa892a2b18d7baad487bfed5 Author: Daniel Ladiges Date: Mon Aug 19 11:56:21 2019 -0700 FHDeX particles now work when a box has zero particles. exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp src_particles/FhdParticleContainer.cpp commit 0e3bddefaa9094bca4aec5bd44f19efac84aba04 Author: Andy Nonaka Date: Mon Aug 19 11:20:19 2019 -0700 includes HydroGrid. Note you need an updated LowMachFHD git repo exec/fluctuatingMembrane/GNUmakefile commit 4df83a272965164451de2b8d3397540d1e187e38 Merge: 2ad94808 87c862bc Author: jbb Date: Fri Aug 16 18:14:01 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2ad9480830e4771f977c826330ae781e5469c845 Author: jbb Date: Fri Aug 16 18:13:26 2019 -0700 cleanup ot 2d GL code exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions_F.H exec/_GL_alt/timeStep.cpp commit 87c862bc420b8e580a0e9acc8df254b2af94e687 Author: Aleksandar Donev Date: Fri Aug 16 20:46:29 2019 -0400 Changed fluctuatingMembrane to have 2 particles with equal and opposite forces to make GMRES solvable exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 commit 1cdc9c1fd70aa0ccd645b291fe26ff23b1ed2bb2 Author: Aleksandar Donev Date: Fri Aug 16 20:32:43 2019 -0400 GMRES not converging yet. CHANGE requests added to membrane_forces exec/fluctuatingMembrane/membrane_forces.F90 commit cd74c536dfd1cf48a13b31cdcf8e356fb835bda3 Author: Aleksandar Donev Date: Fri Aug 16 20:20:31 2019 -0400 GMRES not converging yet exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/membrane_forces.F90 exec/fluctuatingMembrane/write_pview_file.pyc commit 205b32bbb13fa66e289d64dfdcd9c5989a506ce5 Merge: db79c976 81892879 Author: Aleksandar Donev Date: Fri Aug 16 19:57:21 2019 -0400 Updated input file commit db79c976cad728a936350d8e32ff10a7e346bcbd Author: Aleksandar Donev Date: Fri Aug 16 19:54:54 2019 -0400 Updated input file exec/fluctuatingMembrane/inputs_3d commit 81892879a84895a83a498ed114be352ec0dd8935 Merge: 986b9059 facb8a8d Author: Daniel Ladiges Date: Fri Aug 16 16:53:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit facb8a8d92a870413d5ffc9b11fa511b390bf2b1 Author: Aleksandar Donev Date: Fri Aug 16 19:26:22 2019 -0400 Added init and destroy functions to membrane_forces.F90 exec/fluctuatingMembrane/membrane_forces.F90 commit 07ba9477d872fcf914933e44c6bfb0fedc9147a6 Merge: 5b5a2a30 e12e57f4 Author: Aleksandar Donev Date: Fri Aug 16 19:07:26 2019 -0400 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 5b5a2a309d4dcab8198f380d278abf7c8c993e09 Author: Aleksandar Donev Date: Fri Aug 16 19:07:08 2019 -0400 Donev changed makefile to allow to build in external directory, and moved force function to membrane_forces.F90 exec/fluctuatingMembrane/GNUmakefile exec/fluctuatingMembrane/Make.package exec/fluctuatingMembrane/membrane_forces.F90 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit e12e57f4172e227840a221472c915406075473c6 Merge: 077344f5 632bb3f9 Author: jbb Date: Fri Aug 16 14:48:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 077344f566efbdb5b182e9f990b117b4c0770ce7 Author: jbb Date: Fri Aug 16 14:48:04 2019 -0700 cleanup exec/_GL_alt_1D/GL_funcs.F90 exec/_GL_alt_1D/GL_functions.H exec/_GL_alt_1D/GL_functions_F.H exec/_GL_alt_1D/timeStep.cpp commit 986b9059cee00a794cd330ba559e858d0d4267f3 Author: Daniel Ladiges Date: Fri Aug 16 14:24:17 2019 -0700 Membrane marker positions now read from file exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/membrane.dat exec/fluctuatingMembrane/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 632bb3f9d22c608ba313f42891d287745af89bd4 Merge: 4985f79e 152b9857 Author: Andy Nonaka Date: Fri Aug 16 14:03:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4985f79e83d3fdcfae55a350d31c6fd196bbbd01 Author: Andy Nonaka Date: Fri Aug 16 14:02:31 2019 -0700 MkAdvSFluxdiv on gpu. got rid of tracer diffusion so regression will be updated src_hydro/MkAdvSFluxdiv.cpp src_hydro/src_F90/Make.package src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 152b9857189e9a8b1eff215ef4c514e473ff8790 Merge: 4e743f4f 15b65d4d Author: Daniel Ladiges Date: Fri Aug 16 13:42:03 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4e743f4f8f812bd5b961007da7bba2fc83fb8fc9 Author: Daniel Ladiges Date: Fri Aug 16 13:41:52 2019 -0700 Bugfix on membrane code exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 15b65d4d888ac1f9adc8b5783e0f16ac60ca442c Author: jbb Date: Fri Aug 16 13:06:44 2019 -0700 fixed some bugs in GL codes exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/GL_funcs.F90 exec/_GL_alt_1D/inputs_1d exec/_GL_alt_1D/timeStep.cpp commit b455e65d2fe352e2563afb85f53da2db3b0f08ce Merge: 947c197f 32ff9ce5 Author: jbb Date: Fri Aug 16 09:55:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 32ff9ce50e0ebc3bc64cacf4378f2bfcdb0c6066 Author: Andy Nonaka Date: Fri Aug 16 09:15:56 2019 -0700 ported the remaining visc_types in stag_mg_update to gpu src_gmres/StagMGSolver.cpp src_gmres/src_F90/Make.package src_gmres/src_F90/stag_mg_solver.F90 commit 83e29c230d178e1b664b23c670aa8e7749613254 Author: Andy Nonaka Date: Fri Aug 16 08:06:45 2019 -0700 rather than create a temporary alpha, simply multiply alpha by theta_alpha *within* StagApplyOp src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H commit 2ed916ed4a2607d4f6f7bc12c2ac5637732558b8 Author: Andy Nonaka Date: Fri Aug 16 07:58:47 2019 -0700 get these compiling in 3d again; use AMREX_D_DECL macros to help clean up code src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp commit 947c197ffe7426c7c12b0e5a9679fe35e79e72e8 Author: jbb Date: Thu Aug 15 17:24:21 2019 -0700 removed bogus file exec/_GL_alt_1D/-home-kevinluna-FHDeX-exec-_GL_alt_1D_test-.txt commit a457646e057d3fa926dba843c84e3d2fb1079afe Merge: 8b828058 b4b78ac5 Author: jbb Date: Thu Aug 15 17:23:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8b828058d8e4e4c41a0e7cae422969cd0771671c Author: jbb Date: Thu Aug 15 17:22:37 2019 -0700 fixed things so 1d GL would compile exec/_GL_alt/GNUmakefile exec/_GL_alt/timeStep.cpp exec/_GL_alt_1D/fort.7 exec/_GL_alt_1D/timeStep.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_common/src_F90/sqrt_mf.F90 src_rng/rng_functions_F.H commit b4b78ac5dacb0131a1c69b21525c27c5125d894d Author: Andy Nonaka Date: Thu Aug 15 16:02:58 2019 -0700 temporary fix for hydro solver bug src_gmres/StagApplyOp.cpp commit 498de5e226e8b64bcadea31c007dc41e1cccb186 Merge: 152ee694 6d9251bc Author: Daniel Ladiges Date: Thu Aug 15 14:35:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 152ee694ae69bf2f4a4d191391e1b71fb3d221b6 Author: Daniel Ladiges Date: Thu Aug 15 14:34:52 2019 -0700 Added function which pulls particle positions to proc 0, calculates forces, and distributes forces back to original funcs. exec/fluctuatingMembrane/advance.cpp exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/particleGen.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 6d9251bc1a9186bba6ee93209e97bedf227ffc58 Merge: b06a81f7 19aef527 Author: spcarney34 Date: Thu Aug 15 14:10:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b06a81f71b7672850d2e8bdc09650022a458d50d Author: spcarney34 Date: Thu Aug 15 14:08:39 2019 -0700 Previous version of main_driver for debugging purposes. exec/immersedIons/main_driver_OLD.cpp commit 19aef527e784183110a241326a909228f64a226b Author: Daniel Ladiges Date: Thu Aug 15 13:54:37 2019 -0700 Ditto exec/fluctuatingMembrane/debug_functions_F.H commit ed4c479240ed24678c35b463cc2f779f6c759064 Author: Daniel Ladiges Date: Thu Aug 15 13:53:49 2019 -0700 Ditto exec/fluctuatingMembrane/hydro_test_functions.H exec/fluctuatingMembrane/hydro_test_functions_F.H commit 530c3e96b90d62f1edcb6461adaf020a6ec77ee2 Author: Daniel Ladiges Date: Thu Aug 15 13:52:39 2019 -0700 Ditto exec/fluctuatingMembrane/Make_precheck.package commit 39c3d5940748e6d1c989936de041576ead7bcff0 Author: Daniel Ladiges Date: Thu Aug 15 13:50:42 2019 -0700 Ditto. exec/fluctuatingMembrane/DEBUG.F90 commit beaee53509f01bad1cae9b8090879881d0f5ba72 Author: Daniel Ladiges Date: Thu Aug 15 13:49:01 2019 -0700 Added file missing from tracking in membrane exec/fluctuatingMembrane/Make_debug.package commit f1cf3a1014ccab85b9b1c99e772b7d6c7f6c00cc Merge: 18c8259c f0a6e39f Author: Daniel Ladiges Date: Thu Aug 15 11:52:48 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 18c8259c994face41e54ce50a6edafaf50d92068 Author: Daniel Ladiges Date: Thu Aug 15 11:52:18 2019 -0700 Stokes solver is broken, pushing for others to investigate. exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/particleGen.cpp exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit f0a6e39f873a56eb7b7ec51ccc9e5494c1b30566 Author: Andy Nonaka Date: Thu Aug 15 11:38:47 2019 -0700 stag_mg_update: ported visc_type=-1 to GPU src_gmres/StagMGSolver.cpp src_gmres/src_F90/stag_mg_solver.F90 commit cd5a954616a1e640325822d0fb832142a80fbad2 Merge: 3effbd17 9a31cc54 Author: Andy Nonaka Date: Thu Aug 15 11:26:23 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9a31cc5437ff41e858ae81f0b73a6e08319d997c Merge: f3a39899 3a9d2eb8 Author: Johannes Blaschke Date: Thu Aug 15 11:20:50 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit f3a39899a7c8856593c0de48e4a7c9f65d7474fb Author: Johannes Blaschke Date: Thu Aug 15 11:20:40 2019 -0700 searching for why flagellum is moving the wrong way exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test.scaled commit 3effbd173a7208f81fbd25e7361dfaf28a86c5ea Author: Andy Nonaka Date: Thu Aug 15 09:28:52 2019 -0700 some code re-org to help with porting of stag_mg_update to gpu src_gmres/src_F90/stag_mg_solver.F90 commit 3a9d2eb8c75a96cddacff901458603b720ef3403 Author: Andy Nonaka Date: Thu Aug 15 09:18:07 2019 -0700 stag_apply_op: visc_type=-2 on GPU src_gmres/StagApplyOp.cpp src_gmres/src_F90/Make.package src_gmres/src_F90/stag_apply_op.F90 commit 65fae1ba42f83c6972381a146c64683996fc9525 Author: Andy Nonaka Date: Thu Aug 15 09:06:45 2019 -0700 stag_apply_op visc_type=+2 now on gpu src_gmres/StagApplyOp.cpp src_gmres/src_F90/stag_apply_op.F90 commit 55d6e3b37a53db903a07b722faac125e15b11acb Author: Andy Nonaka Date: Thu Aug 15 08:41:48 2019 -0700 stag_apply_op visc_type=-1 now on gpu src_gmres/StagApplyOp.cpp src_gmres/src_F90/stag_apply_op.F90 commit 732b1f821fb570545fee92d31a85fa69323f8c54 Author: Andy Nonaka Date: Wed Aug 14 19:13:26 2019 -0700 another attempt at passing omega src_gmres/StagMGSolver.cpp commit 9a0060abfdf3ec344b70da10be68629c776ac209 Author: Andy Nonaka Date: Wed Aug 14 19:11:44 2019 -0700 pass in stag_mg_omega to gpu src_gmres/StagMGSolver.cpp commit c8103ef1b47caf7eb320f32f50bf9fc03730a46c Merge: 41dd1f63 f8f07668 Author: Andy Nonaka Date: Wed Aug 14 19:08:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 41dd1f63174849dd3e1d1e9f433c6d68078fa438 Author: Andy Nonaka Date: Wed Aug 14 19:07:42 2019 -0700 stag_mg_update for visc_type=+1 complete src_gmres/StagMGSolver.cpp commit f8f07668bef55e7518f5ba9f63bb1030981ce20a Merge: d6963777 9bb5f959 Author: Johannes Blaschke Date: Wed Aug 14 18:05:36 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit d6963777c60b2ce1f086700c68583e494aed404a Author: Johannes Blaschke Date: Wed Aug 14 18:05:31 2019 -0700 update time stepping in flagellum example exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test.scaled src_hydro/MkAdvMFluxdiv.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9bb5f959301b230c60d438b580fa483d73b03830 Merge: b20313c4 51ac44e4 Author: Andy Nonaka Date: Wed Aug 14 17:02:37 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b20313c46ef29862a22bfcb322e4ac95356cab2c Author: Andy Nonaka Date: Wed Aug 14 17:02:17 2019 -0700 use GPUArray instead of array src_hydro/MacProj_hydro.cpp commit 51ac44e44965d470164f6950c64e8542421e887c Author: Daniel Ladiges Date: Wed Aug 14 16:30:53 2019 -0700 Added ability to turn off close range interations between like species src_particles/src_F90/particle_functions.F90 commit 1336c41f078541c90e06a8585468f26621aa3ee3 Author: Daniel Ladiges Date: Wed Aug 14 16:25:39 2019 -0700 Deleted some deprecated functions src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit e3593782b0b81a5b37f4fbc4f96f413f945aeb49 Author: Daniel Ladiges Date: Wed Aug 14 16:11:48 2019 -0700 New directory for fluctuating membrane case exec/fluctuatingMembrane/Data.ipynb exec/fluctuatingMembrane/GNUmakefile exec/fluctuatingMembrane/INS_functions.H exec/fluctuatingMembrane/Make.package exec/fluctuatingMembrane/TimeStep.cpp exec/fluctuatingMembrane/WritePlotFile.cpp exec/fluctuatingMembrane/WritePlotFileHydro.cpp exec/fluctuatingMembrane/advance.cpp exec/fluctuatingMembrane/amrex_to_vtp.py exec/fluctuatingMembrane/convertSeries exec/fluctuatingMembrane/delPlots exec/fluctuatingMembrane/inputs_3d exec/fluctuatingMembrane/main_driver.cpp exec/fluctuatingMembrane/particleGen.cpp exec/fluctuatingMembrane/precheck.F90 exec/fluctuatingMembrane/write_pview_file.py exec/fluctuatingMembrane/write_pview_file.pyc commit fb72adf6051c677cf09cf98b17ca9c4e9a931a91 Author: Daniel Ladiges Date: Wed Aug 14 16:08:37 2019 -0700 Added multispecies sigma to LJ calc. src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit f9cbb46dd59e5894180d056fa5ac3d06f703eabd Author: Daniel Ladiges Date: Wed Aug 14 15:11:03 2019 -0700 more debugging code removed, some additions to the namespace for membrane problem. src_electrostatic/electrostatic.cpp src_particles/src_F90/particle_functions.F90 commit 9666d1a58e79034987206f8d508b2cdc004c7d2c Author: Daniel Ladiges Date: Wed Aug 14 14:20:39 2019 -0700 Removed debugging from electrostatic code after AMReX fix exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_reflect exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_electrostatic/electrostatic.cpp src_particles/src_F90/particle_functions.F90 commit 531590c70188146f69373e3556b69704a39e8a9e Merge: 26e6b0c5 c7aba47a Author: Daniel Ladiges Date: Wed Aug 14 10:05:53 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 26e6b0c5dd03e029a79a94bfe150a6ec5075bf60 Author: Daniel Ladiges Date: Wed Aug 14 10:04:46 2019 -0700 Broken electrostatic code for John/Andy to check exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_reflect exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_electrostatic/electrostatic.cpp commit c7aba47a9ace09c4c4bf8d995d6521c58b19a11a Author: Andy Nonaka Date: Wed Aug 14 08:31:22 2019 -0700 immediately return out of MultiFABPhysBC, MultiFABPhysBCDomainVel, and MultiFABPhysBCMacVel if periodic in all directions src_common/MultiFABPhysBC.cpp commit e75c88b9d96327f513347fd2071f23767bfc4563 Author: Andy Nonaka Date: Wed Aug 14 08:24:51 2019 -0700 code cleanup only; use AMREX_D_DECL macros more src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit 713f77b2b0df58ccf86b2be3755bc1f952778412 Author: Andy Nonaka Date: Wed Aug 14 08:09:22 2019 -0700 pass values in by value to gpu. pass in GPUArray for dx src_common/ComputeDivAndGrad.cpp src_gmres/StagApplyOp.cpp commit dc257f1b618ce5847b8c959bc120717a2ef423a7 Merge: a2f48cc8 b20993ec Author: jbb Date: Tue Aug 13 17:05:33 2019 -0700 Merge branch 'kevin_luna_adaptive_k' commit a2f48cc896858263318f3ada9d911c3a6837a9c2 Author: Andy Nonaka Date: Tue Aug 13 16:16:31 2019 -0700 StagProlongation on GPU src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit ec0beb79db9a0be17a054862df8a14a0dcda2d3b Author: Andy Nonaka Date: Tue Aug 13 14:58:27 2019 -0700 prep the fortran for direction conversion to C++. eliminated all if/else logic and used mod's and multiple loops with stride instead src_gmres/src_F90/stag_mg_solver.F90 commit 48106aaaedb34cc6af2f3126dcf30879b1151e63 Author: Andy Nonaka Date: Tue Aug 13 14:43:50 2019 -0700 EdgeRestriction now on GPU src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit da3bc02780f15fddd060092839f777ed9eb2499f Merge: 2c259ecf 1f5f65a3 Author: Daniel Ladiges Date: Tue Aug 13 12:01:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2c259ecfa9a19c6ecd55ed3a437720d99d8aa112 Author: Daniel Ladiges Date: Tue Aug 13 12:01:12 2019 -0700 Broken Poisson solve, pushing for Andy to look at exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_poisson exec/immersedIons/inputs_3d_reflect exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersedIons/properties.nb src_electrostatic/electrostatic.cpp commit 1f5f65a3756f535e17d7ddfab8b7092b175e9119 Author: Andy Nonaka Date: Tue Aug 13 11:21:27 2019 -0700 StagRestriction now on GPU src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit 597b8900237d8b9863617fcf7fbfdce24d9fc397 Author: Andy Nonaka Date: Tue Aug 13 09:35:01 2019 -0700 move gmres_namelist to src_F90 src_gmres/Make.package src_gmres/src_F90/Make.package src_gmres/src_F90/gmres_namelist.F90 commit 0dbfee9adaafb4c57af77dcad0d30361f88f001e Author: Andy Nonaka Date: Tue Aug 13 09:31:51 2019 -0700 NodalRestriction on GPU src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit 6cf45e801e0bb92358e8990b275337e365682179 Author: Andy Nonaka Date: Tue Aug 13 09:13:44 2019 -0700 cc_restriction on gpu src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit d46deb35ca2284a7e0112ab84560156d86e7a740 Author: Andy Nonaka Date: Tue Aug 13 08:54:11 2019 -0700 cleanup indentation only src_gmres/src_F90/stag_mg_solver.F90 commit 6f81453251bb231838a7e1510a6b09a5eb49893e Merge: 9e11a073 ac363680 Author: Johannes Blaschke Date: Mon Aug 12 17:36:59 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 9e11a0733f6cd5042f22faa88d4adbc47d568208 Author: Johannes Blaschke Date: Mon Aug 12 17:36:56 2019 -0700 wip on stability problem => increase order of time stepping exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test.scaled commit 8f267fd3b6e35772ff3f4f665da05feb7902d9d3 Author: Johannes Blaschke Date: Mon Aug 12 16:38:16 2019 -0700 move marker updating to seperate function exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/src_models/IBMarkerMD.cpp src_immersed-boundary/IBMarkerContainer.cpp commit ac36368072af697b0a2977af375fc1268b9e6d34 Author: Andy Nonaka Date: Mon Aug 12 13:48:51 2019 -0700 much simpler way to do staggered sums on GPU (don't use overlap mask, instead use logic for 1 or 0.5 weighting depending on if you're at the box edge in the nodal direction) src_gmres/NormInnerProduct.cpp commit f253ff40a3777b206b4f70eca4f82074fca517e7 Author: Andy Nonaka Date: Mon Aug 12 13:40:47 2019 -0700 remove debugging statement src_common/common_functions.cpp commit 7ca63b5ec5614d75c112d2b26183cfcc9da414ae Author: Andy Nonaka Date: Mon Aug 12 12:42:53 2019 -0700 made alpha_fc not const exec/immersedIons/INS_functions.H exec/immersedIons/advance.cpp commit da51f2773fadf82d1cd758ffd98b70a9499df5a9 Author: spcarney34 Date: Mon Aug 12 12:42:20 2019 -0700 external debug file for compiling exec/immersedIons/Make_debug.package commit b2485dc968259bf1f325fe42cf692927de2e53a1 Author: Johannes Blaschke Date: Mon Aug 12 12:37:35 2019 -0700 clean up exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 95675fa509040ebf270bb0194b45038acff8546d Merge: 3c95aa04 21216fd0 Author: spcarney34 Date: Mon Aug 12 11:10:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3c95aa04aae8fbf673a1a5c2cfa4a1c650abf06d Author: spcarney34 Date: Mon Aug 12 11:10:13 2019 -0700 Adding p3m with walls + some input files. Testing still ongoing. exec/immersedIons/DEBUG.F90 exec/immersedIons/GNUmakefile exec/immersedIons/debug_functions_F.H exec/immersedIons/inputs_3d exec/immersedIons/inputs_3d_reflect exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit eeb79774ff9b0b6b877f437c770718261800d6c7 Author: Johannes Blaschke Date: Mon Aug 12 10:10:01 2019 -0700 working on increasing the time step exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/inputs_3d_test.scaled commit 21216fd0e2129180fceca359293cbfe083894c7a Merge: 45b3b2c5 b9df3dc2 Author: Johannes Blaschke Date: Fri Aug 9 17:20:03 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit b9df3dc2f704e768973c3f566825e11e19a45d07 Author: Guy Moore Date: Fri Aug 9 17:22:08 2019 -0700 cleaned-up inputs files exec/compressible/inputs_1d exec/compressible/inputs_RT_3d exec/compressible/inputs_equil_3d exec/compressible/inputs_giantfluct_3d exec/compressible/inputs_regression_RT_3d commit 45b3b2c584f1cd3d013692e57c3447659a2fbaaa Author: Johannes Blaschke Date: Fri Aug 9 17:19:57 2019 -0700 work on fixing the instability for small lenght scales exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test.scaled exec/immersed_boundary/flagellum/main_driver.cpp commit 002d5fb96c11b0bb68d6bf9043cc68eeab8b1cfa Author: Guy Moore Date: Fri Aug 9 16:05:02 2019 -0700 Cleaned-up flux scaling for various BCs exec/compressible/octave_tests/large_fluct_analysis.m exec/compressible/octave_tests/large_fluct_grad.mat src_compressible/src_F90/flux_funcs.F90 commit b20993ec5dd233f1d2cf0d551d9580efe4ceaff4 Author: kevinluna Date: Fri Aug 9 14:36:01 2019 -0700 Small tweaks to common src files for 1D code exec/_GL_alt/Python_notebooks_KL_new/EMUS_scripts/Comp_EMU_PMF(step3).ipynb exec/_GL_alt/Python_notebooks_KL_new/EMUS_scripts/Extract_Umbrella_params(step1).ipynb exec/_GL_alt/Python_notebooks_KL_new/EMUS_scripts/Make_meta_files(step2).ipynb commit 701071ff0932d38a2e9f8429eded1f3f2428b4ce Author: kevinluna Date: Fri Aug 9 14:30:06 2019 -0700 Added 1D code src_common/ComputeDivAndGrad.cpp src_common/MultiFABPhysBC.cpp src_common/src_F90/compute_div_and_grad.F90 src_common/src_F90/find_coords.F90 src_common/src_F90/multifab_fill_random.F90 src_common/src_F90/multifab_physbc_mod.F90 commit 76f7bd750000ce19f65347537d121b8384c87d30 Author: kevinluna Date: Fri Aug 9 14:18:06 2019 -0700 Added 1D code exec/_GL_alt_1D/inputs_2d exec/_GL_alt_1D/inputs_2d_LOW_T_Back exec/_GL_alt_1D/inputs_2d_LOW_T_FORWRD exec/_GL_alt_1D/inputs_2d_new commit a5439d97778d3799cea263a25b7448b7303450ca Author: kevinluna Date: Fri Aug 9 14:17:40 2019 -0700 Added 1D code exec/_GL_alt_1D/-home-kevinluna-FHDeX-exec-_GL_alt_1D_test-.txt exec/_GL_alt_1D/.txt exec/_GL_alt_1D/GL_funcs.F90 exec/_GL_alt_1D/GL_functions.H exec/_GL_alt_1D/GL_functions_F.H exec/_GL_alt_1D/GL_namelist.F90 exec/_GL_alt_1D/GNUmakefile exec/_GL_alt_1D/Make.package exec/_GL_alt_1D/exec_functions.H exec/_GL_alt_1D/fort.7 exec/_GL_alt_1D/inputs_1d exec/_GL_alt_1D/inputs_2d exec/_GL_alt_1D/inputs_2d_LOW_T_Back exec/_GL_alt_1D/inputs_2d_LOW_T_FORWRD exec/_GL_alt_1D/inputs_2d_new exec/_GL_alt_1D/main_driver.cpp exec/_GL_alt_1D/mymbar exec/_GL_alt_1D/timeStep.cpp exec/_GL_alt_1D/writePlotFile.cpp commit c72822641ddca0e5603b7908e6d06e4c73806c46 Author: kevinluna Date: Fri Aug 9 12:43:23 2019 -0700 added cleaned up commented python notebooks exec/_GL_alt/Python_notebooks_KL_new/Comp_EMU_PMF(step3).ipynb exec/_GL_alt/Python_notebooks_KL_new/Extract_Umbrella_params(step1).ipynb exec/_GL_alt/Python_notebooks_KL_new/Make_meta_files(step2).ipynb exec/_GL_alt/Python_notebooks_KL_new/Ploting_script.ipynb commit eb3836aeca26ce204599b17ce183ba412fcfb45a Merge: b6f87b48 b675cf42 Author: Johannes Blaschke Date: Thu Aug 8 20:28:22 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit b6f87b48a806c3e995d59a71e9c115f457506bed Author: Johannes Blaschke Date: Thu Aug 8 20:28:09 2019 -0700 gpu grad 3 launches -> 1 src_common/ComputeAverages.cpp src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp src_gmres/StagApplyOp.cpp commit b675cf4287f777c25992b1ce3aaebb405ba9b702 Merge: 61ab64b3 cc478f6a Author: alballow Date: Thu Aug 8 16:55:22 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 61ab64b32ffcaf6e18bf5a9d9e26f615fb7eacc4 Author: alballow Date: Thu Aug 8 16:54:22 2019 -0700 Add a bash script to take out for loop exec/DSMC/bashscript exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit cc478f6a84fd67e181ef0f6214c70b64c9b86a6e Merge: 6ee2b4a1 da225d37 Author: Gang Xu Date: Thu Aug 8 14:32:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6ee2b4a14f0522ac0740ea84a944f031c6758aec Author: Gang Xu Date: Thu Aug 8 14:32:36 2019 -0700 updated according to flagellum folder. Not working yet. exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit a7ed5929fc7d238c6a93bbd0a7b5acfefbc2b99b Author: kevinluna Date: Thu Aug 8 11:20:33 2019 -0700 commented 2d code exec/_GL_alt/inputs_2d_LOW_T_Back exec/_GL_alt/inputs_2d_LOW_T_FORWRD exec/_GL_alt/inputs_2d_new commit 13186e6e8d1e8b13ec04ea59b95944f09781be5b Author: kevinluna Date: Thu Aug 8 11:17:09 2019 -0700 commented 2d code exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt/writePlotFile.cpp commit da225d3780101337762639be53d969649913bd4e Author: Johannes Blaschke Date: Thu Aug 8 09:47:22 2019 -0700 update IB precon for gpu port src_immersed-boundary/IBGMRES.cpp commit 4d2f359159f4e5b7acdeeb551a37113f01c375bb Merge: 27e5bce0 b1bc8b4d Author: Johannes Blaschke Date: Thu Aug 8 09:31:54 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 27e5bce02186a33b2227c236117090f8b3b90770 Author: Johannes Blaschke Date: Thu Aug 8 09:31:50 2019 -0700 fix off-by-one error exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.cpp commit b1bc8b4daba8b2e413ae7e43291f33f0cd8e899a Author: Andy Nonaka Date: Thu Aug 8 04:21:34 2019 -0700 fixed 2 bugs that were preventing compilation: 1. was passing in the default value for findredist in the definition, not the declaration 2. was trying to overwrite a const input parameter src_common/ComputeAverages.cpp commit bb6ee07e7908102f2ce2a1eefbf9708524e3b495 Author: Guy Moore Date: Wed Aug 7 21:37:03 2019 -0700 Found dist. map fix. Needs more debugging exec/compressible/main_driver.cpp src_analysis/StructFact.cpp src_common/ComputeAverages.cpp src_common/common_functions.H commit b566bcc9211d5923383f879d941615dbbdad752b Author: Andy Nonaka Date: Wed Aug 7 17:20:36 2019 -0700 C++ gpu version of the routines in norm_inner_prod.F90 src_gmres/NormInnerProduct.cpp src_gmres/src_F90/Make.package src_gmres/src_F90/norm_inner_prod.F90 commit 01653646c452c7f825af3f27a4ef29cae5b360c2 Author: Andy Nonaka Date: Wed Aug 7 17:01:12 2019 -0700 passing in a Geometry object into SumStag, StagInnerProd, and StagL2Norm in prepration for gpu port src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/NormInnerProduct.cpp src_gmres/gmres_functions.H src_hydro/StochMFlux.cpp commit d29563b6dd7905d07e9f5ec9fd6cbb13c8f74a7f Author: Guy Moore Date: Wed Aug 7 10:53:02 2019 -0700 Large fluctuations test setup. Cleanup needed exec/compressible/init_consvar.F90 exec/compressible/inputs_RT_3d exec/compressible/inputs_giantfluct_3d exec/compressible/main_driver.cpp src_common/ComputeAverages.cpp src_common/Make.package src_common/common_functions.H commit 20c82645a50dca9ad26b64d2af9216a4b2d854bf Merge: fd267dfc c9657787 Author: Guy Moore Date: Wed Aug 7 10:41:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c96577871c965da623db9f98f51a3a0bfcbfab43 Merge: 914fe1d2 b3ede7a1 Author: Johannes Blaschke Date: Wed Aug 7 10:21:26 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 914fe1d2b8516b2da96ac13cbf4bccc511284d2c Author: Johannes Blaschke Date: Wed Aug 7 10:21:23 2019 -0700 add k driving to ib_flagellum namespace exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test src_immersed-boundary/ib_functions.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit b3ede7a10d648c413dda9b2534d4928009ce3810 Merge: 59fb565d 91bea239 Author: Gang Xu Date: Wed Aug 7 10:18:12 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 59fb565d38e2060284332ba4b446feeb5689f8b0 Author: Gang Xu Date: Wed Aug 7 10:15:39 2019 -0700 towards realistic flagellar waveform exec/immersed_boundary/flagellum_chlamy/Explore Data MP.ipynb exec/immersed_boundary/flagellum_chlamy/Render Frames.ipynb exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit 91bea23968f37690fba9a3ac0c32ef30467da9d4 Author: Andy Nonaka Date: Wed Aug 7 09:15:35 2019 -0700 bugfix - error in number of plot variables plotted vs nplot. caused fcompare to break exec/compressible/writePlotFile.cpp commit dd51f8f8fc94fda0875a585e35040bd7d2508561 Author: Johannes Blaschke Date: Tue Aug 6 23:33:05 2019 -0700 almost all flagellum parameters are now set in the inputs file exec/immersed_boundary/flagellum/advance.cpp commit 00dd4edd342549adf41ef36a3fec519514205c57 Author: Johannes Blaschke Date: Tue Aug 6 23:22:29 2019 -0700 load link length from inputs file exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 1d3d806042c9c11b60d3256f7f699e47b848c23c Author: Johannes Blaschke Date: Tue Aug 6 22:56:18 2019 -0700 initialize flagellum from inputs file exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBaseI.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 1cea60d90edea58fd8ae426617354c32b209f592 Author: Johannes Blaschke Date: Tue Aug 6 21:38:34 2019 -0700 load arrays in column-major order exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 586aea3e15f9b45cfc909b482baaaed87592d559 Author: Johannes Blaschke Date: Tue Aug 6 20:20:31 2019 -0700 of course I forgot to actually git-add this file src_immersed-boundary/ib_functions.cpp commit 994864d954d67041ef7e4d954e4765571082b190 Author: Johannes Blaschke Date: Tue Aug 6 17:53:14 2019 -0700 start making use of newly implemented inputs settings for immersed flagella exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 17c1a8cbffa42105417b27e0981b630582561227 Author: Johannes Blaschke Date: Tue Aug 6 16:43:11 2019 -0700 add immersed boundary and ib flagellum namespaces exec/immersed_boundary/flagellum/main_driver.cpp src_compressible/compressible_functions.cpp src_gmres/gmres_functions.H src_immersed-boundary/Make.package src_immersed-boundary/ib_functions.H src_immersed-boundary/ib_functions_F.H src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit cced951bf7ba0d62a6d6dc74cafdbc43f0747a4b Author: Johannes Blaschke Date: Tue Aug 6 13:44:02 2019 -0700 add more properties to ib_flagellum namespace exec/immersed_boundary/flagellum/inputs_3d_test src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit fd267dfc1b1cec89e0fe7a049c05e3663d0788a6 Author: Guy Moore Date: Tue Aug 6 13:34:17 2019 -0700 Compiles with single cell in z-direction exec/compressible/inputs_3d exec/compressible/inputs_RT_3d src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 src_compressible/timeStep.cpp commit f5a1fcf1980876d1a755e632d6aad6ca2eb5a3a8 Merge: 0eda8a5c a6672345 Author: Johannes Blaschke Date: Tue Aug 6 13:16:48 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 0eda8a5c749b46f6429cf0826f0ce29dbfbee6c8 Author: Johannes Blaschke Date: Tue Aug 6 13:16:35 2019 -0700 use seperate namelists for different types of immersed boundary exec/immersed_boundary/flagellum/inputs_3d_test src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 5e08081930bc99c3ae3bf35774524be11efb7dc6 Merge: 97d92d01 29ad0fd0 Author: alballow Date: Tue Aug 6 11:08:00 2019 -0700 Merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 97d92d01b4026048b32ac9a02abab3b0c6e60850 Author: alballow Date: Tue Aug 6 11:07:08 2019 -0700 Trying to add command line controls exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_surfaces/src_F90/surface_functions.F90 commit b87269592c77d4085b3c27c7f71ccfc5853453ff Author: Johannes Blaschke Date: Tue Aug 6 11:03:40 2019 -0700 forgot to add these header files src_immersed-boundary/immbdy_namespace.H src_immersed-boundary/immbdy_namespace_declarations.H commit a6672345ddbce9205e7bc99f8e281170eb236a90 Merge: b47f66bb b8726959 Author: Andy Nonaka Date: Tue Aug 6 11:00:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b47f66bb038ad9ee6ddbf8831720cac1ec06363e Merge: ea445834 ddff0157 Author: Andy Nonaka Date: Tue Aug 6 10:59:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ea4458348d1645fd2fa8bfbeaf096fcec28eb50e Author: Andy Nonaka Date: Tue Aug 6 10:59:28 2019 -0700 new regression test exec/compressible/inputs_regression_RT_3d commit ddff0157b847591a53c8e7001d19b803350dfb49 Merge: 78feab30 29ad0fd0 Author: Johannes Blaschke Date: Tue Aug 6 10:56:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 78feab30ac26d6fffdecdcb34984b6ca39e68780 Author: Johannes Blaschke Date: Tue Aug 6 10:56:23 2019 -0700 work around to load variable list of ib markers exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 29ad0fd0fa84c90d88424d8a704f1f4e17334352 Author: Guy Moore Date: Tue Aug 6 10:02:00 2019 -0700 Fixed coefficients to be evaluated in entire region (valid+ghostcells+corners) src_compressible/src_F90/multispec_funcs.F90 commit 9b674a14cdf531a48720aedafed8d0b35737f721 Merge: 92bf48f0 c7ce4b5e Author: Johannes Blaschke Date: Tue Aug 6 09:40:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 92bf48f0c51106407fd9490622ddb941c076f6f5 Author: Johannes Blaschke Date: Tue Aug 6 09:40:48 2019 -0700 add immersed boundary namespace reading src_common/src_F90/common_namelist.F90 src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/membrane.cpp src_immersed-boundary/Make.package src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/immbdy_namelist.F90 commit c7ce4b5eb7f1ff6eedf7c58fd19862afd0f8b13e Author: Andy Nonaka Date: Tue Aug 6 08:53:21 2019 -0700 now you can read in max_step from the command line and override the inputs file e.g., ./main3d inputs max_step=10 you can use this as a template to read in other parameters from the command line src_common/common_functions.cpp src_common/common_functions_F.H src_common/src_F90/common_namelist.F90 commit 94a0909237d3222518ea351a48cf2f98a7e0d159 Author: Andy Nonaka Date: Tue Aug 6 08:36:43 2019 -0700 accidentally turned off all the visc_types except for visc_type=1. Fixed now, they all should work src_gmres/StagApplyOp.cpp commit f96e1d22ee2b557d0c4ca5ed659366749a1054e6 Author: Andy Nonaka Date: Tue Aug 6 08:24:11 2019 -0700 enable parm parsing of command line for all programs src_common/main.cpp commit 8c3a09ee741ff93bee798c6041c5dfd4e455ac57 Author: Andy Nonaka Date: Tue Aug 6 08:23:15 2019 -0700 fix uninitialized variable exec/hydro/main_driver.cpp commit 03c0c8f52348c38cb39072864f604eb17ab42200 Author: Andy Nonaka Date: Tue Aug 6 04:37:01 2019 -0700 implement plot_base_name for compressible code exec/compressible/writePlotFile.cpp commit a774387384432928e661681c960c85c5b4713b10 Author: Johannes Blaschke Date: Mon Aug 5 20:50:01 2019 -0700 start working on loaded immersed-boundary marker data src_immersed-boundary/src_F90/Make.package src_immersed-boundary/src_F90/immbdy_namelist.F90 commit 773011412f68eb091b66d3a51e6cff51da4b94df Author: Johannes Blaschke Date: Mon Aug 5 20:14:31 2019 -0700 delete trailing spaces src_compressible/src_F90/compressible_namelist.F90 commit b7b9f8c2cb8e790724a3d83feefba7bd133cb17c Merge: e9e7b18a 002f5ca2 Author: Andy Nonaka Date: Mon Aug 5 19:00:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e9e7b18aa6d071bc3fac533d14ae929bb7a25f7f Author: Andy Nonaka Date: Mon Aug 5 19:00:27 2019 -0700 implemented visc_type=1 on gpu src_gmres/StagApplyOp.cpp src_gmres/src_F90/stag_apply_op.F90 commit 002f5ca20b45ba63837557470f17cf3410d73063 Author: Guy Moore Date: Mon Aug 5 18:26:29 2019 -0700 flux functions now support single cell depth - next update BC routines src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/compressible_namespace.H src_compressible/src_F90/flux_funcs.F90 commit a6a91c76fa04474a3008d32b4482c76e1658c3dc Author: Andy Nonaka Date: Mon Aug 5 13:16:36 2019 -0700 random numbers are now controlled by seed_diffusion in the namelist. Default value is 1 exec/compressible/main_driver.cpp commit dba28489ef5216ad8cbc94675ffe562e6c66df48 Author: Andy Nonaka Date: Mon Aug 5 13:14:52 2019 -0700 set the fhdSeed for the compressible code to be 1 by default. no way to control via inputs file at the moment exec/compressible/main_driver.cpp commit e8ee586fa64b01dc1b10d8d3844dc2ffef6557f9 Author: Johannes Blaschke Date: Sun Aug 4 14:47:24 2019 -0700 fix printing src_immersed-boundary/IBMarkerContainer.cpp commit 351459259f4f5986d4eec5e92b858312f2a11fc8 Author: Johannes Blaschke Date: Sun Aug 4 13:29:14 2019 -0700 fix linking error => actually iterate over neighbors exec/immersed_boundary/flagellum/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit b5d0bd195521393453519c428365926cc6d25286 Author: Johannes Blaschke Date: Sun Aug 4 11:21:32 2019 -0700 improve how immersed boundary flagella are initialized on very large grids src_immersed-boundary/IBMarkerContainer.cpp commit 905c2f40948dc4784c5f6b59ad9e7b120dc4b47a Merge: 3e2357b5 1f2c4910 Author: Johannes Blaschke Date: Sat Aug 3 22:20:51 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 3e2357b5679105d366b6e584cb473748a93ace5b Author: Johannes Blaschke Date: Sat Aug 3 22:20:18 2019 -0700 add blob base class to multiblob .gitignore src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 1f2c49105f4bef5aa2f72fefc12d6b0bd53b2335 Merge: 7a93392a 89f59f15 Author: Guy Moore Date: Fri Aug 2 16:44:23 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7a93392a530d9ace03449ef70d4f21d2af035989 Author: Guy Moore Date: Fri Aug 2 16:43:43 2019 -0700 Added true hydrostatic eqm. initial condition exec/compressible/init_consvar.F90 exec/compressible/inputs_RT_3d exec/compressible/main_driver.cpp commit 89f59f15cf83d5087ac5fb0632273211ea6f5f43 Author: Joseph Wagner Date: Fri Aug 2 13:56:16 2019 -0700 calculate the optimal number of amrex particle ghost cells to use exec/immersed_boundary/flagellum/main_driver.cpp commit 2b40d5b3b82f10de3edbc3058ca20d742776ea26 Author: Guy Moore Date: Thu Aug 1 17:44:17 2019 -0700 should now be initialized to hydrostatic equilibrium exec/compressible/compressible_test_functions_F.H exec/compressible/init_consvar.F90 exec/compressible/main_driver.cpp commit ae8764779635f8152350086afb9accdfdd115cf5 Author: Guy Moore Date: Thu Aug 1 15:45:42 2019 -0700 found second BC bug src_compressible/src_F90/bound_funcs.F90 commit f615f169dccbd0a323b183b25d247e99b2392d28 Author: Johannes Blaschke Date: Thu Aug 1 09:36:30 2019 -0700 make flagellum test case longer exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit b1d0eabd9408639ecbe97c8cb771a22172b968d6 Author: Andy Nonaka Date: Thu Aug 1 08:02:13 2019 -0700 bugfix; don't assume alpha_fc has a ghost cell src_gmres/StagApplyOp.cpp commit 35d655b97cb6f8059718fa1a2f665503438fdc35 Author: Andy Nonaka Date: Wed Jul 31 15:35:05 2019 -0700 does not require src_analysis anymore (you can uncomment out the structure factor stuff if you want it back) exec/hydro/GNUmakefile exec/hydro/main_driver.cpp commit bd366e2f666e64fc6057d92aee06fb7d873623a5 Author: Andy Nonaka Date: Wed Jul 31 15:29:58 2019 -0700 moved SqrtMF into src_common. There were two copies, one in src_analysis and src_hydro. now you can build hydro apps without including src_analysis src_analysis/StructFact.H src_analysis/StructFact.cpp src_analysis/StructFact_F.H src_analysis/src_F90/struct_fact.F90 src_common/Make.package src_common/SqrtMF.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/sqrt_mf.F90 src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp src_hydro/hydro_functions_F.H commit cdd36d6b70b0fc65453f319f1833aa28d92e72f3 Merge: f1ebf961 e63728d8 Author: Andy Nonaka Date: Wed Jul 31 14:13:50 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f1ebf9610807a0ef7e4e0d7aa63f099269aa3ff3 Author: Andy Nonaka Date: Wed Jul 31 14:13:36 2019 -0700 more cleanup in prep for gpu src_gmres/src_F90/stag_apply_op.F90 commit e63728d860c8d8c52ec1a565efa820bf70a9ee11 Merge: 1c5d8193 a9e53c6e Author: Gang Xu Date: Wed Jul 31 13:40:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 1c5d8193a08b4ad51a7586e61d6a1ef34307c0be Author: Gang Xu Date: Wed Jul 31 13:39:56 2019 -0700 deleted 'const' for alpha_fc exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.H commit a9e53c6e7b377ff43f7dda98f2124073cdfa9f93 Merge: 780b5fc2 06a5cc90 Author: Andy Nonaka Date: Wed Jul 31 11:14:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 780b5fc2a3839aed77e8ca801094ef8cc7ccc5c8 Author: Andy Nonaka Date: Wed Jul 31 11:13:50 2019 -0700 more gpu prep. plus beginning to fix the positive visc_types for 3d to the simpler constant coefficient formulation src_gmres/src_F90/stag_apply_op.F90 commit 06a5cc90fcf8f95faddb1a7766e6a9487a8321cd Merge: 50d39a8d b71abe1c Author: Gang Xu Date: Wed Jul 31 10:29:10 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 50d39a8dc7e94aabd7fe8fc865777730c8d417bf Author: Gang Xu Date: Wed Jul 31 10:29:01 2019 -0700 corrected shear angle changes in order to produce realistic beat waveform. also fixed the first marker exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit b71abe1c748d0588d3550678776eb3fff6e4e49d Author: msantiago2 Date: Wed Jul 31 09:46:19 2019 -0700 made alpha_fc declared non constant for GMRES updates exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 02b5735d8b4294d7dc69077ced784b51e2c8da7e Merge: 35eeb24d f511e9e0 Author: msantiago2 Date: Tue Jul 30 16:15:19 2019 -0700 merge with master commit 35eeb24d6c6ffe5a973a139f23380cad6b35452c Author: msantiago2 Date: Tue Jul 30 16:14:28 2019 -0700 fixed scaling factor exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 commit f511e9e02b1dbb305f36fdcb3324a72e26916802 Merge: b3893bef d2f1088b Author: Andy Nonaka Date: Tue Jul 30 15:53:28 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b3893bef624bd6509e1ff20705357c32af6fd87a Author: Andy Nonaka Date: Tue Jul 30 15:53:07 2019 -0700 starting to prep StagApplyOp for GPU port exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H src_common/ConvertStag.cpp src_gmres/ApplyMatrix.cpp src_gmres/GMRES.cpp src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/src_F90/stag_apply_op.F90 commit d2f1088ba917e826cf373c4d790e957185b87556 Author: Guy Moore Date: Tue Jul 30 15:38:23 2019 -0700 Added option to toggle: mass, temperature, and velocity BCs independently exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_common/ComputeAverages.cpp src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 commit b2748c59fef04d5f19eff4c973dbdc9b4fb5f896 Author: Andy Nonaka Date: Tue Jul 30 14:43:26 2019 -0700 put mac_solver_hydro stuff on gpu src_hydro/MacProj_hydro.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/mac_solver_hydro.F90 commit 5341a2e1fad7bc5982d79d196dec6cfe28367add Author: Andy Nonaka Date: Tue Jul 30 13:14:21 2019 -0700 combined multiple GPU launch regions into a single launch region src_common/ConvertStag.cpp commit a4abf209374f24c437d80a248b638009b4beacf1 Author: msantiago2 Date: Tue Jul 30 09:42:18 2019 -0700 clean up code exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit f2d8e113104cbbf025a440a6b239dd7ecbd7342e Author: Andy Nonaka Date: Tue Jul 30 09:33:31 2019 -0700 switched all routines to use the new AverageFaceToCC removed the old AverageFaceToCC exec/DiffuisonTest/WritePlotFile.cpp exec/brownian/WritePlotFile.cpp exec/brownian/WritePlotFileHydro.cpp exec/channel/WritePlotFile.cpp exec/hydro/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedParticles/WritePlotFileHydro.cpp exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_rigid/WritePlotFile.cpp exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum_chlamy/WritePlotFile.cpp exec/multispec/WritePlotFile.cpp exec/overdamped/WritePlotFile.cpp src_common/ConvertStag.cpp src_common/common_functions.H commit 950b154ebc4f6cc2ba3a19415f77f23caaa038dc Author: Andy Nonaka Date: Tue Jul 30 09:17:45 2019 -0700 wrote a gpu-version of AverageFaceToCC that performs the loop over all faces. next step: replace all calls in AverageFaceToCC in all of FHDeX with the new interface src_common/ConvertStag.cpp src_common/common_functions.H commit 3cf28ff52b6c734a8e0d629e70a8ab8a31b534f8 Author: Andy Nonaka Date: Tue Jul 30 08:58:40 2019 -0700 code cleanup; use more amrex macros src_common/ComputeDivAndGrad.cpp src_common/ConvertStag.cpp commit 0eb6fa80f810260069ef04bcd386c0cbea805396 Author: msantiago2 Date: Mon Jul 29 16:11:20 2019 -0700 still debugging refinement issue exec/immersed_boundary/channel_soft/inputs_3d_test src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 4ac7afb8567f0ade88ac7ceb39afc8e02c1d6115 Merge: 854688e6 15f84496 Author: msantiago2 Date: Mon Jul 29 15:49:22 2019 -0700 merge with master commit 854688e672a61a326e01c6a3c3c74509934bff43 Author: msantiago2 Date: Mon Jul 29 15:48:28 2019 -0700 debugging refinement issues exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 15f84496b363b72ec0f9db5b02aa7a39395d1fa6 Merge: ea365c10 31fc97df Author: Gang Xu Date: Mon Jul 29 11:22:06 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ea365c107b98f2e23ae8dbf860c0a3afbe29a5b1 Author: Gang Xu Date: Mon Jul 29 11:21:56 2019 -0700 realistic waveform under debugging exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit f95b7f0c34aab5043092a2512702f1cbaca9492b Author: msantiago2 Date: Sat Jul 27 12:48:58 2019 -0700 changed source strength exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 commit 7d50da62faa139d7fe67d1027f722ed30ce3f6e9 Merge: a456096b 31fc97df Author: msantiago2 Date: Sat Jul 27 12:16:11 2019 -0700 merge with master into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit a456096be916b79003231e42dd80c65b4bf1e0c7 Author: msantiago2 Date: Sat Jul 27 12:12:19 2019 -0700 added correct scaling to source strength exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ptsource_fill_2d.F90 src_chem/src_F90/ptsource_fill_3d.F90 commit 31fc97df411f882c964b048c83995fc4724b4eca Author: Daniel Ladiges Date: Fri Jul 26 17:54:10 2019 -0700 Fixed half counting of charge spreading in immersedIons. exec/immersedIons/particleGen.cpp exec/immersedIons/properties.nb src_particles/src_F90/particle_functions.F90 commit a9667a4a76422a2c89f756eea5078c63fa04fa5f Author: Andy Nonaka Date: Fri Jul 26 15:10:17 2019 -0700 fixed a bug in computeCentredGrad (forgot factor of 2 in denominator) ported compute centred grad to gpu note compute_div_and_grad.F90 has been removed src_common/ComputeDivAndGrad.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/compute_div_and_grad.F90 commit e1b029d8f6ac092b0d7396210e1cdca059736c77 Author: Andy Nonaka Date: Fri Jul 26 14:24:34 2019 -0700 average_cc_to_face and shift_face_to_cc now on gpu. convert_stag.F90 completely removed src_common/ConvertStag.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/convert_stag.F90 commit 36e70ad92b5a422b3bfdcff96e3272afc976c02b Author: Andy Nonaka Date: Fri Jul 26 14:02:45 2019 -0700 average_face_to_cc port to gpu src_common/ConvertStag.cpp src_common/common_functions_F.H src_common/src_F90/convert_stag.F90 commit 627571190bcc3acc4ea89914a8d74b30fb563c0f Merge: 63de5753 4d6a6265 Author: Andy Nonaka Date: Fri Jul 26 13:39:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 63de57532f14661cfb65691f34a99150f83c9331 Author: Andy Nonaka Date: Fri Jul 26 13:38:51 2019 -0700 port computeGrad to GPU src_common/ComputeDivAndGrad.cpp src_common/common_functions_F.H src_common/src_F90/compute_div_and_grad.F90 commit f4b8d8c6c18facc6ab02b471f4a93fcdac6aa1c4 Merge: 5287d3c2 262589a5 Author: Andy Nonaka Date: Fri Jul 26 11:10:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4d6a6265e800e9b51142313785b8985b1e6f6456 Merge: 3105bea0 f4b8d8c6 Author: msantiago2 Date: Fri Jul 26 11:09:52 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 5287d3c2230b7cf332e83e7c9069addd482f0f40 Author: Andy Nonaka Date: Fri Jul 26 11:09:44 2019 -0700 ported compute_div to gpu src_common/ComputeDivAndGrad.cpp src_common/common_functions_F.H src_common/src_F90/compute_div_and_grad.F90 commit 3105bea09b91cd72f1772a6c1130a7009b7e938b Author: msantiago2 Date: Fri Jul 26 11:07:54 2019 -0700 fixed visualization exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb src_chem/src_F90/SurfGrad_3d.F90 commit 262589a5e3e037a9ae3378c261aeab503c5beb3e Author: Johannes Blaschke Date: Thu Jul 25 23:32:51 2019 -0700 too many ghost cells exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit a40d98e6cca62963dd28637308a95caf3578a6ae Author: Guy Moore Date: Thu Jul 25 20:12:09 2019 -0700 cleaned up BC function src_compressible/src_F90/bound_funcs.F90 commit e1247e7ac0b5da6586e3319cee084c0e38e02677 Author: Johannes Blaschke Date: Thu Jul 25 19:14:45 2019 -0700 fix broken render frames exec/immersed_boundary/flagellum/Render Frames.ipynb commit 73f3c8a39d119384e0d8e3aa7e07e67b5203a5e0 Author: kevinluna Date: Thu Jul 25 16:02:07 2019 -0700 New outputs added and nonadaptive function restored exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/inputs_2d exec/_GL_alt/inputs_2d_LOW_T_Back exec/_GL_alt/inputs_2d_LOW_T_FORWRD exec/_GL_alt/inputs_2d_new exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit ed49e0dcfe093f7608e91e005307ef3fff05f0c4 Author: msantiago2 Date: Thu Jul 25 15:48:32 2019 -0700 fixed a bug exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/Adv_3d.F90 src_chem/src_F90/ptsource_fill_2d.F90 commit 2b28e1f6ecc94c2af363a1a6a1833c9e78dcc766 Merge: 0012823f 88395ab3 Author: msantiago2 Date: Thu Jul 25 14:55:29 2019 -0700 merge with master commit 0012823febbe950cc75e026d0a3451de3960dc17 Author: msantiago2 Date: Thu Jul 25 14:54:01 2019 -0700 documented files in src_chem exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H commit 88395ab3d2f6bbdb9f61250532a1d9baa8d6ee80 Author: Gang Xu Date: Thu Jul 25 14:17:20 2019 -0700 just 20 markers in a straight line. Keep losing tracking neighbors exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit e1f29ebbf36d5933ec090e16ed5d299f4daca4fd Author: msantiago2 Date: Thu Jul 25 14:03:12 2019 -0700 fixed error in advance.cpp and documented files in src_chem/src_F90 exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/src_F90/Adv_2d.F90 src_chem/src_F90/Adv_3d.F90 src_chem/src_F90/Prob.F90 src_chem/src_F90/SurfGrad_2d.F90 src_chem/src_F90/SurfGrad_3d.F90 src_chem/src_F90/ptsource_fill_2d.F90 src_chem/src_F90/ptsource_fill_3d.F90 commit 67bd94ad4827972b634fbc24958fab7b8d369f2d Author: msantiago2 Date: Thu Jul 25 12:26:45 2019 -0700 documenting files in src_immersed-boundary src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit ddb122c15239208e005535f4bbac67bf4a7edf82 Author: msantiago2 Date: Thu Jul 25 11:59:37 2019 -0700 documenting files in the executable directory exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp commit d0764e495861e1eeb94494f705bb2b36b7477024 Merge: a7e1b5d2 9ee2df54 Author: msantiago2 Date: Thu Jul 25 11:12:15 2019 -0700 merge with master commit a7e1b5d2e7286b6fbade17a50c82462a7c113f54 Author: msantiago2 Date: Thu Jul 25 11:10:45 2019 -0700 fixed the catalyst location with respect to IB orientation src_chem/src_F90/ptsource_fill_3d.F90 src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9ee2df54c83c348fefc205bdfd13bc4edfac9016 Author: Daniel Ladiges Date: Thu Jul 25 11:01:27 2019 -0700 Fixed neff bug and seeding bug in DSMC exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit c9c003efde7a6ea903e9f01cafbc5f258e65d3ad Author: alballow Date: Thu Jul 25 10:20:42 2019 -0700 Small changes to laser src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit b343f604f544f9e6661d8fd3bcb8ab9530b053eb Merge: 4b2c2edb 0fcf7c5e Author: alballow Date: Thu Jul 25 10:20:19 2019 -0700 Merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6f7bf13f7ea1e1970f1d4de2660c54f291188151 Merge: 35506237 0fcf7c5e Author: msantiago2 Date: Wed Jul 24 18:28:42 2019 -0700 merge with master commit 355062379803a5d475b9c443beb1e5464ffc3210 Merge: 84b83fae 086215c2 Author: msantiago2 Date: Wed Jul 24 18:24:26 2019 -0700 Merge branch 'mks/chemistry' of github.com:AMReX-FHD/FHDeX into mks/chemistry commit 84b83fae7368b3bb9f97f7c0b31c603d7d5f2bc5 Author: msantiago2 Date: Wed Jul 24 18:21:26 2019 -0700 fixing git errors exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/Explore Data MP.ipynb exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_averages.F90 src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 0fcf7c5ec005fb0f0ee4604c207bac4f91e99e1f Author: Gang Xu Date: Wed Jul 24 17:38:11 2019 -0700 made a 21-marker flagellum and realistic waveform. Under testing. exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/main_driver.cpp commit 086215c217d32122643a595cd2b0e9111a8968d6 Merge: a9b93649 9d610549 Author: msantiago2 Date: Wed Jul 24 17:31:43 2019 -0700 merge with master commit a9b93649f5164eb873070c10c6831f3947c68dae Author: msantiago2 Date: Wed Jul 24 17:30:47 2019 -0700 added the catalyst location with respect to IB orientation, debugging exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ptsource_fill_2d.F90 src_chem/src_F90/ptsource_fill_3d.F90 src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/IBParticleInfo.H src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9d610549495f0b1880a32484e37a3d7ffbd239e2 Author: Gang Xu Date: Wed Jul 24 16:27:37 2019 -0700 started to add realistic beat waveform exec/immersed_boundary/channel_dumbbell_sol/Explore Data MP.ipynb exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum_chlamy/Explore Data MP.ipynb exec/immersed_boundary/flagellum_chlamy/Explore Data.ipynb exec/immersed_boundary/flagellum_chlamy/GNUmakefile exec/immersed_boundary/flagellum_chlamy/Make.package exec/immersed_boundary/flagellum_chlamy/Render Frames.ipynb exec/immersed_boundary/flagellum_chlamy/WritePlotFile.cpp exec/immersed_boundary/flagellum_chlamy/advance.cpp exec/immersed_boundary/flagellum_chlamy/compute_convfact_2.sh exec/immersed_boundary/flagellum_chlamy/init_funcs.F90 exec/immersed_boundary/flagellum_chlamy/init_s_funcs.F90 exec/immersed_boundary/flagellum_chlamy/inputs_2d exec/immersed_boundary/flagellum_chlamy/inputs_3d exec/immersed_boundary/flagellum_chlamy/inputs_3d_test exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum_chlamy/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum_chlamy/main_driver.H exec/immersed_boundary/flagellum_chlamy/main_driver.cpp exec/immersed_boundary/flagellum_chlamy/main_driver_F.H exec/immersed_boundary/flagellum_chlamy/run_conv_tests_2.sh commit 5c4091d30172d1ca379590d5125d5030cda948a0 Author: msantiago2 Date: Wed Jul 24 15:24:04 2019 -0700 updated time stepping for concentration and added oriendtation into PPVR structure (PPVOR) exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 4b2c2edb995b58802bf022920cef6d2188e00c0e Merge: 2371e85b c604470a Author: alballow Date: Wed Jul 24 14:37:42 2019 -0700 merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2371e85b60227dbb646d8d84368c709e155ba332 Author: alballow Date: Wed Jul 24 14:37:19 2019 -0700 Bug in particle exec/DSMC/inputs_3d src_surfaces/src_F90/surface_functions.F90 commit c604470a4ef5f70cbe471f28451d87ecd6348158 Merge: 0398c366 5f3634e6 Author: Daniel Ladiges Date: Wed Jul 24 14:11:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0398c3660a2cf677dba511332214ae8488fdc37d Author: Daniel Ladiges Date: Wed Jul 24 14:11:31 2019 -0700 Bug fix in particle init for DSMC exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp src_particles/src_F90/collision_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit ad0592cf2e3abc80db56ced6f33cb76336238e40 Author: alballow Date: Wed Jul 24 12:44:31 2019 -0700 Weird plot src_surfaces/src_F90/surface_functions.F90 commit 5f3634e68c372bd43b425f4d7b7e19473454f713 Author: Johannes Blaschke Date: Wed Jul 24 11:11:49 2019 -0700 speed up flagellum exec/immersed_boundary/flagellum/advance.cpp commit b624333c5cee00fd0ab3eecd0a204e0d22318131 Author: alballow Date: Wed Jul 24 10:40:13 2019 -0700 Fixed coefficient issue exec/DSMC/inputs_3d src_surfaces/src_F90/surface_functions.F90 commit 8a42a564b25d716bdab8bd42974e8daf3d429eaa Merge: 06c0ddc7 eea76646 Author: Johannes Blaschke Date: Tue Jul 23 20:37:33 2019 -0700 Merge branch 'master' into jpb/flagellum-init commit 06c0ddc7c856a27a6bc1e6a7c7b1ec3e8c25a9cf Author: Johannes Blaschke Date: Tue Jul 23 20:31:55 2019 -0700 implement heun's method for marker advance exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp commit eea76646e1bd724caaba9139b4a059c747ffb395 Merge: 40a5b0ea fbe375ad Author: spcarney34 Date: Tue Jul 23 19:05:23 2019 -0700 Resolved merge conflict in p3m code for particle_functions. commit 40a5b0ea762b9844487269a8523eeaf2e4435c2e Author: spcarney34 Date: Tue Jul 23 18:59:52 2019 -0700 Added some clarifying comments to the p3m correction . src_particles/src_F90/particle_functions.F90 commit fbe375ad850c0ca7789d2ec9f6dc565ddc0d83cf Author: Guy Moore Date: Tue Jul 23 18:19:18 2019 -0700 pencil redist. in vertical averaging appears to be debugged and working src_common/ComputeAverages.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_averages.F90 commit 42eb28ea29486a2c1bd4e4bcaa2a20da8f94ae66 Author: Johannes Blaschke Date: Tue Jul 23 18:18:31 2019 -0700 fix ghost-particle forces exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp src_immersed-boundary/IBMarkerContainerBaseI.H commit a3635c1b58276f8a7870a68fbcae59d83a578aea Author: msantiago2 Date: Tue Jul 23 18:01:54 2019 -0700 added source strength and scaling factor to input file, scaled source strength by box size exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_2d.F90 src_chem/src_F90/ptsource_fill_3d.F90 src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 62db07475c9ac2785d4cbbfcdd452c0b15f8448d Merge: fc0d51ce 67458847 Author: msantiago2 Date: Tue Jul 23 17:21:28 2019 -0700 merge with master into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit fc0d51ce696931566ba01cb51d3e57ebfdd2e760 Author: msantiago2 Date: Tue Jul 23 17:20:01 2019 -0700 added support for 2D, need 2d normal to levelset exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.cpp src_chem/src_F90/Adv_2d.F90 src_chem/src_F90/ConGrad_2d.F90 src_chem/src_F90/ConGrad_3d.F90 src_chem/src_F90/GradCdotn_CC_3d.F90 src_chem/src_F90/Make.package src_chem/src_F90/SurfGrad_2d.F90 commit 674588470385d7b46e87b671127cd28f35d98e57 Author: Daniel Ladiges Date: Tue Jul 23 15:35:26 2019 -0700 Fixed double counting of momentum exec/DSMC/inputs_3d src_surfaces/src_F90/surface_functions.F90 commit 8ae7bbdbd4c0ccf17a64df2d881d110ed07d596e Author: alballow Date: Tue Jul 23 15:36:16 2019 -0700 Changed density exec/DSMC/inputs_3d commit 25881297a032b6fc72094bd46aee54b4582f0f29 Merge: 39ef3c94 68325cbd Author: alballow Date: Tue Jul 23 15:32:21 2019 -0700 Merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 39ef3c94dc097f63732d42535df2c039ca4f5d22 Author: alballow Date: Tue Jul 23 15:31:43 2019 -0700 Fixed the laser code exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit 68325cbdc5d98b395d18881b70f88734cf8e06f3 Author: Joseph Wagner Date: Tue Jul 23 14:28:14 2019 -0700 added fluxhydro exec/immersed_boundary/flagellum/.advance.cpp.swp exec/immersed_boundary/flagellum/Explore Data MP.ipynb exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp commit 31577d842fdd695847ce85ad45de40cc2217c98a Author: msantiago2 Date: Tue Jul 23 13:30:49 2019 -0700 check to make sure mpi is working exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp commit c5e69116072471b1f1dbea386a6cbdaf5fadc41a Author: jbb Date: Tue Jul 23 12:28:27 2019 -0700 fixed parallel bug exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/timeStep.cpp commit 748cac0226e572cd495385cc285b65a1c88ee3dd Merge: a2023875 7d101770 Author: msantiago2 Date: Mon Jul 22 16:47:12 2019 -0700 merge with master commit a20238754118949b1df613969708d4da8741c7b0 Author: msantiago2 Date: Mon Jul 22 16:40:21 2019 -0700 added correct units to jupyter notebook exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb commit 529988d7c6df78e08b8905fb2f38df2c900fca9b Author: Johannes Blaschke Date: Sun Jul 21 13:26:46 2019 -0700 ease flagellum really slowly into active configuration exec/immersed_boundary/flagellum/Render Frames.ipynb exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp commit 29390ea50ff427900043b5cfd46b8fb0cb1203ab Merge: 9bd6dda0 7d101770 Author: Johannes Blaschke Date: Fri Jul 19 21:23:14 2019 -0700 Merge branch 'master' into jpb/merge_markers commit 7d10177053e76b11be0a5480577ba18b8c027f3b Author: Guy Moore Date: Fri Jul 19 18:19:12 2019 -0700 initialized concentrations for RT exec/compressible/init_consvar.F90 commit d327187b5e531295cedb503bfd6adf51ebdfbb72 Author: Guy Moore Date: Fri Jul 19 18:11:50 2019 -0700 Added gravity and cleaned up exec/compressible/exec_functions.H exec/compressible/inputs_RT_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/stats.cpp commit 5cb9dc993b1f5f833ad3673a6436fd9628981762 Author: Joseph Wagner Date: Fri Jul 19 17:58:51 2019 -0700 changed to 10 exec/immersed_boundary/flagellum/main_driver.cpp commit bbd9784619c23f2559720b6c72299df48ff0138d Author: Joseph Wagner Date: Fri Jul 19 17:55:26 2019 -0700 profiled maindriver exec/immersed_boundary/flagellum/.main_driver.cpp.swp exec/immersed_boundary/flagellum/Explore Data MP.ipynb exec/immersed_boundary/flagellum/Explore Data.ipynb exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp commit 9bd6dda0257e18a2a9bb88653eb88aa10b788a54 Author: Johannes Blaschke Date: Thu Jul 18 22:26:25 2019 -0700 use delegating constructors => IBMarIter inherits correct constructor src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H commit 8e5e9fce6e6fed9907780bce1fc7584324e88a87 Author: Johannes Blaschke Date: Thu Jul 18 21:47:54 2019 -0700 cleanup unused/commented functions src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBase.H commit bbbe5aadb37a7a1224dd464108849a8bd662c6e1 Author: Johannes Blaschke Date: Thu Jul 18 21:01:07 2019 -0700 make sense of the different kinds of itterator src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 26f7f0103f9f0e98e8d770303e397adbd926f8ff Author: msantiago2 Date: Thu Jul 18 15:27:51 2019 -0700 used for poster results exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit e69154e5c0979bf07ccd787dbff8bdec82195bbd Author: Joseph Date: Thu Jul 18 13:17:45 2019 -0700 attempting to fix error exec/immersed_boundary/flagellum/frame_00020.png exec/immersed_boundary/flagellum/frame_00021.png exec/immersed_boundary/flagellum/frame_00022.png 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exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp commit d6842219dd16ced779eafe1d77ac2497ece02666 Author: Gang Xu Date: Thu Jul 18 10:47:39 2019 -0700 upload my explore data file which includes plotting y vs markers exec/immersed_boundary/flagellum/Explore Data MP.ipynb commit b50050e27babb4001195d50693a963d7949c579b Author: Joseph Wagner Date: Thu Jul 18 08:44:17 2019 -0700 more profiling exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00002 exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00003 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00000 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00002 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00003 exec/immersed_boundary/flagellum/inputs_3d_test commit 1b62dbea8b24401d5e4ca1ed5d52b4c4225142b9 Merge: 5aab8ebf b4482130 Author: msantiago2 Date: Wed Jul 17 18:22:25 2019 -0700 merge with master commit 5aab8ebf5226674d83ca7520e0290b7bf7b30764 Author: msantiago2 Date: Wed Jul 17 18:16:05 2019 -0700 adjusted spring constant and cleaned up code exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/src_F90/Adv_3d.F90 commit b44821306ff4acf7f7f707ac87946b6c74c10d09 Author: Joseph Wagner Date: Wed Jul 17 16:40:12 2019 -0700 commented out printstatements src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 03c10e89bd31672e0ad5928f5a93a150de0604ef Author: Johannes Blaschke Date: Wed Jul 17 15:37:56 2019 -0700 ib markers now use IBMarkerContainerBase exec/immersed_boundary/flagellum/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit b2825a47295d68fbdbea259ad08e0238bf7da442 Author: Johannes Blaschke Date: Wed Jul 17 14:33:27 2019 -0700 start inheriting from the IBMarkerBase src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 3871029fb088b1a4261688c3dee7452eedeae1e8 Author: Joseph Wagner Date: Wed Jul 17 12:23:17 2019 -0700 cleaned up exec/immersed_boundary/flagellum/BLProfParser.lex.yy.cpp exec/immersed_boundary/flagellum/BLProfParser.tab.H exec/immersed_boundary/flagellum/BLProfParser.tab.cpp exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_comm_prof_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_call_stats_H_00000 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exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00003 commit e38dba8c0a6bf51718398bdf303ea658bb7ab064 Author: Joseph Wagner Date: Wed Jul 17 12:09:26 2019 -0700 profiling ready for supercomputer exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_comm_prof_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.05395197868/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_call_stats_H_00002 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_call_stats_H_00003 exec/immersed_boundary/flagellum/bl_prof.old.47976088524/bl_comm_prof_H_00000 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exec/immersed_boundary/flagellum/bl_prof.old.57877206802/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.57877206802/bl_comm_prof_H_00002 exec/immersed_boundary/flagellum/bl_prof.old.57877206802/bl_comm_prof_H_00003 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00002 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00003 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00004 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00005 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00006 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_call_stats_H_00007 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00000 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00002 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00003 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00004 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00005 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00006 exec/immersed_boundary/flagellum/bl_prof.old.75209403038/bl_comm_prof_H_00007 exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00000 exec/immersed_boundary/flagellum/bl_prof/bl_call_stats_H_00001 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00000 exec/immersed_boundary/flagellum/bl_prof/bl_comm_prof_H_00001 exec/immersed_boundary/flagellum/inputs_3d_test commit 6c560535ffa55610d05f63bfbb4ac5353652298a Author: Johannes Blaschke Date: Wed Jul 17 11:53:38 2019 -0700 squelch print messages exec/immersed_boundary/channel_dumbbell/inputs_3d_test src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 812810e6014125c531334bca31709eef0c8d103d Author: msantiago2 Date: Wed Jul 17 11:24:22 2019 -0700 fixed issues with ibm exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test commit 002872cee995b27c0d8c29a363317d16613b4e50 Merge: bda04582 53cc98ca Author: msantiago2 Date: Wed Jul 17 10:14:12 2019 -0700 merge with master commit bda045821fcfa2695d843461c8fe456ec6af8445 Author: msantiago2 Date: Wed Jul 17 10:13:36 2019 -0700 still debugging ibm with slip velocity due to concentration exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test commit 53cc98ca887faccfbe4a1818ee453acd420e9581 Author: Joseph Wagner Date: Wed Jul 17 09:57:34 2019 -0700 unbroke profiling exec/immersed_boundary/flagellum/advance.cpp commit b0be3f1ecd8c980b8c124f9911c8dbe80baa18c8 Merge: 0b05d094 075ac8a5 Author: Joseph Date: Wed Jul 17 09:43:45 2019 -0700 Merge remote-tracking branch 'refs/remotes/origin/master' commit 0b05d0948551aa7f3ff5025ced7e3542b7ea01f6 Author: Joseph Date: Wed Jul 17 09:43:36 2019 -0700 more profiling exec/immersed_boundary/flagellum/BLProfParser.tab.H exec/immersed_boundary/flagellum/BLProfParser.tab.cpp exec/immersed_boundary/flagellum/advance.cpp commit 075ac8a58237d706dbcc24ce89b257bf494d5df8 Author: Joseph Wagner Date: Wed Jul 17 09:42:17 2019 -0700 more profiling exec/immersed_boundary/flagellum/BLProfParser.lex.yy.cpp exec/immersed_boundary/flagellum/BLProfParser.tab.H exec/immersed_boundary/flagellum/BLProfParser.tab.cpp exec/immersed_boundary/flagellum/advance.cpp commit 0de2b66a782f2ddba209983f0add80f113d63e0a Author: Johannes Blaschke Date: Tue Jul 16 23:00:59 2019 -0700 fix all them compiler errors src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit a80a43ac29b113a7d389d1339f51a6f15737e68f Author: Johannes Blaschke Date: Tue Jul 16 22:39:40 2019 -0700 make marker data model extensible src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 5db603f3906d2b72a8aa1bea5eeacedcc9fee473 Author: msantiago2 Date: Tue Jul 16 16:54:33 2019 -0700 debugging ibm with slip velocity due to concentration exec/immersed_boundary/channel_soft/advance.cpp commit 0bd689ffc8b654cb4e66f67bfed0670a53036802 Author: msantiago2 Date: Tue Jul 16 16:21:58 2019 -0700 fixed ghost cell issues with advection diffusion with Heun's method, still verifying the method works exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/Adv_3d.F90 src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9eebed6393563c2a6c396df236f351e4537fa434 Merge: 3fd1fa5f 9d7bf08f Author: Joseph Wagner Date: Tue Jul 16 16:12:46 2019 -0700 inputs steps changed and profiling added commit 3fd1fa5fe07297c8a4dc305d9a0ee3365690f986 Author: Joseph Wagner Date: Tue Jul 16 16:07:56 2019 -0700 adding profilling exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test commit 9d7bf08f6fe2882c126af9b161db1eded5b19ddd Merge: f88416ed 34c5f6d2 Author: Johannes Blaschke Date: Tue Jul 16 16:00:26 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f88416edfe93d5d76137c7562d1d06357a43bb56 Author: Johannes Blaschke Date: Tue Jul 16 16:00:23 2019 -0700 build base class for IBMarkers... let the debugging begin src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/IBMarkerContainerBaseI.H commit 34c5f6d2e3d74fda396308814c3e86cecb35ceef Merge: a8ad0465 a6d4adea Author: Gang Xu Date: Tue Jul 16 15:59:15 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a8ad0465a10f328ad0ddc8d0188bcdc8f9e4dc91 Author: Gang Xu Date: Tue Jul 16 15:58:53 2019 -0700 added small sin wave to initial marker position; changed drive period and amplitude exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/main_driver.cpp commit e851dffd978c6dea076bd570946e5d990c5f5ac2 Author: Johannes Blaschke Date: Tue Jul 16 15:21:32 2019 -0700 fix more screwed up indentation src_immersed-boundary/IBMarkerContainer.cpp commit a81ee302297fc0475ca554b99b904132aa8c04b8 Author: Johannes Blaschke Date: Tue Jul 16 15:09:14 2019 -0700 fix screwey indentation src_immersed-boundary/IBMarkerContainer.cpp commit a6d4adea3b8c3972af94cd901edeb68231e4356f Author: Guy Moore Date: Tue Jul 16 08:15:16 2019 -0700 hydro now compiles in 2D src_common/ComputeAverages.cpp commit 3f96110687265b15df4fe6a626645821d5cec072 Author: Johannes Blaschke Date: Mon Jul 15 22:29:28 2019 -0700 we don't need these functions in the base class src_immersed-boundary/IBMarkerContainerBase.H commit 4bb086fe6181795a3cb23d8caa2f23cfa5423116 Author: Johannes Blaschke Date: Mon Jul 15 22:26:30 2019 -0700 begin constructing base template class for IBMarkers src_immersed-boundary/IBMarkerContainerBase.H src_immersed-boundary/Make.package commit 66777f9ec0b2c72ecbb8059f3b5ae155fc420141 Merge: 4f4eb953 fb2666c3 Author: msantiago2 Date: Mon Jul 15 17:11:45 2019 -0700 merge with master commit 4f4eb953cf89e4e9a19734d2c76f80ea502d45dd Author: msantiago2 Date: Mon Jul 15 17:10:48 2019 -0700 still debugging advection diffusion exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_common/Make.package commit fb2666c3abd75b3a926af80176c685ddd3f26286 Author: edrewke <51346504+edrewke@users.noreply.github.com> Date: Mon Jul 15 16:48:07 2019 -0700 make video -- annotate_sphere not working (*_marker does) exec/immersed_boundary/flagellum/Render Frames.ipynb commit 13bf27330120ab4d7828650dcdf7a1b2de484a50 Merge: 617da1e3 9f888d9a Author: Johannes Blaschke Date: Mon Jul 15 16:25:13 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 617da1e3d02d948404e980aab96af9f07d790bac Author: Johannes Blaschke Date: Mon Jul 15 16:25:09 2019 -0700 start converting IBMarkerMarker to template class src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.H commit 9f888d9af40be8cb0dedac2a09f52c5a42651654 Merge: 697a133d 3d4a1f82 Author: msantiago2 Date: Mon Jul 15 14:48:34 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 697a133d9ed1a4defaedaceb418ccd7120005085 Author: msantiago2 Date: Mon Jul 15 14:47:28 2019 -0700 updated to correct time integration for concentrations, still debugging exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit 3d4a1f827f7dd2f9a4942eae647c6d4a72c432cd Author: Guy Moore Date: Fri Jul 12 18:59:38 2019 -0700 Added pencil redistribution src_common/ComputeAverages.cpp src_common/src_F90/compute_averages.F90 commit 24dc2ce43203d7f7e3d2e0b35634de58530b0c9d Merge: d4e7bc5a 2d85c205 Author: Guy Moore Date: Fri Jul 12 18:50:37 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d4e7bc5a68898f3a461f5817fb6537f908d5e440 Author: Guy Moore Date: Fri Jul 12 18:50:26 2019 -0700 Almost done with averaging routines exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 2d85c205eb5b446c8536fca829ddbfc7c78bca0d Author: msantiago2 Date: Fri Jul 12 16:31:52 2019 -0700 updated code to make it easier to use correct method for concentration exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit f6aac8d18b09c12e4469bcbf3059a7018b29478b Merge: a8eb26bf 99e31994 Author: msantiago2 Date: Fri Jul 12 15:43:00 2019 -0700 merge with master commit a8eb26bf1cdf6005b676c51ddea999d665f7be84 Author: msantiago2 Date: Fri Jul 12 15:41:27 2019 -0700 updated advance.F90 to make it easier to implement Heun's method for the concentration exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/Adv_3d.F90 src_immersed-boundary/src_F90/ib_fort_utils.F90 commit a8a186d808ca6184b313f3bafbf00e0fd2db5066 Merge: f5001389 99e31994 Author: alballow Date: Fri Jul 12 14:11:57 2019 -0700 merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f500138970b064a848a1af0e81aa5451b0bbf538 Author: alballow Date: Fri Jul 12 14:04:53 2019 -0700 small changes src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 99e319945365597f889cccd8dc2c2631a3a68ec5 Author: alballow Date: Fri Jul 12 13:36:32 2019 -0700 small changes to coefficeints src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 68a5381c14dbb2dbc1c63ecf62124d335c73994e Merge: 8c8d6ce9 d601bcb2 Author: alballow Date: Fri Jul 12 12:29:55 2019 -0700 merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8c8d6ce912f67e27ac27271c72fc0e363a9dbbbe Author: alballow Date: Fri Jul 12 12:29:21 2019 -0700 fix conflicts exec/DSMC/inputs_3d src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 3ddab4dcad1163c62957357b4b76f3ccf952dd5c Merge: 81bb17ac 68a5381c Author: alballow Date: Fri Jul 12 12:08:14 2019 -0700 fixed conflicts Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 81bb17ac87b1c488845d0545a673fc4ccc26fc71 Author: alballow Date: Fri Jul 12 12:05:13 2019 -0700 Moving files exec/DSMC/inputs_3d src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit d601bcb2017c2de1e209e7d06681a470c08fe4eb Merge: f6fb2701 bdd8d122 Author: Gang Xu Date: Fri Jul 12 10:52:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f6fb2701b5416b2ef505d507ff2cc080a3c52e44 Author: Gang Xu Date: Fri Jul 12 10:52:10 2019 -0700 minor updates in MoveMarkers src_immersed-boundary/IBMarkerContainer.cpp commit bdd8d1227afd4527c4b171c4c8c4288f7b19a724 Author: alballow Date: Fri Jul 12 09:41:29 2019 -0700 Added laser forcing factor exec/DSMC/inputs_3d src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 commit c2959bb270c655d42f7ac7cd21e6bc7fb77bb5ce Merge: 27c8e4e5 a7f1ab54 Author: Daniel Ladiges Date: Thu Jul 11 17:55:53 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 27c8e4e5a6db1f22b0f8f2d5968692cc0c23734f Author: Daniel Ladiges Date: Thu Jul 11 17:55:30 2019 -0700 Geometry update for dsmc graphene probelm exec/DSMC/surfaces.dat exec/DSMC/surfaces.nb commit a7f1ab54c0e9ead59101744abc7d090f5fd97cbb Merge: 0e4984e5 b613a2b2 Author: Johannes Blaschke Date: Thu Jul 11 16:41:59 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 0e4984e514ca6a766bfa8cf180fb7162e6d66d0e Author: Johannes Blaschke Date: Thu Jul 11 16:41:16 2019 -0700 Store IBMarkers as single object (let it manage levels) src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 40505d64ab945c4c4c4b00c5483c35c37767b779 Author: kevinluna Date: Thu Jul 11 15:54:30 2019 -0700 finer resolution input files added exec/_GL_alt/inputs_2d_LOW_T_Back exec/_GL_alt/inputs_2d_LOW_T_Forward commit 763a0e8f07fa6bfc3095dbce947ce2aacafabc45 Author: kevinluna Date: Thu Jul 11 15:49:44 2019 -0700 finer resolution input files added exec/_GL_alt/inputs_2d_LOW_T_Back exec/_GL_alt/inputs_2d_LOW_T_Forward commit cfc26f5259583ba6f76e6704a390999351b92fe4 Merge: 81afd9ea b613a2b2 Author: Guy Moore Date: Thu Jul 11 15:47:36 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 81afd9eafa2155e8e5b971037272fcdc046c6d9f Author: Guy Moore Date: Thu Jul 11 15:47:28 2019 -0700 strange main driver merge exec/compressible/main_driver.cpp commit b613a2b22858e12f048fab270f3905c9e2c1b808 Author: Daniel Ladiges Date: Thu Jul 11 15:42:57 2019 -0700 Removed structfact refferences from immersedIons exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit 61bba22e111e6143125a64a4d7ba171dfe231631 Author: Johannes Blaschke Date: Thu Jul 11 10:27:02 2019 -0700 don't need struct factor stuff here? src_hydro/StochMFlux.cpp commit a035f52bdc6743391b3f3018c3d9e063da624be3 Author: Johannes Blaschke Date: Thu Jul 11 10:15:14 2019 -0700 make work on cori exec/immersed_boundary/flagellum/GNUmakefile commit 3b1a3c3b16ee71819f7d9126802ac0ee679f7c77 Merge: d3362712 8288b9aa Author: jbb Date: Thu Jul 11 09:59:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d336271287a40932296a37a465e1fac3cd440c44 Author: jbb Date: Thu Jul 11 09:54:39 2019 -0700 minor tweaks exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/timeStep.cpp exec/compressible/main_driver.cpp commit 8288b9aa2e0ce8d3064804a21a0238053ecf1d12 Merge: d87dbe35 467d02b2 Author: Guy Moore Date: Wed Jul 10 20:13:15 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d87dbe355aa0bf72e6d1543a0894756f40f4a3ef Author: Guy Moore Date: Wed Jul 10 20:13:08 2019 -0700 Fixed pressure BC bug exec/compressible/inputs_3d src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 commit 467d02b2365ebf5cdd94880586491884c1bc8630 Merge: 2ad7faf1 a18769e0 Author: Daniel Ladiges Date: Wed Jul 10 19:26:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2ad7faf12bc0584a3a162c8f70a6672c2cfef8e2 Author: Daniel Ladiges Date: Wed Jul 10 19:25:57 2019 -0700 Trimmed the plotfile output for big runs in immersedIons exec/DSMC/surfaces.nb exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/main_driver.cpp commit 5ade3d45128d6659ac5b842dfbe1ec9894adec9f Author: kevinluna Date: Wed Jul 10 18:39:08 2019 -0700 reverse adaptive steps exec/_GL_alt/umbrella00000000.txt commit 6c386a25f22355ffe6beb3a7a93f8751c708b315 Author: kevinluna Date: Wed Jul 10 18:38:12 2019 -0700 reverse adaptive steps exec/_GL_alt/inputs_2d_Bkwrd exec/_GL_alt/umbrella00000000.txt commit ae51a954a43b88523a319b08e6da9afcf4c40230 Author: kevinluna Date: Wed Jul 10 18:02:05 2019 -0700 reverse adaptive steps exec/_GL_alt/timeStep.cpp commit 939638e414c1f2a151894a7aaceb98da91d7669c Author: kevinluna Date: Wed Jul 10 18:00:32 2019 -0700 reverse adaptive steps exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/inputs_2d_Bkwrd exec/_GL_alt/timeStep.cpp commit 8c1c5b416639e52c50516cd9368ba5fcbb2fb939 Author: msantiago2 Date: Wed Jul 10 17:16:27 2019 -0700 added enforced slip velocities to plot file exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp commit b46eb664acc796407d4161d5622aac328fe15848 Author: msantiago2 Date: Wed Jul 10 16:22:35 2019 -0700 immersed boundary forcing consistent with Heun's method in fluid solver exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp src_immersed-boundary/IBMarkerContainer.cpp commit 637bd582720558cfadd4b41a5fdacbaada519ac5 Author: kevinluna Date: Wed Jul 10 16:10:54 2019 -0700 reverse adaptive steps exec/_GL_alt/MID_T_UMB commit 230f4694079aca31578e08d53c2bc0a843ba956b Author: kevinluna Date: Wed Jul 10 16:10:10 2019 -0700 reverse adaptive steps exec/_GL_alt/Data.ipynb exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/GL_namelist.F90 exec/_GL_alt/MID_T_UMB exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/inputs_2d exec/_GL_alt/inputs_2d_new exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit 96f9ffd71f8effcca234aa12f0e3bd3a14056496 Author: Guy Moore Date: Wed Jul 10 14:26:37 2019 -0700 changed species wall bc in namelist exec/compressible/inputs_3d src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 commit a18769e08963b0b1451da60c2cd7a670dc46df74 Merge: 8760c64d bd0adfb2 Author: msantiago2 Date: Wed Jul 10 13:05:16 2019 -0700 merge with mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit bd0adfb248ab45b873430dffd68bb52de188762d Author: msantiago2 Date: Wed Jul 10 13:03:34 2019 -0700 added concentration gradient as surface velocity of sphere, runs still debugging exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test commit 4488d6e91eb4cfca5e12d9dee59d48b8f618da91 Author: Guy Moore Date: Wed Jul 10 11:23:46 2019 -0700 Added more boundary condition routines exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/timeStep.cpp commit 6a6bb8186389476e86734dbff9f1e8a067802962 Merge: ad994493 8760c64d Author: Guy Moore Date: Wed Jul 10 11:22:22 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8760c64d836e8bac00598f0ad6329a019ace21cc Author: Andy Nonaka Date: Wed Jul 10 11:13:51 2019 -0700 comment out structure factor stuff for now, so this compiles exec/hydro/main_driver.cpp commit ad994493c9c86e4cda830e9755c7cb682aebcc55 Author: Guy Moore Date: Tue Jul 9 17:11:55 2019 -0700 Added compressible namespace and wall concentration values exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions.cpp src_compressible/compressible_functions_F.H src_compressible/compressible_namespace.H src_compressible/compressible_namespace_declarations.H src_compressible/src_F90/Make.package src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/compressible_namelist.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 commit 99a727907f00af5fd303ad995995d4ce28fd8810 Merge: 00f8f1af 5adaf181 Author: msantiago2 Date: Tue Jul 9 16:51:25 2019 -0700 merge with master commit 00f8f1afb446391c4f5d18e5cd7f079c050cd5f6 Author: msantiago2 Date: Tue Jul 9 16:50:24 2019 -0700 improved cell centered gradients and fixed boundary issues with face centered gradients exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb src_chem/AmrCoreAdv.cpp src_chem/src_F90/SurfGrad_3d.F90 commit 5adaf181d5ad7131d78820310091a74e62389a9d Author: alballow Date: Tue Jul 9 15:38:56 2019 -0700 Changed orders of coeffiecent saving exec/DSMC/inputs_3d src_surfaces/src_F90/surface_functions.F90 commit 6ba80fe13e1bcccf2f3cc7acd009849466770eec Merge: 55da495d 7b3d1eca Author: Daniel Ladiges Date: Tue Jul 9 15:21:11 2019 -0700 Confilict fixMerge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 55da495d6f02f3d5917af7ae17a825753923d5cf Author: Daniel Ladiges Date: Tue Jul 9 15:17:36 2019 -0700 Modified c in DSMC graphene. exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/surfaces.dat src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 7b3d1ecaf14c96ed41fccc6a5a63329321bfb169 Merge: b35ac31c e2b15ef7 Author: alballow Date: Tue Jul 9 15:13:05 2019 -0700 Pulled Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b35ac31c7ba0d32e9f411e9488e4728b6f33a415 Author: alballow Date: Tue Jul 9 15:12:13 2019 -0700 Changed order of creating coeffiecents src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit e2b15ef7d906df9743e090ec1e93022979dad6cb Merge: 2ab99c12 b0eb3b9b Author: Gang Xu Date: Tue Jul 9 15:11:04 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2ab99c12fef3c68bb16b07695b05d74fec24a7e3 Author: Gang Xu Date: Tue Jul 9 15:10:54 2019 -0700 added z constraints exec/immersed_boundary/flagellum/advance.cpp commit b0eb3b9bb2df494114bbb3957f6aeaed5d6f3ec1 Author: Johannes Blaschke Date: Tue Jul 9 14:34:41 2019 -0700 fix build system error exec/immersed_boundary/channel_soft/GNUmakefile src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMultiBlobContainer.H commit 05a5fa514eca8a5d6b9dd0346fe4f8a0fc723c29 Merge: 150c08d1 84ceccd6 Author: Johannes Blaschke Date: Tue Jul 9 14:25:27 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 150c08d1d5eefa5dfbbd5be640514a00750a6a2f Author: Johannes Blaschke Date: Tue Jul 9 13:59:03 2019 -0700 add method of fill marker positions src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.H commit ead6ee1ef37a64a475ac47a6d1f480c2dd22af1d Author: msantiago2 Date: Tue Jul 9 13:34:51 2019 -0700 fixed face centered and cell centered tangential gradients exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ConGrad_3d.F90 src_chem/src_F90/GradCdotn_CC_3d.F90 src_chem/src_F90/Make.package src_chem/src_F90/SurfGrad_3d.F90 commit 84ceccd6e4e4d82fb07e9b838ba8e57f141569f2 Author: Daniel Ladiges Date: Tue Jul 9 13:04:40 2019 -0700 Updates to DSMC exec/DSMC/inputs_3d exec/DSMC/surfaces.nb src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 07dfc6596c0820b62bd773e61b335638dae6ac0b Merge: fdb37b4e d00458c5 Author: alballow Date: Tue Jul 9 12:03:46 2019 -0700 Pulled Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fdb37b4ea8d0c7b0786da4e0d6396f0b175b471c Author: alballow Date: Tue Jul 9 12:03:22 2019 -0700 Added particles at the top exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit d00458c5b41155b0512b981a43353b1b1ec3383b Author: Johannes Blaschke Date: Tue Jul 9 10:53:07 2019 -0700 fix input parameters exec/immersed_boundary/flagellum/inputs_3d_test commit dcc3f96e27426e13154560c4a56866b2549a681a Author: Johannes Blaschke Date: Tue Jul 9 10:50:48 2019 -0700 add time-dependent driving exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp commit 3c42482bd5d88f5edc158ef01a9940333222ba54 Author: Johannes Blaschke Date: Tue Jul 9 10:42:02 2019 -0700 remove beding force, add driving force exec/immersed_boundary/flagellum/advance.cpp commit ebc099aa79ca57bc875e3865fabca4b476d1f8c1 Author: Johannes Blaschke Date: Tue Jul 9 10:32:29 2019 -0700 remove walls exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.2 src_immersed-boundary/IBMarkerContainer.cpp commit 8db861e710f57b99c9ff52740b71eefc17bb6d33 Author: Johannes Blaschke Date: Tue Jul 9 10:29:22 2019 -0700 stupid error, now fixed src_immersed-boundary/IBMarkerContainer.cpp commit 50995b4c97e0de4e3c464f99b43427665e447b4f Author: Johannes Blaschke Date: Tue Jul 9 10:29:07 2019 -0700 start adding flagellum exec/immersed_boundary/flagellum/Explore Data MP.ipynb exec/immersed_boundary/flagellum/Explore Data.ipynb exec/immersed_boundary/flagellum/GNUmakefile exec/immersed_boundary/flagellum/Make.package exec/immersed_boundary/flagellum/WritePlotFile.cpp exec/immersed_boundary/flagellum/advance.cpp exec/immersed_boundary/flagellum/compute_convfact_2.sh exec/immersed_boundary/flagellum/init_funcs.F90 exec/immersed_boundary/flagellum/init_s_funcs.F90 exec/immersed_boundary/flagellum/inputs_2d exec/immersed_boundary/flagellum/inputs_3d exec/immersed_boundary/flagellum/inputs_3d_test exec/immersed_boundary/flagellum/inputs_3d_test.2 exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_2d exec/immersed_boundary/flagellum/inputs_incomp_equil_fluct_3d exec/immersed_boundary/flagellum/main_driver.H exec/immersed_boundary/flagellum/main_driver.cpp exec/immersed_boundary/flagellum/main_driver_F.H exec/immersed_boundary/flagellum/run_conv_tests_2.sh commit 1c74a522037173d5792897824eed9f6189c392de Merge: 24b2525d 384dd512 Author: Johannes Blaschke Date: Tue Jul 9 10:22:50 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 24b2525d15d2711f67dbfd9c7cefcd803f1b532b Author: Johannes Blaschke Date: Tue Jul 9 10:22:48 2019 -0700 fix small things exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/src_models/IBMarkerMD.H src_immersed-boundary/IBMarkerContainer.H commit 384dd512512899e1b350287748613deca1a73f34 Author: edrewke <51346504+edrewke@users.noreply.github.com> Date: Tue Jul 9 08:02:27 2019 -0700 add loops for multiple particles exec/immersed_boundary/channel_dumbbell_sol/Explore Data MP.ipynb commit 0b56170832a5441735d3ef77992d47aba0af43cf Author: Johannes Blaschke Date: Mon Jul 8 23:23:36 2019 -0700 fix sign error exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 7677193ed1fa7c5cda85991b59e0c1a145cab786 Author: Johannes Blaschke Date: Mon Jul 8 23:04:13 2019 -0700 track marker sequence number exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test src_immersed-boundary/IBMarkerContainer.cpp commit a08834b18b148faf26bfcabbcd5381cfac58f87f Author: Johannes Blaschke Date: Mon Jul 8 22:33:39 2019 -0700 using D_DECL like this wouldn't work because *z* vars are not defined for DIM<3 exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 7fadef4ea5962271b03d8b459ea4bdd35d94bd69 Author: Johannes Blaschke Date: Mon Jul 8 22:17:15 2019 -0700 add driving force calculation exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 60dcf8310f809add1287ae05c30c552f9a47cbea Merge: 23fbadcf 0a6064ed Author: msantiago2 Date: Mon Jul 8 17:03:52 2019 -0700 Merge branch 'mks/chemistry' commit 0a6064edc3e0f980226e4f1740ce2da47d63bb1d Author: msantiago2 Date: Mon Jul 8 17:03:15 2019 -0700 debugging surface gradient, runs still verifying exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb src_chem/AmrCoreAdv.cpp commit 23fbadcf0f0739de3670c3b0dd030276fa3135f0 Author: Johannes Blaschke Date: Mon Jul 8 16:41:20 2019 -0700 build numerical derivatives for active beding force exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit f847bf2bfc8c276726f5bee06cf16a06f09c8953 Merge: f405c622 f0c3d734 Author: msantiago2 Date: Mon Jul 8 16:22:53 2019 -0700 merge with master commit f405c622cf1b7c5473abc21d2c401942916154cc Author: msantiago2 Date: Mon Jul 8 16:21:42 2019 -0700 fixed issues at boundary, still debugging exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ConGrad_3d.F90 commit f0c3d734b81a9cf89aa1e2ec5548534074c132db Author: Johannes Blaschke Date: Mon Jul 8 16:13:54 2019 -0700 add bending potential exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit c45d68377a72da17bfe98790da4c2d48f47aaccb Merge: f915efd2 7487aea4 Author: Anthony Date: Mon Jul 8 18:04:06 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f915efd2285b3833648770afe71e052fd0f02645 Author: Anthony Date: Mon Jul 8 18:03:12 2019 -0400 stochastic flux is sampled from the LDT result. Euler time-stepping implemented. exec/low_density/inputs_3d exec/low_density/main_driver.cpp src_low-density/compressible_functions.H src_low-density/compressible_functions_F.H src_low-density/src_F90/flux_funcs.F90 src_low-density/src_F90/time_step_funcs.F90 src_low-density/timeStep.cpp commit 7487aea45ff451aa517483b2a49054d6c5a0258f Merge: d3c73fec 10286c1a Author: Gang Xu Date: Mon Jul 8 14:33:46 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 10286c1a30290b3bb57755c6ae02e0e040bb1f0f Merge: 715a4384 822a7a4f Author: Daniel Ladiges Date: Mon Jul 8 14:29:59 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 715a4384080a3f7cd97e9f693a24f86ccc87a22c Author: Daniel Ladiges Date: Mon Jul 8 14:29:15 2019 -0700 Settings for Cori. exec/immersedIons/GNUmakefile exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit 822a7a4f0d5cb85e27c4a6261c4e5b5ae01ba420 Author: Anthony Date: Mon Jul 8 14:31:02 2019 -0400 bug fix to support of proposal distribution exec/low_density/inputs_3d src_low-density/src_F90/flux_funcs.F90 commit e7ec8def42d80396cdd95b13bba16f0764b9c054 Merge: 613165e9 759ab8f9 Author: Anthony Date: Mon Jul 8 14:28:20 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 613165e91ecdb469ac9c620e94f362988e4f84bb Author: Anthony Date: Mon Jul 8 14:27:48 2019 -0400 uniform rejection sampler done exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/surfaces.dat exec/low_density/inputs_3d src_low-density/src_F90/flux_funcs.F90 commit 666827f2bf291d72e68ba3305da843abf0e29e87 Author: msantiago2 Date: Mon Jul 8 10:53:27 2019 -0700 debugging surface gradients src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/GradCdotn_CC_3d.F90 commit 3619296d446e51eae856ebd35e15087871e1e20a Author: kevinluna Date: Mon Jul 8 09:49:59 2019 -0700 fixed adamtive step bug exec/_GL_alt/AVG_DATA.txt commit 40b3128a00809c847355991a1d323a58a7d1ceb5 Author: kevinluna Date: Mon Jul 8 09:49:31 2019 -0700 fixed adamtive step bug exec/_GL_alt/AVG_DATA.txt exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit d3c73fec787057a3aa772764a59247eec622b38a Merge: c7aee126 759ab8f9 Author: Johannes Blaschke Date: Mon Jul 8 06:33:54 2019 -0700 Merge branch 'master' into jpb/experiments/dumbbell_sol commit c7aee1267a0e4e2666679520071c45f5ccf54337 Author: Johannes Blaschke Date: Mon Jul 8 06:33:32 2019 -0700 10 markers exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit 79ef9c616fc02424cc20d370bbd1997e274e9074 Author: Johannes Blaschke Date: Sun Jul 7 16:11:07 2019 -0700 5-point filament exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb commit a3c1534d29d048a42b18c2aeb50b0963d1812c3b Merge: f335b178 759ab8f9 Author: msantiago2 Date: Sat Jul 6 08:02:29 2019 -0700 merge with master commit f335b178459052298a74e2f33134289882482fd3 Author: msantiago2 Date: Sat Jul 6 08:01:05 2019 -0700 added cell centered concentration gradient to plot files, runs but still debugging exec/immersed_boundary/channel_soft/Explore_Chemistry_checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/SurfGrad_3d.F90 commit 108e0a28e0bf0800ae266df9e13f0e41b38bd0e4 Author: Johannes Blaschke Date: Fri Jul 5 21:22:27 2019 -0700 fix sign error exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test commit 213b521eadf59a0992f62988ee1f246d1b40e59f Author: Johannes Blaschke Date: Fri Jul 5 21:04:07 2019 -0700 add bending forces back in exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit c432799c3b9f5ac2dd937c0eb6c9dff26f3dabc9 Author: Johannes Blaschke Date: Fri Jul 5 20:53:36 2019 -0700 yay! this is stable exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit 759ab8f9273757e883d65d3cf6a2e3332cb4b619 Author: Guy Moore Date: Fri Jul 5 18:23:29 2019 -0700 Added multispecies BC functionality - needs wall species conc's src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp commit cd8eb182c91081e3182a5338216f37c997981dc0 Author: Guy Moore Date: Fri Jul 5 18:21:25 2019 -0700 Corrected eqm. covariance scaling exec/compressible/main_driver.cpp commit b4979dbf218989bf494acfc6639b43383d690e22 Author: Anthony Date: Fri Jul 5 19:00:17 2019 -0400 testing rejection sampler. Need to run DSMC test cases for effect of changing cell sizes src_low-density/src_F90/flux_funcs.F90 commit 2e030f0286cfcd3d2590caf4222d2b22bfb12514 Author: Anthony Date: Fri Jul 5 15:59:10 2019 -0400 setting up stochastic flux to sample from LDT distribution exec/DSMC-LDT/fluxStats.py exec/low_density/GNUmakefile exec/low_density/delPlots exec/low_density/inputs_3d exec/low_density/main_driver.cpp src_low-density/src_F90/flux_funcs.F90 commit d2077c37a74f2977c9f8880d837bd0ff76a01498 Author: kevinluna Date: Fri Jul 5 11:14:39 2019 -0700 adaptive cont. parameter exec/_GL_alt/Ploting_script.ipynb commit 2c5cdcd5eb2ce379239dc99e86de5e3bef9d0629 Author: kevinluna Date: Fri Jul 5 11:14:02 2019 -0700 adaptive cont. parameter exec/_GL_alt/timeStep.cpp commit c88956d7aecb88f1fa1e1829fa25cb1e0883de36 Author: kevinluna Date: Fri Jul 5 10:01:50 2019 -0700 adaptive cont. parameter exec/_GL_alt/.txt exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/GL_namelist.F90 exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/exec_functions.H exec/_GL_alt/inputs_2d exec/_GL_alt/inputs_2d_new exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt/writePlotFile.cpp commit 35fe0150b33538d2ba95754da5c587aa69381a95 Author: Johannes Blaschke Date: Thu Jul 4 14:03:14 2019 -0700 cleaned up some force calculation exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 9e3c365778b6400788bf5be962d1a36a6559ece5 Author: Johannes Blaschke Date: Thu Jul 4 13:52:19 2019 -0700 fix error in holding first 2 markers in place exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 1d508391220f1d7b097b20780e3be8437e7fd90a Author: Johannes Blaschke Date: Wed Jul 3 22:03:57 2019 -0700 predictor uses compact syntax exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 0ad34862ccc8743adb402bfe9ed80f4bb2f80a83 Merge: 53cb5e10 d62cf532 Author: Johannes Blaschke Date: Wed Jul 3 20:52:48 2019 -0700 Merge branch 'master' into jpb/experiments/dumbbell_sol commit 53cb5e1097aefbcfa08d9e2558170d9ce6f94751 Author: Johannes Blaschke Date: Wed Jul 3 20:46:24 2019 -0700 use loops to iterate over rdata => more compact syntax exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit d62cf5324dfa6fb77e436214cd041a29f432b5d7 Merge: 6835d18c c2d10a73 Author: Daniel Ladiges Date: Wed Jul 3 16:57:54 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6835d18c2e7c8aaa250a78817e189327c0e0a1b8 Author: Daniel Ladiges Date: Wed Jul 3 16:57:31 2019 -0700 More pruning of LDT diffusion code exec/low_density/Make.package exec/low_density/compressible_test_functions_F.H exec/low_density/indexshift/index_shift.sh exec/low_density/init_consvar.F90 exec/low_density/inputs_1d exec/low_density/main_driver.cpp src_low-density/Make.package src_low-density/compressible_functions.H src_low-density/compressible_functions_F.H src_low-density/conservedPrimitiveConversions.cpp src_low-density/membrane.cpp src_low-density/src_F90/Make.package src_low-density/src_F90/bound_funcs.F90 src_low-density/src_F90/conv_funcs.F90 src_low-density/src_F90/flux_funcs.F90 src_low-density/src_F90/matrix.f src_low-density/src_F90/matrixnp.f src_low-density/src_F90/membrane_funcs.F90 src_low-density/src_F90/multispec_funcs.F90 src_low-density/src_F90/stats_funcs.F90 src_low-density/src_F90/trans_funcs.F90 src_low-density/stats.cpp src_low-density/transCoeffs.cpp commit c2d10a737b80e31f591de73a936a82949a12490c Author: Guy Moore Date: Wed Jul 3 16:28:49 2019 -0700 'Full' eqm. covariances exec/compressible/inputs_3d exec/compressible/main_driver.cpp commit 4e566f47e11c5e5d68daaaafba80bd8c9cd6aa65 Merge: 6262b732 39e270ca Author: Daniel Ladiges Date: Wed Jul 3 16:17:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6262b7328f0375d6001da10199848ba282d4c553 Author: Daniel Ladiges Date: Wed Jul 3 16:16:29 2019 -0700 Started stripping down copy of compressible code for conversion into LDT diffusion. exec/DSMC/inputs_3d exec/DSMC/surfaces.nb exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/low_density/exec_functions.H exec/low_density/inputs_3d exec/low_density/main_driver.cpp exec/low_density/writePlotFile.cpp src_low-density/compressible_functions.H src_low-density/compressible_functions_F.H src_low-density/flux.cpp src_low-density/src_F90/flux_funcs.F90 src_low-density/src_F90/time_step_funcs.F90 src_low-density/timeStep.cpp commit 39e270ca9f92d0159b0c9b84296b9b6c9d5be51e Merge: 9bfd6981 8671a3be Author: Gang Xu Date: Wed Jul 3 16:15:28 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9bfd69813e6717eabaf9bec4910404e65c6f014e Author: Gang Xu Date: Wed Jul 3 16:15:07 2019 -0700 updated bending forces with right position vectors. But 3rd marker gets no neighbors exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 7ac040069a2acabc3381d1765ac0b5c5dc8282af Merge: 8b087f56 8671a3be Author: msantiago2 Date: Wed Jul 3 15:51:07 2019 -0700 merge with master commit 8b087f56b1fbf323ac5277043f4f62fe8d70c217 Author: msantiago2 Date: Wed Jul 3 15:49:54 2019 -0700 computing the tangential gradient using correct grids compiles but doesn't run still debugging exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/GradCdotn_CC_3d.F90 src_chem/src_F90/Make.package src_chem/src_F90/SurfGrad_3d.F90 commit 8671a3becf106bfd4358317c01dda32eb590468b Merge: de90b417 04e8842a Author: Anthony Date: Wed Jul 3 18:18:04 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit de90b417b50602c6d9d581f280b267e58aa11a4f Author: Anthony Date: Wed Jul 3 18:16:52 2019 -0400 spin off compressible code to test large deviation result for low densities exec/low_density/GNUmakefile exec/low_density/Make.package exec/low_density/compressible_test_functions_F.H exec/low_density/exec_functions.H exec/low_density/indexshift/index_shift.sh exec/low_density/init_consvar.F90 exec/low_density/inputs_1d exec/low_density/inputs_3d exec/low_density/interpAnalysis.nb exec/low_density/main_driver.cpp exec/low_density/stressTensor.nb exec/low_density/writePlotFile.cpp src_low-density/Make.package src_low-density/boundary.cpp src_low-density/compressible_functions.H src_low-density/compressible_functions_F.H src_low-density/conservedPrimitiveConversions.cpp src_low-density/flux.cpp src_low-density/membrane.cpp src_low-density/src_F90/Make.package src_low-density/src_F90/bound_funcs.F90 src_low-density/src_F90/conv_funcs.F90 src_low-density/src_F90/flux_funcs.F90 src_low-density/src_F90/matrix.f src_low-density/src_F90/matrixnp.f src_low-density/src_F90/membrane_funcs.F90 src_low-density/src_F90/multispec_funcs.F90 src_low-density/src_F90/stats_funcs.F90 src_low-density/src_F90/time_step_funcs.F90 src_low-density/src_F90/trans_funcs.F90 src_low-density/stats.cpp src_low-density/timeStep.cpp src_low-density/transCoeffs.cpp commit 04e8842a871856569ad9243e662f63015c5423c2 Merge: 45c5841c 23f850d5 Author: Johannes Blaschke Date: Wed Jul 3 12:55:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 45c5841c4edf4434be12467c37c7172ab1e53a3a Author: Johannes Blaschke Date: Wed Jul 3 12:55:34 2019 -0700 fix compile exec/immersed_boundary/channel_dumbbell/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H commit 23f850d5c81ee01ae1cb859d1737243c7988b768 Author: Gang Xu Date: Wed Jul 3 12:15:52 2019 -0700 will abort due to NAN forces exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test commit d011331d2300748ff6a0100ce2799b6145999570 Merge: 73552e17 e920e7d2 Author: Gang Xu Date: Wed Jul 3 12:15:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 73552e175e3c24dcdb54645aaf5dc28e755337d5 Author: Gang Xu Date: Wed Jul 3 12:14:53 2019 -0700 will abort due to NAN forces exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit e920e7d2472aa85e90d33887c2ae7db74ed21a2a Merge: 2f9e6254 bcb7f341 Author: Daniel Ladiges Date: Wed Jul 3 11:35:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2f9e62549e2e21188f2e041c72cd5e2b38638239 Author: Daniel Ladiges Date: Wed Jul 3 11:34:33 2019 -0700 Possible fix for neighbour list error. exec/immersedIons/main_driver.cpp commit bcb7f3417e04b17fb2b9b5541a8e8df74648eb38 Merge: 40dfe105 2ed2667f Author: Anthony Date: Wed Jul 3 13:30:02 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 40dfe1050bec1f442365653e3f6ec73dcfb04fcf Author: Anthony Date: Wed Jul 3 13:29:39 2019 -0400 fixed a bug when a box has less than 2 particles exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp commit a78a28fefc889cf7dd5407c939bcbaa6a534888c Merge: 56d5e2ff 2ed2667f Author: Gang Xu Date: Wed Jul 3 08:15:26 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 56d5e2ffba663c733c184435b7524ecc9813445f Author: Gang Xu Date: Wed Jul 3 08:14:07 2019 -0700 added bunch of Print() to trace forces exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 2ed2667f128181fbf32a9d9b1a98bbefbd049146 Merge: d39de154 d57a4c50 Author: Johannes Blaschke Date: Tue Jul 2 23:06:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d39de154e6ccdeb3da6b3f15313a355d01086e1e Author: Johannes Blaschke Date: Tue Jul 2 23:06:27 2019 -0700 redo the way we treat the ghost region in spread/interpolate exec/immersed_boundary/channel_dumbbell/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit d57a4c501a60d2c975fc5e976c5bf18f56da6046 Author: Guy Moore Date: Tue Jul 2 18:51:08 2019 -0700 starting to update BCs & add toggles exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/flux.cpp src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 commit 30e9c66ef6c5069f0f699013fb8dc917a7c17e6d Merge: 5ff34749 91450db6 Author: msantiago2 Date: Tue Jul 2 18:02:21 2019 -0700 merge with master into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 5ff3474925a8c5d0b45d57110356303b072e0177 Author: msantiago2 Date: Tue Jul 2 18:00:38 2019 -0700 correcting gradient location, still debugging exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ConGrad_3d.F90 src_chem/src_F90/Make.package src_chem/src_F90/SurfGrad_3d.F90 commit 91450db6893f4081d369ef0b8c5a26b7ca54d33e Author: Daniel Ladiges Date: Tue Jul 2 16:51:46 2019 -0700 Commented out line causing segfault in boundary intersection detection. Not sure why yet. src_surfaces/src_F90/surface_functions.F90 commit ee037489d36f24194f16d38f960be27948bfc709 Merge: 12bba8c8 bdc66847 Author: alballow Date: Tue Jul 2 15:50:14 2019 -0700 Conflicts fixed Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 12bba8c8cc0689813b19d88a11092bcd5176675b Author: alballow Date: Tue Jul 2 15:49:35 2019 -0700 Visualization exec/DSMC/inputs_3d src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit bdc66847ebfd4b3aed1805d0b03d6a97bdb7cf9a Author: Daniel Ladiges Date: Tue Jul 2 14:08:26 2019 -0700 Fixed misnamed header file after structure fact change exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_hydro/StochMFlux.cpp commit 150f3d79273aec1349a479f75718fbef66354fe3 Merge: 96b5f79a 16d520e7 Author: Daniel Ladiges Date: Tue Jul 2 13:58:37 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 16d520e70a79becedce7a8026e8e0f61cc916829 Author: Guy Moore Date: Tue Jul 2 11:20:55 2019 -0700 Cleaned up StructFact and modified plotfile names for each step src_analysis/Make.package src_analysis/StructFact.H src_analysis/StructFact.cpp src_analysis/StructFact_F.H src_analysis/src_F90/struct_fact.F90 commit 99fb44fc9b8af2e8b7c5dc61113c7e711e47d0fd Merge: c15b90ef 708905ad Author: Anthony Date: Tue Jul 2 12:23:45 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c15b90efe4a585c34e2899b9a87677ba64a3cee0 Author: Anthony Date: Tue Jul 2 12:23:14 2019 -0400 thermostatting actually works now. added re-sampler for particle positions and velocities within their current cell exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp src_particles/FhdParticleContainer.H commit 708905ad1ea4f8b2b47b3d250f8730b4e1dfd4bf Author: Guy Moore Date: Mon Jul 1 18:25:54 2019 -0700 Fixed StructFact MF copy + set k=0 cell to zero. Fixed other scaling in main_driver exec/compressible/main_driver.cpp src_analysis/StructFact.cpp src_analysis/src_F90/struct_fact.F90 src_compressible/src_F90/conv_funcs.F90 commit a29c9bedd0606299dbde24cc8df274a278d0b4db Merge: 21e58fbb f3c1f87a Author: Gang Xu Date: Mon Jul 1 17:43:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 21e58fbb966daaf7639a9cd87db9888c2884930d Author: Gang Xu Date: Mon Jul 1 17:43:28 2019 -0700 more debugging done, but no forces on markers so far exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit f3c1f87a063aa9b70036428f51d75f4ad47a11fb Author: alballow Date: Mon Jul 1 15:56:35 2019 -0700 Fixed warning src_surfaces/src_F90/surface_functions.F90 commit 96b5f79af44c78f9017c6909f7d267c7380d47a1 Merge: df81a720 f8b2621b Author: Daniel Ladiges Date: Mon Jul 1 15:54:29 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit df81a72044445e8eb6f363e26898b34ab3cdcc67 Author: Daniel Ladiges Date: Mon Jul 1 15:54:04 2019 -0700 Comment out struct fact in immersedIons, fix later. exec/immersedIons/main_driver.cpp src_surfaces/surfaces.cpp commit f8b2621bc9e89cbf2126a97278f86b3e5fc76f2c Merge: 8c5770a5 c0e080cc Author: alballow Date: Mon Jul 1 15:52:15 2019 -0700 merge Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8c5770a582d8714e7866d46d16c9c85a2d436565 Author: alballow Date: Mon Jul 1 15:51:25 2019 -0700 Fixed variables exec/DSMC/inputs_3d src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/surfaces.cpp commit c0e080cc9d15fc1c646e304caae08776e859850d Author: Guy Moore Date: Mon Jul 1 13:00:33 2019 -0700 Changed structure factor scaling and plotting functions exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 3475d86ad1c3cb6731204c3ce2f8bfc62bc21528 Merge: 5f293d8a bdafbf89 Author: alballow Date: Mon Jul 1 11:33:50 2019 -0700 Fixed conflictsMerge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5f293d8aaa54eab61141e14ea290da24300d03b7 Merge: 57965b58 beec9b60 Author: alballow Date: Mon Jul 1 11:32:52 2019 -0700 Fixed conflicts Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bdafbf89acb201d255c70708470280da43644e6d Merge: bd38905a beec9b60 Author: Anthony Date: Mon Jul 1 14:30:04 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bd38905a7a6178bee3704cb155377d9e7ead372a Author: Anthony Date: Mon Jul 1 14:29:40 2019 -0400 "working" 3d dsmc exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/surfaces.dat exec/DSMC-LDT/thermostat.F90 commit 57965b580838aae0bbf11d0cabe2f996a1fce8f5 Author: alballow Date: Mon Jul 1 11:25:29 2019 -0700 Renamed variables src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit beec9b60f5bb30b97eaec3171930150659fba871 Author: Daniel Ladiges Date: Mon Jul 1 11:22:07 2019 -0700 Uncommented some stuff from debugging. src_surfaces/src_F90/surface_functions.F90 commit ab1a5f881472f836fa87a3aa4a9b4261ab86654e Author: Daniel Ladiges Date: Mon Jul 1 11:18:43 2019 -0700 Fixed wrong function signature for particleInit in DSMC exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp commit 9c5e2a3622dd0f18bb88f6989f321121468791d9 Merge: 352edb8c 993badee Author: Daniel Ladiges Date: Sun Jun 30 23:51:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 352edb8ca3391923ba4e8e05599830170c03dd50 Author: Daniel Ladiges Date: Sun Jun 30 23:50:42 2019 -0700 Fixed surface definition bug. exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit 993badee9d442cbfdab4e485d2eadd3c6452c496 Author: Guy Moore Date: Sat Jun 29 12:28:26 2019 -0700 Finished conservative variable interpolation for hyperbolic fluxes. Large oscillations fixed that were seen in primitive interp. exec/compressible/inputs_3d src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 8cee3aa9f5aa4eb13f257d1e52830e807cc3dc46 Merge: 00736c49 48840915 Author: msantiago2 Date: Fri Jun 28 18:21:08 2019 -0700 merge with master commit 00736c497a495021bf43e909ebf033230fe8faf9 Author: msantiago2 Date: Fri Jun 28 18:20:02 2019 -0700 put the levelset and derivatives of concentration in the correct box arrays exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ConGrad_3d.F90 commit 48840915ef188224cd6516f912b70e80d4414f5a Merge: 3b398f62 3fa9d25d Author: Guy Moore Date: Fri Jun 28 17:53:29 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3b398f6200bfc91e5a740b8cd35231c7072a1555 Author: Guy Moore Date: Fri Jun 28 17:53:25 2019 -0700 starting to add conserved hypflux src_compressible/flux.cpp src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 commit 3fa9d25d75dbced7190e52cbfd7cda10b20418c3 Merge: 7333c8aa 55b82934 Author: Anthony Date: Fri Jun 28 19:15:03 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7333c8aaf96e20b28cc9c0f4ac404426ef85a4ac Author: Anthony Date: Fri Jun 28 19:14:37 2019 -0400 fix for when a box has only 1 particle exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp commit b2a42585d8cff011a21dff30ce4a49ae4759b531 Merge: 993f315c 55b82934 Author: msantiago2 Date: Fri Jun 28 15:59:50 2019 -0700 merge with master commit 993f315c68bb41e672da8a2e117193830d8100ae Author: msantiago2 Date: Fri Jun 28 15:54:27 2019 -0700 fixed unique pointer error exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit 55b829349154a1ac31cb2dd12507d6c42f3028a9 Author: Daniel Ladiges Date: Fri Jun 28 15:45:11 2019 -0700 Commented out some unfinshed code so FHDeX will compile src_surfaces/src_F90/surface_functions.F90 commit 199f16bfa78e08041a82a6a96bc77300c53968b3 Merge: eda58cc8 fdd8d592 Author: alballow Date: Fri Jun 28 15:40:56 2019 -0700 Fixed Conflict Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit eda58cc82694f03c021d4eff009263fe85f333df Author: alballow Date: Fri Jun 28 15:33:43 2019 -0700 Modified changes exec/DSMC-LDT/inputs_3d commit ffda25af041f7552dbb247067b02db2ce00e4a79 Author: Guy Moore Date: Fri Jun 28 15:26:29 2019 -0700 fixed correct scaling of molecular_mass exec/compressible/inputs_2d src_compressible/src_F90/multispec_funcs.F90 src_compressible/transCoeffs.cpp commit fdd8d592b3271886012995cfd74313a4619c8e1c Merge: ed69e992 0b2e0fa1 Author: Daniel Ladiges Date: Fri Jun 28 15:25:12 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ed69e9928b4715e24f08b35239778aac8f0da2e5 Author: Daniel Ladiges Date: Fri Jun 28 15:24:28 2019 -0700 Changes to method of graphene surface vel update exec/immersedIons/inputs_3d exec/immersedIons/properties.nb src_surfaces/src_F90/surface_functions.F90 commit 0b2e0fa15698fc995dad77d927f7b8d5a063f3b7 Author: Anthony Date: Fri Jun 28 18:24:06 2019 -0400 merge conflict exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp commit 774cbcd401b6971617fa0678ceabc7b16a52dc31 Merge: 74094ab1 5ddc118a Author: Gang Xu Date: Fri Jun 28 15:21:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 74094ab1711bae54988a7eb87b9e9e487995d88a Author: Gang Xu Date: Fri Jun 28 15:21:11 2019 -0700 Three markers version with spring and bending forces. Now compiles and runs. exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 5ddc118aaa9d0b01beffb958e0065f0e947d6a73 Merge: c71b9e4b a24fac3c Author: Anthony Date: Fri Jun 28 18:11:41 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c71b9e4bfa71165e05287b48bac588ae830635cf Author: Anthony Date: Fri Jun 28 18:11:23 2019 -0400 updated for velocities in 3D exec/DSMC-LDT/particleGen.cpp commit f2279294bdabf1c53b326b6171732019e68e508c Author: Anthony Date: Fri Jun 28 18:10:37 2019 -0400 updated to have velocity in 3D exec/DSMC-LDT/INS_functions.H exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/thermostat.F90 commit a24fac3cad9459abf2577b44c389fe14ea1b9c33 Merge: ce5eba8c 949c74e0 Author: alballow Date: Fri Jun 28 14:57:58 2019 -0700 Changed conflict Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ce5eba8c0fd00af90c9551eb9909e683c7f9fb84 Author: alballow Date: Fri Jun 28 14:42:00 2019 -0700 Constant changes exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit ef0d065233b2bbab4483a589d22e056fea30fd30 Author: msantiago2 Date: Fri Jun 28 10:51:21 2019 -0700 still debugging unique pointer error src_chem/AmrCoreAdv.cpp commit 949c74e0e13d028cbe3fa22253737bcb72da5411 Author: Johannes Blaschke Date: Fri Jun 28 10:33:03 2019 -0700 add marker data to plot file exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell/main_driver.H exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.H src_immersed-boundary/IBMultiBlobContainer.H commit c3509756707eec17055b859aea16877f2c8dc8fc Merge: e8611c12 cee0de7c Author: msantiago2 Date: Thu Jun 27 18:37:08 2019 -0700 merge with master commit e8611c1212497aa4b18567964852487625ebc347 Author: msantiago2 Date: Thu Jun 27 18:36:02 2019 -0700 debugging errors with unique pointers src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit cee0de7c219e8ba692fc9e61525299144bd11dc5 Author: Guy Moore Date: Thu Jun 27 18:01:50 2019 -0700 Multispecies compiles and runs. Sensible results (chi & Dij). Currently over-writing visc & thermal coefficients with Daniel's calcs - need to fix exec/compressible/main_driver.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/matrix.f src_compressible/src_F90/multispec_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/transCoeffs.cpp commit 5d37836c88f9f31d98601c4bc6bb4f77bdf72e6e Merge: 70e5283d d7f168d7 Author: Gang Xu Date: Thu Jun 27 16:58:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 70e5283d3cd958974eecb9bd7b61dc6e99c93274 Author: Gang Xu Date: Thu Jun 27 16:56:46 2019 -0700 Corrected the spring force calculation and Incorperated bending force calculation for three markers exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit 2640713a9b91f8ea830e2e1b1c887dcbbe43e224 Author: msantiago2 Date: Thu Jun 27 16:26:39 2019 -0700 put derivatives on cell faces, still debugging exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/ConGrad_3d.F90 src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBParticleContainer.H commit d7f168d72248098928ab54549e0418640d920403 Merge: c82c443f 5843f889 Author: Anthony Date: Thu Jun 27 14:27:46 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c82c443f750587082c14490a20a54f3b7e9e1d5c Author: Anthony Date: Thu Jun 27 14:27:28 2019 -0400 python file to do statistics on fluxes exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp commit 5843f8895eab6450cc994d3f41ede273eabbb8e8 Author: Johannes Blaschke Date: Thu Jun 27 10:56:18 2019 -0700 fix issue with dumbbell forcing (causing non-zero divergence) exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit 3d768b7ed010721cd8a631e9d84fa82589fa1f15 Author: Johannes Blaschke Date: Wed Jun 26 22:33:42 2019 -0700 dumbell implemented properly exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit 6ccd29e401fc979bd991551ee6ea36f0beef9bb9 Author: Johannes Blaschke Date: Wed Jun 26 20:49:20 2019 -0700 fix issue with predictor position exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit d188c6e22e0e306c7f89c5e429c9d27684da6d80 Author: Guy Moore Date: Wed Jun 26 17:39:13 2019 -0700 Identified one bug. Now trying to debug QR decomp. Singular matrix input? exec/compressible/main_driver.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit aea0eef597562d2414e4868c899a2dd376bd3a91 Author: Anthony Date: Wed Jun 26 20:23:10 2019 -0400 removed unnecessary function def from particleGen exec/DSMC-LDT/particleGen.cpp commit a74ee8cc5e6ce8df050cc2f414f5797c10690998 Merge: 0ede5719 aea0eef5 Author: Johannes Blaschke Date: Wed Jun 26 17:22:29 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 0ede571927cdbb17d0e5ce55f67af6de81dc96e3 Author: Johannes Blaschke Date: Wed Jun 26 17:22:25 2019 -0700 debugging dumbbell exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/main_driver.cpp commit 1e454e606ac7955d2988e3b4b5283e04c49e7750 Merge: 894cb635 b9c0c93b Author: Anthony Date: Wed Jun 26 20:20:14 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 894cb635e5a0a980630dbdab1547645b5f78525a Author: Anthony Date: Wed Jun 26 20:19:19 2019 -0400 thermostat handles 2 particles in box by re-drawing from maxwell distribution. working on getting average flux over samples in python script. exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/thermostat.F90 commit b9c0c93b4273220efb52ec0841351d3c3a216e05 Merge: a88cd6f9 a497dc52 Author: Johannes Blaschke Date: Wed Jun 26 17:00:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a88cd6f90e6ad6a9347aeeb64cf4ece49cef2f86 Author: Johannes Blaschke Date: Wed Jun 26 17:00:18 2019 -0700 buffer before interpolating exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/main_driver.cpp commit a497dc524520806f17c9f6aa39499035aae7d26e Merge: 04a02223 42bd4742 Author: Daniel Ladiges Date: Wed Jun 26 16:58:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 04a02223db6c8538b057a39dc86291f0e8be2f59 Author: Daniel Ladiges Date: Wed Jun 26 16:56:18 2019 -0700 Fixed structure factor using wrong geometry exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.H commit 42bd4742b26e7883871729b4ee88aaf669ce4c7b Merge: 4d7693ff b8eacaa1 Author: spcarney34 Date: Wed Jun 26 16:18:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4d7693ffd44e4104f9649daacec952ab146e52d4 Author: spcarney34 Date: Wed Jun 26 16:18:16 2019 -0700 Changed name of p3m interaction radius for clarity. exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit b8eacaa139716180218aa957def8be420d8fe944 Merge: ebb18ab4 1f418b2f Author: Johannes Blaschke Date: Wed Jun 26 16:12:34 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit ebb18ab49638e7f943a73c3437d9120ee47b036e Author: Johannes Blaschke Date: Wed Jun 26 16:12:30 2019 -0700 fix segfault exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/inputs_3d_test src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 1f418b2f012bbecf97c9745fa8d7fea885155f7e Merge: da1e0ece c70fb71f Author: Daniel Ladiges Date: Wed Jun 26 15:45:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit da1e0ecee21122b700500947d1fdf8da9cf40950 Author: Daniel Ladiges Date: Wed Jun 26 15:45:19 2019 -0700 Bug fix in pppm radius definition exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp commit c70fb71ff50c6bbba80ddc95bd2acf384f8b40ed Merge: 05bdb4e9 6625c26d Author: Johannes Blaschke Date: Wed Jun 26 15:38:48 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 05bdb4e963912bcbf9d54d9f95d45a0e4eb931fe Author: Johannes Blaschke Date: Wed Jun 26 15:38:45 2019 -0700 debugging segfault exec/immersed_boundary/channel_dumbbell/advance.cpp commit 6625c26d4e9ddb84f49a048e1f1a09b13cc76999 Merge: 6f01d5ce 9b1c8d14 Author: Andy Nonaka Date: Wed Jun 26 14:43:36 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6f01d5ce861bee1d254af50036ba8d7e6f297a8a Author: Andy Nonaka Date: Wed Jun 26 14:43:07 2019 -0700 sign error in bulk viscosity (not being used in testing now anyway) exec/hydro/advance.cpp commit 9b1c8d14ea51c340c489ea28199266045f099cfc Author: Guy Moore Date: Wed Jun 26 14:22:11 2019 -0700 Dangerous: Adjusted QR decomp tolerance. Now appears to successfully perform decomp without 'singular matrix' error. Needs further testing/validation src_compressible/src_F90/matrix.f commit 3b73f65ec417be5858095626fb0ae3f702a0903d Author: Guy Moore Date: Wed Jun 26 14:05:41 2019 -0700 Ported multicomponent diffusion coefficients. Singular matrix error in QR decomposition src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/src_F90/Make.package src_compressible/src_F90/matrix.f src_compressible/src_F90/matrixnp.f src_compressible/src_F90/multispec_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp commit 9db2c257c034f841902c07286f2bffd2a4e1c5fa Merge: ce97b5eb b0c19c8e Author: Andy Nonaka Date: Wed Jun 26 12:50:57 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 964a61954f10d4f8b668627604ca1ca10de7ea2b Author: kevinluna Date: Wed Jun 26 11:16:03 2019 -0700 adaptive cont. parameter exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions_F.H exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit b0c19c8e3bd9390946b4668d97c5f3a8a8fb9b9f Author: Daniel Ladiges Date: Wed Jun 26 10:52:42 2019 -0700 Added structure factor measurement for charge to immersedIons exec/immersedIons/main_driver.cpp src_common/common_namespace_declarations.H commit fac0e143a947ca2d088437683c92395bee3e9238 Merge: 230a08e1 9384d497 Author: msantiago2 Date: Wed Jun 26 09:51:04 2019 -0700 merge with master commit 9384d49741d32a0b15b20f98070dd8b5569d5ff3 Merge: de504fec 36b1097e Author: Anthony Date: Wed Jun 26 12:50:39 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit de504fecb78b4d4d041f2a11dad7f69488f33c51 Author: Anthony Date: Wed Jun 26 12:50:21 2019 -0400 python script to make histograms from flux data exec/DSMC-LDT/fluxStats.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp commit 230a08e140e0dcb160717cfb552ed563252fe315 Merge: 6985a73c d9aa1f4a Author: msantiago2 Date: Wed Jun 26 09:49:26 2019 -0700 Merge branch 'mks/chemistry' of github.com:AMReX-FHD/FHDeX into mks/chemistry commit 6985a73ca62b374cb1a4796fe830e69053a503e2 Author: msantiago2 Date: Wed Jun 26 09:48:15 2019 -0700 fix branching issue src_compressible/src_F90/multispec_funcs.F90 commit 7c74375c3187c4ffc310344a8515e38caa22c4cc Author: kevinluna Date: Tue Jun 25 23:54:19 2019 -0700 adaptive cont. parameter exec/_GL_alt/AVG_DATA.txt exec/_GL_alt/Umbrela_01_step/Data.ipynb exec/_GL_alt/Umbrela_01_step/Data_Script.py exec/_GL_alt/Umbrela_01_step/FE.txt exec/_GL_alt/Umbrela_01_step/PltFiles/Data_Script.py exec/_GL_alt/Umbrela_01_step/PltFiles/data0.050 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.060 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.070 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.080 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.090 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.100 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.110 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.120 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.130 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.140 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.150 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.160 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.170 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.180 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.190 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.200 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.210 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.220 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.230 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.240 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.250 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.260 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.270 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.280 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.290 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.300 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.310 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.320 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.330 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.340 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.350 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.360 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.370 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.380 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.390 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.400 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.410 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.420 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.430 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.440 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.450 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.460 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.470 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.480 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.490 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.500 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.510 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.520 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.530 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.540 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.550 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.560 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.570 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.580 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.590 exec/_GL_alt/Umbrela_01_step/data/data0.05 exec/_GL_alt/Umbrela_01_step/data/data0.060000000000000005 exec/_GL_alt/Umbrela_01_step/data/data0.07 exec/_GL_alt/Umbrela_01_step/data/data0.08 exec/_GL_alt/Umbrela_01_step/data/data0.09 exec/_GL_alt/Umbrela_01_step/data/data0.1 exec/_GL_alt/Umbrela_01_step/data/data0.11 exec/_GL_alt/Umbrela_01_step/data/data0.12000000000000001 exec/_GL_alt/Umbrela_01_step/data/data0.13 exec/_GL_alt/Umbrela_01_step/data/data0.14 exec/_GL_alt/Umbrela_01_step/data/data0.15000000000000002 exec/_GL_alt/Umbrela_01_step/data/data0.16 exec/_GL_alt/Umbrela_01_step/data/data0.16999999999999998 exec/_GL_alt/Umbrela_01_step/data/data0.18 exec/_GL_alt/Umbrela_01_step/data/data0.19 exec/_GL_alt/Umbrela_01_step/data/data0.2 exec/_GL_alt/Umbrela_01_step/data/data0.21000000000000002 exec/_GL_alt/Umbrela_01_step/data/data0.22000000000000003 exec/_GL_alt/Umbrela_01_step/data/data0.22999999999999998 exec/_GL_alt/Umbrela_01_step/data/data0.24 exec/_GL_alt/Umbrela_01_step/data/data0.25 exec/_GL_alt/Umbrela_01_step/data/data0.26 exec/_GL_alt/Umbrela_01_step/data/data0.27 exec/_GL_alt/Umbrela_01_step/data/data0.28 exec/_GL_alt/Umbrela_01_step/data/data0.29 exec/_GL_alt/Umbrela_01_step/data/data0.3 exec/_GL_alt/Umbrela_01_step/data/data0.31 exec/_GL_alt/Umbrela_01_step/data/data0.32 exec/_GL_alt/Umbrela_01_step/data/data0.33 exec/_GL_alt/Umbrela_01_step/data/data0.33999999999999997 exec/_GL_alt/Umbrela_01_step/data/data0.35 exec/_GL_alt/Umbrela_01_step/data/data0.36 exec/_GL_alt/Umbrela_01_step/data/data0.37 exec/_GL_alt/Umbrela_01_step/data/data0.38 exec/_GL_alt/Umbrela_01_step/data/data0.39 exec/_GL_alt/Umbrela_01_step/data/data0.4 exec/_GL_alt/Umbrela_01_step/data/data0.41 exec/_GL_alt/Umbrela_01_step/data/data0.42 exec/_GL_alt/Umbrela_01_step/data/data0.43 exec/_GL_alt/Umbrela_01_step/data/data0.44 exec/_GL_alt/Umbrela_01_step/data/data0.45 exec/_GL_alt/Umbrela_01_step/data/data0.46 exec/_GL_alt/Umbrela_01_step/data/data0.47 exec/_GL_alt/Umbrela_01_step/data/data0.48 exec/_GL_alt/Umbrela_01_step/data/data0.49 exec/_GL_alt/Umbrela_01_step/data/data0.5 exec/_GL_alt/Umbrela_01_step/data/data0.51 exec/_GL_alt/Umbrela_01_step/data/data0.52 exec/_GL_alt/Umbrela_01_step/data/data0.53 exec/_GL_alt/Umbrela_01_step/data/data0.54 exec/_GL_alt/Umbrela_01_step/data/data0.55 exec/_GL_alt/Umbrela_01_step/data/data0.56 exec/_GL_alt/Umbrela_01_step/data/data0.5700000000000001 exec/_GL_alt/Umbrela_01_step/data/data0.5800000000000001 exec/_GL_alt/Umbrela_01_step/data/data0.5900000000000001 exec/_GL_alt/Umbrela_01_step/mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/__init__.py exec/_GL_alt/Umbrela_01_step/pymbar/bar.py exec/_GL_alt/Umbrela_01_step/pymbar/confidenceintervals.py exec/_GL_alt/Umbrela_01_step/pymbar/exp.py exec/_GL_alt/Umbrela_01_step/pymbar/mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/mbar_solvers.py exec/_GL_alt/Umbrela_01_step/pymbar/old_mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/__init__.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_covariance.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_utils.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/__init__.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/gaussian_work.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/utils.py exec/_GL_alt/Umbrela_01_step/pymbar/utils_for_testing.py exec/_GL_alt/Umbrela_01_step/pymbar/version.py commit 902b0c16cd771d474d4c29f148d50f6262e81413 Author: kevinluna Date: Tue Jun 25 23:49:16 2019 -0700 adaptive cont. parameter exec/_GL_alt/Umbrella_100Samp_4Umb_K50/Data.ipynb exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.05 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.1 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.15000000000000002 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.2 exec/_GL_alt/Umbrella_Full_J_Run/Data.ipynb exec/_GL_alt/Umbrella_Full_J_Run/FE.txt exec/_GL_alt/Umbrella_Full_J_Run/Ploting_script.ipynb exec/_GL_alt/Umbrella_Full_J_Run/Result1.png exec/_GL_alt/Umbrella_Full_J_Run/data/data0.000 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.001 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.002 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.003 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.004 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.005 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.006 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.007 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.008 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.009 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.010 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.011 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.012 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.013 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.014 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.015 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.016 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.017 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.018 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.019 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.020 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.021 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.022 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.023 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.024 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.025 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.026 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.027 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exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/__init__.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_covariance.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_mbar.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_utils.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/__init__.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/gaussian_work.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/utils.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/utils_for_testing.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/version.py commit ec516d2e9d4332e87a71bf03f89042eadb285a58 Author: kevinluna Date: Tue Jun 25 23:44:53 2019 -0700 adaptive cont. parameter exec/_GL_alt/AVG_DATA.txt exec/_GL_alt/Data.ipynb exec/_GL_alt/Data_Script.py exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/Ploting_script.ipynb exec/_GL_alt/Python_Scripts/Ploting_script.ipynb exec/_GL_alt/Umbrela_01_step/Data.ipynb exec/_GL_alt/Umbrela_01_step/Data_Script.py exec/_GL_alt/Umbrela_01_step/FE.txt exec/_GL_alt/Umbrela_01_step/PltFiles/Data_Script.py exec/_GL_alt/Umbrela_01_step/PltFiles/data0.050 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.060 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.070 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.080 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.090 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.100 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.110 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.120 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.130 exec/_GL_alt/Umbrela_01_step/PltFiles/data0.140 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exec/_GL_alt/Umbrela_01_step/pymbar/confidenceintervals.py exec/_GL_alt/Umbrela_01_step/pymbar/exp.py exec/_GL_alt/Umbrela_01_step/pymbar/mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/mbar_solvers.py exec/_GL_alt/Umbrela_01_step/pymbar/old_mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/__init__.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_covariance.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_mbar.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/tests/test_utils.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/__init__.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/gaussian_work.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/Umbrela_01_step/pymbar/testsystems/timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/timeseries.py exec/_GL_alt/Umbrela_01_step/pymbar/utils.py exec/_GL_alt/Umbrela_01_step/pymbar/utils_for_testing.py exec/_GL_alt/Umbrela_01_step/pymbar/version.py exec/_GL_alt/Umbrella_100Samp_4Umb_K50/Data.ipynb exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.05 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.1 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.15000000000000002 exec/_GL_alt/Umbrella_100Samp_4Umb_K50/data/data0.2 exec/_GL_alt/Umbrella_Full_J_Run/FE.txt exec/_GL_alt/Umbrella_Full_J_Run/Ploting_script.ipynb exec/_GL_alt/Umbrella_Full_J_Run/Result1.png exec/_GL_alt/Umbrella_Full_J_Run/mbar.py exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/pymbar/__init__.py exec/_GL_alt/pymbar/bar.py exec/_GL_alt/pymbar/confidenceintervals.py exec/_GL_alt/pymbar/exp.py exec/_GL_alt/pymbar/mbar.py exec/_GL_alt/pymbar/mbar_solvers.py exec/_GL_alt/pymbar/old_mbar.py exec/_GL_alt/pymbar/tests/__init__.py exec/_GL_alt/pymbar/tests/test_covariance.py exec/_GL_alt/pymbar/tests/test_mbar.py exec/_GL_alt/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/pymbar/tests/test_timeseries.py exec/_GL_alt/pymbar/tests/test_utils.py exec/_GL_alt/pymbar/testsystems/__init__.py exec/_GL_alt/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/pymbar/testsystems/gaussian_work.py exec/_GL_alt/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/pymbar/testsystems/timeseries.py exec/_GL_alt/pymbar/timeseries.py exec/_GL_alt/pymbar/utils.py exec/_GL_alt/pymbar/utils_for_testing.py exec/_GL_alt/pymbar/version.py exec/_GL_alt/timeStep.cpp commit 36b1097ebbd524630fac0cec1397afc900f131cf Author: Johannes Blaschke Date: Tue Jun 25 22:22:49 2019 -0700 fix issue with initializing linked IBMarkers in different cores exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp commit 14a484c8f09f07e0c8ff99b38af2e7a72826bd75 Author: Johannes Blaschke Date: Tue Jun 25 22:02:26 2019 -0700 modernize finding neighbor markers exec/immersed_boundary/channel_dumbbell/advance.cpp commit 05fdc5b1cb00ef544dc1cdadca2ad80e7a773ce1 Merge: c3aa5a4d 74e1836e Author: Johannes Blaschke Date: Tue Jun 25 21:45:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c3aa5a4d4e0c3ba9d87ce3eaaecbeb5ddf8a6fa4 Author: Johannes Blaschke Date: Tue Jun 25 21:45:01 2019 -0700 migrating dumbell solution into dumbbell directory exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/Make.package exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/hydro_test_functions.H exec/immersed_boundary/channel_dumbbell/hydro_test_functions_F.H exec/immersed_boundary/channel_dumbbell/main_driver.H exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell/main_driver_F.H exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 74e1836e671adf0f8f6113900375aa9e2e147b7f Author: Guy Moore Date: Tue Jun 25 19:14:25 2019 -0700 Fixed which random fluxes are being filled. Need to populate diffusion matrix src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp commit 9341c3b034f4d167de319a78869ec8c59ed58ed7 Author: msantiago2 Date: Tue Jun 25 19:00:58 2019 -0700 fixed reset mistake exec/DSMC-LDT/surfaces.nb exec/compressible/writePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/ConGrad_3d.F90 src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp src_particles/src_F90/particle_functions.F90 commit d9aa1f4aa83de7274d35e9dcff31f40ce771b946 Merge: 874380e8 538358ac Author: msantiago2 Date: Tue Jun 25 18:42:48 2019 -0700 merge with master commit 874380e826e212722772c6996825f1db55be1465 Author: msantiago2 Date: Tue Jun 25 18:41:48 2019 -0700 fixed concentration derivatives exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb src_chem/src_F90/ConGrad_3d.F90 commit 538358ac754c8a7c1871034704061ac1f3e8b97a Author: Guy Moore Date: Tue Jun 25 18:40:31 2019 -0700 Added stochastic multispecies fluxes. Needs testing exec/compressible/writePlotFile.cpp src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/multispec_funcs.F90 src_compressible/timeStep.cpp commit d4b6200f6fe644f7725bb65cdca2df39682a7207 Author: msantiago2 Date: Tue Jun 25 18:08:44 2019 -0700 concentration gradients are passed to advance.cpp but not used exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.H commit 031c5018edace3fe69e21122b407ec66f052c7a0 Author: Daniel Ladiges Date: Tue Jun 25 18:04:32 2019 -0700 p3m bugfix src_particles/src_F90/particle_functions.F90 commit a34c302ae0aa6a3ee8e01435497825fa9fd5523e Author: msantiago2 Date: Tue Jun 25 17:30:56 2019 -0700 visualization for the tangential concentration gradient and it's magnitude exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/ConGrad_3d.F90 commit cd330eb8b0192dd68ea2d2236966efe33c674870 Merge: fe4f9fe6 3cf5fa01 Author: Daniel Ladiges Date: Tue Jun 25 16:32:21 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fe4f9fe6c0f90c509beea5b20cade91c3e4bad7d Author: Daniel Ladiges Date: Tue Jun 25 16:32:08 2019 -0700 LM HYdro debugging exec/DSMC-LDT/surfaces.nb exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/src_F90/particle_functions.F90 commit 3cf5fa01418d0ef8bc9e7b25b0d2a4361172e79c Merge: 86c68aa9 10fd6694 Author: Gang Xu Date: Tue Jun 25 16:31:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 86c68aa9f158f4ec394193f19ed39ca8489522e1 Author: Gang Xu Date: Tue Jun 25 16:26:18 2019 -0700 added bending forces for both predictor and corrector. Fixed the first markers in place. exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit ce97b5ebacb5b7cf06f29b12fa48609ae37e015d Author: Andy Nonaka Date: Tue Jun 25 16:22:01 2019 -0700 cleanup only exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp commit cac0df291a99e39c0ce7f3ea6626e7c1ea2944a4 Merge: 15eaa8a6 10fd6694 Author: msantiago2 Date: Tue Jun 25 16:19:13 2019 -0700 merge with master commit 15eaa8a686903719115b0b7bc49692d32a63eba3 Author: msantiago2 Date: Tue Jun 25 16:18:16 2019 -0700 added visualization of the dot product of the concentration gradient with the normal of the interface exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/src_F90/ConGrad_3d.F90 src_immersed-boundary/IBCore.H commit 377554b88640c819d7d60b97ae6682b5bee9d561 Merge: 85cb3736 10fd6694 Author: alballow Date: Tue Jun 25 16:02:03 2019 -0700 Fixed typo Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 85cb3736e22e15164e03a8cd7cb45c252032fb4f Author: alballow Date: Tue Jun 25 15:58:51 2019 -0700 reconsilating versions exec/DSMC/inputs_3d src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit 10fd66946f2590a317ebb409e6ee14157924e3d2 Merge: 8651a1a1 fced868e Author: Anthony Date: Tue Jun 25 18:54:27 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8651a1a10b5a860264fac2d291e2855465e088a7 Author: Anthony Date: Tue Jun 25 18:53:05 2019 -0400 thermostatting in parallel is done. moveparticlesDSMC now checks how many particles cross a given surface and in which direction. It needs a new final argument, int flux[2]. exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit fced868e293a56a47a1e6877bedd5c04ebf33082 Merge: 3d01481f efe40ea3 Author: Johannes Blaschke Date: Tue Jun 25 15:33:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3d01481f63e6309c2640eeb04ca8ab2d6f12a448 Author: Johannes Blaschke Date: Tue Jun 25 15:33:22 2019 -0700 add function to find previous/next markers in chained ibmarkers exec/immersed_boundary/channel_dumbbell_sol/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit efe40ea3789f028fab88c134a8ac82a700dd12aa Author: Anthony Date: Tue Jun 25 18:03:31 2019 -0400 thermostatting works in parallel exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/thermostat.F90 commit 0c0b678cf73d5181edf96e86606972dd2cebe19b Merge: 36293459 fa3a8ad7 Author: Anthony Date: Tue Jun 25 17:18:14 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 36293459d0d0461df43c293374e0ac372a0f0a29 Author: Anthony Date: Tue Jun 25 17:17:38 2019 -0400 working on thermostat in parallel framework. works up to a reduction. exec/DSMC-LDT/INS_functions.H exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/thermostat.F90 commit fa3a8ad79d29389a944675dbea47abb001a22f8c Author: Guy Moore Date: Tue Jun 25 13:56:27 2019 -0700 Identified source of error in cons->prim conversions: energy and mass fraction scaling. More consideration to BCs needed exec/compressible/main_driver.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/trans_funcs.F90 commit ec15739bbdb763a40cbea326910b4f8b8f6371e8 Author: Anthony Date: Tue Jun 25 16:09:10 2019 -0400 added thermostat_tog to input parser exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/thermostat.F90 src_common/common_functions.cpp src_common/common_functions_F.H src_common/src_F90/common_namelist.F90 commit cbcc0b704637e2791d7811a93f4bd1cbb233298f Merge: e83d4d3d a3bb74c5 Author: msantiago2 Date: Tue Jun 25 11:34:30 2019 -0700 merge with master commit a3bb74c5cac8072a61edf159575e11e764d5c254 Merge: 6a17acf7 912490c7 Author: Anthony Date: Tue Jun 25 14:14:09 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6a17acf71ae53b0bba7cd4c8e33a08f3fce2d9b4 Author: Anthony Date: Tue Jun 25 14:12:33 2019 -0400 Generating different numbers of particles in different regions of the domain works in parallel. exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp src_particles/FhdParticleContainer.H commit 912490c7de4b134e903f3c38f2aac32de4f6dbb9 Author: Guy Moore Date: Tue Jun 25 11:10:22 2019 -0700 Added multispecies functionality to hyp. fluxes and conversion functions src_compressible/src_F90/Make.package src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 commit 046ec3a303990c6e79e8be287252186b6b78f8de Author: Johannes Blaschke Date: Mon Jun 24 22:18:11 2019 -0700 use umac buffer for interpolation => no need to use 6 ghost cells in gmres exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp commit ef4e0c3f0ecedbe41b56eea6194921f6c600e168 Author: Johannes Blaschke Date: Mon Jun 24 20:52:30 2019 -0700 I can't explain why atm, but we need 6 ghost cells here... exec/immersed_boundary/channel_soft/main_driver.cpp commit e83d4d3d9351300d2bc05e743560a20875634df0 Merge: 507fa592 bb17b493 Author: msantiago2 Date: Mon Jun 24 19:26:04 2019 -0700 merge with master commit 507fa592802ab518c099bcbeca84e929182c3640 Author: msantiago2 Date: Mon Jun 24 19:24:48 2019 -0700 added some visualization of gradients vs phi and theta exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb exec/immersed_boundary/channel_soft/inputs_3d_test commit bb17b493cfac916c6651e6782ad00008e8a3ccfd Author: Guy Moore Date: Mon Jun 24 18:12:19 2019 -0700 diffusive multispecies implemented exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp commit 1dfeaa1eb1b64478b8f84cc53fc1b2727dbcbf19 Merge: cc247a24 a9fd1f5f Author: Johannes Blaschke Date: Mon Jun 24 17:41:46 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit cc247a2463d174d16cb56bb79a839f587fcc24e0 Author: Johannes Blaschke Date: Mon Jun 24 17:41:44 2019 -0700 debug plt file and divergence exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test commit a9fd1f5fc4ac52ab12d6dd826d39bad304b6dbd0 Merge: 392c9dff 3c089fd8 Author: Gang Xu Date: Mon Jun 24 16:55:03 2019 -0700 Try to merge changes in advance.cpp for predictor bending force. Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 392c9dff6f7f3ac546d1380eca9b95f5fbde2b78 Author: Gang Xu Date: Mon Jun 24 16:44:00 2019 -0700 added in the bending force calculation for the predictor exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit 5031b887b0b9bad6e3ee1e2282c0949123fd3d8f Author: alballow Date: Mon Jun 24 16:12:43 2019 -0700 Adding correct constants exec/DSMC-LDT/inputs_3d exec/DSMC/inputs_3d src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 6011e33119bf9085aaad976b1105f35f8a9fd5bf Author: msantiago2 Date: Mon Jun 24 15:16:03 2019 -0700 added overlaying quiver plots to visualization exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb commit 3c089fd8967295e14b41093a900fc5879e7f4010 Merge: 1cc65611 6c16ef47 Author: Anthony Date: Mon Jun 24 17:44:13 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 1cc65611b2a09b3c27d5db1e71bb1d29141e6d8a Author: Anthony Date: Mon Jun 24 17:43:19 2019 -0400 outputs particle flux per timestep to txt file exec/DSMC-LDT/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit ed250c45ec3c0dc48ef983f1a1d6b911359174d5 Merge: 3456038d 3c089fd8 Author: msantiago2 Date: Mon Jun 24 14:42:11 2019 -0700 merge with master into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 3456038d960595624f322abf89de3644b87474bd Author: msantiago2 Date: Mon Jun 24 14:41:07 2019 -0700 updated concentration gradient multifab to only be visible at the interface exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb src_chem/src_F90/ConGrad_3d.F90 commit 6c16ef475f409c505fe7721cd2d4a0d3bb5a05b7 Merge: 7f1209aa e1daa799 Author: Johannes Blaschke Date: Mon Jun 24 14:39:53 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 7f1209aad52d017a7711b970307aba8596c2587e Author: Johannes Blaschke Date: Mon Jun 24 14:39:49 2019 -0700 fix problem with ghost cells exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.H commit e1daa79926946122dde244e7b5cb5264147e8a7a Merge: 0e814cb8 7c72eeea Author: Daniel Ladiges Date: Mon Jun 24 13:32:49 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0e814cb8eb7ce9e39fc0c22702269fc9c63aa4ef Author: Daniel Ladiges Date: Mon Jun 24 13:32:21 2019 -0700 Bug fix for LDT-DSMC surface definitions exec/DSMC-LDT/surfaces.dat exec/immersedIons/inputs_3d exec/immersedIons/particleGen.cpp exec/immersedIons/properties.nb commit 7c72eeeaa761f80a994fd834d5ff6c292c0c52ff Author: Anthony Date: Mon Jun 24 16:24:06 2019 -0400 added thermostat toggle to common namespace exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 35f632014cd56657d8ac45a34ef56c580d9bf063 Author: Johannes Blaschke Date: Mon Jun 24 11:34:52 2019 -0700 add init src_immersed-boundary/IBMultiBlobContainer.cpp commit f72f8bb797329af1dc4813b2cb29a92bde116b9d Merge: 32755b26 23fb28dd Author: msantiago2 Date: Mon Jun 24 11:28:56 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 32755b2624e4bdbdd662e752e6620f220ac4b615 Author: msantiago2 Date: Mon Jun 24 11:28:15 2019 -0700 added visualization file exec/immersed_boundary/channel_soft/Explore Chemistry-checkpoint.ipynb commit 23fb28ddadc6735b09e55826e6eb9acd518468bb Merge: a4f59ea8 03bf8bec Author: Johannes Blaschke Date: Mon Jun 24 11:07:31 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit a4f59ea8fddc07dd69afeb538ddf22e60cceaa42 Author: Johannes Blaschke Date: Mon Jun 24 11:07:29 2019 -0700 add include src_hydro/StochMFlux.cpp commit 03bf8bec1d4f25c525c37dd6a3040c8e57015216 Merge: b46eb012 d46684cb Author: Anthony Date: Mon Jun 24 14:02:30 2019 -0400 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b46eb01251c089440432cd560022bb9fa69bcec6 Author: Anthony Date: Mon Jun 24 13:59:50 2019 -0400 set up DSMC-LDT to do thermostatting. Added a DSMC init particles and thermostatting function to the particle container class. Added the option for a specularly reflecting BC in surfaces. exec/DSMC-LDT/INS_functions.H exec/DSMC-LDT/Make.package exec/DSMC-LDT/amrex_to_vtp.py exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/thermostat.F90 exec/channel/inputs_3d src_particles/FhdParticleContainer.H src_surfaces/surfaces.cpp commit d46684cb0750477d6d5a21df94051bc633883c18 Merge: e2cb2c51 151cada1 Author: Guy Moore Date: Mon Jun 24 10:28:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e2cb2c5175b38085a745970bd94e5789ad92bd5f Author: Guy Moore Date: Mon Jun 24 10:28:18 2019 -0700 forgot rng_functions.H ! src_rng/rng_functions.H commit 151cada17accddc15cba7382963796de9c08fd2f Author: Daniel Ladiges Date: Mon Jun 24 10:23:42 2019 -0700 ditto exec/DSMC/particleGen.cpp commit ab090db4eafff22b2d0323a3480f2de761150ac2 Author: Daniel Ladiges Date: Mon Jun 24 10:16:27 2019 -0700 Added precheck.f90 to DSMC dir exec/DSMC/precheck.F90 commit 19f0eb5ad91a45a2801fa43cfca50739ab893ba0 Merge: 7113ae0a b7fadafc Author: Guy Moore Date: Mon Jun 24 09:53:00 2019 -0700 Merge remote-tracking branch 'origin/gcm/compressible/multispecies' commit b7fadafc159bd0091bb6cb5f654cd5e940a06af7 Author: Guy Moore Date: Mon Jun 24 09:49:50 2019 -0700 Moved MultiFABFillRandom & cleaned-up makefile exec/compressible/GNUmakefile exec/compressible/indexshift/index_shift.sh exec/compressible/main_driver.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_compressible/timeStep.cpp src_rng/Make.package src_rng/MultiFABFillRandom.cpp src_rng/rng_functions_F.H src_rng/src_F90/Make.package src_rng/src_F90/multifab_fill_random.F90 commit 7113ae0a924f4f868ee43d1214e2dcf8e776d56c Author: Johannes Blaschke Date: Sun Jun 23 22:52:16 2019 -0700 work on multi-blob container src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp commit 16a452d5b8ca983ddb913255da56e426c8d4faa0 Author: Johannes Blaschke Date: Sun Jun 23 21:26:42 2019 -0700 build a better soft immersed boundary container src_immersed-boundary/IBMultiBlobContainer.H src_immersed-boundary/IBMultiBlobContainer.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/Make.package commit 17f6f83cfe93c1d6207fa4da13d466b13557d012 Author: Johannes Blaschke Date: Sun Jun 23 20:48:09 2019 -0700 noodling with debuging soft ib exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.H commit 3fd181970c713c93acc83a0ad986c86faabafe8a Author: Johannes Blaschke Date: Sun Jun 23 15:19:39 2019 -0700 cleanup exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 921cebf23b9a4c0ed811b00dd22f7b395e6c862e Author: Johannes Blaschke Date: Sun Jun 23 15:17:27 2019 -0700 example bending for calculation added to main driver exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp commit 73ee691270362c03628d99a48c8ee33c7755d187 Author: Johannes Blaschke Date: Sun Jun 23 15:16:53 2019 -0700 fix delegating constructors exec/immersed_boundary/src_models/IBMarkerMD.cpp commit bf7fa8ddf899561a6bec1aea344e7d721f4e9201 Author: Johannes Blaschke Date: Sun Jun 23 13:58:22 2019 -0700 use namespaces exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 0a3e4f56f9d0767491998d2e5d3fbb1a889dbf87 Author: Johannes Blaschke Date: Sun Jun 23 12:40:05 2019 -0700 helper function to compute bending forces from 3 positions exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit a3daaf0a149e30536ab792b5ba17a1111a92bc69 Author: Johannes Blaschke Date: Sun Jun 23 12:29:40 2019 -0700 update Edge data model to be more secure exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 7320730304bf08969ff552d475f452309ab467a1 Author: Johannes Blaschke Date: Sun Jun 23 12:13:24 2019 -0700 reference vectors, don't copy them exec/immersed_boundary/src_models/IBMarkerMD.cpp commit 776a50a4066f0d6620b03598c57d3c86c41524ef Author: Johannes Blaschke Date: Sun Jun 23 12:11:51 2019 -0700 add bending force calculation exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp commit dfc736fb69b2a9da1a1cedf2bd747ea77490b007 Author: Johannes Blaschke Date: Sat Jun 22 21:02:16 2019 -0700 start working on implementing bending forces exec/immersed_boundary/channel_dumbbell_sol/GNUmakefile exec/immersed_boundary/src_models/IBMarkerMD.H exec/immersed_boundary/src_models/IBMarkerMD.cpp exec/immersed_boundary/src_models/Make.package commit ab70753f2bb104e8117aab0bce1fc0a42070754d Author: Johannes Blaschke Date: Thu Jun 20 21:05:30 2019 -0700 write ib marker data to plotfile exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_soft/Explore Data.ipynb commit 80c8264cdb6fe0fc9ce5dc208e4539bf47dd1193 Merge: 65e45dc2 f1e4a37e Author: Johannes Blaschke Date: Thu Jun 20 20:49:38 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 65e45dc2e2853560ff5a19f5a78a7eb16dc393ff Author: Johannes Blaschke Date: Thu Jun 20 20:49:23 2019 -0700 restructure header files exec/immersed_boundary/channel_dumbbell_sol/Make.package exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.H exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver_F.H commit c68864cd9a90b6d14c8624ab5a7e41216f19d1a7 Author: Johannes Blaschke Date: Thu Jun 20 20:26:17 2019 -0700 clean up .H files exec/immersed_boundary/channel_dumbbell_sol/hydro_test_functions.H exec/immersed_boundary/channel_dumbbell_sol/hydro_test_functions_F.H commit f1e4a37e12d0f17c6cd0ab4ad79e2d2da10ab33c Author: Daniel Ladiges Date: Thu Jun 20 19:23:23 2019 -0700 Finished adding inertial option to ion code. Velocity fluctuations dont look quite right. exec/DSMC-LDT/inputs_3d exec/immersedIons/INS_functions.H exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 2450ae605e45b6d226822a74f91eb35c24f879ec Merge: d8f8532a 15575b24 Author: Daniel Ladiges Date: Thu Jun 20 14:58:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d8f8532aee39aca08c8a91ac46c22ac2a9114c8a Author: Daniel Ladiges Date: Thu Jun 20 14:58:22 2019 -0700 LDT-DSMC debugging. exec/DSMC-LDT/main_driver.cpp commit 15575b2445aee6f30a43019dc9d28833904bf06f Merge: 10f74a46 aa884824 Author: Guy Moore Date: Thu Jun 20 14:58:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 10f74a46fa4c973608117b94ffc2d11db2f53584 Author: Guy Moore Date: Thu Jun 20 14:57:37 2019 -0700 Moved random fill to correct location in time stepping scheme src_compressible/flux.cpp src_compressible/timeStep.cpp commit aa884824e708b981ad6201b6bb5e472f2d6918e1 Author: Anthony Date: Thu Jun 20 17:56:30 2019 -0400 setting up DSMC to place particles in 2 cells. Also commented out a print statement in collision_functions exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp src_particles/src_F90/collision_functions.F90 commit 298511702ad60458ffb0daf903d9aead67e423d3 Author: Gang Xu Date: Thu Jun 20 14:24:01 2019 -0700 debug dumbbell exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit e54da9cb26591c349461006e1babcf422aa48e83 Merge: 3bdc8450 62891815 Author: Gang Xu Date: Thu Jun 20 14:09:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3bdc84506bd62fa1127cb6d8d2b47cb2d135c276 Author: Gang Xu Date: Thu Jun 20 14:09:20 2019 -0700 fiddle with dumbbell forcing exec/channel/inputs_3d_test exec/immersedParticles/inputs_3d exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test src_immersed-boundary/IBMarkerContainer.cpp commit 62891815489a6070f818ac29c574e841af40fed7 Author: Daniel Ladiges Date: Thu Jun 20 13:56:04 2019 -0700 Added default value for graphene_tog src_common/src_F90/common_namelist.F90 commit 099b95e3347296d1995ac25bf2c1467446dfb971 Merge: 5c177643 38bee70f Author: Daniel Ladiges Date: Thu Jun 20 13:54:49 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5c177643522d196251b0b891ed987a6a8dec7650 Author: Daniel Ladiges Date: Thu Jun 20 13:54:34 2019 -0700 More stuff for LDT DSMC exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/precheck.F90 exec/immersedIons/Eanalysis.nb exec/immersedIons/inputs_3d commit 38bee70fc2428abcbcde2b679339c1ce1ffd25ab Merge: 4f0d7254 c9cf44c2 Author: alballow Date: Thu Jun 20 13:53:07 2019 -0700 fixed conflicts Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4f0d7254229e452c560c11691d41d78eae8cb355 Author: alballow Date: Thu Jun 20 13:46:12 2019 -0700 Added moving graphene boundary exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/precheck.F90 src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit c4c5d6d3bb4f0a4acc0258638105fda2443e2187 Merge: c699399b c9cf44c2 Author: msantiago2 Date: Thu Jun 20 09:44:23 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit c9cf44c2fc84e00eda8736c7a9b48e944d607972 Author: Daniel Ladiges Date: Thu Jun 20 09:19:52 2019 -0700 precheck file change for ldt-dsmc exec/DSMC-LDT/precheck.F90 commit 80f8d4b5f771b8ba2e784df87e6503e92103e413 Merge: 9ff2f1f8 94773917 Author: Daniel Ladiges Date: Thu Jun 20 08:59:29 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9ff2f1f897d460c78fbe2b58ec9dbb4dee06a29c Author: Daniel Ladiges Date: Thu Jun 20 08:59:07 2019 -0700 Spin off DSMC version for LDT testing exec/DSMC-LDT/GNUmakefile exec/DSMC-LDT/INS_functions.H exec/DSMC-LDT/Make.package exec/DSMC-LDT/Make_precheck.package exec/DSMC-LDT/TimeStep.cpp exec/DSMC-LDT/WritePlotFile.cpp exec/DSMC-LDT/cellvols.F90 exec/DSMC-LDT/convertSeries exec/DSMC-LDT/delPlots exec/DSMC-LDT/inputs_3d exec/DSMC-LDT/main_driver.cpp exec/DSMC-LDT/particleCheck.cpp exec/DSMC-LDT/particleGen.cpp exec/DSMC-LDT/precheck.F90 exec/DSMC-LDT/surfaces.dat exec/DSMC-LDT/surfaces.nb exec/DSMC-LDT/write_pview_file.py commit c699399bb26877eed7be58bebf4e4a77004b884c Author: msantiago2 Date: Wed Jun 19 18:39:59 2019 -0700 clean up code exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/Make.package~ commit 947739172007fb4cf200c4084f5feee0f41bdccc Merge: 63768004 00b8f2b0 Author: Guy Moore Date: Wed Jun 19 17:43:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 63768004d75f6aae43707d2f40eca7d267ebd009 Author: Guy Moore Date: Wed Jun 19 17:43:06 2019 -0700 Fixed indexing of hyperbolic flux function - needs converting from primitive to conserved src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 00b8f2b000f1c1f29206a53868b1dd5cd1b8a145 Merge: 8757e12d 26275ab6 Author: msantiago2 Date: Wed Jun 19 17:38:11 2019 -0700 Merge branch 'master' into mks/chemistry commit 8757e12d9fda378a5c2e6898fa3fa4c7f8bbe57a Author: msantiago2 Date: Wed Jun 19 17:36:30 2019 -0700 Fixed code so it runs with MPI, only support for 3D exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.cpp commit eca2f471f0e0139b09c3a210256d4a0a599358a5 Author: Gang Xu Date: Wed Jun 19 17:12:07 2019 -0700 just add forces for the predictor step exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 26275ab67869d2c5d72f5dae73c64f960137fa62 Author: Guy Moore Date: Wed Jun 19 16:14:15 2019 -0700 corrected stochastic weighting and other indexing issues - valgrind report clean exec/compressible/index_shift.sh exec/compressible/indexshift/index_shift.sh exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp commit ded93eabe25083f9158ece2e16f9b189a6ef9cc9 Author: msantiago2 Date: Wed Jun 19 15:29:06 2019 -0700 johannes screwed up.. fixed it! src_immersed-boundary/IBParticleContainer.cpp commit b5e35c0f89594bc030a1c12d427c16f836dcda51 Merge: 0cd09092 c8002f7c Author: Johannes Blaschke Date: Wed Jun 19 15:20:36 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 0cd090922f41130d7fcb1bbab3672de636bedc1f Author: Johannes Blaschke Date: Wed Jun 19 15:20:33 2019 -0700 basic example for looping over neighbors exec/immersed_boundary/channel_dumbbell_sol/advance.cpp src_immersed-boundary/IBMarkerContainer.H commit d23e4e728eab284dc342896db320bc2d581c12a7 Merge: cdcecd2f c8002f7c Author: msantiago2 Date: Wed Jun 19 14:58:29 2019 -0700 Merge branch 'master' into mks/chemistry commit cdcecd2feb4664733900f1ebfaab20f1a704de61 Author: msantiago2 Date: Wed Jun 19 14:56:54 2019 -0700 debugging continued exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_particles/src_F90/particle_functions.F90 commit c8002f7c7cf96f9dacd8e277100d2ee46a9a54a0 Merge: 9318f6f0 f02e4a62 Author: msantiago2 Date: Wed Jun 19 14:54:05 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit de51f0aceb76d67fe441b22e2cfb1ca8f8c1ac01 Author: msantiago2 Date: Wed Jun 19 14:53:22 2019 -0700 debugging exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/src_F90/ptsource_fill_3d.F90 commit f02e4a62ace38d792665910cdfb996a0d2a1283f Author: Johannes Blaschke Date: Wed Jun 19 11:19:38 2019 -0700 playing with neighbor lists exec/immersed_boundary/channel_dumbbell_sol/advance.cpp src_immersed-boundary/IBMarkerContainer.H commit 9318f6f0f3fe2e838234c2c327fe55fcada9ee1f Author: msantiago2 Date: Wed Jun 19 11:14:40 2019 -0700 diffusion coefficient read in from inputs file fixed exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_immersed-boundary/IBParticleContainer.cpp commit f7e205a04d323a94af10947b9856b3c338695bd0 Author: Johannes Blaschke Date: Wed Jun 19 11:06:44 2019 -0700 debug exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 2c8f5ab889b8e211cbe7bae8b074068b93e6a5d3 Merge: c8d02554 37785c05 Author: Daniel Ladiges Date: Tue Jun 18 19:11:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c8d0255499a30a50c8383167e3d7233f634be32c Author: Daniel Ladiges Date: Tue Jun 18 19:11:06 2019 -0700 Found bug in spread op, for now es and fluid kernels must be same size. exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_particles/src_F90/particle_functions.F90 commit 37785c05d0d91f7e39bec34973fcf5e949c55ef3 Merge: 8da656f7 97db4324 Author: msantiago2 Date: Tue Jun 18 18:31:38 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 8da656f7b8a4d20821a58a1af46c17b96c7b4e48 Author: msantiago2 Date: Tue Jun 18 18:30:00 2019 -0700 diffusion works, advection remains to be verified exec/brownian/INS_functions.cpp src_chem/AmrCoreAdv.cpp src_immersed-boundary/IBParticleContainer.cpp commit 97db43247e79afc7dafe50da4f0155422780b033 Author: Gang Xu Date: Tue Jun 18 16:58:48 2019 -0700 use umacNew in IB corrector step exec/immersed_boundary/channel_dumbbell_sol/advance.cpp commit 5c5e42f6dbcfaf7ac24458a08a75c0bf17e96041 Merge: 8a9ff359 777ce290 Author: msantiago2 Date: Tue Jun 18 16:39:54 2019 -0700 update master acking branch 'refs/remotes/origin/master' # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 8a9ff359342227889d2c47ee9e099ab303a394f6 Author: msantiago2 Date: Tue Jun 18 16:38:48 2019 -0700 chemistry work in progress exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/Adv_3d.F90 src_chem/src_F90/ptsource_fill_3d.F90 src_immersed-boundary/IBParticleContainer.cpp commit 777ce290e4f1ae5521c2ba56e8dd0573cb9fa58a Merge: d04de485 b5d762ef Author: Johannes Blaschke Date: Tue Jun 18 16:38:48 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit d04de48598fef25a6ed3094cc46a41a239acfdd2 Author: Johannes Blaschke Date: Tue Jun 18 16:38:41 2019 -0700 add forcing example exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test commit b5d762efaa4a67d59cd7050143a878021243294b Author: spcarney34 Date: Tue Jun 18 16:29:14 2019 -0700 Bug fix in short range force calculation--particle(nl(j)) now called instead particle(j) src_particles/src_F90/particle_functions.F90 commit 8082309e320f3faebd7b770ab356d37987f55225 Merge: 3384c972 8dae52f4 Author: Daniel Ladiges Date: Tue Jun 18 16:02:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3384c97273e95d07d023ff36c1d05338e856fb10 Author: Daniel Ladiges Date: Tue Jun 18 16:02:08 2019 -0700 PPPM bugfix exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/particleGen.cpp src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 8dae52f4a3090fbea53a36bade43e9371c4d96c5 Author: Johannes Blaschke Date: Tue Jun 18 15:41:04 2019 -0700 add function to reset marker and predictor velocity exec/immersed_boundary/channel_dumbbell_sol/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 0bd912f83b03a4570f1583c6b41feca95058720e Author: Johannes Blaschke Date: Tue Jun 18 15:39:00 2019 -0700 make a dumbbell slution directory using the new ib marker container exec/immersed_boundary/channel_dumbbell_sol/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell_sol/GNUmakefile exec/immersed_boundary/channel_dumbbell_sol/Make.package exec/immersed_boundary/channel_dumbbell_sol/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell_sol/advance.cpp exec/immersed_boundary/channel_dumbbell_sol/compute_convfact_2.sh exec/immersed_boundary/channel_dumbbell_sol/hydro_test_functions.H exec/immersed_boundary/channel_dumbbell_sol/hydro_test_functions_F.H exec/immersed_boundary/channel_dumbbell_sol/init_funcs.F90 exec/immersed_boundary/channel_dumbbell_sol/init_s_funcs.F90 exec/immersed_boundary/channel_dumbbell_sol/inputs_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test exec/immersed_boundary/channel_dumbbell_sol/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell_sol/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell_sol/main_driver.cpp exec/immersed_boundary/channel_dumbbell_sol/run_conv_tests_2.sh commit cf887a85a0f940aed35f7caf075557b555f4bab3 Author: Johannes Blaschke Date: Tue Jun 18 14:42:37 2019 -0700 fix predictor interpolation src_immersed-boundary/IBMarkerContainer.cpp commit 7ebbdb76214b7a83fd6f03cbfdaab46fc6e26dcf Merge: 4c50f710 6384b021 Author: Johannes Blaschke Date: Tue Jun 18 14:15:01 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 4c50f71057e3060d225d1650e91ee9a9c10d9365 Author: Johannes Blaschke Date: Tue Jun 18 14:14:54 2019 -0700 make sure to flag total weights = -1 => standard interpolation function src_immersed-boundary/IBMarkerContainer.cpp commit 660d59e48b7ad2497c33b52f5709b7e69e1b2394 Author: Johannes Blaschke Date: Tue Jun 18 14:03:29 2019 -0700 should be ng src_immersed-boundary/IBMarkerContainer.cpp commit 6384b0216b9159c421b879ecf8ad4e16f2c43860 Author: spcarney34 Date: Tue Jun 18 13:31:08 2019 -0700 Linear interp based on tabulated values for correction force exists. src_particles/src_F90/particle_functions.F90 commit 276efa5b40f601d71ac923a3bc432e9fa3553729 Merge: f2fbf642 f1b5498d Author: Johannes Blaschke Date: Tue Jun 18 11:29:27 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit f2fbf64287cd94a2aeeb7a81060a6a95975e15ea Author: Johannes Blaschke Date: Tue Jun 18 11:29:24 2019 -0700 fix interpolate markers src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit f1b5498d3736fa3c0b92e5ef96162669ddb1d9fb Author: Daniel Ladiges Date: Tue Jun 18 11:17:00 2019 -0700 Added tables for 6 point pppm correction. exec/immersedIons/inputs_3d exec/immersedIons/p3mcalc2.nb src_particles/src_F90/particle_functions.F90 commit 58fcd9d3e8ee2449aa0c02961f17b64198dea13a Merge: b2ed640a fb7d62a1 Author: Johannes Blaschke Date: Tue Jun 18 11:01:36 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit b2ed640ae2080eb2ddd059f4f7657e7314ef583b Author: Johannes Blaschke Date: Tue Jun 18 11:01:34 2019 -0700 fix spread maker src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 5549297b9ceb69e2a012be7c62df17eeb525d6e9 Merge: 486f4c04 fb7d62a1 Author: Daniel Ladiges Date: Tue Jun 18 10:59:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 486f4c0491169f07ede1fe87668afc18444b8afa Author: Daniel Ladiges Date: Tue Jun 18 10:59:30 2019 -0700 More PPPM stuff exec/immersedIons/main_driver.cpp exec/immersedIons/p3mcalc2.nb exec/immersedIons/particleGen.cpp src_particles/src_F90/particle_functions.F90 commit fb7d62a1dc6f41289f9e189d21da6d6e830087e6 Author: spcarney34 Date: Tue Jun 18 10:57:17 2019 -0700 P3M framework in place (for periodic boundaries and peskin kernel of order 6), just need to implement function to get tabulated correction integral as function of separation distance. src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 0f15ff2012bdb09aab25df0782d6d7e5ade28e81 Author: Johannes Blaschke Date: Mon Jun 17 23:52:13 2019 -0700 working on better way to spread predictor/corrector (old way could get neighbor data confused) src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit d44e7ee57f4ff08bfc70d3648e475dcf1ab9756c Merge: e5bbc430 f1ef73bc Author: Guy Moore Date: Mon Jun 17 17:38:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e5bbc4308dce15c0d29d322db3eb7dcfc505c142 Author: Guy Moore Date: Mon Jun 17 17:38:13 2019 -0700 wrote bash script to correct indexing for nodality exec/compressible/index_shift.sh commit 20f67db94a9aa9f601cb2710391e24078e76bc07 Merge: 5560cb90 f1ef73bc Author: Daniel Ladiges Date: Mon Jun 17 17:24:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5560cb90509dfd843a36ba395b57bc2a76c51452 Author: Daniel Ladiges Date: Mon Jun 17 17:24:17 2019 -0700 Started tabulation of coulomb correction exec/immersedIons/inputs_3d exec/immersedIons/p3mcalc2.nb exec/immersedIons/particleGen.cpp src_particles/src_F90/particle_functions.F90 commit f1ef73bc6495d36176d85579c7c7324cac53d89a Author: Johannes Blaschke Date: Mon Jun 17 16:33:27 2019 -0700 add predictor velocity interpolation to maker predictor velocity fields src_immersed-boundary/IBMarkerContainer.cpp commit 78f2492c57f09e9a7cbf6886a40b2adcdf4cbe31 Author: Johannes Blaschke Date: Mon Jun 17 16:30:17 2019 -0700 should be interpolation to vel, not force src_immersed-boundary/IBMarkerContainer.cpp commit 6e53c9a5c3929e1b61e68ad70544bd568390f963 Author: Johannes Blaschke Date: Mon Jun 17 16:28:03 2019 -0700 add velocity interpolation to maker force fields src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit faaf106bb000153f5ed836fa6e0d6c2bb4fdf8f7 Author: Johannes Blaschke Date: Mon Jun 17 16:10:40 2019 -0700 add predictor force spreading from maker force fields src_immersed-boundary/IBMarkerContainer.cpp commit 43021bf4d8e79eb689ce394fb5d6e5f5c74a2569 Author: Johannes Blaschke Date: Mon Jun 17 16:03:59 2019 -0700 add force spreading from maker force fields src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit c0a06ce93d834931d29d689331e28f02da208edf Author: Johannes Blaschke Date: Mon Jun 17 15:25:00 2019 -0700 fortran marker type needs to match the c++ version src_immersed-boundary/src_F90/ib_fort_utils.F90 commit e1e8e305ea718e221cf174721378b9534d99c174 Merge: 5aae6050 56e27cbf Author: Johannes Blaschke Date: Mon Jun 17 15:19:06 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 5aae60507653269610365fd330499a37452de4e0 Author: Johannes Blaschke Date: Mon Jun 17 15:19:03 2019 -0700 add move predictor/marker exec/immersed_boundary/channel_dumbbell/advance.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 56e27cbf87b10b87f310c845e16d30002de6baaa Author: kevinluna Date: Mon Jun 17 15:10:24 2019 -0700 Full run data files exec/_GL_alt/Umbrella_Full_J_Run/Data.ipynb exec/_GL_alt/Umbrella_Full_J_Run/FE.txt exec/_GL_alt/Umbrella_Full_J_Run/Ploting_script.ipynb exec/_GL_alt/Umbrella_Full_J_Run/Result1.png exec/_GL_alt/Umbrella_Full_J_Run/data/data0.000 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.001 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.002 exec/_GL_alt/Umbrella_Full_J_Run/data/data0.003 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exec/_GL_alt/Umbrella_Full_J_Run/pymbar/exp.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/mbar.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/mbar_solvers.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/old_mbar.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/__init__.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_covariance.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_mbar.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/tests/test_utils.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/__init__.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/gaussian_work.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/testsystems/timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/timeseries.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/utils.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/utils_for_testing.py exec/_GL_alt/Umbrella_Full_J_Run/pymbar/version.py commit 202300e9686f8fcf7c342b7f8dd81d154959e9d7 Merge: e3c94054 d3aa9254 Author: kevinluna Date: Mon Jun 17 15:00:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a7e8993db04cd9ea98a0ed13a619c7742befd742 Author: msantiago2 Date: Mon Jun 17 14:54:03 2019 -0700 working advection diffusion solver linked with FHDeX exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 commit e3c94054c143b3c7228467d8b85dea707cfc8ca5 Author: kevinluna Date: Mon Jun 17 14:52:29 2019 -0700 python scripts for anlysis exec/_GL_alt/Python_Scripts/Data.ipynb exec/_GL_alt/Python_Scripts/Ploting_script.ipynb exec/_GL_alt/Python_Scripts/PltFile2DataFile.py exec/_GL_alt/Python_Scripts/mbar.py exec/_GL_alt/Python_Scripts/pymbar/__init__.py exec/_GL_alt/Python_Scripts/pymbar/bar.py exec/_GL_alt/Python_Scripts/pymbar/confidenceintervals.py exec/_GL_alt/Python_Scripts/pymbar/exp.py exec/_GL_alt/Python_Scripts/pymbar/mbar.py exec/_GL_alt/Python_Scripts/pymbar/mbar_solvers.py exec/_GL_alt/Python_Scripts/pymbar/old_mbar.py exec/_GL_alt/Python_Scripts/pymbar/tests/__init__.py exec/_GL_alt/Python_Scripts/pymbar/tests/test_covariance.py exec/_GL_alt/Python_Scripts/pymbar/tests/test_mbar.py exec/_GL_alt/Python_Scripts/pymbar/tests/test_mbar_solvers.py exec/_GL_alt/Python_Scripts/pymbar/tests/test_timeseries.py exec/_GL_alt/Python_Scripts/pymbar/tests/test_utils.py exec/_GL_alt/Python_Scripts/pymbar/testsystems/__init__.py exec/_GL_alt/Python_Scripts/pymbar/testsystems/exponential_distributions.py exec/_GL_alt/Python_Scripts/pymbar/testsystems/gaussian_work.py exec/_GL_alt/Python_Scripts/pymbar/testsystems/harmonic_oscillators.py exec/_GL_alt/Python_Scripts/pymbar/testsystems/timeseries.py exec/_GL_alt/Python_Scripts/pymbar/timeseries.py exec/_GL_alt/Python_Scripts/pymbar/utils.py exec/_GL_alt/Python_Scripts/pymbar/utils_for_testing.py exec/_GL_alt/Python_Scripts/pymbar/version.py commit bf1ee785b841bdb2428c2ff17eb2aee50db3eacb Merge: af899ef9 d3aa9254 Author: msantiago2 Date: Mon Jun 17 10:10:17 2019 -0700 merge with master commit d3aa9254a9b12cf98a2db9e2914c53eb9bc41893 Author: Johannes Blaschke Date: Sun Jun 16 14:23:29 2019 -0700 blacklist all _H and _D_ (multifab) files .gitignore commit 0317a1177d1499308bca49272f739629cf3af74b Merge: 507b2b02 03b37fab Author: Johannes Blaschke Date: Sun Jun 16 14:16:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 507b2b02bd097582b6d66eea89c072059f8301db Author: Johannes Blaschke Date: Sun Jun 16 14:16:23 2019 -0700 enable communication for extra ib-marker data src_immersed-boundary/IBMarkerContainer.cpp commit 03b37fab1175fce8e0da5469db75b8a461ab3400 Author: spcarney34 Date: Sun Jun 16 12:08:05 2019 -0700 Typo in coulombRadiusFactor fix. src_particles/src_F90/particle_type.F90 commit 16c48f90f0a4d2374c2497e2c72f23c14e743896 Merge: 7c1e9401 1da674ee Author: spcarney34 Date: Sun Jun 16 12:06:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7c1e9401e2ef5007871d73285e00b49a12e5c786 Author: spcarney34 Date: Sun Jun 16 12:06:11 2019 -0700 coulombRadiusFactor exists for particle class--used for short, Coulomb part of P3M method. Currently initializes to sigma from the sr_forces (LJ). Routine for actually computing coulomb interaction for every particle within coulombRadiusFactor also exists. Just need to correctly implement correction force to get P3M online. exec/immersedIons/particleGen.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 010ed7429e53996b608a0ca72d0cd0e43b92db47 Author: Johannes Blaschke Date: Sun Jun 16 11:15:11 2019 -0700 add position predictor to ib marker src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 1da674eec34fdc859d444e59ad146bd60a4a8699 Merge: c18cf1bb 15611b32 Author: Johannes Blaschke Date: Sun Jun 16 00:07:50 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c18cf1bbd0ee3d250eb19f3e78b2f39a6cbdd58b Author: Johannes Blaschke Date: Sun Jun 16 00:07:45 2019 -0700 add diagnostic printing exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 15611b323a65d975c1db285031eb85c4bde2b11d Author: Johannes Blaschke Date: Sat Jun 15 23:52:52 2019 -0700 Update LEGAL LEGAL commit 0547212edeb7532dde13cdacebb2444feb28fad5 Merge: 0ce9b536 9bbc91f5 Author: Johannes Blaschke Date: Sat Jun 15 23:17:26 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0ce9b536144829a4503befda59cc4d0523b1c56e Author: Johannes Blaschke Date: Sat Jun 15 23:16:59 2019 -0700 update fortran marker info data types src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 9bbc91f5d6f9948800d0e9b3f29b228056c0c475 Author: Daniel Ladiges Date: Sat Jun 15 20:28:55 2019 -0700 Added mathematica notebook with correction calc. exec/immersedIons/p3mcalc2.nb commit a9b55cd81480b3920f24f1928a4ac77f88b1f26c Merge: aed37a2e 071f86ca Author: Daniel Ladiges Date: Sat Jun 15 20:28:21 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit aed37a2e7805208e72ad0bae6a302ea396a95489 Author: Daniel Ladiges Date: Sat Jun 15 20:27:21 2019 -0700 More framework for subgrid correction. Fixed charge spreading bug for overlapping kernels. exec/DSMCstatcheck/inputs_3d exec/immersedIons/inputs_3d exec/immersedIons/particleGen.cpp src_particles/src_F90/particle_functions.F90 commit 071f86ca4dbf90befc7d5d0140d5420996f2741e Author: Johannes Blaschke Date: Fri Jun 14 22:49:42 2019 -0700 add fillNeighbors exec/immersed_boundary/channel_dumbbell/advance.cpp commit 184f1b7235305cf216caf6aef07427f9ca413ec8 Author: Johannes Blaschke Date: Fri Jun 14 22:49:15 2019 -0700 add critical pragmas when compiling particle list src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.cpp commit af899ef9612b3167a6d336eeeda6272138c7a58e Author: msantiago2 Date: Fri Jun 14 17:46:01 2019 -0700 did some troubleshooting with initialization, still getting incorrect solutions for AD equation exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/src_F90/Prob.F90 commit 88acaac8c92427aeea2144d868c417b288dcd652 Author: Johannes Blaschke Date: Fri Jun 14 17:41:28 2019 -0700 started working on ib marker example exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/hydro_test_functions.H exec/immersed_boundary/channel_dumbbell/main_driver.cpp src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp commit 23192896ccb8a4b9b6cb2aec8a2d1f3d028b6674 Merge: 05155583 0e679d4a Author: msantiago2 Date: Fri Jun 14 16:27:13 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 0515558365cc375a4fab6257b2be3f7eba0ad1e0 Author: msantiago2 Date: Fri Jun 14 16:25:02 2019 -0700 runs but has bugs that give incorrect solution exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.cpp commit 0e679d4a1ce297d27b6aa539b511659f2b24f12c Author: Johannes Blaschke Date: Fri Jun 14 16:01:32 2019 -0700 fix stupid spelling mistake exec/immersed_boundary/channel_dumbbell/Explore Data.ipynb exec/immersed_boundary/channel_dumbbell/GNUmakefile exec/immersed_boundary/channel_dumbbell/Make.package exec/immersed_boundary/channel_dumbbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbbell/advance.cpp exec/immersed_boundary/channel_dumbbell/compute_convfact_2.sh exec/immersed_boundary/channel_dumbbell/hydro_test_functions.H exec/immersed_boundary/channel_dumbbell/hydro_test_functions_F.H exec/immersed_boundary/channel_dumbbell/init_funcs.F90 exec/immersed_boundary/channel_dumbbell/init_s_funcs.F90 exec/immersed_boundary/channel_dumbbell/inputs_2d exec/immersed_boundary/channel_dumbbell/inputs_3d exec/immersed_boundary/channel_dumbbell/inputs_3d_test exec/immersed_boundary/channel_dumbbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbbell/main_driver.cpp exec/immersed_boundary/channel_dumbbell/run_conv_tests_2.sh commit db651a15f3ccbea5053a7dc487f84e6b97c89ca0 Author: Johannes Blaschke Date: Fri Jun 14 15:27:34 2019 -0700 we got interpolation and spreading now, yay! src_immersed-boundary/IBMarkerContainer.cpp commit 1fadad84d1c5d9bc1daa5c6d0853925e4d016165 Merge: e3b50f79 553eb493 Author: Johannes Blaschke Date: Fri Jun 14 15:17:40 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e3b50f79423f2a96e1c4519d9107b096ff804386 Author: Johannes Blaschke Date: Fri Jun 14 15:17:38 2019 -0700 debugged marker spreading src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 553eb493767dc97595d7c3674a5afb29a17e910e Merge: 38496da8 b20d21e6 Author: Daniel Ladiges Date: Fri Jun 14 14:14:51 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 38496da8e3efb1e226f9db9b0dd58f03ce092f23 Author: Daniel Ladiges Date: Fri Jun 14 14:14:13 2019 -0700 Added DSMC exec deirectory for checking against compressible exec/DSMCstatcheck/GNUmakefile exec/DSMCstatcheck/INS_functions.H exec/DSMCstatcheck/Make.package exec/DSMCstatcheck/Make_precheck.package exec/DSMCstatcheck/TimeStep.cpp exec/DSMCstatcheck/WritePlotFile.cpp exec/DSMCstatcheck/amrex_to_vtp.py exec/DSMCstatcheck/cellvols.F90 exec/DSMCstatcheck/convertSeries exec/DSMCstatcheck/delPlots exec/DSMCstatcheck/inputs_2d exec/DSMCstatcheck/inputs_3d exec/DSMCstatcheck/main_driver.cpp exec/DSMCstatcheck/makeBoth exec/DSMCstatcheck/particleCheck.cpp exec/DSMCstatcheck/particleGen.cpp exec/DSMCstatcheck/precheck.F90 exec/DSMCstatcheck/surfaces.dat exec/DSMCstatcheck/surfaces.nb exec/DSMCstatcheck/write_pview_file.py src_surfaces/surfaces.cpp commit 09d1b415904d8aad84196493cd8b0f02a6024e55 Author: msantiago2 Date: Fri Jun 14 14:12:05 2019 -0700 successfully added chemistry variables to plot files exec/immersed_boundary/channel_soft/WritePlotFile.cpp commit 4dcba295142f83e12562301aefdf35a27c7ffe53 Author: msantiago2 Date: Fri Jun 14 13:13:32 2019 -0700 runs but doesn't add the correct variables to plotfile exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/main_driver.H src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit b20d21e6c33d1da29f3c7a003ed81121a5efd191 Author: Johannes Blaschke Date: Fri Jun 14 10:33:48 2019 -0700 start work on dumbell example exec/immersed_boundary/channel_dumbell/Explore Data.ipynb exec/immersed_boundary/channel_dumbell/GNUmakefile exec/immersed_boundary/channel_dumbell/Make.package exec/immersed_boundary/channel_dumbell/WritePlotFile.cpp exec/immersed_boundary/channel_dumbell/advance.cpp exec/immersed_boundary/channel_dumbell/compute_convfact_2.sh exec/immersed_boundary/channel_dumbell/hydro_test_functions.H exec/immersed_boundary/channel_dumbell/hydro_test_functions_F.H exec/immersed_boundary/channel_dumbell/init_funcs.F90 exec/immersed_boundary/channel_dumbell/init_s_funcs.F90 exec/immersed_boundary/channel_dumbell/inputs_2d exec/immersed_boundary/channel_dumbell/inputs_3d exec/immersed_boundary/channel_dumbell/inputs_3d_test exec/immersed_boundary/channel_dumbell/inputs_3d_test.2 exec/immersed_boundary/channel_dumbell/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_dumbell/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_dumbell/main_driver.cpp exec/immersed_boundary/channel_dumbell/run_conv_tests_2.sh commit 1c183d2448d575063ce3e91d4f78eb0f65807846 Author: Johannes Blaschke Date: Fri Jun 14 10:24:58 2019 -0700 debugging src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBParticleInfo.H commit 2f7b26ea2fc82b52d3bf342f4e748099aa579f75 Merge: 36ed2631 b432d3f1 Author: Johannes Blaschke Date: Fri Jun 14 10:18:24 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 36ed26318cfdacd31a656e94ae33ff67f6d9ba3d Author: Johannes Blaschke Date: Fri Jun 14 10:18:22 2019 -0700 working on generalized IB container src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleInfo.H commit b432d3f1b4b3fae1f797fdd3d5b6d08f7b286694 Merge: d77e3b79 56dd93f1 Author: msantiago2 Date: Fri Jun 14 10:06:39 2019 -0700 Merge branch 'master' of github.com:AMReX-FHD/FHDeX commit 56dd93f1b9be4d106e50f9fb2d8b2dd62bd488a4 Merge: 48224a16 0207dc78 Author: Daniel Ladiges Date: Fri Jun 14 09:59:21 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 48224a16b9c139d65077378154472108b71a657e Author: Daniel Ladiges Date: Fri Jun 14 09:58:12 2019 -0700 More framework for Poisson correction. src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 commit 1f27f98f5c44f7d0078ecf295f165d475f83bc9a Author: Johannes Blaschke Date: Fri Jun 14 09:55:03 2019 -0700 start adding genrealized IB src_immersed-boundary/IBMarkerContainer.H src_immersed-boundary/IBMarkerContainer.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/Make.package commit d50b43b2972ba485be9c25f58ff7fc0b612bebbd Author: Johannes Blaschke Date: Fri Jun 14 09:54:01 2019 -0700 squelch compiler warnings src_chem/src_F90/Make.package commit d77e3b79ba50a9657038ee4c854bb77c0bda7048 Author: msantiago2 Date: Fri Jun 14 09:25:33 2019 -0700 added Con_Grad3d.F90 and Con_Grad_2D.F90 src_chem/src_F90/ConGrad_2d.F90 src_chem/src_F90/ConGrad_3d.F90 commit 0207dc78f11c1167f1bf1201806e53442f3bbc37 Merge: cc5bb4a5 37958e25 Author: msantiago2 Date: Thu Jun 13 18:12:01 2019 -0700 merge with master successful commit cc5bb4a5cc371a27ae284dda5623db993309e334 Author: msantiago2 Date: Thu Jun 13 18:07:03 2019 -0700 Updating plotfiles in progress exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp commit 37958e25ea04649f18764b4777659864e2d26aaf Author: Daniel Ladiges Date: Thu Jun 13 18:03:09 2019 -0700 Passed through all necessary vars to short range correction function exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 2022da99179a9ec16094b51cfc7627fc756ef0b7 Merge: 105c9a70 093ac094 Author: spcarney34 Date: Thu Jun 13 17:08:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 105c9a7032cf33aed31b040db558c86f819125bc Author: spcarney34 Date: Thu Jun 13 17:08:08 2019 -0700 added coulomb radius factor. src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 093ac09434648b93d76caf2227df9b281ea4a239 Merge: 28c204ce a06b747c Author: Daniel Ladiges Date: Thu Jun 13 16:59:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 28c204ce71a3ef1fda8e1c30cb8524a0f9749402 Author: Daniel Ladiges Date: Thu Jun 13 16:58:14 2019 -0700 Added pppm function to nl forces cpp function. Called when es_tog == 3 exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit aafad33d70b0d7b73574b8452c721ec2c15ced3e Author: msantiago2 Date: Thu Jun 13 16:55:36 2019 -0700 added some files I forgot to add last commit src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 73635615da009ce39930d6d87e60b0b8fb043ced Merge: e9ff1ee0 27bb75ee Author: msantiago2 Date: Thu Jun 13 16:53:20 2019 -0700 merge with master and renamed phi to con commit a06b747cadb0caa068e1f1aaf9b476152368e5aa Merge: a4ded8b0 ae9891ff Author: Johannes Blaschke Date: Thu Jun 13 16:48:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a4ded8b0448778408dcd2139b2118678e0c3a277 Author: Johannes Blaschke Date: Thu Jun 13 16:48:42 2019 -0700 work on letting IBParticleContainer track marker velocities and forces exec/immersed_boundary/channel_soft/main_driver.H src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit ae9891ff43a756e5404261b900cb00699c172575 Author: Daniel Ladiges Date: Thu Jun 13 16:34:06 2019 -0700 Now passing charge dist to spread_ions exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit be4d4ab46d1327903b4df550c6c3a0f69185fd3a Merge: 0c65234d 373f6b7f Author: Daniel Ladiges Date: Thu Jun 13 16:20:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0c65234de9899a400f5ff8f7cfcbe288f8cde4a5 Author: Daniel Ladiges Date: Thu Jun 13 16:20:35 2019 -0700 Another conflict fix src_common/common_namespace.H src_common/common_namespace_declarations.H commit 373f6b7fbb153b8b408f67ec7bd6a67c420584f5 Author: SeanPCarney Date: Thu Jun 13 16:08:57 2019 -0700 Added a function to perform calculation of correction force for the P3M method. Needs to be written. src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit e9ff1ee0cff335c96a7cbfadda25729c4e68f65d Author: msantiago2 Date: Thu Jun 13 14:49:05 2019 -0700 code compiles and runs but has errors, no plot files for concentration exec/immersed_boundary/channel_soft/inputs_3d_test src_chem/AmrCoreAdv.cpp src_chem/src_F90/ptsource_fill_3d.F90 commit 27bb75ee4dcfe0cdacac8742e8dcba4e40fb0666 Merge: 51cdf586 bba947a1 Author: Daniel Ladiges Date: Thu Jun 13 13:58:45 2019 -0700 Conflict fix Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 51cdf586ac9ce6564142e13ee59cc19d8986a937 Author: Daniel Ladiges Date: Thu Jun 13 13:56:04 2019 -0700 Started adding inertial option exec/compressible/inputs_3d exec/immersedIons/INS_functions.H exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit cdd1ef93605316af06fd1b439114db93d84e9df4 Merge: 2727ef38 bba947a1 Author: msantiago2 Date: Thu Jun 13 09:57:22 2019 -0700 sucessfully merged with master commit 2727ef38c7362dc60dd872ffa5830349e4a9f981 Author: msantiago2 Date: Thu Jun 13 09:52:07 2019 -0700 Linked advection diffusion to FHDeX solver, compiles but doesn't run exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit f11ac0b5da86a03e45bee8a4da6cb88e442b308a Author: msantiago2 Date: Thu Jun 13 09:50:07 2019 -0700 Linked advection diffusion to FHDeX solver, compiles but doesn't run exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft_chem/Explore Data.ipynb exec/immersed_boundary/channel_soft_chem/GNUmakefile exec/immersed_boundary/channel_soft_chem/Make.package exec/immersed_boundary/channel_soft_chem/Test Sphere Markers.ipynb exec/immersed_boundary/channel_soft_chem/WritePlotFile.cpp exec/immersed_boundary/channel_soft_chem/advance.cpp exec/immersed_boundary/channel_soft_chem/compute_convfact_2.sh exec/immersed_boundary/channel_soft_chem/init_funcs.F90 exec/immersed_boundary/channel_soft_chem/init_s_funcs.F90 exec/immersed_boundary/channel_soft_chem/inputs_2d exec/immersed_boundary/channel_soft_chem/inputs_3d exec/immersed_boundary/channel_soft_chem/inputs_3d_test exec/immersed_boundary/channel_soft_chem/inputs_3d_test.2 exec/immersed_boundary/channel_soft_chem/inputs_3d_test.3 exec/immersed_boundary/channel_soft_chem/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft_chem/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft_chem/main_driver.H exec/immersed_boundary/channel_soft_chem/main_driver.cpp exec/immersed_boundary/channel_soft_chem/main_driver_F.H exec/immersed_boundary/channel_soft_chem/run_conv_tests_2.sh exec/immersed_boundary/channel_soft_chem/sphere_markers.txt src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit bba947a10ee03ac462f9214db7773196c7565b26 Author: Johannes Blaschke Date: Wed Jun 12 19:08:29 2019 -0700 no longer needed exec/immersed_boundary/channel_soft/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 8af81c63c86a442d7445d6f8571d68ed9933f87a Merge: 2035ae13 4725bab0 Author: Johannes Blaschke Date: Wed Jun 12 19:03:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2035ae138c3c46b97942ff192805d426b2a88d62 Author: Johannes Blaschke Date: Wed Jun 12 19:03:17 2019 -0700 getting list of colloids is a common problem => write function to do that exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 8a851be1077721776d2c8ded77d72771a1b56678 Merge: ed2af652 4725bab0 Author: msantiago2 Date: Wed Jun 12 18:58:31 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit ed2af6525534d2f8886694d01305a1e176f2a5f4 Author: msantiago2 Date: Wed Jun 12 18:56:54 2019 -0700 velocity linked to advection diffusion, issue with copy function in EvolveChem.cpp exec/immersed_boundary/channel_soft/advance.cpp src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp commit 4725bab0baa7b80c6d6b6798c6b256bcfaef2dee Author: Guy Moore Date: Wed Jun 12 18:39:21 2019 -0700 Cleaned up flux functions exec/compressible/inputs_3d src_compressible/src_F90/flux_funcs.F90 commit 10a18e1c2fb1c73bbc23e9dae9f41c6227edf018 Merge: 0fee06ef 698c3ab3 Author: Guy Moore Date: Wed Jun 12 17:17:53 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0fee06ef67ccc4e8b3c6d5f022638b83f6c60e13 Author: Guy Moore Date: Wed Jun 12 17:17:49 2019 -0700 Added toggle between diffusion and stochastic tensor forms as visc_type exec/compressible/inputs_2d exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 698c3ab35bd3210b684b37cdd8bdc00b534a94d3 Author: jbb Date: Wed Jun 12 16:07:01 2019 -0700 tweaked notebook and set up new inputs file exec/_GL_alt/Data.ipynb exec/_GL_alt/inputs_2d_new commit b52d1465b23463f35b0aeeccf17f0c96b74efb29 Merge: c286d1d8 97deec3f Author: SeanPCarney Date: Wed Jun 12 14:31:25 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX - commit 93711714358f73f21496667d590a880a9e7a538b Author: msantiago2 Date: Wed Jun 12 14:22:32 2019 -0700 access tagged interface cells in advance.cpp exec/immersed_boundary/channel_soft/advance.cpp src_immersed-boundary/IBCore.H commit 87467e62d1bd055bf064dc663c4ebe36510afa15 Merge: a3f48e9c 97deec3f Author: msantiago2 Date: Wed Jun 12 13:41:08 2019 -0700 Merge branch 'master' into mks/chemistry commit 97deec3f832115288a44c4d1ab1725dabaac1ce4 Author: Guy Moore Date: Wed Jun 12 13:15:55 2019 -0700 Generalized FFT shift for single cell deep exec/compressible/inputs_2d exec/compressible/main_driver.cpp src_analysis/src_F90/struct_fact.F90 src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit c286d1d8263cbafcb38a79ce7d4aa76be518ac0e Author: SeanPCarney Date: Wed Jun 12 11:52:13 2019 -0700 Potential for each particle now initialized to zero (previously was unspecified). exec/immersedIons/particleGen.cpp commit a3f48e9c9d559ba5645fddb314f3dc4fee5c4c2c Author: msantiago2 Date: Wed Jun 12 11:24:30 2019 -0700 passing AmrCoreAdv through advance successfully exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp commit 3a1fbbee4f866324a77d65ab279f18584d3ed0dd Author: msantiago2 Date: Wed Jun 12 11:09:33 2019 -0700 added necessary parameters for chemistry src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit e4bdc15b82a3563fa824d983b192d5341baf2e05 Author: Johannes Blaschke Date: Wed Jun 12 08:46:29 2019 -0700 forgot to update immersed-boundary forces after advance, my bad! exec/immersed_boundary/channel_soft/advance.cpp commit 3cf8f294d525a50ae64dd52ffa142ac4c6d5724a Author: Johannes Blaschke Date: Tue Jun 11 23:51:28 2019 -0700 fix instability in soft IB algorithm exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp commit 767a09636bd7beb383caca5b3df36da6f8f5b79a Merge: 339654f1 40a77f71 Author: Johannes Blaschke Date: Tue Jun 11 23:32:58 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 339654f11b25ca1fcc137448b10122b995aaef4c Author: Johannes Blaschke Date: Tue Jun 11 23:32:53 2019 -0700 replace cumbersome notation exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp commit 2558531b29441a09c3561b0863612e0f319bd843 Author: msantiago2 Date: Tue Jun 11 18:36:29 2019 -0700 added one parameter for chemistry exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 40a77f7116e762d95973bdc26ac0807b68369bdb Merge: 0b2a7edc ca51e999 Author: msantiago2 Date: Tue Jun 11 17:39:03 2019 -0700 fixed mistake commit ca51e9992d0a62bbd396389f81430a17d650e903 Author: msantiago2 Date: Tue Jun 11 17:29:30 2019 -0700 additions to channel soft, broken will fix exec/immersed_boundary/channel_soft/main_driver.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 0b2a7edc4aaa0006caa8c5dd12c480cff52c51ab Merge: d9d1656b 62863aee Author: msantiago2 Date: Tue Jun 11 17:11:06 2019 -0700 merge with master r' into mks/chemistry # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit d9d1656b33093aeea7e036572923b4f46f6e5837 Author: msantiago2 Date: Tue Jun 11 17:06:12 2019 -0700 initalize chemistry in main_driver.cpp exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/channel_soft/inputs_3d exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/main_driver.cpp src_chem/AmrCoreAdv.cpp commit 62863aee104c6c9f2f67674618844bec8839da1d Author: Guy Moore Date: Tue Jun 11 16:26:05 2019 -0700 Corrected membrane BC fix for non-periodic exec/compressible/main_driver.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/timeStep.cpp commit 1b5c7c1512e42d1d0458f7793abc9aa415ea7368 Author: Guy Moore Date: Tue Jun 11 16:11:19 2019 -0700 corrected flux BC src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit 432683ef86d0f9eeec976a6cdcbdebd4c37a9634 Merge: 9f21939b 6e576872 Author: Johannes Blaschke Date: Tue Jun 11 15:15:23 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9f21939b884e4e0ba45708a417c885012a76b941 Author: Johannes Blaschke Date: Tue Jun 11 15:15:07 2019 -0700 single step in advance exec/immersed_boundary/channel_soft/advance.cpp commit 6e5768726b3bf88012e52e85fbd092744a7c3557 Merge: 75ceb5ca 9655659a Author: msantiago2 Date: Tue Jun 11 14:56:02 2019 -0700 merge with mks/chemistry y' # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. commit 9655659a575bfbadf2fd4bcf862a531c4dde2d34 Author: msantiago2 Date: Tue Jun 11 14:53:30 2019 -0700 fixed with alot of help, now compiles src_chem/AmrCoreAdv.cpp src_chem/src_F90/Adv_2d.F90 src_chem/src_F90/Adv_3d.F90 src_chem/src_F90/Make.package src_chem/src_F90/Make.package~ src_chem/src_F90/PhiGrad_2d.F90 src_chem/src_F90/PhiGrad_3d.F90 src_chem/src_F90/Prob.F90 src_chem/src_F90/Tagging_nd.F90 src_chem/src_F90/bc_fill_nd.F90 src_chem/src_F90/compute_flux_2d.F90 src_chem/src_F90/compute_flux_3d.F90 src_chem/src_F90/ptsource_fill_2d.F90 src_chem/src_F90/ptsource_fill_3d.F90 src_chem/src_F90/slope_2d.F90 src_chem/src_F90/slope_3d.F90 commit 75ceb5ca30f181c0664213c08ce265aef0c32db5 Author: Guy Moore Date: Tue Jun 11 14:03:01 2019 -0700 Fixed membrane boundary issue exec/compressible/inputs_2d exec/compressible/main_driver.cpp src_common/MultiFABFillRandom.cpp src_compressible/timeStep.cpp commit c4205271768484a58c53aa6c88d208d4030475d3 Merge: 9c1da438 8644ca68 Author: msantiago2 Date: Tue Jun 11 13:21:58 2019 -0700 Merge branch 'mks/chemistry' commit 8644ca68a8672ad3d3f6f57ede54f04b06ed9935 Author: msantiago2 Date: Tue Jun 11 13:16:48 2019 -0700 commit update still won't compile exec/immersed_boundary/channel_soft_chem/GNUmakefile src_chem/Adv_2d.F90 src_chem/Adv_3d.F90 src_chem/AmrCoreAdv_F.H src_chem/Make.package src_chem/PhiGrad_2d.F90 src_chem/PhiGrad_3d.F90 src_chem/Prob.F90 src_chem/Tagging_nd.F90 src_chem/bc_fill_nd.F90 src_chem/compute_flux_2d.F90 src_chem/compute_flux_3d.F90 src_chem/ptsource_fill_2d.F90 src_chem/ptsource_fill_3d.F90 src_chem/slope_2d.F90 src_chem/slope_3d.F90 commit 9c1da438b35fe5c91f8ea880eeba7055fb18824a Merge: 65f98480 a1ef0d6a Author: Guy Moore Date: Tue Jun 11 11:09:48 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 65f98480d39b17574bf87a58073d20c5adb9db04 Author: Guy Moore Date: Tue Jun 11 11:09:44 2019 -0700 found minor fix, still debugging periodic case exec/compressible/inputs_2d exec/compressible/main_driver.cpp src_common/MultiFABFillRandom.cpp src_common/src_F90/multifab_fill_random.F90 src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit a1ef0d6a3140ca14ec3bcae3391d924e706f36c6 Merge: 849c8719 de53ae8d Author: msantiago2 Date: Mon Jun 10 18:04:37 2019 -0700 Merge branch 'master' into mks/chemistry commit de53ae8d54204ef3484bf9ac29def49e520dc839 Author: Guy Moore Date: Mon Jun 10 18:04:31 2019 -0700 Temp gradient test now appears to be working in x & y exec/compressible/inputs_2d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_analysis/src_F90/struct_fact.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/trans_funcs.F90 commit 849c8719aca80732e77ddd71585283e48cd88b2d Author: msantiago2 Date: Mon Jun 10 18:01:01 2019 -0700 added make files for chemistry, doesn't compile exec/immersed_boundary/channel_soft_chem/Explore Data.ipynb exec/immersed_boundary/channel_soft_chem/GNUmakefile exec/immersed_boundary/channel_soft_chem/Make.package exec/immersed_boundary/channel_soft_chem/Test Sphere Markers.ipynb exec/immersed_boundary/channel_soft_chem/WritePlotFile.cpp exec/immersed_boundary/channel_soft_chem/advance.cpp exec/immersed_boundary/channel_soft_chem/compute_convfact_2.sh exec/immersed_boundary/channel_soft_chem/init_funcs.F90 exec/immersed_boundary/channel_soft_chem/init_s_funcs.F90 exec/immersed_boundary/channel_soft_chem/inputs_2d exec/immersed_boundary/channel_soft_chem/inputs_3d exec/immersed_boundary/channel_soft_chem/inputs_3d_test exec/immersed_boundary/channel_soft_chem/inputs_3d_test.2 exec/immersed_boundary/channel_soft_chem/inputs_3d_test.3 exec/immersed_boundary/channel_soft_chem/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft_chem/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft_chem/main_driver.H exec/immersed_boundary/channel_soft_chem/main_driver.cpp exec/immersed_boundary/channel_soft_chem/main_driver_F.H exec/immersed_boundary/channel_soft_chem/run_conv_tests_2.sh exec/immersed_boundary/channel_soft_chem/sphere_markers.txt src_chem/Adv_2d.F90 src_chem/Adv_3d.F90 src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/Make.package src_chem/PhiGrad_2d.F90 src_chem/PhiGrad_3d.F90 src_chem/Prob.F90 src_chem/Tagging_nd.F90 src_chem/compute_flux_2d.F90 src_chem/compute_flux_3d.F90 src_chem/face_velocity_2d.f90 src_chem/face_velocity_3d.f90 src_chem/ptsource_fill_2d.F90 src_chem/ptsource_fill_3d.F90 src_chem/slope_2d.F90 src_chem/slope_3d.F90 commit f5abd2f0efb411ff7544e4a448c52eaedf123d52 Merge: cbd7b798 9981936d Author: Johannes Blaschke Date: Mon Jun 10 17:55:12 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit cbd7b798a381ce4b0307b6b6986bbc155efc5843 Author: Johannes Blaschke Date: Mon Jun 10 17:55:09 2019 -0700 cleanup soft immersed boundary exec/immersed_boundary/channel_soft/advance.cpp commit fee1b15cec6a3e86d7b8b1ab64de2578e131272f Merge: 6f9b0aac 9981936d Author: kevinluna Date: Mon Jun 10 15:02:57 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9981936dd02f608a13bc4313d2db00e0cc304013 Merge: e2b9bb0a 3b241254 Author: kklymko Date: Mon Jun 10 14:27:14 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e2b9bb0a2340c161bc0aabc1df2a061a152fb045 Author: kklymko Date: Mon Jun 10 14:27:07 2019 -0700 made mbar read files more easily exec/_GL_alt/mbar.py commit 3b241254cea3b04e774b744c5165cf4620ae66ba Author: msantiago2 Date: Mon Jun 10 13:47:22 2019 -0700 add colloid chemistry src_chem/Adv_2d.f90 src_chem/Adv_3d.f90 src_chem/AmrCoreAdv.H src_chem/AmrCoreAdv.cpp src_chem/AmrCoreAdv_F.H src_chem/CMakeLists.txt src_chem/Make.package src_chem/PhiGrad_2d.f90 src_chem/PhiGrad_3d.f90 src_chem/Prob.f90 src_chem/README src_chem/Tagging_nd.f90 src_chem/bc_fill_nd.F90 src_chem/compute_flux_2d.f90 src_chem/compute_flux_3d.f90 src_chem/face_velocity_2d.f90 src_chem/face_velocity_3d.f90 src_chem/main.cpp src_chem/ptsource_fill_2d.f90 src_chem/ptsource_fill_3d.f90 src_chem/slope_2d.f90 src_chem/slope_3d.f90 commit 6f9b0aac778f3b66f3a6ef9999352efe7a2c8155 Author: kevinluna Date: Mon Jun 10 13:29:13 2019 -0700 input file exec/_GL_alt/inputs_2d commit 830b7462511b509417e7f1cd21812eef33b0b897 Author: Johannes Blaschke Date: Sun Jun 9 22:26:07 2019 -0700 yay, soft immersed boundaries are converging fast enough exec/immersed_boundary/channel_soft/advance.cpp commit afb0701f7407cfde6558328497eae3cdb3fe62dd Author: Johannes Blaschke Date: Sun Jun 9 22:00:46 2019 -0700 wip on soft immersed boundaries exec/immersed_boundary/channel_soft/advance.cpp commit d2b1861f3356bfbef277735db9f74c74c3d5858b Author: Johannes Blaschke Date: Sat Jun 8 23:16:59 2019 -0700 compute soft ibm particle forces in predictor exec/immersed_boundary/channel_soft/advance.cpp src_immersed-boundary/IBGMRES.cpp commit 6fe131b0e8dc75dd87810b10a484b52f86935a9c Author: Johannes Blaschke Date: Sat Jun 8 22:31:53 2019 -0700 soft immersed boundary does not need IBGMRES exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/inputs_3d_test commit 63681fd9315dd639f217aaf2e6ee238deec7a006 Author: Johannes Blaschke Date: Sat Jun 8 22:02:27 2019 -0700 strip out debug code from rigid ibm code exec/immersed_boundary/channel_soft/main_driver.cpp commit b4234419da8dd2e1cd8d8325880878b835e8332d Author: Johannes Blaschke Date: Sat Jun 8 19:19:00 2019 -0700 begin working on soft particles: based on channel_hard exec/immersed_boundary/channel_soft/Explore Data.ipynb exec/immersed_boundary/channel_soft/GNUmakefile exec/immersed_boundary/channel_soft/Make.package exec/immersed_boundary/channel_soft/Test Sphere Markers.ipynb exec/immersed_boundary/channel_soft/WritePlotFile.cpp exec/immersed_boundary/channel_soft/advance.cpp exec/immersed_boundary/channel_soft/compute_convfact_2.sh exec/immersed_boundary/channel_soft/init_funcs.F90 exec/immersed_boundary/channel_soft/init_s_funcs.F90 exec/immersed_boundary/channel_soft/inputs_2d exec/immersed_boundary/channel_soft/inputs_3d exec/immersed_boundary/channel_soft/inputs_3d_test exec/immersed_boundary/channel_soft/inputs_3d_test.2 exec/immersed_boundary/channel_soft/inputs_3d_test.3 exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_soft/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_soft/main_driver.H exec/immersed_boundary/channel_soft/main_driver.cpp exec/immersed_boundary/channel_soft/main_driver_F.H exec/immersed_boundary/channel_soft/run_conv_tests_2.sh exec/immersed_boundary/channel_soft/sphere_markers.txt commit 504123aac0b9b0e1ccf55ff35faec4912fe03087 Author: Johannes Blaschke Date: Sat Jun 8 17:10:47 2019 -0700 create a seperate immersed_boundary subdirectory in the exe folder exec/channel_ibm/GNUmakefile exec/immersed_boundary/channel_rigid/Explore Data.ipynb exec/immersed_boundary/channel_rigid/GNUmakefile exec/immersed_boundary/channel_rigid/Make.package exec/immersed_boundary/channel_rigid/Test Sphere Markers.ipynb exec/immersed_boundary/channel_rigid/WritePlotFile.cpp exec/immersed_boundary/channel_rigid/advance.cpp exec/immersed_boundary/channel_rigid/compute_convfact_2.sh exec/immersed_boundary/channel_rigid/init_funcs.F90 exec/immersed_boundary/channel_rigid/init_s_funcs.F90 exec/immersed_boundary/channel_rigid/inputs_2d exec/immersed_boundary/channel_rigid/inputs_3d exec/immersed_boundary/channel_rigid/inputs_3d_test exec/immersed_boundary/channel_rigid/inputs_3d_test.2 exec/immersed_boundary/channel_rigid/inputs_3d_test.3 exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_2d exec/immersed_boundary/channel_rigid/inputs_incomp_equil_fluct_3d exec/immersed_boundary/channel_rigid/main_driver.H exec/immersed_boundary/channel_rigid/main_driver.cpp exec/immersed_boundary/channel_rigid/main_driver_F.H exec/immersed_boundary/channel_rigid/run_conv_tests_2.sh exec/immersed_boundary/channel_rigid/sphere_markers.txt commit 9aad192813b614c898b932026dccaca8c433c45f Merge: 36b21517 bf370eed Author: Johannes Blaschke Date: Sat Jun 8 16:57:02 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 36b21517fa4612481ce8727586ea594fe7bc4971 Author: Johannes Blaschke Date: Sat Jun 8 16:56:52 2019 -0700 work on finding proper inverse to J operator exec/channel_ibm/inputs_3d_test exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit bf370eedffa4df9ee4ff3c14c14b31837309b546 Merge: 3345b602 921edfbd Author: Guy Moore Date: Fri Jun 7 19:04:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3345b602e76a7ebd84fac969b43ee14948f27675 Author: Guy Moore Date: Fri Jun 7 19:04:14 2019 -0700 Added more debugging tools - initialize conserved variables exec/compressible/Make.package exec/compressible/compressible_test_functions_F.H exec/compressible/init_consvar.F90 exec/compressible/inputs_2d exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/src_F90/flux_funcs.F90 commit 921edfbd33ae2d2b6a23157b3f14c65866f2522c Author: alballow Date: Fri Jun 7 16:43:47 2019 -0700 Added momentum clculation on surface src_surfaces/src_F90/surface_functions.F90 commit d5b1750a917a503b49d00df39109cde15295a5ce Merge: bf8895e9 e1a9676d Author: alballow Date: Fri Jun 7 14:42:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bf8895e9708a401ca33f1d3a9f459661e5178962 Author: alballow Date: Fri Jun 7 14:41:15 2019 -0700 Added subroutine to call previous commit src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit e1a9676d04c1108bff73ec9523638d7b7f06457a Merge: 2758f8d1 83a97ac1 Author: Daniel Ladiges Date: Fri Jun 7 14:21:47 2019 -0700 Trying to fix conflict... Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2758f8d1de038a3d48b5afa6cbe7c49332edc614 Author: Daniel Ladiges Date: Fri Jun 7 14:19:53 2019 -0700 Fixed git tracking mixup. exec/DSMC/amrex_to_vtp.py exec/DSMC/convertSeries exec/DSMC/write_pview_file.py exec/DSMC/write_pview_file.pyc commit c87c655ae06a1532a6780d52f0f55a75f294eaf0 Author: Daniel Ladiges Date: Fri Jun 7 14:18:14 2019 -0700 Added some parameters to surface type for use in DSMC src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H commit 18bdef26473cbc33a6b297db2a058c6aa3cd54bf Author: alballow Date: Fri Jun 7 14:13:51 2019 -0700 Print those particles that hit the top and bottom boundary of the cylinder and their coordinates exec/DSMC/GNUmakefile src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 83a97ac12f1e95ac0556c4165095ef83af988ac8 Author: KKlymko Date: Fri Jun 7 12:14:50 2019 -0700 clarified some of the inputs in the analysis exec/_GL_alt/Data.ipynb commit db627d1a6b5f6f284ebd4d6bf7715367d4c263bc Author: Guy Moore Date: Thu Jun 6 17:01:00 2019 -0700 Structure factor class included - ready for testing! exec/compressible/GNUmakefile exec/compressible/inputs_3d exec/compressible/main_driver.cpp commit 4888e28b1bda3ce282adbafb9eb9ac49b080a029 Author: Guy Moore Date: Thu Jun 6 11:48:13 2019 -0700 Code appears to compile & run in 3D exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_common/Make.package src_common/MultiFABFillRandom.cpp src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 commit dccce8f7c4f80199c469351c1ed376a4295d6330 Merge: 77497808 061456e7 Author: alballow Date: Wed Jun 5 16:45:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 061456e7e9da6cc64efbc5453cd0e4ef7a32556c Merge: d45dee8f 687d64bb Author: Guy Moore Date: Wed Jun 5 16:35:14 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d45dee8fe2419f978c7bcc6ddd19d89876cd2dc0 Author: Guy Moore Date: Wed Jun 5 16:33:21 2019 -0700 uncommented 3D flux funcs src_compressible/src_F90/flux_funcs.F90 commit 687d64bbc4fa2d4640c9df7f41e39b24fd4e7582 Author: Daniel Ladiges Date: Wed Jun 5 16:08:38 2019 -0700 Setup some demo settings for DSMC exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp src_particles/src_F90/collision_functions.F90 commit 350a73ad86a5d4bbf58a387bb376bfb5b38f1d11 Author: Daniel Ladiges Date: Wed Jun 5 15:03:36 2019 -0700 Added some particle utilities to DSMC exec/DSMC/GNUmakefile exec/DSMC/amrex_to_vtp.py exec/DSMC/convertSeries exec/DSMC/inputs_3d exec/DSMC/write_pview_file.py exec/DSMC/write_pview_file.pyc commit 75976af5096710905bf50e648a8f6b35c9ff8424 Merge: d40f18e3 aeee9e99 Author: Daniel Ladiges Date: Wed Jun 5 14:45:38 2019 -0700 Fixed conflict in makefile Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d40f18e32286a2378040721bf3d457ebf4b5beab Author: Daniel Ladiges Date: Wed Jun 5 14:36:40 2019 -0700 Various exec/DSMC/surfaces.nb exec/compressible/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/particleGen.cpp exec/immersedIons/properties.nb src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 885f9183ab595483a4807d33acb21a3b1d68e007 Author: Daniel Ladiges Date: Wed Jun 5 14:35:02 2019 -0700 Now tracking delPlots exec/DSMC/delPlots commit aeee9e992ea4e1232eb8f1bc527618068a81f298 Author: Guy Moore Date: Wed Jun 5 10:32:44 2019 -0700 First commit of 3D compressible + made new branch for 1D exec/compressible/main_driver.cpp src_compressible/src_F90/trans_funcs.F90 src_compressible/transCoeffs.cpp commit 7749780891b4898add54bf84dd9468f2a632e640 Author: alballow Date: Tue Jun 4 15:44:07 2019 -0700 commited LEGAL commit 114b11695157bfc279d6c5484b4bf14788060db7 Author: Guy Moore Date: Mon Jun 3 18:45:34 2019 -0700 Code compiles and runs - debugging for 3D exec/compressible/GNUmakefile exec/compressible/inputs_1d exec/compressible/inputs_3d commit 3c81ffc3f7f284cc5502d71ece369ca79222e7d0 Author: Johannes Blaschke Date: Fri May 31 17:55:28 2019 -0700 add inverse interpolation/spreading operators src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit b8090d9861d43e3ed047eecd237aa411195f73ed Author: Johannes Blaschke Date: Fri May 31 16:49:12 2019 -0700 messing about with speeding up preconditioner exec/channel_ibm/inputs_3d_test exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp commit 08c04b4a9018a0164fb9a0b286d35d576376f43e Author: Johannes Blaschke Date: Fri May 31 15:47:36 2019 -0700 I was trying to fill too many cells src_immersed-boundary/src_F90/ib_fort_utils.F90 commit b6d2d93ec4a5fb2ee4b57b86ad0dc4844d155a43 Merge: 9517e388 61dc283f Author: Johannes Blaschke Date: Wed May 29 22:43:15 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9517e3887588242846307cc8f54e9f56eaec3580 Author: Johannes Blaschke Date: Wed May 29 22:43:11 2019 -0700 we might have convergences... yay! exec/channel_ibm/inputs_3d_test exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp commit 61dc283fdaec059173d866d83ed357ac34b0f0b4 Merge: 714c1f0e 27f5311b Author: kklymko Date: Wed May 29 13:49:40 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 714c1f0eba7e22a91ef25f09fef246b9676a739e Author: kklymko Date: Wed May 29 13:49:30 2019 -0700 more MBAR exec/_GL_alt/mymbar commit 27f5311b3976893892c383979945a8d661d1bb55 Merge: 8fb2173d 12b72bc5 Author: Johannes Blaschke Date: Tue May 28 15:50:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8fb2173d67e1f4bb9c595635500ca42c4f486a94 Author: Johannes Blaschke Date: Tue May 28 15:50:14 2019 -0700 immersed-boundary inner products need to be mpi-compatible src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 12b72bc5c1b48ea58bd8d9f9898310c229dd4ae2 Author: kklymko Date: Tue May 28 13:35:47 2019 -0700 reconstruction files exec/_GL_alt/mbar.py commit d0e2a422556f1a3de21c555eef541fa850814723 Author: Johannes Blaschke Date: Mon May 27 14:51:27 2019 -0700 apply scaling to IBM operator exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBGMRES.cpp commit 1d8047e9b4e7549263b6e6dbdb09d3211f5efc77 Author: Johannes Blaschke Date: Sat May 25 18:31:34 2019 -0700 use parallel reduce to make sure all cores have the same result on all ranks exec/channel_ibm/inputs_3d_test src_gmres/ApplyMatrix.cpp src_immersed-boundary/IBGMRES.cpp commit fd1e3cd1b194e55daf174dc3e8e71ae2c89b5340 Author: Johannes Blaschke Date: Sat May 25 14:56:26 2019 -0700 add scaling exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBGMRES.cpp commit 4acafdf3262c1d42d669dadc2dae903ba0f5ab1a Author: Johannes Blaschke Date: Fri May 24 12:46:52 2019 -0700 work on v convergence rate in IBGMRES exec/channel_ibm/inputs_3d_test exec/channel_ibm/inputs_3d_test.3 exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp commit dc79304d42a85539294bf4c1b0fe0354b92cd46b Author: Johannes Blaschke Date: Thu May 23 21:04:05 2019 -0700 who would have thought that only itterating over the relevant cells will speed things up exec/channel/inputs_3d_test exec/channel_ibm/advance.cpp exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 63fe00465d87515012baa6cc231a42f0d95eb0fc Author: Johannes Blaschke Date: Thu May 23 14:25:52 2019 -0700 clear pervious marker forces in precon exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.cpp commit 36558b9e6cedae2bd81ca460d82d801f094360c5 Merge: 34c5d3b5 18aee18b Author: Johannes Blaschke Date: Wed May 22 14:39:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 34c5d3b5c85cd367fcf25086bca5a170ab39e527 Author: Johannes Blaschke Date: Wed May 22 14:39:32 2019 -0700 create non double-counting interpolating function <= Debugging preconditioner exec/channel_ibm/inputs_3d_test exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 18aee18bf45aeb7a99576a17ea0e11bd3f817ded Author: Daniel Ladiges Date: Wed May 22 13:21:13 2019 -0700 Tested cell vol calc and added cell volumes to output in DSMC exec/DSMC/INS_functions.H exec/DSMC/cellvols.F90 exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp commit 9e2699b31df5cef4f07400fcd2dbffc6357ab35e Author: Daniel Ladiges Date: Wed May 22 12:49:46 2019 -0700 Added cell volume calculation. Untested. exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/WritePlotFile.cpp exec/DSMC/cellvols.F90 exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.dat exec/DSMC/surfaces.nb commit 963d4bd4c64270502bbacb07aa3bcade1ac9a15c Author: Daniel Ladiges Date: Tue May 21 19:26:20 2019 -0700 More internal geometry code, and fixed bug where domain origin had to be at 0,0,0 exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/particleGen.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.dat exec/DSMC/surfaces.nb src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit 1acf08c4135ef0e0afe8a2ec0d346ab38747275f Author: Daniel Ladiges Date: Tue May 21 15:07:55 2019 -0700 Updates for immersedIons and DSMC to work with new particle gen procedure. exec/DSMC/particleGen.cpp exec/immersedIons/Make.package exec/immersedIons/particleGen.cpp commit 05ca0a4033b46e88d7b6078e8e0d97c9037f5369 Author: Daniel Ladiges Date: Tue May 21 14:51:55 2019 -0700 Moved FhdParticleContainer::InitParticles into file local to exec/... Updated one line in response to WQ's Slack message. exec/DSMC/Make.package exec/DSMC/surfaces.dat src_hydro/MacProj_hydro.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit 5f6a0e52fbaca189c82e0dcfd066d174646d7895 Author: Daniel Ladiges Date: Mon May 20 18:28:00 2019 -0700 Finished updating DSMC to incorporate changes for immersed particles. Started adding setup for managing geometry. exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_surfaces/surfaces.cpp commit 598d0471802a2cde9227c2566005725707ce4c2e Author: Daniel Ladiges Date: Mon May 20 16:13:48 2019 -0700 Domain diffuse BC now pulls temperature from input file. exec/DSMC/main_driver.cpp src_surfaces/surfaces.cpp commit 3eed5efd6840fa0cd64818a5fd3c32f8d65211cd Author: Daniel Ladiges Date: Mon May 20 16:05:24 2019 -0700 Moved surface definitions into src_surfaces exec/DSMC/GNUmakefile exec/DSMC/Make_surface.package exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp exec/immersedIons/GNUmakefile exec/immersedIons/Make_surface.package exec/immersedIons/surfaces.cpp src_surfaces/Make.package src_surfaces/surfaces.cpp commit 34377f4a9880f78e5e755d101c481b3f96e7de21 Merge: 874454c6 c5411be3 Author: Daniel Ladiges Date: Mon May 20 15:33:34 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 874454c69da340d85c4c34a8de98f6dcc78e83b5 Author: Daniel Ladiges Date: Mon May 20 15:32:04 2019 -0700 Started bringing DSMC up to date with changes to immersedIons. Started adding functionality for graphene resonator problem. exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/surfaces.nb exec/immersedIons/inputs_3d exec/immersedIons/properties.nb src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 1b8cd8cab514b40acddbd4736b8da427dc3f546d Author: Johannes Blaschke Date: Sat May 18 20:35:33 2019 -0700 fix fill boundary src_immersed-boundary/IBGMRES.cpp commit c5411be3231e633e8a0838700d72f8f54a0d3718 Author: Johannes Blaschke Date: Fri May 17 17:48:24 2019 -0700 update IB-lambda solution src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit e93afdc1398314327a3c6639549c4b47edcc0ef9 Author: Johannes Blaschke Date: Fri May 17 17:10:06 2019 -0700 update krylov space src_immersed-boundary/IBGMRES.cpp commit f70680bb6a065a85a3f7dc0004c8edfa8f5bfdcb Merge: f8c175d6 446cd00d Author: Johannes Blaschke Date: Fri May 17 16:58:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f8c175d6ecaaac541458d9fbe453f321940eb844 Author: Johannes Blaschke Date: Fri May 17 16:58:01 2019 -0700 add ib markers to hessenberger matrix src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit a753abd3aabf0ef523345d74321c8669ae720a1f Author: Johannes Blaschke Date: Fri May 17 16:35:50 2019 -0700 start working on IBM hessenberg matrix src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 446cd00d511e00da329ab7a48df6e4739ed6dc3b Merge: a0da3b87 a737592a Author: Daniel Ladiges Date: Fri May 17 15:36:08 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a0da3b87813210c068020ac6eff25a9cbaa0c9c4 Author: Daniel Ladiges Date: Fri May 17 15:35:44 2019 -0700 Added framework for analysing potential energy exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit b9b45a3f52539a03b0646adb74429ed480fdee38 Author: Johannes Blaschke Date: Fri May 17 15:34:26 2019 -0700 add ib marker krylov vector src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit a8f3f3a4e4f2a02022364d0c118371e9fea6cd1e Merge: 34de81cd a737592a Author: Johannes Blaschke Date: Fri May 17 14:27:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 34de81cd8a088b5c2b22cf47853a134cf2540229 Author: Johannes Blaschke Date: Fri May 17 14:27:39 2019 -0700 fix handling of ib marker quantities src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit a737592ac75afcf125fba838a3411f4af79653ca Merge: 0d256dcb 773a0874 Author: KKlymko Date: Fri May 17 11:36:50 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0d256dcb711c3154f4701300806b02b430db046f Author: KKlymko Date: Fri May 17 11:36:36 2019 -0700 analysis and some modifications exec/_GL_alt/Data.ipynb exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp commit ad20bad0ccab8a3863e070ee4870dc06f30ba74b Author: Johannes Blaschke Date: Thu May 16 18:06:25 2019 -0700 compute lambda and w norms src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 773a0874d41c31880a10f97178243b828824b755 Merge: a03f9417 ad20bad0 Author: Daniel Ladiges Date: Thu May 16 18:05:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a03f94175f41c9db213e9e35e5867dd2832b2416 Author: Daniel Ladiges Date: Thu May 16 18:04:35 2019 -0700 Unit debug. Now getting correct zero concentration limit conductivity. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit aae8b55553e7a236d91e4600c7e2b0121eaba4b2 Author: Johannes Blaschke Date: Thu May 16 16:58:33 2019 -0700 add function to compute tmp_lambda src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit d7d2b0a552fbb6c7378b4fe3a642925ca82ed417 Author: Johannes Blaschke Date: Thu May 16 16:47:18 2019 -0700 create the IBM equivalent of `ApplyMatrix` src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit f9908ac7b23623f57496f6a8d91ee21adb63f280 Author: Johannes Blaschke Date: Thu May 16 15:49:04 2019 -0700 add IB apply op src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit f6d6c29ea1a9a59c9638f762d76dad44a1f320b1 Author: Johannes Blaschke Date: Thu May 16 13:03:03 2019 -0700 remove debug output exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp commit 901ebd4974351d3f05d1a9f034b27604e3da73fb Author: Johannes Blaschke Date: Thu May 16 12:49:54 2019 -0700 fix sign error src_immersed-boundary/IBGMRES.cpp commit ebf580d4e516260431edd12f59aa742712317703 Author: Johannes Blaschke Date: Thu May 16 12:47:52 2019 -0700 use std::map::at instead of std::map::operator for non-initizing access src_immersed-boundary/IBGMRES.cpp commit b4e86e8ade726af6c44a4070c3abb7b070cbd9b9 Author: Johannes Blaschke Date: Thu May 16 12:30:21 2019 -0700 remove broken code src_immersed-boundary/IBGMRES.cpp commit dcc81feec587d91595d49d08e39873a74f1cf081 Author: Johannes Blaschke Date: Thu May 16 12:25:40 2019 -0700 finish implementing JAS preconditioner src_immersed-boundary/IBGMRES.cpp commit 587f77282f4388141f634e4c44c20986dd79459c Author: Johannes Blaschke Date: Thu May 16 10:43:13 2019 -0700 added V compents due to the JLS preconditioner src_immersed-boundary/IBGMRES.cpp commit 2fe9cb24e78735e8c5ab8f6727c6cd3b221573cf Author: Johannes Blaschke Date: Thu May 16 10:09:25 2019 -0700 added (JL^{-1}S)^{-1} = JAS preconditioner src_immersed-boundary/IBGMRES.cpp commit 5e94d4c1b7baece2e61b423b8223e3cfbc817a18 Merge: 4096d6b1 8ca7305c Author: Johannes Blaschke Date: Wed May 15 18:09:56 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4096d6b1d66a24133c2484d377bbd5dbfc94b434 Author: Johannes Blaschke Date: Wed May 15 18:09:51 2019 -0700 added (JL^{-1}S)^{-1} RHS term src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 8ca7305ccb8140e363edb2698a29d72cc0a55d6c Author: KKlymko Date: Wed May 15 17:52:29 2019 -0700 added analysis notebook exec/_GL_alt/Data.ipynb commit 69a278a0849e7c9cbeb4181f97ffe9c57c817481 Author: Johannes Blaschke Date: Wed May 15 17:21:06 2019 -0700 add JA^{-1}G\phi src_immersed-boundary/IBGMRES.cpp commit 471cb9c2c1d9d39c4c7a8c92d4831d6da412e79b Author: Johannes Blaschke Date: Wed May 15 17:13:13 2019 -0700 add JA^{-1}g + W src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.cpp commit 5909f78b3eb085ddcb953e3cd4fade336ab76162 Merge: 30e1cb96 c53050b0 Author: Johannes Blaschke Date: Wed May 15 16:08:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 30e1cb9688a849320e8840e9d8a368a6326ee895 Author: Johannes Blaschke Date: Wed May 15 16:07:26 2019 -0700 use const member functions correctly, also be careful with std::map::operator[] src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions.H commit c53050b035d44ebed90f6b07f97fe878490bfa0d Merge: 4845b4e9 cdcb07a4 Author: jbb Date: Wed May 15 13:45:30 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 4845b4e9727d93377cfb1d85ba9ec2059e1896ff Author: jbb Date: Wed May 15 13:37:14 2019 -0700 fix to enable continuation in phi0 exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/GL_namelist.F90 exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit cdcb07a45d1968904d52b7d3681a752cc0702f53 Merge: dcc174c7 8e40d4b7 Author: Johannes Blaschke Date: Tue May 14 19:09:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit dcc174c7af8e11de79d2a72dc4fe9d79d3b24f80 Author: Johannes Blaschke Date: Tue May 14 19:09:44 2019 -0700 continute work on ib-aware preconditioner: document maths src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit d15d4d124e5869750abba6694d0f58209491236b Author: Daniel Ladiges Date: Tue May 14 17:07:37 2019 -0700 Fluid mean & var added to plotfile output exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/src_F90/compute_basic_stats.F90 commit 8e40d4b7c4edf26b6eab38f0a35d99eeaab60ff7 Merge: c208f70b 318cde0b Author: Daniel Ladiges Date: Tue May 14 16:28:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c208f70b12dfe267862c770e62fe059578912f5a Author: Daniel Ladiges Date: Tue May 14 16:27:55 2019 -0700 bugfix in stats function exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/main_driver.cpp src_common/src_F90/compute_basic_stats.F90 commit 70a1259a299ccfc17f4138312bd5e08bfabf3769 Merge: 0ebdf37e 318cde0b Author: Johannes Blaschke Date: Tue May 14 16:21:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 318cde0b319f9e4b0705df6fb649b819472bbcc6 Merge: 262d9827 4d31fb60 Author: Johannes Blaschke Date: Tue May 14 16:18:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 262d9827b588d46d2d5f778a8c1672cfde84c4d8 Author: Johannes Blaschke Date: Tue May 14 16:18:15 2019 -0700 fix sign error exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBGMRES.cpp commit 0ebdf37edfecedf99ab7d803a39efe5584463f55 Merge: 2b9cf4c2 4d31fb60 Author: Johannes Blaschke Date: Tue May 14 16:16:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2b9cf4c2dbbfe1d17e5ecc8a0d9f040c9889ce79 Author: Johannes Blaschke Date: Tue May 14 16:16:43 2019 -0700 need seperate ib-aware precon function src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 216cc366a23cd0b123ffb1be1d867655e90d2d55 Author: Daniel Ladiges Date: Tue May 14 16:07:53 2019 -0700 Added basic stats recording for fluid in immersedIons exec/immersedIons/main_driver.cpp commit 4d31fb60303490be0e95fb5642720120d8bb4eba Merge: 748de60f a0295db9 Author: Daniel Ladiges Date: Tue May 14 15:22:00 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 748de60f368d688f31cca7ed4472e30052a06bbf Author: Daniel Ladiges Date: Tue May 14 15:21:22 2019 -0700 Added some functions for recording means and vars of arbitrary multifab. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/ComputeBasicStats.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/compute_basic_stats.F90 commit a0295db904825fe01a819913d2fc3827dfd38387 Author: Johannes Blaschke Date: Mon May 13 22:53:07 2019 -0700 fiddle with first call to precon src_immersed-boundary/IBGMRES.cpp commit 4d05d11ad862988a4eac6a29870c65e03f479842 Merge: 75737751 1eec01ab Author: Johannes Blaschke Date: Mon May 13 21:29:20 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 75737751ae67df44b31db043929e76fd9ff3edfe Author: Johannes Blaschke Date: Mon May 13 21:29:18 2019 -0700 working on ib-aware preconditioners exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBGMRES.cpp commit 1eec01abd89db6e0b3ca25ec79db859dd046e06a Merge: bcad9b6c 74e0627e Author: Daniel Ladiges Date: Mon May 13 19:45:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bcad9b6c8f2c232003e76a266fec7d1085195bce Author: Daniel Ladiges Date: Mon May 13 19:41:53 2019 -0700 Finished dry particle mobility stuff. Further testing required to determine some details of mobility close to a wall. exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/delPlots exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 74e0627ee8e215d8920889207245875298c35d23 Merge: f54b72dd a43301eb Author: jbb Date: Mon May 13 17:29:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f54b72dd97bd15635d1a284ec4bf343e1a965104 Author: jbb Date: Mon May 13 17:28:41 2019 -0700 fixed to print integral occasionally exec/_GL_alt/GL_functions.H exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp commit a43301ebef7c3d03e88229b07b7d4f09ab6db4c0 Merge: d9c8623c f424c061 Author: Daniel Ladiges Date: Mon May 13 17:01:51 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d9c8623ceca0565854c64e2c48d38f1a61678a99 Author: Daniel Ladiges Date: Mon May 13 17:01:26 2019 -0700 Finished mobility calculation src_particles/src_F90/particle_functions.F90 commit f424c061a409d44c74e79b2456312a134e6f6409 Merge: 946dfd9c c3ef6744 Author: Johannes Blaschke Date: Mon May 13 16:56:02 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 946dfd9cb6e527c1cd88daec300fc49696505d1e Author: Johannes Blaschke Date: Mon May 13 16:55:59 2019 -0700 add option to avoid repeats due to ghost particles src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/IBParticleInfo.H commit c3ef67443d78d0886ef4f5282547f592d34114b9 Merge: 7faa19d4 1d52cece Author: jbb Date: Mon May 13 16:31:05 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7faa19d4097b69b411237315448dceae3d5cdd9d Author: jbb Date: Mon May 13 16:30:10 2019 -0700 tweak to fortran version of GL exec/GinzburgLandau/GL.f90 exec/GinzburgLandau/inputs src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 commit 9697f9a6bf89544374976c2811e8cba79a4587c2 Author: jbb Date: Mon May 13 16:28:17 2019 -0700 amrex GL code exec/_GL_alt/GL_funcs.F90 exec/_GL_alt/GL_functions.H exec/_GL_alt/GL_functions_F.H exec/_GL_alt/GL_namelist.F90 exec/_GL_alt/GNUmakefile exec/_GL_alt/Make.package exec/_GL_alt/exec_functions.H exec/_GL_alt/inputs_2d exec/_GL_alt/main_driver.cpp exec/_GL_alt/timeStep.cpp exec/_GL_alt/writePlotFile.cpp commit 1d52cece6cc810d0443fc125d524b3545498d4ba Author: Daniel Ladiges Date: Mon May 13 15:23:06 2019 -0700 Added Fortran type for species, added more stuff for dry mobility calculation. exec/immersedIons/main_driver.cpp src_common/src_F90/Make.package src_common/src_F90/species_type.F90 src_particles/particle_functions.H src_particles/particle_functions_F.H src_particles/particle_mobility.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 290d72bd11c78dfbe1edbfc811fda90bb0f0f718 Merge: 18c7fddd c7931be2 Author: Daniel Ladiges Date: Mon May 13 13:41:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 18c7fdddc6f16831bbaf9bca30e617a5a2d88c21 Author: Daniel Ladiges Date: Mon May 13 13:38:57 2019 -0700 Forgot to add untracked file exec/immersedIons/main_driver.cpp src_particles/particle_functions.H src_particles/particle_functions_F.H src_particles/particle_mobility.cpp src_particles/src_F90/particle_functions.F90 commit c7931be2dfda8d17f96a8dfd16584790ccd4628e Merge: 5d769fee 7927d8f0 Author: Johannes Blaschke Date: Mon May 13 12:03:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5d769fee162be699a7135a9ad4e75b42656cf9ed Author: Johannes Blaschke Date: Mon May 13 12:02:11 2019 -0700 fiddle with data management exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.H src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 7927d8f0e006a504abca6699d46c9ba7810415a9 Merge: f12a643a ddf18667 Author: Daniel Ladiges Date: Mon May 13 11:52:54 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f12a643a60b7adfc575f3eb7970949f2d6b30532 Author: Daniel Ladiges Date: Mon May 13 11:52:14 2019 -0700 Chased compilation error all morning. Added framework for particle mobility calc. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/Make.package src_particles/particle_functions.H commit 079caf0fdaf50c2b538a5686bfc1bab67da7db6d Author: Johannes Blaschke Date: Mon May 13 11:27:43 2019 -0700 take out old (faulty) IB code exec/channel_ibm/advance.cpp commit ddf186671c0e9c2c924caf21fcea8346eaedfb4d Author: Johannes Blaschke Date: Mon May 13 11:23:48 2019 -0700 tie IBGMRES into exec/channel_ibm exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.H exec/channel_ibm/main_driver.cpp src_immersed-boundary/Make.package commit 021703b4bbc9ebe597598723f3722f6d34c48356 Author: Johannes Blaschke Date: Mon May 13 11:23:12 2019 -0700 IB-aware GMRES lives in its own seperate translation unit ( => avoids dependency hell) src_immersed-boundary/IBGMRES.cpp src_immersed-boundary/ib_functions.H commit 383efddb0c9b2b2ec1aa3d4c68c83b43b1087880 Author: Johannes Blaschke Date: Mon May 13 11:02:23 2019 -0700 annotate some gmres, putting in immersed bdy precon next src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp commit ad7c33c3f852ee472034e54c1fc33f42fdd58236 Author: Johannes Blaschke Date: Sun May 12 19:07:47 2019 -0700 remove unncessary stuff from stag mg solver and tidy up some of the gmres stuff, so that it's easier to add the immersed boundary preconditioner exec/channel_ibm/main_driver.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit d1d014a1b295b386b969ac59e5f3faa4a382979d Author: Johannes Blaschke Date: Sat May 11 22:31:46 2019 -0700 add ibm interpolation operator exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit ebe250d3f38136d30a32a0b6646e602d72f37a0a Author: Johannes Blaschke Date: Sat May 11 18:53:21 2019 -0700 add marker interpolation function src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 892124f2e57463e34bd6bc6a0fcceb32ebe78283 Author: Johannes Blaschke Date: Fri May 10 22:11:34 2019 -0700 spreading operator works now... yay! exec/channel_ibm/main_driver.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 309ff57d53a1f1d6cfcecec402ffb8acbef4f0e1 Author: Johannes Blaschke Date: Fri May 10 21:59:16 2019 -0700 machinery in place for the IB spreading operator exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/IBParticleInfo.H commit f0a678ed6fcb6188a03b182e3bd15d79263dedab Merge: 11952acd 28acc588 Author: Johannes Blaschke Date: Fri May 10 20:23:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 11952acd2e4a818704a114fc154368efd981dc7a Author: Johannes Blaschke Date: Fri May 10 20:23:29 2019 -0700 testing fortran interface src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 843722a6884c4cfc5a7afcabda2244a518f10d96 Author: Daniel Ladiges Date: Fri May 10 17:28:05 2019 -0700 Added potential fill to electrostatic loop, removed some debug code. src_common/MultiFABPhysBC.cpp src_electrostatic/electrostatic.cpp commit 28acc5881154a40562967d219dae1ad45bc1ff8b Merge: c3c77b4d 3fdb449c Author: Daniel Ladiges Date: Fri May 10 17:09:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c3c77b4d2a3ed819c228e33ca374502d9112cc0e Author: Daniel Ladiges Date: Fri May 10 17:08:55 2019 -0700 Fixed potential ghost cell fill so electric field is correct near non periodic boundaries. src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/src_F90/common_namelist.F90 src_common/src_F90/multifab_physbc_mod.F90 commit 3fdb449c39f9632f2fd6133ead4516e05baf425c Author: jbb Date: Fri May 10 14:57:24 2019 -0700 annoted inputs and how to build exec/GinzburgLandau/README commit b3a7ed1168a5fbbb3cc88cb135f3c9db5b03ee8b Author: jbb Date: Fri May 10 14:54:11 2019 -0700 fxed but in spring for umbrella sampling exec/GinzburgLandau/GL.f90 commit 2e3480b4791f2c96ac9262db62202df9c011fa9e Author: Johannes Blaschke Date: Fri May 10 14:47:38 2019 -0700 add prototype spreading function src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit add1850b8009c09201abee872250bd41078a6615 Merge: 5db58404 469d3aca Author: Daniel Ladiges Date: Fri May 10 14:01:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5db584047c7dbcaba926481af3052314b7c657af Author: Daniel Ladiges Date: Fri May 10 13:58:42 2019 -0700 Started fixing electric field calc to include boundary conditions. exec/immersedIons/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_electrostatic/electrostatic.cpp commit 469d3acaba5b634edc61e3200851eac5063e62d0 Author: jbb Date: Fri May 10 13:49:52 2019 -0700 hacked up Ginzburg Landau model -- first-order exec/GinzburgLandau/GL.f90 exec/GinzburgLandau/Precision.f90 exec/GinzburgLandau/README exec/GinzburgLandau/Random.f90 exec/GinzburgLandau/inputs exec/GinzburgLandau/output.f90 commit 34cef9c53e7c7cf0f95f1c15f60508d16a13eb6f Merge: b5cd80fd 971694ef Author: Daniel Ladiges Date: Thu May 9 18:24:10 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b5cd80fd8cf9360e3ed986cbd7eb003994f3152a Author: Daniel Ladiges Date: Thu May 9 18:23:44 2019 -0700 Fixed another short range interaction bug. exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit 971694efe2b94e4a74c8ad82d9ffee2d2372cfd5 Author: Johannes Blaschke Date: Thu May 9 17:06:03 2019 -0700 found it, and some syntax cleanup src_common/FindCoords.cpp src_common/common_functions.H src_immersed-boundary/IBParticleContainer.cpp commit 9f3e26f6996c29623943b17601d11aff7527df43 Author: Johannes Blaschke Date: Thu May 9 16:53:33 2019 -0700 tracking down segfault src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 4f2b00b75fdf7340c133bc5eee8b739364492961 Author: Johannes Blaschke Date: Thu May 9 15:55:09 2019 -0700 update IBParticle API exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 866df5a25659d77532c2aa1631d7d3bba2cbb4a1 Author: Daniel Ladiges Date: Thu May 9 14:45:01 2019 -0700 Fixed another dry update bug. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/surfaces.cpp src_particles/src_F90/particle_functions.F90 commit a03da3a52d7ec98835c3253bd7cc87f196c5c652 Author: Daniel Ladiges Date: Thu May 9 13:50:14 2019 -0700 Added charge BC update to electrostatic solve exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp commit ba50aa6570bb68852d3ac4579054711064c1459c Author: Johannes Blaschke Date: Thu May 9 12:33:45 2019 -0700 replace cast to string to substring => more efficient src_immersed-boundary/src_F90/testing/Analyse Test.ipynb commit 712b07d2df799f6c022ef6469859879b22a9434f Author: Johannes Blaschke Date: Thu May 9 12:31:51 2019 -0700 finished testing positions of markers, seems to work exec/channel_ibm/Test Sphere Markers.ipynb commit 6c19fed7d41babee071cbbfd359b554c22bbb8c6 Author: Daniel Ladiges Date: Thu May 9 11:40:43 2019 -0700 Finished peskin charge BCs src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 commit d436ba1036d677d0a3f9f56fc110f6303c369e82 Merge: 648baecd 2bc9db35 Author: Daniel Ladiges Date: Thu May 9 11:09:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 648baecd74c39f03c3855efeaeb6701374600cc7 Author: Daniel Ladiges Date: Thu May 9 11:08:32 2019 -0700 Added electostatic bcs as seperate input option. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_common/src_F90/multifab_physbc_mod.F90 src_particles/src_F90/particle_functions.F90 commit 2bc9db357f063eff252e17e9cadefc1f08694f55 Merge: 7a058444 52a73512 Author: Johannes Blaschke Date: Thu May 9 10:24:27 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7a058444242d67d9d373aa6d393b8f4a105fea0d Author: Johannes Blaschke Date: Thu May 9 10:24:25 2019 -0700 debug marker placement on sphere exec/channel_ibm/main_driver.cpp exec/channel_ibm/sphere_markers.txt src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 52a73512debcdbff17f36247afeca6233685e5b6 Author: Daniel Ladiges Date: Wed May 8 17:25:27 2019 -0700 Fixed unit mistake in dry calc. exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit d01423bd27ab381960916dcc2c554cb7213f481c Merge: fe17969d 02b96c79 Author: Daniel Ladiges Date: Wed May 8 16:48:03 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fe17969dbcc526f3292171d6f4d9aa0461bfe6f2 Author: Daniel Ladiges Date: Wed May 8 16:47:47 2019 -0700 various exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 02b96c796f95730551dad76f76b1afde229ad660 Merge: a466252c 962e5345 Author: Johannes Blaschke Date: Wed May 8 11:07:00 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a466252c8f8ee0ca6b83be2c73c7a880af1406d7 Author: Johannes Blaschke Date: Wed May 8 11:06:55 2019 -0700 fixed channel_ibm case to use the updated BCs API exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.cpp commit 962e534557d2528aa2854da85092a69eaa6b5780 Merge: 75222f82 5779945a Author: Daniel Ladiges Date: Wed May 8 11:04:26 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 75222f82b485d04a59db2e52814985c0c9b6afb5 Author: Daniel Ladiges Date: Wed May 8 11:04:04 2019 -0700 Fixed dt factor in dry update exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit 5779945aee15be76ccbf293a71de06b71aff7251 Author: Johannes Blaschke Date: Wed May 8 10:54:59 2019 -0700 fixed channel case to use the updated BCs API exec/channel/advance.cpp exec/channel/main_driver.cpp src_common/MultiFABPhysBC.cpp commit c287984feb26bf6d877f2412d6af047d0dcdba27 Merge: 375579c1 3be2ba88 Author: Daniel Ladiges Date: Tue May 7 20:04:55 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 375579c189f196c3b8fac7322b45d4aa6b09ab07 Author: Daniel Ladiges Date: Tue May 7 20:02:12 2019 -0700 An error appears to have crept into our diffusion at some point, added some debugging code. exec/immersedIons/inputs_3d exec/immersedIons/properties.nb commit ae54c76d30aebdd8cf3aae494702a92b1b42baf8 Author: Daniel Ladiges Date: Tue May 7 20:00:47 2019 -0700 Adjusted dry update to return velocity rather that displacement, this allows proper boundary detection exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 3be2ba88af34ecf65a800859f99d75181669450f Merge: c64a1de0 7d043d76 Author: KKlymko Date: Tue May 7 18:29:29 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c64a1de06d1acb0482668c6a3515e644b4b6a847 Author: KKlymko Date: Tue May 7 18:27:19 2019 -0700 adding structfact back and python notebook exec/immersedIons/Data.ipynb exec/immersedIons/main_driver.cpp commit 7d043d76052ef1fd70302751affe8ef8c6bcfeef Merge: 9f32cd83 5c1d8616 Author: Johannes Blaschke Date: Tue May 7 18:20:37 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9f32cd83c8d6392af870b95a697a8ef5881a9717 Author: Johannes Blaschke Date: Tue May 7 18:20:31 2019 -0700 debug 6pt kernel src_immersed-boundary/src_F90/ib_fort_utils.F90 src_immersed-boundary/src_F90/testing/Analyse Test.ipynb src_immersed-boundary/src_F90/testing/test_data.txt src_immersed-boundary/src_F90/testing/test_kernel_6p src_immersed-boundary/src_F90/testing/test_kernel_6p.F90 commit 5c1d8616cbcd6f10fcd707c215de5f082d19695f Author: Daniel Ladiges Date: Tue May 7 16:45:46 2019 -0700 Added 2D versions of all src_common functions that were missing one. src_common/src_F90/find_coords.F90 src_common/src_F90/multifab_physbc_mod.F90 commit 17d841db10affc4ecc3bf5b131261fb6519b8e06 Merge: f1228170 9054c141 Author: Daniel Ladiges Date: Tue May 7 16:18:42 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f12281701403ffb70ac54a125ce0833d8664eb02 Author: Daniel Ladiges Date: Tue May 7 16:18:02 2019 -0700 Partial change for 2D compilation src_common/src_F90/multifab_physbc_mod.F90 commit 9054c1419f65d6b1b0cfc495ace0118e41ea95ef Merge: 33499633 fb28b8ce Author: Johannes Blaschke Date: Tue May 7 14:44:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 33499633cbad37a3b077f2425d29c67f45d1a77b Author: Johannes Blaschke Date: Tue May 7 14:44:31 2019 -0700 test 6-point kernel function src_immersed-boundary/src_F90/ib_fort_utils.F90 src_immersed-boundary/src_F90/testing/GNUmakefile src_immersed-boundary/src_F90/testing/test_data.txt src_immersed-boundary/src_F90/testing/test_kernel_6p src_immersed-boundary/src_F90/testing/test_kernel_6p.F90 commit fb28b8ce18760fa9951dbe74e6fae7e5752867c1 Author: Andy Nonaka Date: Tue May 7 12:37:08 2019 -0700 fix a 2d compilation error src_common/src_F90/multifab_physbc_mod.F90 commit b89db025f79c6156d675cc0960a8c097361b38ef Author: Daniel Ladiges Date: Mon May 6 15:55:18 2019 -0700 Ascii plot files is now an input option exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 7a1416ea1f4b132acddeacb5faaaecd2b8e0e52b Author: Daniel Ladiges Date: Mon May 6 15:28:52 2019 -0700 External field now an input option exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit f9de08f33298d2e017f4bfed7668e44bd0fc42e5 Author: Daniel Ladiges Date: Mon May 6 15:03:40 2019 -0700 images in pairwise calc is now an input option exec/immersedIons/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit e214218263dd99fc9536a5e25108908bc69e5168 Author: Daniel Ladiges Date: Mon May 6 13:42:23 2019 -0700 Added peskin interpolation boundary condition for the electric field - this will probably be necessary for the dry part? src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 src_electrostatic/electrostatic.cpp commit 107be492e27f918724a47e10abb4ff523364281a Author: Daniel Ladiges Date: Mon May 6 13:13:01 2019 -0700 Poisson BCs now set from input value exec/immersedIons/inputs_3d src_electrostatic/electrostatic.cpp commit 14322bce77304163f5268e2aa177bf0b5c72fab9 Author: Daniel Ladiges Date: Fri May 3 19:17:41 2019 -0700 'Hard' boundary conditions are now set by input boundary conditions. Using specular condition, in practice particle mobility is too low near walls for accidental boundary crossings. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/inputs_3d exec/immersedIons/surfaces.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 574065832c8c984753d8a2f7db3dfc246ffeced6 Author: Daniel Ladiges Date: Fri May 3 18:29:29 2019 -0700 Finished & tested fluid velocity and stress peskin boundary conditions exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/surfaces.cpp src_common/src_F90/multifab_physbc_mod.F90 src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 1000dde859a94bd9cf16a2e3c3813daf62b0e167 Author: Daniel Ladiges Date: Fri May 3 10:52:45 2019 -0700 Added peskin stress BC - untested. exec/immersedIons/inputs_3d src_common/src_F90/multifab_physbc_mod.F90 commit 150cff864dff30e99e6a8a82e12da40d45907a9e Author: Daniel Ladiges Date: Fri May 3 10:33:55 2019 -0700 Fluid BC bugfix #2, everything looks good now. exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 src_gmres/ApplyMatrix.cpp src_gmres/StagMGSolver.cpp src_hydro/MacProj_hydro.cpp src_hydro/StochMFlux.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit becf78a5238f3c75f1efefdcde978240102ae42f Author: Daniel Ladiges Date: Thu May 2 19:42:02 2019 -0700 Fixed boundary condition bug. Added framework for peskin particle BCs, need to discuss correct implementation. exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_physbc_mod.F90 src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 6649b08b469369f2ce95c9bd7b6ec33e063aece5 Author: Daniel Ladiges Date: Thu May 2 14:52:18 2019 -0700 These input values look like a stable test case. exec/immersedIons/inputs_3d exec/immersedIons/properties.nb src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 commit 5f5b6d5ef6b55bafac4b1af1432c068f457a11b4 Author: Daniel Ladiges Date: Thu May 2 12:58:41 2019 -0700 This input file has a reasonably functional set of parameters for the close range forces. exec/immersedIons/inputs_3d exec/immersedIons/properties.nb commit 023cd6f8af0ffe7bc537de6ef07854ef42c97110 Author: Daniel Ladiges Date: Thu May 2 12:29:51 2019 -0700 Removed debugging code. src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit f93d9f13bb1f2def12605cde5c62577066ec66af Author: Daniel Ladiges Date: Thu May 2 12:27:40 2019 -0700 Short range looks correct now. exec/immersedIons/Eanalysis.nb exec/immersedIons/inputs_3d exec/immersedIons/properties.nb src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 3ab8b0227e6f637062222776486173823e8160ac Author: Daniel Ladiges Date: Thu May 2 11:14:54 2019 -0700 Repulsive force bugfix. src_particles/src_F90/particle_functions.F90 commit adca3da95035f12032fbaf65007eaf76e38513cb Author: Daniel Ladiges Date: Thu May 2 11:12:21 2019 -0700 Repulsive force bugfix. exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 2015c6ab14d80f15f4ba8b8e1f996363671e0d91 Merge: b11ffc0f cc9b6090 Author: Daniel Ladiges Date: Thu May 2 10:06:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b11ffc0f2aecd07bb9a551e96e80f338a5858607 Author: Daniel Ladiges Date: Thu May 2 10:06:23 2019 -0700 Started some mods of close range calc exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit cc9b6090257464056d42aadaac76bf1ba31278c0 Merge: 6233bf68 6fe40df2 Author: Johannes Blaschke Date: Wed May 1 18:25:39 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6233bf6880ca3f3037e2efd8c0638adea650d184 Author: Johannes Blaschke Date: Wed May 1 18:25:37 2019 -0700 add 6pt ibm kernel exec/channel_ibm/Explore Data.ipynb exec/channel_ibm/main_driver.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 6fe40df2afc9873a44bcbccea5adac342a37f193 Author: KKlymko Date: Wed May 1 18:10:26 2019 -0700 cleaning up and some notes src_particles/src_F90/particle_functions.F90 commit 97ee4de220bd33a45c860615b9e096039f738fff Merge: ac13695d dd76151b Author: Daniel Ladiges Date: Wed May 1 18:07:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ac13695ddd0994966586d312aff594e6d8a98a02 Author: Daniel Ladiges Date: Wed May 1 18:06:43 2019 -0700 Removed debugging stuff while Andrew hunts for neighbor list problem. exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit dd76151b58a7009d392afbfe95a07d03d6b015ab Author: KKlymko Date: Wed May 1 17:18:53 2019 -0700 more dry src_particles/src_F90/particle_functions.F90 commit ee187f68df0c222f2a6d7a26cc9aa481dcdcdbfe Merge: 64e3ba80 dc5a4432 Author: Daniel Ladiges Date: Wed May 1 16:39:52 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 64e3ba80aee4c42ee0d5634dd5b665e803356b12 Author: Daniel Ladiges Date: Wed May 1 16:39:35 2019 -0700 Seg faulting version for debugging exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit dc5a4432252afc609a9751a857627d4b65b045d0 Author: KKlymko Date: Wed May 1 16:30:51 2019 -0700 call dry function in move_ions src_particles/src_F90/particle_functions.F90 commit df7db221654358452bc3ce1d1175f669c6dacbf6 Author: KKlymko Date: Wed May 1 11:58:39 2019 -0700 dry terms src_particles/src_F90/particle_functions.F90 commit 612e6ec2df5846f5a4f302b72733f8af79a648e4 Author: Daniel Ladiges Date: Wed May 1 11:09:09 2019 -0700 Moved force zeroing to end of rfd. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 3a06a499388ab21067c672450414adcbf3073766 Merge: 227cc19a e24111d1 Author: KKlymko Date: Tue Apr 30 16:41:28 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 227cc19ad4583706c864251d233008eac2ae0641 Author: KKlymko Date: Tue Apr 30 16:41:11 2019 -0700 cleaned up a bit src_particles/src_F90/particle_functions.F90 commit e24111d18c1cb174d7e9bfba88fee92b591cbd91 Merge: 6e0637a8 d89904eb Author: Daniel Ladiges Date: Tue Apr 30 16:13:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6e0637a818b0fd6bdda2fd785517e32c9ae4d9e2 Author: Daniel Ladiges Date: Tue Apr 30 16:11:48 2019 -0700 Added cell checking depth for neighbor list as input value. Something in the short ranged interaction appears to be hanging program, checking now. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/src_F90/particle_functions.F90 commit d89904ebdb82eab84fb6ddfb21b4c9a5c90c839a Merge: 17ea6225 cb8ef0c5 Author: Johannes Blaschke Date: Tue Apr 30 15:51:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 17ea62255fac5cd0c24e9efbfba40688d3591e9a Author: Johannes Blaschke Date: Tue Apr 30 15:51:29 2019 -0700 debugging diffusion process exec/channel_ibm/Explore Data.ipynb exec/channel_ibm/main_driver.cpp commit cb8ef0c5de9ebe4f43eb45656af7b9dd5f9eeb2a Author: Daniel Ladiges Date: Tue Apr 30 15:46:09 2019 -0700 Switched amrex_compute_forces_nl to use 'cell_sorted_particle_module' and removed 'short_range_particle_module' as it appears to be redundant - Katie let me know if this is a problem, easy to undo. src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 40d8677441647a2eec48774e2e296e1113b5cb3f Author: Daniel Ladiges Date: Tue Apr 30 15:42:55 2019 -0700 Short range calc now uses particle carried values for sigma and eepsilon (still needs to be made multispec) exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/species.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 7bd54fad2440a090a085de3cb48db209fca2d18f Author: Daniel Ladiges Date: Tue Apr 30 15:36:15 2019 -0700 Added sigma and eepsilon parameters to particle type. exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.H src_particles/src_F90/particle_type.F90 commit a7c7dc64c36451d49579a76ddcc36cdd61a66f74 Author: Daniel Ladiges Date: Tue Apr 30 15:30:38 2019 -0700 Deleted constants for min_r and cutoff and changed them to input vars. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit f0c4da683ed0716af076747c0691cbbc90619ac2 Merge: fe6818ea 610cd638 Author: Daniel Ladiges Date: Tue Apr 30 14:23:54 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fe6818ea46929aa5b16babb39391131a6f91ccd2 Author: Daniel Ladiges Date: Tue Apr 30 14:23:34 2019 -0700 Moved RFD toggle to reflect previous change. src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 6f1ebc5e9f2f08742492c0f26f27871c454f6e20 Author: Daniel Ladiges Date: Tue Apr 30 14:21:49 2019 -0700 Spun RFD calc out into seperate mfiter loop to accomodate neighbor list force calculation. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit f4dfa5b9f6d93d18668430b9e8803b72b271d0de Author: Daniel Ladiges Date: Tue Apr 30 14:04:17 2019 -0700 Changed repulsive force to use radius stored with particle - this is the value calculated from diffusion coefficients. We need to make this formula multispecies. Commented out 'neighbor_t' type, we don't appear to be using it. Delete if this is ok. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 610cd63883bb7d40deeb7a14dd21a596d2ca4092 Merge: e5da186e fab6e543 Author: Johannes Blaschke Date: Tue Apr 30 14:00:00 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e5da186e90544cdb337c2d65e880b2c00dd3956d Author: Johannes Blaschke Date: Tue Apr 30 13:59:58 2019 -0700 label the particle data exec/channel_ibm/Explore Data.ipynb exec/channel_ibm/WritePlotFile.cpp src_immersed-boundary/IBParticleContainer.H commit fab6e543cd45987dd652db19001b0671ad39d552 Author: Daniel Ladiges Date: Tue Apr 30 13:39:42 2019 -0700 Moved rfd calc to start of spreading loop. This preserves the value of part%force for use in the dry velocity update. src_particles/src_F90/particle_functions.F90 commit 74403babf1f1602cc80e0e8de590226507f60566 Author: Daniel Ladiges Date: Mon Apr 29 19:02:27 2019 -0700 Added a comment to dry(..) and answered questions. src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 714f5dffc4cc6d5f832f655424da1c7096ba483a Merge: ad3cdb72 f323585a Author: Daniel Ladiges Date: Mon Apr 29 18:13:17 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ad3cdb7264cd07c3f44faa6b568d60a20c2d4e27 Author: Daniel Ladiges Date: Mon Apr 29 18:12:22 2019 -0700 Added checking of midpoint update rejections and tested that not too many are occuring. Value is now output each timestep. exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit f323585a9bb80046d5892498693eb64ee973de0f Author: KKlymko Date: Mon Apr 29 17:29:18 2019 -0700 making dry a function call and questions src_particles/src_F90/particle_functions.F90 commit 375372b8ead02349fa163d009097cdd942411cf9 Author: Daniel Ladiges Date: Mon Apr 29 14:29:26 2019 -0700 Added electrostatic kernel volume correction, bugfix in coulomb calc. exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit 433b1c03a30ccf91cfd797847678a6e76f015186 Author: Daniel Ladiges Date: Mon Apr 29 13:20:24 2019 -0700 Dry diffusion coefficient is now calculated using Peskin kernel, grid size, and either input diameter or input diff coefficient. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/src_F90/common_namelist.F90 commit f602556c5859f0a24ed9b33372294f3755c2caa6 Author: Daniel Ladiges Date: Mon Apr 29 13:05:51 2019 -0700 Dry diffusion coefficient is now calculated from input particle diameter. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 0a5158f93b6fda1521dbb69a3e8cdaf1f465e45b Author: Daniel Ladiges Date: Mon Apr 29 12:12:06 2019 -0700 Drag calc is now toggled from input src_particles/src_F90/particle_functions.F90 commit b32031f361db69a5fbbaf5062fcb93aa679cdbf5 Merge: a5256035 e7ce3bed Author: Daniel Ladiges Date: Mon Apr 29 12:06:57 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a52560352376c7b9995fd04d9a93aaa34fe6ceed Author: Daniel Ladiges Date: Mon Apr 29 12:06:33 2019 -0700 Fixed namelist bug exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/src_F90/common_namelist.F90 commit e7ce3bed7729aa07d8b8538449951e26c9c0bc68 Merge: ec4ad580 7a803685 Author: Johannes Blaschke Date: Mon Apr 29 11:25:03 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ec4ad5808a8cdc27a317325a03993146dbed294b Author: Johannes Blaschke Date: Mon Apr 29 11:25:00 2019 -0700 demonstrate loading particle data using yt exec/channel_ibm/Explore Data.ipynb commit 516aeeb4c6c90cd79e8d93be25db115db0b38a16 Author: Johannes Blaschke Date: Mon Apr 29 11:24:33 2019 -0700 store particle data in plt file exec/channel_ibm/WritePlotFile.cpp exec/channel_ibm/main_driver.H exec/channel_ibm/main_driver.cpp commit 7a80368506b91566bc314aa05cdbf271923b3a70 Author: Daniel Ladiges Date: Mon Apr 29 11:20:59 2019 -0700 Added total, wet and dry diffusion to both particle and species types. exec/immersedIons/inputs_3d src_common/species.H commit 69797fde04bfb8bad9fee7946a412f58cefcb600 Author: Daniel Ladiges Date: Mon Apr 29 11:10:58 2019 -0700 Added input variables for total diffusion coefficient and to toggle dry movement exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/src_F90/particle_type.F90 commit bb5b5b16499104c3566b0c6fced7ac17d78d2a34 Author: Johannes Blaschke Date: Mon Apr 29 09:42:19 2019 -0700 stop git from bothering me .gitignore commit 1991062b5b28d689a42a5ba37c4e8cac65a20f64 Author: Daniel Ladiges Date: Sun Apr 28 18:35:23 2019 -0700 Particle movement now toggled from input exec/immersedIons/main_driver.cpp commit 4e3490b24e20a6f1e564c852d5389c869e80e158 Author: Daniel Ladiges Date: Sun Apr 28 18:31:53 2019 -0700 All kernel types now work with both fluid and es. exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 5818c85be2d5e20e992c89a285c0cd9323e8bd0d Author: Daniel Ladiges Date: Sun Apr 28 18:10:13 2019 -0700 Removed unused staggered electric field stuff. exec/immersedIons/main_driver.cpp commit 7a948f281507e341509d73efd02fb5f6b458cb6a Author: Daniel Ladiges Date: Sun Apr 28 18:05:31 2019 -0700 Seperate ghost cell depths for the three grids. exec/immersedIons/main_driver.cpp commit 10fb34133d1b4c80dbd17cedf519707538b7fefc Author: Daniel Ladiges Date: Sun Apr 28 17:53:30 2019 -0700 Electrostatic calculation type now in input file. Removed move_particle_fhd functions, most functionality has been moved to other functions. Simplified pairwise Coulomb calling format. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit b2640680b5674ecc86180acb4e71b1a828a744d7 Author: Daniel Ladiges Date: Sat Apr 27 19:54:27 2019 -0700 Fluid update now toggled from input exec/immersedIons/main_driver.cpp commit 200e6240e2332d23b0fa778c9ee94149ce221309 Author: Daniel Ladiges Date: Sat Apr 27 19:52:28 2019 -0700 RFD calc now toggled from input src_particles/src_F90/particle_functions.F90 commit 6edcc5e8df2220f01cbdbbf900bc9a7189e8394e Author: Daniel Ladiges Date: Sat Apr 27 19:49:45 2019 -0700 RFD calc turned back into function call src_particles/src_F90/particle_functions.F90 commit b9efdc899e8aae93966f846c710ff8ed9d228240 Author: Daniel Ladiges Date: Sat Apr 27 19:32:20 2019 -0700 Grid refining/coarsening now an input option. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit baac89d1f45db104091d859f2713165091de2960 Author: Daniel Ladiges Date: Sat Apr 27 19:24:18 2019 -0700 Added a bunch of new input parameters exec/immersedIons/inputs_3d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit a695dfa0089c4109904726ff2879779190e8074d Author: Daniel Ladiges Date: Sat Apr 27 19:00:45 2019 -0700 Removed need to do initializing particle move. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit b00cab69a702c7108fbe121acaf81fa4b07d31e5 Author: Daniel Ladiges Date: Sat Apr 27 18:57:22 2019 -0700 Updated particle init functions for multispecies support. Positive and negative ions are now treated as seperate species. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 06a4d76e416592d6987ac7a7bcf739583fd504aa Merge: 1d1d3480 01ad5b4c Author: Daniel Ladiges Date: Sat Apr 27 18:11:49 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 1d1d348097c0f84e2b06017efe2143814ac85db5 Author: Daniel Ladiges Date: Sat Apr 27 18:11:33 2019 -0700 Made qval a vector. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.cpp commit 01ad5b4cad1808a95394f8b61484b96405b1fa03 Author: Johannes Blaschke Date: Fri Apr 26 20:49:49 2019 -0700 avoid repeat searches of the particle list .gitignore src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp commit 218791ebf0917b64abeb43905b4e5ca141527789 Author: Johannes Blaschke Date: Fri Apr 26 20:30:39 2019 -0700 git stop bugging me .gitignore commit 2c386a56ad908dfed789081d4022519726c1333a Merge: 0aaf07f3 24409fc2 Author: Johannes Blaschke Date: Fri Apr 26 20:23:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0aaf07f33c44095f82d01b9138953eba944a02fc Author: Johannes Blaschke Date: Fri Apr 26 20:23:42 2019 -0700 remove hackery from ibm force interpolation src_immersed-boundary/IBCore.cpp commit 24409fc225e987fa3b00a393f471db4d3fef4859 Merge: 41b704a0 efebac58 Author: Daniel Ladiges Date: Fri Apr 26 18:33:16 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 41b704a0f06610d3d680026b55c9bad699a5f95a Author: Daniel Ladiges Date: Fri Apr 26 18:31:57 2019 -0700 Added fluid BCs, simple test case appears to work well. exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit efebac58947d9b7c9175faea5af572e68865d152 Author: Johannes Blaschke Date: Fri Apr 26 17:39:40 2019 -0700 finish analysis notebook for finding the local x, y, and z temperatures exec/channel/Explore Data.ipynb commit 561e71d83780d113112353c8518cda0921283051 Author: Johannes Blaschke Date: Fri Apr 26 11:07:08 2019 -0700 document some of the data analysis exec/channel/Explore Data.ipynb commit 6749911701c15764e12797d1486274ba385b1da2 Author: Johannes Blaschke Date: Fri Apr 26 10:45:31 2019 -0700 play with data using YT exec/channel/Explore Data.ipynb commit db8cd374613f15c510ed76a0a6ab6b15b2562bec Author: Johannes Blaschke Date: Thu Apr 25 19:38:25 2019 -0700 fiddling with the divergence part of the inverse-mobility matrix exec/channel_ibm/advance.cpp commit ce18d710270bd5cfe29dbf499dc9c258889d2385 Merge: 73fee195 051886c7 Author: Johannes Blaschke Date: Thu Apr 25 17:42:22 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 73fee19567ffd85891a5ba63680762a38df74c57 Author: Johannes Blaschke Date: Thu Apr 25 17:42:18 2019 -0700 fixed intermittend deadlock src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp commit 051886c71491fa934e01352d64cca7eb3f4dc684 Author: Daniel Ladiges Date: Thu Apr 25 12:50:57 2019 -0700 Finally figured out correct implementation of image charges. Poisson and Coulomb implementations now match in all cases. src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit f470dc01b75d4db7298152c7abfce22e8fb9f9d2 Merge: ec9110ba 1ecdb2f0 Author: Daniel Ladiges Date: Wed Apr 24 19:57:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ec9110baef2420fc7634a4b481e0387f273ae3a7 Author: Daniel Ladiges Date: Wed Apr 24 19:55:37 2019 -0700 Now putting efield on cell centers. Greatly improved Poisson solution but still seems to be a scaling issue. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/analysis.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_div_and_grad.F90 src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 1ecdb2f0cb84e61826433d1a5fb434639fa289f7 Author: Johannes Blaschke Date: Wed Apr 24 18:30:58 2019 -0700 fix mpi comms deadlock exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp commit 20ecb48ee119b5f6be78adf0e54c257b0ad59ec9 Author: Johannes Blaschke Date: Wed Apr 24 18:13:23 2019 -0700 consistent treatment of cc and fc arrays src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 377b431276d6766e570aadd7dd0e32ffacbbe590 Merge: aa7d7123 bb6acb6a Author: Daniel Ladiges Date: Mon Apr 22 18:08:32 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit aa7d71238f1e260da472d49e61531f7908378bf0 Author: Daniel Ladiges Date: Mon Apr 22 18:08:00 2019 -0700 Fixed symmetry bug in pairwise coloumb calculation. Still doesn't match Poisson. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit bb6acb6a34dbe410371f9424cfa702223d307a44 Author: Johannes Blaschke Date: Mon Apr 22 18:07:14 2019 -0700 MultiFab -> Vector for local buffers exec/channel_ibm/inputs_3d_test src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp commit e09e79a69f6325b667d0714ea8772b25826ca972 Author: Johannes Blaschke Date: Sun Apr 21 17:46:53 2019 -0700 found it src_immersed-boundary/IBParticleContainer.cpp commit 93f45baad84ddf50ec593e5a4c3c76d6dca8f9cd Author: Johannes Blaschke Date: Sun Apr 21 14:14:34 2019 -0700 tracking down errand particle index exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit fb49957a34761245741786cffac11a5de80d1790 Author: Johannes Blaschke Date: Sun Apr 21 12:39:55 2019 -0700 move particle time-steping in IBParticleContainer src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 3cf7d51898ec59693e001d51cbeb00fb11bb9d2c Author: Johannes Blaschke Date: Fri Apr 19 22:20:01 2019 -0700 function to store translational forces in index->force map src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 476c6175a10f5dd6fd0d0e64f5b165c93bfdc0e2 Author: Johannes Blaschke Date: Fri Apr 19 18:04:09 2019 -0700 no longer need a list of particle indices src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp commit 848324e85c1534ce8c4cd1b2ccea366e5f83813e Author: Johannes Blaschke Date: Fri Apr 19 17:44:16 2019 -0700 build a map from particle index->immersed boundary index src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H commit 91d60d423b736ac5c5b1478d4e5eb8ffe48e4737 Author: Johannes Blaschke Date: Thu Apr 18 21:06:43 2019 -0700 fix issue with ghost cells exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBCore.cpp commit c65083be96b639c807179ff53bae13007bb84678 Author: Johannes Blaschke Date: Thu Apr 18 20:43:56 2019 -0700 work on force interpolation exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp commit 8b39c66f6cac74f4fbc857f24fa7d02a5c9e9d98 Author: Johannes Blaschke Date: Thu Apr 18 17:16:01 2019 -0700 save force (acting on immersed boundaries) data exec/channel_ibm/WritePlotFile.cpp exec/channel_ibm/main_driver.H exec/channel_ibm/main_driver.cpp commit 6191dc14bf9ba4f557324a1ce910ed6e1d4425a7 Author: Johannes Blaschke Date: Thu Apr 18 17:15:36 2019 -0700 add const qualifier to divergence input data src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/compute_div_and_grad.F90 commit d46c72cdc3718c1fe9e6feac59b74e2634f0ab2b Author: Johannes Blaschke Date: Thu Apr 18 16:01:08 2019 -0700 forgot to initialize this src_immersed-boundary/IBCore.cpp commit d86888200899dc4f1e838e75090fcb82ac52ccc0 Merge: 7d9a758d c878acf0 Author: Johannes Blaschke Date: Thu Apr 18 15:51:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7d9a758dd43590f5cce77ca21f93f4c02dfe016c Author: Johannes Blaschke Date: Thu Apr 18 15:51:40 2019 -0700 got segfault => transfer to anguirus src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/IBParticleInfo.H src_immersed-boundary/src_F90/ib_fort_utils.F90 commit c878acf0a42a06c8366e6f347969f78843479ddf Author: Daniel Ladiges Date: Thu Apr 18 15:44:58 2019 -0700 RFD bug fixed? Test running now. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit e90c1361cd5d79f79871d615aad278d28605bbde Author: Johannes Blaschke Date: Thu Apr 18 13:15:26 2019 -0700 add local level-set for each mpi rank src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/ib_functions_F.H commit 631dc2197aa775dc25fe4552cb2c0bca164f7471 Author: Daniel Ladiges Date: Wed Apr 17 19:28:39 2019 -0700 Fixed weight update error in RFD. Result still very wrong. exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 51880e481f0d261b15a80c759fa88e5883405cab Merge: 2e369d0f e12dd1ef Author: Daniel Ladiges Date: Wed Apr 17 19:08:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2e369d0f6dc67f351bbca3d13b558e9dd2b70c51 Author: Daniel Ladiges Date: Wed Apr 17 19:04:24 2019 -0700 Re added ES force check - still doesn't match src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit e12dd1ef9633d1f641dc228c45b5c1d1e3c35aee Merge: 3bc7b71f 1b1ebaa0 Author: Johannes Blaschke Date: Wed Apr 17 19:03:56 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3bc7b71fc607ab9fe707dfbca182fe4e66290190 Author: Johannes Blaschke Date: Wed Apr 17 19:03:51 2019 -0700 add fortran function to fill single-particle level-set data src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 1b1ebaa07bf6cafcfe3a257f58e34e02845e7e01 Merge: b28359aa 42b4b399 Author: Daniel Ladiges Date: Wed Apr 17 18:56:54 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b28359aa10836349877b572f572e89136d80d256 Author: Daniel Ladiges Date: Wed Apr 17 18:55:49 2019 -0700 Broke rfd, drag, and spreading operators out into seperate function from interpolate and move. Put main loop in correct order. exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 42b4b3993056504ab5a755ac4db4bc7241453437 Author: Johannes Blaschke Date: Wed Apr 17 16:54:22 2019 -0700 clean up immersed-boundary tagging function calls src_immersed-boundary/IBCore.cpp commit 6562b71f044f66c223bcd5d7ecd29f9866de3053 Author: Johannes Blaschke Date: Wed Apr 17 16:10:06 2019 -0700 update change the way particle-container data is managed in IBCore exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp commit 86fee65f02af2506b821dfa5ad61abe95ed94617 Merge: 52b759de e4656833 Author: Johannes Blaschke Date: Tue Apr 16 17:05:14 2019 -0700 merge commit 52b759dedd8fbd7731620d954166c79fcf809743 Author: Johannes Blaschke Date: Tue Apr 16 17:04:39 2019 -0700 update IBParticleContainer api exec/channel_ibm/advance.cpp src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/src_F90/constant_mod.F90 src_immersed-boundary/src_F90/param_mod.F90 src_immersed-boundary/src_F90/set_particle_properties.F90 commit e46568334df7205ad8adbef63d14e1e079606370 Author: Andy Nonaka Date: Tue Apr 16 14:40:10 2019 -0700 comments only exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 0942fb2d69f086ebd03126b34c11018c28e5b38a Author: Andy Nonaka Date: Tue Apr 16 11:14:41 2019 -0700 started going through immersedIons/main_driver.cpp and added "AJN" comments/questions in the source code exec/immersedIons/main_driver.cpp commit 405db5e26cb7ad786eabbc93d2b641523a26587e Author: Andy Nonaka Date: Tue Apr 16 11:14:18 2019 -0700 stochMfluxdiv does not need ghost cells exec/hydro/main_driver.cpp commit f4d145a3d14c3398e619d65418461047ea92a7e0 Author: Johannes Blaschke Date: Mon Apr 15 18:24:59 2019 -0700 level-set index type should be nodal src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H commit ca01bec0fb8ed25e6034e9963afb8276aff7f0f8 Author: Johannes Blaschke Date: Sun Apr 14 21:37:43 2019 -0700 fix error where no fluctuations would not advance solution exec/channel_ibm/main_driver.cpp commit 83881e588c3aae6d30b07f62e7b0a4bda6aba61c Author: Johannes Blaschke Date: Sun Apr 14 21:33:19 2019 -0700 store IBM as initial guess for next time step exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.H exec/channel_ibm/main_driver.cpp commit 4f78cc28fb20f917c0257cb6f0f34f57655343c1 Author: Johannes Blaschke Date: Sun Apr 14 21:13:48 2019 -0700 for some reason this fixed the compile issues I was having exec/channel_ibm/Make.package exec/channel_ibm/WritePlotFile.cpp exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.H exec/channel_ibm/main_driver.cpp exec/channel_ibm/main_driver_F.H src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/set_particle_properties.F90 commit 525c8d3c2c53ae9f4931f88cb6e2561032fdbff9 Author: Johannes Blaschke Date: Sun Apr 14 17:49:41 2019 -0700 fix cell-centered => face-centered indexing exec/channel_ibm/advance.cpp exec/channel_ibm/hydro_test_functions.H exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit 45863aca14fc328f9ae7680b283c95c3258992a3 Author: Johannes Blaschke Date: Fri Apr 12 17:52:33 2019 -0700 pass IBCore instance to fluid advance exec/channel_ibm/advance.cpp exec/channel_ibm/hydro_test_functions.H exec/channel_ibm/main_driver.cpp commit 0118e47d11b54a48d57beb388fda43c77ecda7f6 Merge: 41f2b329 f9a7c4cf Author: Johannes Blaschke Date: Fri Apr 12 17:18:12 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 41f2b329e036c9a571b89e246f6799564e1f4acc Author: Johannes Blaschke Date: Fri Apr 12 17:18:09 2019 -0700 force tagging on interface only src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit f9a7c4cfe3fce1af53bba773354908bf825fcc39 Author: Andy Nonaka Date: Fri Apr 12 16:09:08 2019 -0700 remove extra call to amrex::finalize that was causing segfault exec/immersedIons/main_driver.cpp commit f9daf7de39beb794932e6d17db20c1f8dd2b7975 Merge: 9e5ff2f5 87ba229a Author: Andy Nonaka Date: Fri Apr 12 16:04:03 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9e5ff2f5ab7d5d1a4f778d37dc2f645bd221549a Author: Andy Nonaka Date: Fri Apr 12 16:03:38 2019 -0700 bugfix; the computation of dx was commented out, causing crashes when in DEBUG mode src_particles/src_F90/particle_functions.F90 commit 87ba229a0371ff592c2066987026d08b60ff2223 Author: Johannes Blaschke Date: Fri Apr 12 15:52:45 2019 -0700 ensure that IBCore's grids have the right index type src_immersed-boundary/IBCore.cpp src_immersed-boundary/src_F90/ib_fort_utils.F90 commit f0d3a0bb4d61850896a74ecaae0366c471d5b33f Author: Johannes Blaschke Date: Fri Apr 12 15:32:01 2019 -0700 fiddle with the right kind of tiling... at least this seems to work at the moment exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit d098fca4e9eff035452c7a853caa295c394d61fd Author: Johannes Blaschke Date: Thu Apr 11 22:36:59 2019 -0700 tagging works now src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.cpp commit ed42dc66f3fd53bab2f593564385dc413878e49c Author: Johannes Blaschke Date: Thu Apr 11 22:01:01 2019 -0700 fix segfault exec/channel_ibm/main_driver.cpp commit e92962bb15234c21842d07837e311e3faf0524a6 Author: Johannes Blaschke Date: Thu Apr 11 21:51:14 2019 -0700 debugging tagging exec/channel_ibm/main_driver.cpp commit 246537eefbf757d646aed7ca37e95a1276fe13ac Author: Johannes Blaschke Date: Thu Apr 11 21:16:57 2019 -0700 hack parmparse database exec/channel_ibm/main_driver.cpp commit 09750305b4b7e93accf8063f242c6c5dfcb1bab3 Author: Johannes Blaschke Date: Thu Apr 11 16:22:52 2019 -0700 debugged exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.cpp commit 8ddd62b86ad9dd1c3ad68632268e44e9c2bab8bc Author: Johannes Blaschke Date: Thu Apr 11 15:48:19 2019 -0700 debugging with Andrew exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 2e537d2a9fa54495fc7f315c3c0080fa4cb5359c Author: Johannes Blaschke Date: Thu Apr 11 14:03:34 2019 -0700 ib particle container needs constructor that takes pargdb exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp commit 67628ffeef326fe765f65007c0a9533fae6c3aab Author: Johannes Blaschke Date: Thu Apr 11 13:35:46 2019 -0700 update ib particle container to make it compatible to updates to amrex exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.cpp src_immersed-boundary/IBParticleContainer.H commit e08f44e5f593a7777880aba3f478b2f09e2c2d50 Author: Johannes Blaschke Date: Thu Apr 11 13:28:03 2019 -0700 still not happy with this, but I gotta move on... exec/channel_ibm/advance.cpp commit 7c5f45dca184de0625442787403c13e6f770111c Author: Johannes Blaschke Date: Wed Apr 10 22:02:15 2019 -0700 deal with ghost cells exec/channel_ibm/advance.cpp commit ed25a1bc050b8b63188ce5b9786a7cff6a281716 Author: Johannes Blaschke Date: Wed Apr 10 18:11:44 2019 -0700 improve performance exec/channel_ibm/advance.cpp commit 9ebdb224761555b840a7e3f5c79ed45026d5c6cd Author: Johannes Blaschke Date: Wed Apr 10 17:31:14 2019 -0700 fixed it by remembering the ibm pressure (implicit) term exec/channel_ibm/advance.cpp commit f387f8a5e3fe5f3c12b2cb001b8e6849882baf21 Author: Johannes Blaschke Date: Tue Apr 9 18:57:46 2019 -0700 hrm... fiddling with divergence part of the ibm constraint forces exec/channel_ibm/advance.cpp commit 4e0fc9174d68d4851634768265fb5e21a63a6ad2 Merge: 827bbe77 ea2f1b06 Author: Johannes Blaschke Date: Tue Apr 9 18:47:55 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 827bbe777f6eba904ef6aadceed275ba2f2ae581 Author: Johannes Blaschke Date: Tue Apr 9 18:47:52 2019 -0700 broke it again... but I know what's going on? exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.cpp src_common/MultiFABPhysBC.cpp src_hydro/StochMFlux.cpp commit ea2f1b06edc2983ca982bab40de3a1813ab735ba Author: jbb Date: Tue Apr 9 15:08:36 2019 -0700 fixed code to reflect updates to amrex exec/DiffuisonTest/main_driver.cpp exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp commit 62637bfca93b65b2c2af4b4163aa69535ba50d81 Author: KKlymko Date: Tue Apr 9 13:40:01 2019 -0700 added neighborlist calculation and testing on dry particle moves exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 6cc98df9575f3bd5d31e075e5aecad4d6668c3d4 Author: Johannes Blaschke Date: Tue Apr 9 11:25:05 2019 -0700 strip out debug code exec/channel_ibm/main_driver.cpp commit 183644dfb4f76e536c5ef15ea95f9b634e3a136b Author: KKlymko Date: Mon Apr 8 17:56:42 2019 -0700 more NL src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit b86e2c52d8e3ef04e01843591fea2b3bdac0234c Author: KKlymko Date: Mon Apr 8 16:13:53 2019 -0700 more NL src_particles/particle_functions_F.H commit 8ea8d5957c83ce522d49ae58f51ca8d4e7bc2c1e Merge: 1e42328f 439ce02b Author: KKlymko Date: Mon Apr 8 16:02:38 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 1e42328f59d386f0fedcb02633dc04b88fc611d5 Author: KKlymko Date: Mon Apr 8 16:02:20 2019 -0700 more neighborlist fixes src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 439ce02b20db238b8624b73625edc58afc000fb1 Merge: e6411baa fe99065f Author: Johannes Blaschke Date: Mon Apr 8 14:50:43 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit e6411baae51e54107ba041cc986b19f934f7a2d5 Author: Johannes Blaschke Date: Mon Apr 8 14:50:40 2019 -0700 this somehow fixed it ... huh! exec/channel_ibm/advance.cpp commit fe99065fdb93e799f3c864edfadd292e92fce78f Author: KKlymko Date: Mon Apr 8 13:50:35 2019 -0700 fixing neighborlist src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 2c4ec247cb5a6ee98c6abb6b72ff50dc793c6578 Author: kklymko Date: Mon Apr 8 13:21:44 2019 -0700 added neighbor list src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 767f1266e2c33a18e406cee39f0c1b62e6f3ff41 Author: Johannes Blaschke Date: Sat Apr 6 16:08:14 2019 -0700 remove more prints exec/channel_ibm/advance.cpp commit 51e8c6ab83a3fc16b39c3c66c0e9b48c1b353e3d Author: Johannes Blaschke Date: Sat Apr 6 16:02:18 2019 -0700 get rid of some debug code exec/channel_ibm/advance.cpp exec/channel_ibm/main_driver.cpp commit 151f9b7b93453d8e7befdf13810b6f3eb0e7c608 Author: Johannes Blaschke Date: Fri Apr 5 21:42:42 2019 -0700 p_f is scalar exec/channel_ibm/advance.cpp commit 6118f9d40721db9ed57948e16d270f4911a6c15a Merge: 2e262b16 0abb3662 Author: Johannes Blaschke Date: Fri Apr 5 19:59:07 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2e262b164932c96d881d00f0da97dc960093c1b6 Author: Johannes Blaschke Date: Fri Apr 5 19:58:47 2019 -0700 I think I have the ibm-gmres thing more-or-less figured out exec/channel_ibm/advance.cpp exec/channel_ibm/inputs_3d_test exec/channel_ibm/main_driver.cpp src_gmres/ApplyMatrix.cpp commit 0abb36621f9e505b4d386b053901fafac85b9918 Author: KKlymko Date: Wed Apr 3 18:45:29 2019 -0700 fixed muo dynamics in dry particles--running in brownian exec/brownian/GNUmakefile exec/brownian/INS_functions.H exec/brownian/WritePlotFile.cpp exec/brownian/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit d71d30ab9ccfae602a2a9f403656e348622bf153 Author: Daniel Ladiges Date: Fri Mar 29 20:55:57 2019 -0700 Added self image interaction, although this should sum to zero? src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit fd08121bf4d0ccdd0e7d2d76053ec8fa6fc4432c Author: Daniel Ladiges Date: Fri Mar 29 20:31:19 2019 -0700 Turned on midpoint correction exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit b0a019aff2b15499a2d46e3d430f97ae8a377b88 Author: Daniel Ladiges Date: Fri Mar 29 20:14:40 2019 -0700 Test setup for em interactions. Poisson solution behaves sensibly, missmatch with coulomb solution appears to be due to error in image charge calculation? exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/precheck.F90 src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit e694dc7bd6a2e78d831fab8d905e360924a82852 Merge: 573c4f60 8639f3f0 Author: Daniel Ladiges Date: Fri Mar 29 17:27:53 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 573c4f60f239a306f5fa96a98a898915ad214ce9 Author: Daniel Ladiges Date: Fri Mar 29 17:27:20 2019 -0700 Added particle interactions with e field exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 8639f3f0b1475578e3aac9f8fd1c24cd5a5e0033 Merge: a97fff35 e56a620e Author: Katherine Klymko Date: Fri Mar 29 16:00:33 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a97fff35f0dd2f37c414d617b3cfe4d6519ae799 Author: Katherine Klymko Date: Fri Mar 29 16:00:27 2019 -0700 fixed period problems in dry src_particles/src_F90/particle_functions.F90 commit e56a620efbc449e98fdc303facb40347d52a1cd1 Author: Daniel Ladiges Date: Fri Mar 29 15:42:19 2019 -0700 Deleted old move ion function src_particles/src_F90/particle_functions.F90 commit 21a776c8a091dc4f384636a6d5bc665caa77b08f Merge: 0c727253 89c178eb Author: Daniel Ladiges Date: Fri Mar 29 15:22:55 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0c727253687686d61c0e2115ff71088326770209 Author: Daniel Ladiges Date: Fri Mar 29 15:22:31 2019 -0700 Electric field calculation, including external field. exec/immersedIons/main_driver.cpp src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp commit 89c178ebdd22939ebf6de79dae45da2c63a7d5dc Merge: 386aa5bc 604d3bcf Author: Katherine Klymko Date: Fri Mar 29 13:37:47 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 386aa5bceb7ff9c479e0961d5659bafdf2d79cd9 Author: Katherine Klymko Date: Fri Mar 29 13:37:38 2019 -0700 added dry particles src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 604d3bcff9eb4ff38cecc394c85b36921cd7650b Author: Daniel Ladiges Date: Fri Mar 29 13:31:36 2019 -0700 Potential calculation working. exec/immersedIons/main_driver.cpp src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp src_particles/src_F90/particle_functions.F90 commit 0ec8d47c2c71530e6d139d1b786bffdd608debef Author: Daniel Ladiges Date: Fri Mar 29 12:22:50 2019 -0700 Added various parameters to common namespace exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/delPlots exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_common/src_F90/find_coords.F90 src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp src_particles/src_F90/particle_functions.F90 commit 8ba2bb985062e221a143afa6b27a8a5748fbee4f Merge: ad32b053 f32e71b0 Author: Daniel Ladiges Date: Thu Mar 28 10:49:11 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ad32b0534658b124d1a32a157855afb86c83e45f Author: Daniel Ladiges Date: Thu Mar 28 10:48:01 2019 -0700 FhdParticleContainer now inherits from NeighborParticleContainer exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit f32e71b034f17f51f4c40ba8784d0a68cdd27426 Author: Andy Nonaka Date: Wed Mar 27 15:21:59 2019 -0700 fix regression test plot_base_name exec/hydro/inputs_regression_2d exec/hydro/inputs_regression_3d commit 1687ef7b0b211485f7419055d79cc25509799b91 Author: Andy Nonaka Date: Wed Mar 27 15:16:29 2019 -0700 properly initialize plot/chk_base_name from fortran into c++ namespace src_common/common_functions.cpp commit 1e4a9e60083437c13be00182dec1fbc595f9848c Author: Andy Nonaka Date: Wed Mar 27 13:08:12 2019 -0700 plot_base_name for regression testing exec/hydro/inputs_regression_2d exec/hydro/inputs_regression_3d commit f18878c748e8194e4224eb6766d4284f2e2ef6ca Author: Andy Nonaka Date: Wed Mar 27 13:07:20 2019 -0700 enable plot_base_name exec/DiffuisonTest/WritePlotFile.cpp exec/channel/WritePlotFile.cpp exec/channel_ibm/WritePlotFile.cpp exec/multispec/WritePlotFile.cpp exec/overdamped/WritePlotFile.cpp commit 84911598f4f4f22fac4f9b37aecdc2cd1587077d Author: Andy Nonaka Date: Wed Mar 27 13:05:34 2019 -0700 enable plot_base_name exec/hydro/WritePlotFile.cpp commit 976087516888cdf66ed6ef95985be77a80463292 Author: Andy Nonaka Date: Wed Mar 27 12:19:39 2019 -0700 bugfix; don't resize string in the common namespace src_common/common_functions.cpp commit 1708fa25cd188e8b50a3086f13c93d12ef19176a Author: Andy Nonaka Date: Wed Mar 27 10:42:57 2019 -0700 regression tests exec/hydro/inputs_regression_2d exec/hydro/inputs_regression_3d commit 469e6d8443e4acb802ee06bf6a465419585fa68b Author: Andy Nonaka Date: Wed Mar 27 10:39:49 2019 -0700 remove static multifab (caused segfault at amrex:finalize) src_gmres/StagMGSolver.cpp commit b7b2117df1adfa1111242d4d97894103f96ddd9e Author: Andy Nonaka Date: Wed Mar 27 10:08:38 2019 -0700 bugfix - was trying to use a multifab mult() on ghost cells when there weren't any exec/hydro/advance.cpp commit 497397a000cdbee850209092f77deea668b0a61f Author: Katherine Klymko Date: Tue Mar 26 18:15:11 2019 -0700 fixed dx name in force calculation src_particles/src_F90/particle_functions.F90 commit 5e6272d957c66826b10118b17fa8ba8991bf2db5 Author: Andy Nonaka Date: Tue Mar 26 15:42:37 2019 -0700 old inputs exec/hydro/inputs_2d exec/hydro/inputs_3d commit 4f0a048fd1aa9f74632f50637196635f8e5b3b29 Merge: bf742008 28ae311e Author: Daniel Ladiges Date: Tue Mar 26 14:13:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit bf7420086a5d5ccd540bf28fb8120efb3c7e73aa Author: Daniel Ladiges Date: Tue Mar 26 14:13:01 2019 -0700 Various exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 28ae311ea32dde6754fdc106c05bac89e51606f2 Author: Andy Nonaka Date: Mon Mar 25 17:20:14 2019 -0700 remove incomplete, unused example exec/gmres/GNUmakefile exec/gmres/inputs_2d exec/gmres/main_driver.cpp commit 5f2b43e9613af3fb473c9ab5774ace56fac26e22 Author: Daniel Ladiges Date: Mon Mar 25 14:12:11 2019 -0700 Removed some debug messages src_particles/src_F90/particle_functions.F90 commit 03bd0fb0869c5413ee7533f06dd256e903bb0891 Author: Daniel Ladiges Date: Mon Mar 25 14:04:27 2019 -0700 Version which compiles exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit cb8f7c0d4de23a86d326dafdf5b8535b57cc20d2 Merge: 22154962 dbb6daae Author: Daniel Ladiges Date: Mon Mar 25 14:02:54 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 22154962c0316a6909c3c162661d848acdc920cc Author: Daniel Ladiges Date: Mon Mar 25 14:02:32 2019 -0700 Fixed fill/sum boundary bug in source MF exec/immersedIons/analysis.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit dbb6daae00481a27d0067606b42a3311d6c13c87 Author: Katherine Klymko Date: Mon Mar 25 11:51:03 2019 -0700 fixed WCA repulsion src_particles/src_F90/particle_functions.F90 commit e949db2a6d4699fe095f292ab7ea9f2e5ae08e47 Author: Katherine Klymko Date: Mon Mar 25 11:46:52 2019 -0700 added WCA repulsion src_particles/src_F90/particle_functions.F90 commit b7ae369d0208c87fa14e2a1195f08bd87665f44f Merge: 77016bd6 0fe0088d Author: Katherine Klymko Date: Fri Mar 22 15:02:59 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 77016bd66b00d48e3f965b9e5213f136fd22687f Author: Katherine Klymko Date: Fri Mar 22 15:02:42 2019 -0700 not sure src_particles/src_F90/particle_functions.F90 commit 0fe0088dda005c3696e5b31d875f1dff53d9be94 Author: Daniel Ladiges Date: Fri Mar 22 14:51:21 2019 -0700 Working random finite difference and midpoint correctors exec/immersedIons/analysis.nb exec/immersedIons/delPlots exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit b2ccba271200f4945b4528c53e19671763eb73ea Author: Daniel Ladiges Date: Thu Mar 21 20:14:58 2019 -0700 Added random finite difference and midpoint timestepping exec/immersedIons/analysis.nb exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/properties.nb src_particles/src_F90/particle_functions.F90 commit f37d019b53a4c800c9e14a29ec6d14c34d82f912 Merge: b1f483e0 794a8d7a Author: Daniel Ladiges Date: Thu Mar 21 17:41:06 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b1f483e0abe407c65d06675a96579c637e7c2036 Author: Daniel Ladiges Date: Thu Mar 21 17:40:36 2019 -0700 removed drag calculation from spreading function exec/immersedIons/inputs_3d exec/immersedIons/properties.nb src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 794a8d7a863f0d6f846e3b21fb434ea06fedae5d Merge: 20c4c5ac 5dd8332b Author: Katherine Klymko Date: Thu Mar 21 16:08:59 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 20c4c5ac67d33f785141d9caa9ec028d123d4805 Author: Katherine Klymko Date: Thu Mar 21 16:08:08 2019 -0700 fixed force directions src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 5dd8332b3e8cb1b51cec3722e6cf82c11c0939e5 Author: Daniel Ladiges Date: Thu Mar 21 15:47:25 2019 -0700 added useful mathematica notebooks exec/immersedIons/analysis.nb exec/immersedIons/properties.nb commit 3c40be3a369fb08283db8721c722ad28f65ee4a8 Author: Daniel Ladiges Date: Thu Mar 21 14:56:16 2019 -0700 Katie pull this version to work on. src_particles/src_F90/particle_functions.F90 commit 46cf913f4a8c380bec29f61b121be9b460c62fc7 Merge: 235171a7 80ded7b9 Author: Daniel Ladiges Date: Thu Mar 21 14:41:42 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 235171a7d7b0a203e6e65f891076cb35aadc184e Author: Daniel Ladiges Date: Thu Mar 21 14:41:03 2019 -0700 Various bugfixes, ascii plotfiles now work with multiple boxes. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/outputAscii.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 80ded7b9673e48029d2f5dd281e2139412fd7afd Author: Guy Moore Date: Thu Mar 21 14:04:04 2019 -0700 Diffusive bubble appears to be working - needs convergence verification exec/multispec/GNUmakefile exec/multispec/advance.cpp exec/multispec/inputs_bubble_2d exec/multispec/main_driver.cpp src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/MatvecMul.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/matvec_mul.F90 commit 5247b89394214b34e94b0851754cdc73c5471a29 Author: Daniel Ladiges Date: Tue Mar 19 17:10:49 2019 -0700 Ascii output functions. exec/immersedIons/WritePlotFile.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/Make.package src_common/common_functions.H src_common/outputAscii.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 90737db682465f31aec19f25f7118b1608fedfde Author: Daniel Ladiges Date: Tue Mar 19 13:00:11 2019 -0700 particle electrostatic debugging exec/immersedIons/inputs_3d src_particles/src_F90/particle_functions.F90 commit a35994fb1cb6ca83cbd8a44f4672bcaff585ddfd Merge: bcff3689 b64a5f3f Author: Daniel Ladiges Date: Tue Mar 19 12:49:09 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b64a5f3fde360090bbc23cea7e9da8ba8bd7d1e3 Author: Katherine Klymko Date: Tue Mar 19 12:50:37 2019 -0700 repulsive interactions src_particles/src_F90/particle_functions.F90 commit bcff368987d049931a505ce4fd6eb1fb4759a9c8 Author: Daniel Ladiges Date: Tue Mar 19 12:48:59 2019 -0700 Mods to particle init exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit d329bb9edc9e5d7620d8d3a487e55af115e448ae Author: Katherine Klymko Date: Tue Mar 19 12:24:28 2019 -0700 repulsive interactions src_particles/src_F90/particle_functions.F90 commit 2f393088d3e0ba7e404a56c540ef990e3eda9824 Merge: 3e691f91 d329bb9e Author: Daniel Ladiges Date: Tue Mar 19 12:23:45 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3e691f91f3be30542c552f7da385f35fb899c5db Author: Daniel Ladiges Date: Tue Mar 19 12:23:15 2019 -0700 Continued work on Poisson solver exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 46aa373cad1ba2ccf2ea4fc026fd2a5848ef02ba Author: Daniel Ladiges Date: Tue Mar 19 10:37:59 2019 -0700 New version of coloumb force src_particles/src_F90/particle_functions.F90 commit c22231c775ef2a7dbd58bce1cd1f2362e88a045d Author: Daniel Ladiges Date: Mon Mar 18 18:41:42 2019 -0700 Added option to turn off both interpolation and spreading exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 8f3eddf6083e8be0e2e1ce2ccf348284ace2e3fc Merge: 8d533f63 7f690e69 Author: Daniel Ladiges Date: Mon Mar 18 18:16:57 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7f690e697530a6a9554fe14ddf59d798013ad61b Author: Katherine Klymko Date: Mon Mar 18 18:15:03 2019 -0700 fixed infinite loops in force calculation src_particles/src_F90/particle_functions.F90 commit 8d533f6389cebf4bffcba8a667ec1d666192afd0 Author: Daniel Ladiges Date: Mon Mar 18 18:13:32 2019 -0700 MOre work on stats exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 09283b7301cde2a9cca141a251e0d9824764f70d Merge: 630452b7 d65fd633 Author: Daniel Ladiges Date: Mon Mar 18 17:38:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 630452b734e48dc0409f854ce2d4bdd034afa184 Author: Daniel Ladiges Date: Mon Mar 18 17:38:06 2019 -0700 Halfway through updating stats exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit d65fd633cd5be6d4b84e5ded778bbfeee465b1ce Author: Katherine Klymko Date: Mon Mar 18 17:33:24 2019 -0700 added repuslive potential src_particles/src_F90/particle_functions.F90 commit 93bf8065c11804a3f7f072b32ec56d9b3bcecd70 Author: Katherine Klymko Date: Mon Mar 18 16:33:59 2019 -0700 more on particle forces src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 991c1b8f7363872eb4a2d93cc9ee8b5da80d071b Merge: c638d60d 06f041d0 Author: Daniel Ladiges Date: Fri Mar 15 17:02:50 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c638d60dda372b111d0210613551a00282e6083a Author: Daniel Ladiges Date: Fri Mar 15 17:02:27 2019 -0700 Added function for finding cell centers exec/immersedIons/main_driver.cpp src_common/FindCoords.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/find_coords.F90 src_particles/src_F90/particle_functions.F90 commit 06f041d0417a4afb4e303676b8c9a8dc30b02a80 Merge: aa7b4858 4ea5e044 Author: Katherine Klymko Date: Fri Mar 15 15:52:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit aa7b48580c696e4fdc612fffdd4159b32998ae20 Author: Katherine Klymko Date: Fri Mar 15 15:51:51 2019 -0700 fixed electrostatic force src_particles/src_F90/particle_functions.F90 commit 4ea5e0446b7d7cdfd05f25af022155b16445651c Author: Daniel Ladiges Date: Fri Mar 15 13:28:02 2019 -0700 Update to particle type definition. Added more electrostatic stuff. src_electrostatic/Make.package src_electrostatic/electrostatic.H src_electrostatic/electrostatic.cpp src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 903a812bcd94dda6970b96b3b94ec84af5685eff Merge: f0de1c69 7677f321 Author: Daniel Ladiges Date: Fri Mar 15 12:50:22 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f0de1c6988206bec6486677fe4e45a97f44a6041 Author: Daniel Ladiges Date: Fri Mar 15 12:45:32 2019 -0700 Started function for collecting charge distribution exec/immersedIons/GNUmakefile exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 7677f321cbfe15b318e949c7dac0bde136fa9775 Author: Katherine Klymko Date: Fri Mar 15 11:08:50 2019 -0700 adding electrostatic calc src_particles/src_F90/particle_functions.F90 commit 0f777294260aebbe656ca71c993f8ff6ee505a0b Author: Katherine Klymko Date: Fri Mar 15 10:36:31 2019 -0700 fixing force calculation src_particles/src_F90/particle_functions.F90 commit dafc441117a23be5f2ff9770d593ccd0ee75eff6 Merge: 6c0d5e14 640782c4 Author: Katherine Klymko Date: Fri Mar 15 10:04:41 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 6c0d5e14f24b7ce30f3c35497738b32212ed7cf0 Author: Katherine Klymko Date: Fri Mar 15 10:02:35 2019 -0700 started interparticle force calculations src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 640782c430a294cab1b82bd0dd94fda51cecc01f Merge: 425e48c2 69282dec Author: Johannes Blaschke Date: Thu Mar 14 22:15:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 425e48c23c3af86238640cecfa905dbefd9628ac Author: Johannes Blaschke Date: Thu Mar 14 22:15:16 2019 -0700 added implicit forcing to staggered MG solver (untested) src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit 69282dec67c5bf8cc4babfbee6886f5650285739 Author: Daniel Ladiges Date: Thu Mar 14 14:23:25 2019 -0700 Started adding parts for electrostatic solver exec/brownian/inputs_3d exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit 33425a9407e19ef7f96136eee01a2ad97f8add55 Author: Johannes Blaschke Date: Wed Mar 13 22:37:02 2019 -0700 this might not be necessary, but at least it's safer exec/channel/main_driver.cpp exec/channel_ibm/main_driver.cpp src_gmres/StagMGSolver.cpp commit 74b14e3ad88ab8461eadcfaa8ee429d775241625 Author: Johannes Blaschke Date: Wed Mar 13 17:58:21 2019 -0700 start by implementing implicit forcing in StagMGSolver src_gmres/StagMGSolver.cpp commit 500b58a691ed1d7ab320ea53e549eb886000ad79 Author: Johannes Blaschke Date: Wed Mar 13 17:19:47 2019 -0700 start work on implicit forcing src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 951139c341efd6b7959f891170be9cee77c1ee44 Author: Johannes Blaschke Date: Wed Mar 13 15:33:17 2019 -0700 clean up in lieu of adding implicit forcing src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.cpp commit a208ec600e602b2eb07dc7e917f25a79576db3c4 Merge: a01e9e5c 69637318 Author: Johannes Blaschke Date: Wed Mar 13 14:25:31 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 69637318dffb339918c1a7566622babdc8c5f8cc Merge: b35e784c 738bd656 Author: Daniel Ladiges Date: Wed Mar 13 14:17:19 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b35e784c66df753f9c8289f1fde0ee8fb7cc1287 Author: Daniel Ladiges Date: Wed Mar 13 14:15:46 2019 -0700 Added various parameters to input files. Added some extra properties to particle definition. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit a01e9e5ca41564165dbf860d5d418afd53a5a7a9 Author: Johannes Blaschke Date: Wed Mar 13 13:20:52 2019 -0700 add pure attribute the BC functions => guarantee no side-effects exec/channel/advance.cpp exec/channel_ibm/advance.cpp src_common/src_F90/multifab_physbc_mod.F90 src_gmres/GMRES.cpp src_hydro/src_F90/hydro_bounds_mod.F90 commit 95874fb4279a145a8614cba21e974b2f420f8827 Merge: 89511be4 738bd656 Author: Johannes Blaschke Date: Wed Mar 13 10:28:42 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 89511be4710cb7cd08071d6f0e3a4eb5c29bd626 Author: Johannes Blaschke Date: Wed Mar 13 10:28:40 2019 -0700 added comment explaining boundary conditions exec/channel/inputs_3d_test commit 738bd656b201305c9adf077a9ddd4aed5424f60a Author: Johannes Blaschke Date: Tue Mar 12 22:02:43 2019 -0700 clean up makefiles exec/channel/GNUmakefile exec/channel_ibm/GNUmakefile commit 5e0acea6ff477a0dd50bc82bcc1e288f0c9480f9 Author: Johannes Blaschke Date: Tue Mar 12 21:57:24 2019 -0700 start adding colloid to channel flow exec/channel_ibm/GNUmakefile exec/channel_ibm/Make.package exec/channel_ibm/WritePlotFile.cpp exec/channel_ibm/advance.cpp exec/channel_ibm/compute_convfact_2.sh exec/channel_ibm/hydro_test_functions.H exec/channel_ibm/hydro_test_functions_F.H exec/channel_ibm/init_funcs.F90 exec/channel_ibm/init_s_funcs.F90 exec/channel_ibm/inputs_2d exec/channel_ibm/inputs_3d exec/channel_ibm/inputs_3d_test exec/channel_ibm/inputs_3d_test.2 exec/channel_ibm/inputs_incomp_equil_fluct_2d exec/channel_ibm/inputs_incomp_equil_fluct_3d exec/channel_ibm/main_driver.cpp exec/channel_ibm/run_conv_tests_2.sh commit 6a1b3c8fc4a10223358c100f2418813a02c1779e Author: Johannes Blaschke Date: Tue Mar 12 16:53:36 2019 -0700 added 2D version for pressure BCs src_hydro/src_F90/hydro_bounds_mod.F90 commit db70e80145fbb631079a65fb429db4a5a1cbbe19 Merge: db3c6fde 75e2783b Author: Johannes Blaschke Date: Tue Mar 12 16:38:44 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit db3c6fdefff82541ad1a4ed07554decc8b56eda0 Author: Johannes Blaschke Date: Tue Mar 12 16:38:37 2019 -0700 cleanup main driver exec/channel/advance.cpp exec/channel/main_driver.cpp src_hydro/src_F90/hydro_bounds_mod.F90 commit 75e2783b56b1ba5317feec1482e28a70b1f4c966 Merge: 8e4dbe46 23c22043 Author: Daniel Ladiges Date: Mon Mar 11 18:56:35 2019 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8e4dbe4674250838c260336a953045366a32f8a9 Author: Daniel Ladiges Date: Mon Mar 11 18:52:03 2019 -0700 Various bug fixes, diffusion coefficient appears to be correct. exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_hydro/StochMFlux.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 23c22043b30f7105bf0b8b4a34e22be9b07f4889 Author: Guy Moore Date: Mon Mar 11 16:35:40 2019 -0700 Fixed multispec namespace error src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/multispec_namelist.F90 commit 1dc784ee4fa49f61c82567200b9884010c0a1b1e Author: Guy Moore Date: Mon Mar 11 08:08:51 2019 -0700 Cleaned up main_driver and advance routines in hydro and multispec. Also ComputeMassFluxdiv exec/hydro/advance.cpp exec/hydro/main_driver.cpp exec/multispec/WritePlotFile.cpp exec/multispec/advance.cpp exec/multispec/init_funcs.F90 exec/multispec/inputs_2d exec/multispec/inputs_bubble_2d exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H exec/multispec/multispec_test_functions_F.H src_multispec/ComputeMassFluxdiv.cpp src_multispec/multispec_functions.H commit 87079603ac0a1b8791f1a4f4c2476927e271057b Merge: b622dd0a 8c4d40a7 Author: Daniel Ladiges Date: Sat Mar 9 18:47:59 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b622dd0a888eb817156bc2784767935e19ea3713 Author: Daniel Ladiges Date: Sat Mar 9 18:46:01 2019 -0800 Added more robust handling of periodic bcs. Added diffusion test. Currently measured diff. coef is way to large. exec/brownian/inputs_3d exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 8c4d40a7e8bd10e27cc0de49ed4d74316cedb039 Author: Johannes Blaschke Date: Sat Mar 9 09:29:18 2019 -0800 forgot to actually _add_ the file src_hydro/HydroBCs.cpp src_hydro/src_F90/hydro_bounds_mod.F90 commit d88ef07a223f4472452893caf42689b03baa2297 Merge: d11142da 81fe5ea7 Author: Johannes Blaschke Date: Fri Mar 8 20:08:44 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d11142dab107880aff07ac4b408e734da0d3449a Author: Johannes Blaschke Date: Fri Mar 8 20:08:39 2019 -0800 add periodic pressure inlet boundary conditions exec/channel/GNUmakefile exec/channel/advance.cpp exec/channel/inputs_3d_test exec/channel/main_driver.cpp src_common/MuliFABFillRandom.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_common/src_F90/multifab_physbc_mod.F90 src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package commit 81fe5ea7011397d8ee91830d1b4edf5bbc09be42 Author: Daniel Ladiges Date: Fri Mar 8 18:52:32 2019 -0800 Added tracking of non-periodic position for meansqr displacement calc exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit 8d690761110a22167e36e886f670379d2a091eff Author: Daniel Ladiges Date: Fri Mar 8 17:50:24 2019 -0800 turned off test electro forcing. src_particles/src_F90/particle_functions.F90 commit ac2de19d8d982e79034593b7aa901efc34a4df97 Author: Daniel Ladiges Date: Fri Mar 8 17:48:17 2019 -0800 bugfix in particle init Input file has 'correct' hydro diameter that matches peskin kernel, producing correct fluid response for this cell size. exec/brownian/inputs_3d exec/brownian/main_driver.cpp exec/immersedIons/inputs_3d src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 67ae2aeb73cac4439b15e2a199b13226530bd864 Author: Daniel Ladiges Date: Fri Mar 8 15:06:35 2019 -0800 Fixed source update bug - timestepping now probably works correctly. Added charge property to particles Added fixed field forcing term for testing exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/species.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit c6e21bc9072ef4ba3301e8c694012da24f435de6 Author: Daniel Ladiges Date: Fri Mar 8 12:31:30 2019 -0800 Working on timestepping exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp commit 8fce388ee4e5a787c6aa6b36b881937fff43c757 Author: Daniel Ladiges Date: Thu Mar 7 19:36:15 2019 -0800 Added interpolation operator and simple timestepping exec/brownian/init_funcs.F90 exec/brownian/init_s_funcs.F90 exec/brownian/main_driver.cpp exec/immersedIons/init_funcs.F90 exec/immersedIons/init_s_funcs.F90 exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 9643db1b6135a4c34c2912b855dfe30c1fc31d8d Author: Daniel Ladiges Date: Thu Mar 7 17:40:07 2019 -0800 Spreading and stokes operators impelemented for single time step. exec/brownian/GNUmakefile exec/brownian/INS_functions.H exec/brownian/Make.package exec/brownian/WritePlotFile.cpp exec/brownian/WritePlotFileHydro.cpp exec/brownian/advance.cpp exec/brownian/delPlots exec/brownian/inputs_3d exec/brownian/main_driver.cpp exec/immersedIons/INS_functions.H exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/advance.cpp exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedParticles/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 9a3be587df04833715f2f798232346559fc37388 Author: Johannes Blaschke Date: Thu Mar 7 12:16:53 2019 -0800 fix variable name exec/channel/advance.cpp src_common/MultiFABPhysBC.cpp src_common/src_F90/multifab_physbc_mod.F90 commit 5a657e3c9830994153c99bdec6bfdc170228a7a7 Author: Johannes Blaschke Date: Thu Mar 7 11:16:43 2019 -0800 Use Nonaka indexing in main_driver exec/channel/main_driver.cpp commit 34deb0eab63cea442c0ebf26183e05500cd9b84d Author: Johannes Blaschke Date: Thu Mar 7 11:07:11 2019 -0800 Expand concept of Nonaka indexing to edges src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit cec8b16f5f7b5391d891fed1ccc9b239b0c36558 Author: Andy Nonaka Date: Thu Mar 7 08:21:01 2019 -0800 more cleanup exec/overdamped/main_driver.cpp commit 09d3e0e4b06974ea11fd8cb79db6e951dbe94bb0 Author: Andy Nonaka Date: Thu Mar 7 08:03:50 2019 -0800 cleanup/simplify overdamped integrator exec/overdamped/advance.cpp exec/overdamped/main_driver.cpp commit 6101eca1c465afa5337344498a341b347f91db71 Author: Andy Nonaka Date: Thu Mar 7 07:58:02 2019 -0800 introduced a a vector: "nodal_flag_dir". So instead of using AMREX_D_TERM to define vectors of nodal data, you can use loops if you like. e.g., you can replace AMREX_D_TERM(alpha_fc[0].define(convert(ba,nodal_flag_x), dmap, 1, 1);, alpha_fc[1].define(convert(ba,nodal_flag_y), dmap, 1, 1);, alpha_fc[2].define(convert(ba,nodal_flag_z), dmap, 1, 1);); with for (int d=0; d Date: Wed Mar 6 22:07:43 2019 -0800 Re-enable corner cases for BC filling src_common/MultiFABPhysBC.cpp commit 6dee4496cc6a0945dc00296a91c18978f2c16b28 Author: Johannes Blaschke Date: Wed Mar 6 22:00:02 2019 -0800 Moved BC functions to src_common src_common/Make.package src_common/MuliFABFillRandom.cpp src_common/MultiFABPhysBC.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/multifab_physbc_mod.F90 src_gmres/ApplyMatrix.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_hydro/Make.package src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMFlux.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package commit 84cf2adfb0c847b8bacb54e8f7876323847e58c7 Author: Johannes Blaschke Date: Wed Mar 6 21:22:43 2019 -0800 Debug.o (from Debug.cpp) and debug.o (from debug.F90) collide on (case insensitive) macOS file system. src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/debug_mod.F90 commit 64d18a531bfd6578e064a8a224d28edca3631703 Author: Daniel Ladiges Date: Wed Mar 6 20:50:24 2019 -0800 Temporarily FhdParticleContainer::InitParticles into FhdParticleContainer::InitParticlesBrownian for seperate development of electrostatic stuff. src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit fe6d2293f18b036cb5d02d1a7888f305a0edf841 Author: Daniel Ladiges Date: Wed Mar 6 20:35:11 2019 -0800 Added shell/python scripts to immersedIons and brownian for particle visuals exec/brownian/amrex_to_vtp.py exec/brownian/convertSeries exec/brownian/write_pview_file.py exec/brownian/write_pview_file.pyc exec/immersedIons/amrex_to_vtp.py exec/immersedIons/convertSeries exec/immersedIons/write_pview_file.py exec/immersedIons/write_pview_file.pyc commit 00083eb4573f9f533b43d35c6a51fa5f98980402 Merge: ef3d634d b90ed47b Author: Daniel Ladiges Date: Wed Mar 6 20:29:54 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit ef3d634d42a64c9f4f566e5d6f59349f1c73ba1e Author: Daniel Ladiges Date: Wed Mar 6 20:22:44 2019 -0800 Impelemented 3pt Peskin kernel exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp python/convertSeries src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit b90ed47b92e8eeaaa753763b3883ce4c398e635d Merge: f7ec9563 0d65c6fb Author: Johannes Blaschke Date: Wed Mar 6 17:47:45 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f7ec9563b0d0297e2f755544bcad35d95850e4a7 Author: Johannes Blaschke Date: Wed Mar 6 17:47:40 2019 -0800 fix tracer diffusion, and remove diagnostic print statements exec/channel/WritePlotFile.cpp exec/channel/advance.cpp exec/channel/main_driver.cpp src_gmres/src_F90/stag_apply_op.F90 src_hydro/src_F90/bound_funcs.F90 commit 0d65c6fb5a1edcad15088d99b0d9fd9a1c4b68e6 Author: Andy Nonaka Date: Wed Mar 6 17:10:43 2019 -0800 bugfix; didn't implement theta_alpha in stag_applyop. overdamped integrator runs fast now (12 GMRES iters) exec/overdamped/advance.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 5a04f8e0f52b6408d77ee5dcdf4653b1bd29fdb1 Author: Andy Nonaka Date: Wed Mar 6 16:14:21 2019 -0800 visc_type=2 exec/overdamped/inputs_incomp_equil_fluct_3d commit 952ad300c97e224140611c8c2e5c0a46d1d657b3 Author: Andy Nonaka Date: Wed Mar 6 16:13:18 2019 -0800 first cut at overdamped integrator... it runs but converges too slowly exec/overdamped/.#main_driver.cpp exec/overdamped/advance.cpp exec/overdamped/hydro_test_functions.H exec/overdamped/inputs_incomp_equil_fluct_2d exec/overdamped/inputs_incomp_equil_fluct_3d exec/overdamped/main_driver.cpp commit 850462ca25a7c0b529edac195c3fd984021defaa Author: Andy Nonaka Date: Wed Mar 6 15:41:51 2019 -0800 whittling down the inertial integrator for overdamped steady-stokes (WIP) exec/overdamped/.#main_driver.cpp exec/overdamped/GNUmakefile exec/overdamped/Make.package exec/overdamped/WritePlotFile.cpp exec/overdamped/advance.cpp exec/overdamped/hydro_test_functions.H exec/overdamped/hydro_test_functions_F.H exec/overdamped/init_funcs.F90 exec/overdamped/inputs_incomp_equil_fluct_2d exec/overdamped/inputs_incomp_equil_fluct_3d exec/overdamped/main_driver.cpp commit 42bc4f9ce378343ea70879d1b29e2e2a77508889 Author: Andy Nonaka Date: Wed Mar 6 15:16:45 2019 -0800 tidy up convergence readme and script exec/hydro/README_CONVERGENCE exec/hydro/compute_convergence_rate.sh commit b0bb8cce264bc42cba53939beec72968a2988e62 Author: Andy Nonaka Date: Wed Mar 6 15:16:21 2019 -0800 smoother tanh profile for vortex (to help get convergence back to 2nd order) exec/hydro/init_funcs.F90 commit a0ccfc9687fddcc3de1e508fa8d93114f049d7e3 Author: Andy Nonaka Date: Wed Mar 6 15:07:50 2019 -0800 add a PrintMF function to write out the contents of a cell-centered multifab. parallel safe in that it writes ou the contents of 1 grid at a time (in the order they appear in the boxArray) src_common/Debug.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/debug.F90 commit 69f7307320bee2a26efd1a90dc2bef5f275a4b9e Merge: fbb3f003 32637a1d Author: Daniel Ladiges Date: Wed Mar 6 13:56:43 2019 -0800 Fixed conflict Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fbb3f0031e7a52b71bf4b6241c7f891c408aba19 Author: Daniel Ladiges Date: Wed Mar 6 13:54:51 2019 -0800 Started setup for particle testing exec/hydro/GNUmakefile exec/immersedIons/GNUmakefile exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp src_common/src_F90/init_funcs.F90 src_gmres/GMRES.cpp src_particles/src_F90/particle_functions.F90 commit 32637a1d5adec6d17837414f13df9232e967550d Author: Johannes Blaschke Date: Wed Mar 6 13:39:43 2019 -0800 fix uninitialized data exec/channel/advance.cpp src_gmres/StagMGSolver.cpp src_hydro/MacProj_hydro.cpp commit 211af306c0800cd1ab32d6ce5e5d0148eb6c3e08 Author: Johannes Blaschke Date: Tue Mar 5 21:22:57 2019 -0800 comment out NaN test src_gmres/src_F90/stag_apply_op.F90 src_hydro/src_F90/bound_funcs.F90 commit 91c4d308a871447ac82f76aeb33a867c368bdb84 Author: Johannes Blaschke Date: Tue Mar 5 21:12:41 2019 -0800 added 2d versions of boundary conditions src_hydro/src_F90/bound_funcs.F90 commit e88924a13b34eb3283cd481bc37f00833d9f6675 Author: Johannes Blaschke Date: Tue Mar 5 20:55:23 2019 -0800 fix makefile exec/channel/GNUmakefile commit 8a7960eec557855e33b4bc32d94ba80aba362080 Merge: 070ade45 3d46ac4a Author: Johannes Blaschke Date: Tue Mar 5 20:44:14 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 070ade4596bb64309c2b03e043e70d3f1ca6bad7 Author: Johannes Blaschke Date: Tue Mar 5 20:43:59 2019 -0800 fix: boundary conditions now work with coarsened geometries exec/channel/GNUmakefile exec/channel/advance.cpp exec/channel/inputs_3d_test exec/channel/main_driver.cpp src_common/MuliFABFillRandom.cpp src_gmres/ApplyMatrix.cpp src_gmres/GMRES.cpp src_gmres/StagMGSolver.cpp src_gmres/src_F90/stag_apply_op.F90 src_gmres/src_F90/stag_mg_solver.F90 src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMFlux.cpp src_hydro/boundary.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/bound_funcs.F90 commit 3d46ac4a44c1fbb34943869d1ca63c559ac5d044 Author: Andy Nonaka Date: Tue Mar 5 18:47:45 2019 -0800 F_BaseLib no longer required exec/hydro/GNUmakefile exec/multispec/GNUmakefile commit 9f7cdd85cb16de751a9991f76595d9dd1cffcd29 Author: Andy Nonaka Date: Tue Mar 5 17:38:36 2019 -0800 remove antiquated example exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/Make.package exec/INS/Make_precheck.package exec/INS/Make_surface.package exec/INS/TimeStep.cpp exec/INS/WritePlotFile.cpp exec/INS/inputs_2d exec/INS/inputs_3d exec/INS/main_driver.cpp exec/INS/precheck.F90 exec/INS/surfaces.cpp commit 439d472658997c4ac7ad6618ff57846a6e1bee31 Merge: 82512e76 228620f8 Author: Daniel Ladiges Date: Tue Mar 5 16:37:07 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 82512e76e2c7f98396e03dc6185851627594b3e7 Author: Daniel Ladiges Date: Tue Mar 5 16:34:52 2019 -0800 Moved minimal necessary functionality for random number calls from within Fortran. All necessary code now lives in src_rng, refs to fbaselib and fboxlib may be removed from makefiles. src_particles/FhdParticleContainer.H src_particles/src_F90/particle_functions.F90 src_rng/Make.package src_rng/bl_random_c.H src_rng/bl_random_c.cpp src_rng/src_F90/Make.package src_rng/src_F90/bl_random.F90 src_rng/src_F90/rng_functions.F90 commit 228620f87cafec0318166da73e02630f4a281c36 Merge: de8e50d3 b0e9015b Author: Johannes Blaschke Date: Wed Feb 27 17:03:52 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit de8e50d32c7e57588e78eff2a6b7e8d2226d7449 Author: Johannes Blaschke Date: Wed Feb 27 17:03:48 2019 -0800 working on fixing boundary conditions src_hydro/boundary.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/bound_funcs.F90 commit c93463d7cd4dd665a2222ab174a17bf5182e8bcd Author: Johannes Blaschke Date: Wed Feb 27 15:49:31 2019 -0800 update makefile to work with fboxlib exec/channel/GNUmakefile commit b0e9015baae1565f0406ecfdfe7f76d9c2b6bebd Author: Daniel Ladiges Date: Wed Feb 27 14:41:58 2019 -0800 Added simplified move ions functions. exec/immersedIons/GNUmakefile exec/immersedIons/INS_functions.H exec/immersedIons/Make.package exec/immersedIons/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 75e238695e476f3d36865ee3fa777621284e4c58 Author: Daniel Ladiges Date: Wed Feb 27 12:38:49 2019 -0800 Added working directory for immersed ions exec/immersedIons/GNUmakefile exec/immersedIons/INS_functions.H exec/immersedIons/Make.package exec/immersedIons/Make_precheck.package exec/immersedIons/Make_surface.package exec/immersedIons/TimeStep.cpp exec/immersedIons/WritePlotFile.cpp exec/immersedIons/WritePlotFileHydro.cpp exec/immersedIons/advance.cpp exec/immersedIons/hydro_test_functions.H exec/immersedIons/hydro_test_functions_F.H exec/immersedIons/inputs_2d exec/immersedIons/inputs_3d exec/immersedIons/main_driver.cpp exec/immersedIons/precheck.F90 exec/immersedIons/surfaces.cpp commit a30c9f70381aa621b5d2cc20606f810a58cd4da7 Merge: f0efe1bb 16ea69fa Author: Johannes Blaschke Date: Wed Feb 27 00:18:36 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit f0efe1bb744b8a5251f5fec4f2bc944c13145ecc Author: Johannes Blaschke Date: Tue Feb 26 23:49:39 2019 -0800 add no-slip boundary conditions... still needs stochastic fluxes and cleanup exec/channel/advance.cpp exec/channel/main_driver.cpp src_common/ComputeDivAndGrad.cpp src_common/MuliFABFillRandom.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/src_F90/stag_apply_op.F90 src_hydro/MacProj_hydro.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMFlux.cpp src_hydro/boundary.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/bound_funcs.F90 commit 16ea69fab035730856be89ce5fac97a3b60b0525 Author: Daniel Ladiges Date: Tue Feb 26 14:36:55 2019 -0800 compressible stuff exec/compressible/GNUmakefile exec/compressible/inputs_3d src_compressible/src_F90/membrane_funcs.F90 src_compressible/timeStep.cpp commit af4930abdcaffef30e063991c2a827282a19464d Author: Katherine Klymko Date: Thu Feb 21 15:04:28 2019 -0800 fixed spelling :) exec/brownian/GNUmakefile exec/brownian/INS_functions.H exec/brownian/Make.package exec/brownian/Make_precheck.package exec/brownian/Make_surface.package exec/brownian/TimeStep.cpp exec/brownian/WritePlotFile.cpp exec/brownian/WritePlotFileHydro.cpp exec/brownian/advance.cpp exec/brownian/delPlots exec/brownian/hydro_test_functions.H exec/brownian/hydro_test_functions_F.H exec/brownian/inputs_2d exec/brownian/inputs_3d exec/brownian/main_driver.cpp exec/brownian/makeBoth exec/brownian/precheck.F90 exec/brownian/surfaces.cpp commit 642b59ec8147effb70581e40fe8bc3209744dafc Author: Daniel Ladiges Date: Wed Feb 20 20:21:11 2019 -0800 Testing temporary work around for imminent death of F_BaseLib. Discuss tomorrow. exec/compressible/GNUmakefile commit 592eed24db6a574198e29ef8a3506380b3a2adf4 Merge: 59fa7013 b1edc0f8 Author: Daniel Ladiges Date: Tue Feb 19 16:40:00 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 59fa701333b3afc5f0ed14786cd7f75eb570f833 Author: Daniel Ladiges Date: Tue Feb 19 16:38:29 2019 -0800 Added exec dir for brownian motion. Currently copy of immersed boundary with hydro commented out exec/browninian/GNUmakefile exec/browninian/INS_functions.H exec/browninian/Make.package exec/browninian/Make_precheck.package exec/browninian/Make_surface.package exec/browninian/TimeStep.cpp exec/browninian/WritePlotFile.cpp exec/browninian/WritePlotFileHydro.cpp exec/browninian/advance.cpp exec/browninian/delPlots exec/browninian/hydro_test_functions.H exec/browninian/hydro_test_functions_F.H exec/browninian/inputs_2d exec/browninian/inputs_3d exec/browninian/main_driver.cpp exec/browninian/makeBoth exec/browninian/precheck.F90 exec/browninian/surfaces.cpp exec/compressible/inputs_3d src_particles/src_F90/particle_functions.F90 commit b1edc0f8dd3097c9b61879ff49fbe90e36fbca42 Author: Guy Moore Date: Sat Feb 16 15:38:50 2019 -0800 Added advance routines exec/hydro/Make.package exec/hydro/advance.cpp exec/hydro/hydro_test_functions.H exec/multispec/Make.package exec/multispec/advance.cpp exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H src_hydro/Make.package src_hydro/MkAdvSFluxdiv.cpp src_hydro/hydro_functions.H src_multispec/ComputeMassFluxdiv.cpp src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H commit cf206216b2ea77652026d5b80d6da9a8ab72c9c8 Merge: 14d643c1 302d6486 Author: Guy Moore Date: Sat Feb 16 12:41:15 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 302d6486ff12dcdfd86e70449ddbdf1bbac96f83 Author: Johannes Blaschke Date: Thu Feb 14 15:56:20 2019 -0800 add pressure bcs src_hydro/boundary.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/bound_funcs.F90 commit cd6b8dc317f114560478b81620364da6261b5bdb Author: Johannes Blaschke Date: Thu Feb 14 13:49:57 2019 -0800 set neumann mlgm bcs src_gmres/ApplyPrecon.cpp src_gmres/MacProj.cpp src_hydro/MacProj_hydro.cpp commit f90c96fbe1aee3e88f21f37465be53fd936793fa Author: Johannes Blaschke Date: Thu Feb 14 10:08:27 2019 -0800 fix typo exec/channel/inputs_3d_test exec/channel/inputs_3d_test.2 src_hydro/src_F90/bound_funcs.F90 commit 32ed4b357b27befaf50d1f0cc10467425a817cdf Author: Johannes Blaschke Date: Wed Feb 13 16:08:28 2019 -0800 debuging deterministric bcs exec/channel/advance.cpp exec/channel/inputs_3d_test exec/channel/main_driver.cpp src_gmres/MacProj.cpp src_hydro/MacProj_hydro.cpp src_hydro/boundary.cpp src_hydro/hydro_functions.H commit 5b9198527485c36e471a0ddfdcb64673188bc62f Author: Johannes Blaschke Date: Wed Feb 13 14:13:48 2019 -0800 added note for stochastic BCs exec/channel/advance.cpp src_hydro/StochMFlux.cpp commit 6ee8603d58bfd2a750c2db97da746dd14c641255 Author: Johannes Blaschke Date: Wed Feb 13 11:25:57 2019 -0800 finish implementing deterministic part of nsw src_hydro/src_F90/bound_funcs.F90 commit 1db6605822c6e266ec93a8d91e15e477783655bd Author: Johannes Blaschke Date: Wed Feb 13 09:44:55 2019 -0800 we don't need them pesky backtraces in the git .gitignore commit 14d643c135aeb0e03c1a74ce3cab85e73a6ca7fc Merge: dfe179bc 44629300 Author: Guy Moore Date: Tue Feb 12 23:38:10 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 44629300a32c9c2d39b2246fc51c192a87105382 Author: Johannes Blaschke Date: Tue Feb 12 17:05:38 2019 -0800 added alternative way of specifying local variables/paths .gitignore exec/channel/GNUmakefile tools/Path.local.template commit 0f488d9a99200bcb8b99c6da44e897b9aca521b1 Author: Johannes Blaschke Date: Tue Feb 12 15:50:54 2019 -0800 fix typo src_hydro/src_F90/bound_funcs.F90 commit 84ab50b8085e1d05d7095db83f5d85dbeca36b12 Author: Johannes Blaschke Date: Tue Feb 12 15:50:12 2019 -0800 implement hi-end of no-slip bcs src_hydro/boundary.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/bound_funcs.F90 commit 92a752450954cc84464086bfaa721cadc654c6d9 Author: Katherine Klymko Date: Tue Feb 12 14:31:41 2019 -0800 further work on boundary for channel exec/channel/advance.cpp src_hydro/hydro_functions.H src_hydro/src_F90/bound_funcs.F90 commit d29faf844d4d631b94f9cb20202041cf2bf88603 Author: Johannes Blaschke Date: Mon Feb 11 21:44:57 2019 -0800 begin adding immersed boundaries... oh, and pushed after daniel exec/channel/GNUmakefile src_immersed-boundary/IBCore.H src_immersed-boundary/IBCore.cpp src_immersed-boundary/IBParticleContainer.H src_immersed-boundary/IBParticleContainer.cpp src_immersed-boundary/IBParticleInfo.H src_immersed-boundary/MFUtil.H src_immersed-boundary/Make.package src_immersed-boundary/ib_functions_F.H src_immersed-boundary/src_F90/Make.package src_immersed-boundary/src_F90/constant_mod.F90 src_immersed-boundary/src_F90/ib_fort_utils.F90 src_immersed-boundary/src_F90/param_mod.F90 src_immersed-boundary/src_F90/set_particle_properties.F90 commit 30d01fc65db26b33b704de2f244621868d032e3d Merge: 3130e348 f20f25a0 Author: Daniel Ladiges Date: Mon Feb 11 19:28:59 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 3130e348bfd73aaebc4cb35ef509dac7c9114bac Author: Daniel Ladiges Date: Mon Feb 11 19:28:32 2019 -0800 I pushed later than Johannes. exec/DSMC/surfaces.cpp exec/compressible/inputs_3d src_compressible/src_F90/membrane_funcs.F90 commit f20f25a0f339e665e0e8918c7f8d2b49a86c3296 Author: Johannes Blaschke Date: Mon Feb 11 19:03:15 2019 -0800 update gitignore .gitignore commit dfe179bcded346249eb3e46512050bdc380dcc3c Merge: 94c83723 a9e7c512 Author: Guy Moore Date: Sat Feb 9 18:42:59 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit a9e7c512fa1bbd1d5d97815dca07219a0c5986ce Author: Guy Moore Date: Sat Feb 9 18:07:15 2019 -0800 Cleaned-up and improved convergence testing capabilities: new inputs files and improved scripts with README exec/hydro/README_CONVERGENCE exec/hydro/compute_convergence_rate.sh exec/hydro/inputs_dtrmnistic_convergence_2d exec/hydro/inputs_dtrmnistic_convergence_3d exec/hydro/main_driver.cpp exec/hydro/run_conv_tests_2.sh exec/hydro/run_convergence_tests.sh src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 94c837233699e2be46e06549b2f61d63ebfd4fcc Merge: 9b0c8709 0eac7dd5 Author: Guy Moore Date: Sat Feb 9 11:45:37 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 0eac7dd597a3c22ff6f1fc1c82dcfab06d23bdc4 Author: Katherine Klymko Date: Fri Feb 8 19:21:24 2019 -0800 started adding boundaries for channel src_hydro/Make.package src_hydro/boundary.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/bound_funcs.F90 commit 4fcca9e6a65835b9edaaa4b66195de42d0a265d8 Author: Johannes Blaschke Date: Wed Feb 6 17:43:14 2019 -0800 experiment with channel example exec/channel/inputs_3d src_common/ConvertStag.cpp src_gmres/gmres_functions.H src_gmres/src_F90/stag_apply_op.F90 src_hydro/MkAdvMFluxdiv.cpp src_hydro/StochMFlux.cpp src_hydro/src_F90/mk_advective_m_fluxdiv.F90 src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 10bea6573689d510523caf71f713518c78093b33 Merge: 12f4747b d7167e79 Author: Johannes Blaschke Date: Tue Feb 5 18:14:47 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 12f4747b41d804beae63468222e0c31b7db945f0 Author: Johannes Blaschke Date: Tue Feb 5 18:14:39 2019 -0800 clean up channel example exec/channel/inputs_3d exec/channel/main_driver.cpp src_common/src_F90/convert_stag.F90 src_gmres/MacProj.cpp src_hydro/MacProj_hydro.cpp src_hydro/src_F90/mac_solver_hydro.F90 commit d7167e79d9321bc717c36b2596937df65bc1c405 Author: Andy Nonaka Date: Tue Feb 5 14:15:54 2019 -0800 test commit 3 LEGAL commit 435fa2b4f65e3fca3d05b6330abee2ca196329e9 Author: Andy Nonaka Date: Tue Feb 5 14:12:31 2019 -0800 test commit 2 LEGAL commit f23e523a0710c0e3520bef5a4f26742427093dc2 Author: Andy Nonaka Date: Tue Feb 5 14:05:47 2019 -0800 test commit LEGAL commit 0aff537b59d349c9ae8094e4ceed907fa03b631c Author: Johannes Blaschke Date: Tue Feb 5 12:42:39 2019 -0800 fix DIM<3 problem exec/channel/main_driver.cpp commit 9b0c8709628fabe679df747119ac2010b2f188fc Author: Guy Moore Date: Tue Feb 5 12:42:21 2019 -0800 Added mixture property routines src_multispec/ComputeMassFluxdiv.cpp src_multispec/ComputeMixtureProperties.cpp src_multispec/Make.package src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/compute_mixture_properties.F90 commit 9359330d2ad0a6d2d4276263dd51420a1fc8e90d Merge: 35887f10 3a02db40 Author: Johannes Blaschke Date: Tue Feb 5 10:28:40 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 35887f105f09ea3ca3f164b6375b6de87d194bfb Author: Johannes Blaschke Date: Tue Feb 5 10:28:35 2019 -0800 more cleaning up of main driver exec/channel/main_driver.cpp commit 3a02db4011e0ab1e0bac3c2b66471dd3438dda84 Author: Guy Moore Date: Mon Feb 4 17:44:20 2019 -0800 Updated multispec fxns and changed ComputeGrad() in src_common to take a const scalar field "phi" src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_common/common_functions_F.H src_multispec/ComputeMassFluxdiv.cpp src_multispec/multispec_functions.H src_multispec/src_F90/compute_mass_fluxdiv.F90 commit f0c86e81aad4cebbbc5da23ccec0d512a9f66962 Merge: 22720841 96660f21 Author: Guy Moore Date: Mon Feb 4 17:02:13 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 22720841ae880a37982e39a03b408dd5ce074957 Author: Guy Moore Date: Mon Feb 4 17:01:30 2019 -0800 Added flux correction routines src_multispec/CorrectionFlux.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/Make.package src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/correction_flux.F90 src_multispec/src_F90/matvec_mul.F90 commit 96660f21ab82f37ea0ed257e73c2ee26d3daf517 Author: Johannes Blaschke Date: Mon Feb 4 13:41:00 2019 -0800 make makefile compatible with macOS, and delete commented code exec/channel/GNUmakefile exec/channel/main_driver.cpp commit 3a19faa1a9a456257e064cd392f303f1e987d735 Author: Daniel Ladiges Date: Sun Feb 3 18:50:57 2019 -0800 Working Langevin membrane exec/DSMC/surfaces.cpp src_compressible/src_F90/membrane_funcs.F90 commit 1ece995551d8f84f1f2956cd44910689729ecef2 Author: Guy Moore Date: Sun Feb 3 11:23:24 2019 -0800 Added "diffusive mass fluxdiv" capabilities - more flux correction functions needed src_multispec/ComputeMassFluxdiv.cpp src_multispec/DiffusiveMassFluxdiv.cpp src_multispec/Make.package src_multispec/MatvecMul.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions_F.H src_multispec/src_F90/Make.package src_multispec/src_F90/matvec_mul.F90 commit 9adc045c89fcf79117133d99674b72a358dbd235 Author: Johannes Blaschke Date: Fri Feb 1 18:15:53 2019 -0800 continue cleaning up main_driver exec/channel/main_driver.cpp commit ab6d08637bc467a36060ff5f1177ca14259aec15 Author: Johannes Blaschke Date: Fri Feb 1 16:44:40 2019 -0800 clean up main driver exec/channel/main_driver.cpp src_common/src_F90/common_namelist.F90 commit 29372db90de79411c2401ddf15ed0f4cf53d1879 Author: Johannes Blaschke Date: Fri Feb 1 14:54:09 2019 -0800 start working on channel flow example .gitignore exec/channel/GNUmakefile exec/channel/Make.package exec/channel/WritePlotFile.cpp exec/channel/advance.cpp exec/channel/compute_convfact_2.sh exec/channel/hydro_test_functions.H exec/channel/hydro_test_functions_F.H exec/channel/init_funcs.F90 exec/channel/init_s_funcs.F90 exec/channel/inputs_2d exec/channel/inputs_3d exec/channel/inputs_incomp_equil_fluct_2d exec/channel/inputs_incomp_equil_fluct_3d exec/channel/main_driver.cpp exec/channel/run_conv_tests_2.sh exec/hydro/advance.cpp exec/hydro/main_driver.cpp src_common/common_namespace_declarations.H src_common/main.cpp src_gmres/GMRES.cpp src_gmres/StagApplyOp.cpp src_hydro/StochMFlux.H src_hydro/hydro_functions.H src_rng/src_F90/rng_functions.F90 commit 58348b02952215adca6eeffdc711570eab2f9b1e Author: Guy Moore Date: Thu Jan 31 20:44:51 2019 -0800 Ported some "mass fluxdiv" functions & added new multispec exec directory exec/multispec/GNUmakefile exec/multispec/Make.package exec/multispec/WritePlotFile.cpp exec/multispec/advance.cpp exec/multispec/init_funcs.F90 exec/multispec/init_s_funcs.F90 exec/multispec/inputs_2d exec/multispec/inputs_3d exec/multispec/main_driver.cpp exec/multispec/multispec_test_functions.H exec/multispec/multispec_test_functions_F.H src_multispec/ComputeMassFluxdiv.cpp src_multispec/Make.package src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/src_F90/Make.package src_multispec/src_F90/compute_mass_fluxdiv.F90 src_multispec/src_F90/mass_flux_utilities.F90 src_multispec/src_F90/matrix_utilities.F90 commit 280d30466942add8357f316865c7d7c7f521dabc Merge: 9ca87fe5 6bc9c610 Author: Daniel Ladiges Date: Tue Jan 29 19:00:13 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 9ca87fe5c2e97f23ff2f3f2e461a7d60042ea49a Author: Daniel Ladiges Date: Tue Jan 29 18:59:09 2019 -0800 Fixed bug which was resetting stats every n_steps_skip exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/membrane.cpp src_compressible/src_F90/membrane_funcs.F90 src_compressible/ssa.cpp commit 6bc9c610ad3f7bb40a59bbeb8072a04bba8656e2 Author: Guy Moore Date: Mon Jan 28 10:53:13 2019 -0800 Added zero initial velocity for prob_type=0 exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d commit 9274708ddd20853c561cf890aec13c76a04355af Author: Andy Nonaka Date: Fri Jan 25 10:28:39 2019 -0800 turn on fluctuations; fix an issue with the 2d inputs file having a 3rd bc_comp exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d commit 34016cc2cd50d532e676ee9d14bd81cd47a3b563 Author: Guy Moore Date: Thu Jan 24 17:33:27 2019 -0800 Fixed struct. fact. test input files, in addition to 3D tracer fluxdiv routine exec/hydro/inputs_3d exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 742fce206f54501f3591d6f2b317d7aeca918d2d Author: Daniel Ladiges Date: Thu Jan 24 13:05:42 2019 -0800 Started adding Langevin version of membrane exec/DSMC/GNUmakefile exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/membrane.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/ssa.cpp src_compressible/timeStep.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 commit e0d1d29be36dab673b1330bb04362224921dce25 Author: Guy Moore Date: Tue Jan 22 18:21:01 2019 -0800 Fixed namelist and C binding for Fortran functions src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/mass_flux_utilities.F90 src_multispec/src_F90/multispec_namelist.F90 commit 8845b2e5f6d29021fa5943bce0ee0b1934cdfb76 Merge: cc32dec5 6e152aad Author: Guy Moore Date: Tue Jan 22 15:49:52 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit cc32dec5e028a9ef314b0f8636f6fbdb7d384408 Author: Guy Moore Date: Tue Jan 22 15:48:54 2019 -0800 Ported mass-flux utilities - needs debugging src_multispec/Make.package src_multispec/MassFluxUtil.cpp src_multispec/multispec_functions.H src_multispec/multispec_functions.cpp src_multispec/multispec_functions_F.H src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/Make.package src_multispec/src_F90/compute_mass_fluxdiv.F90 src_multispec/src_F90/mass_flux_utilities.F90 src_multispec/src_F90/multispec_namelist.F90 commit 6e152aad07f97c17ca58e8d010f8624f47aceba3 Author: Andy Nonaka Date: Fri Jan 18 12:49:11 2019 -0800 license LEGAL LICENSE commit 304d57a1cfd1dd228f0c3fd09a31d9a764263aa2 Author: Guy Moore Date: Thu Jan 3 16:13:35 2019 -0800 Added src_multispec directory with namespace(&)list src_multispec/Make.package src_multispec/multispec_namespace.H src_multispec/multispec_namespace_declarations.H src_multispec/src_F90/Make.package src_multispec/src_F90/multispec_namelist.F90 commit da220806903dda3d1ff40024c2d92d39f145e23f Merge: 20dedbbd 22bf313e Author: Guy Moore Date: Thu Jan 3 12:37:43 2019 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 22bf313ec30a20ad1aa6652d39abe648c04390f0 Author: Daniel Ladiges Date: Fri Dec 21 16:07:31 2018 -0800 Compressible: changed hyperbolic interpolation to conserve pressure. exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/compressible/GNUmakefile exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/flux.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 commit ba487c7e1e6706f6a9dd88052636dee705e0d143 Author: Daniel Ladiges Date: Wed Dec 19 14:16:44 2018 -0800 Bugfix in particle temperature variance calculation exec/DSMC/GNUmakefile exec/DSMC/Make.package exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp exec/compressible/exec_functions.H exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_compressible/compressible_functions.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/stats.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 commit 6b36ea46f3c97f85d0a50ba92a9f31fa7d6fdbcd Author: Daniel Ladiges Date: Thu Dec 13 12:34:17 2018 -0800 Implemented correct stencil for 3D viscous tensor - some mild debugging remaining. exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit efdd7c574849dc52585e4ca8fe9464379c3931d7 Author: Daniel Ladiges Date: Thu Dec 6 13:46:43 2018 -0800 Removed one more duplication src_common/src_F90/Make.package commit b74a0bd62081bfb61c6666185f66b572d9b34163 Author: Daniel Ladiges Date: Thu Dec 6 13:35:15 2018 -0800 Removed duplicate module name preventing compilation with intel compiler exec/immersedParticles/Make.package src_common/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 src_gmres/src_F90/stag_mg_solver.F90 commit 7a8149a5853065f709042bb52a2ef79ce11a5cb2 Merge: 7828ca78 81a1da6b Author: Daniel Ladiges Date: Thu Dec 6 12:08:43 2018 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 7828ca78b99192473b2e2beea0f006af3205a561 Author: Daniel Ladiges Date: Thu Dec 6 12:06:35 2018 -0800 Removed structure factor stuff from compressible makefile so it will compile on Cori. We will have to address this for incompressible code. exec/compressible/GNUmakefile exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_compressible/compressible_functions_F.H src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit 81a1da6bdec706f41fcc07bbd793910dbe451cb1 Author: Andy Nonaka Date: Wed Dec 5 09:05:52 2018 -0800 remove unused stuff src_hydro/Make.package src_hydro/advance_timestep_inertial.cpp src_hydro/hydro_functions.H commit ea806de008ff34e53b5f266a5e00006cfdc673b6 Author: Daniel Ladiges Date: Tue Dec 4 20:07:42 2018 -0800 Minor compressible bugfixes? exec/compressible/inputs_3d src_compressible/src_F90/flux_funcs.F90 src_compressible/ssa.cpp src_particles/src_F90/particle_functions.F90 commit 77f427e71c3d3fbefba830f00d5681efd78838cf Author: Daniel Ladiges Date: Mon Dec 3 19:51:01 2018 -0800 minor bugfixes to particle code exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/compressible/inputs_3d exec/compressible/writePlotFile.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/timeStep.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 commit 20dedbbdeed397d40fe174c3ec52dabc474943e6 Merge: 18aa8420 01bfc433 Author: Guy Moore Date: Mon Dec 3 15:22:41 2018 -0800 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 01bfc4336c54293605c5653fd079ffc41cbfc017 Author: Daniel Ladiges Date: Fri Nov 30 14:29:36 2018 -0800 ImmersedParticles/DSMC: -Added most particle parameters to input file. -Particle origin is now stored for mean square displacement calcs. exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_3d exec/DSMC/surfaces.cpp exec/compressible/inputs_3d exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/species.H src_common/src_F90/common_namelist.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 18aa84204e3147c63d7d07c0ed2026327bea0038 Author: Guy Moore Date: Wed Nov 28 19:19:46 2018 -0800 Tracer diffusion coef. condition corrected - minimum (cell reynolds) instead of maximum limit exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/inputs_incomp_equil_fluct_2d src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 901ac0cedf054880faaf2cb8f3213c5d4706ef35 Author: Daniel Ladiges Date: Wed Nov 28 17:15:28 2018 -0800 Added cross correlation cell to input files to avoid possible out of bounds error in immersedParticles exec/DSMC/inputs_3d exec/compressible/inputs_3d src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp src_particles/src_F90/collision_functions.F90 commit 6be1dbda2fdd814619f4f37ed65d1301c0e47f6b Author: Daniel Ladiges Date: Wed Nov 28 16:51:49 2018 -0800 Added additional cross correlation mesurements to DSMC & compressible. Updated immersedParticles to be compatible. Added switches for stochastic terms to input file for immersedParticles. exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/stats.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit c9b359ebd3adc25e6b0c1a48f1496e4dfc3ad03f Author: Guy Moore Date: Wed Nov 28 16:32:36 2018 -0800 Added random flux switch using variance_coef_mom & Daniel helped fix "ngc" initialization exec/hydro/advance.cpp exec/hydro/main_driver.cpp src_common/src_F90/common_namelist.F90 src_common/src_F90/multifab_fill_random.F90 commit f9d32da27015bce1b43846da8fa1ec78beaf648b Author: Daniel Ladiges Date: Tue Nov 27 19:38:23 2018 -0800 Compressible FHD - Began adding code for averaging cross correlations over spatial ensemble. exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/stressTensor.nb src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/stats.cpp commit 145c1bc133a70b0834be5f363d98e70fa5bfc4d5 Author: Daniel Ladiges Date: Mon Nov 26 15:10:38 2018 -0800 Restored 3D functionality and added function to average output quantaties over the yz axes. exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_common/MuliFABFillRandom.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp commit 46951d282127a79bc007d482498d1cd5d64e21d8 Author: Daniel Ladiges Date: Fri Nov 16 12:03:51 2018 -0800 removed particle boundaries exec/immersedParticles/surfaces.cpp commit 6ac09444ed76295ffe3932f7423d3719c54e3e2f Author: Daniel Ladiges Date: Thu Nov 15 17:31:16 2018 -0800 Program now takes periodicity from input file. Hydro runs correctly. exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp commit c1596ae357bd916a6a48f2f00ffc7fd5ceda11de Author: Daniel Ladiges Date: Thu Nov 15 17:25:12 2018 -0800 Fixed plotfile function. Now seperate functions for outputing particle and hydro components exec/compressible/GNUmakefile exec/compressible/inputs_3d exec/immersedParticles/INS_functions.H exec/immersedParticles/Make.package exec/immersedParticles/WritePlotFile.cpp exec/immersedParticles/WritePlotFileHydro.cpp exec/immersedParticles/hydro_test_functions.H exec/immersedParticles/main_driver.cpp commit b237f9275a4791c15125f79896a3e87afc717c2e Author: Daniel Ladiges Date: Thu Nov 15 13:06:45 2018 -0800 fixed temperature bug exec/immersedParticles/main_driver.cpp commit fe8041d3f85f383536373131d843894666a0cc42 Author: Daniel Ladiges Date: Thu Nov 15 12:54:14 2018 -0800 immersed Particle bugfixing exec/compressible/GNUmakefile exec/immersedParticles/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 commit bd9e7b8f257a2d9ee310a31484dc868ff0640046 Author: Daniel Ladiges Date: Thu Nov 15 12:17:48 2018 -0800 addded hydro advance function to immersed particles exec/immersedParticles/advance.cpp exec/immersedParticles/hydro_test_functions.H exec/immersedParticles/hydro_test_functions_F.H commit 7863cb8f71da41e8985bd1a2e9111cf30f55fb4f Author: Daniel Ladiges Date: Thu Nov 15 12:07:28 2018 -0800 forgot to push makefile exec/compressible/main_driver.cpp commit 5f6e1bc3f1c0bc45c35c928a1e30c36983640218 Author: Daniel Ladiges Date: Wed Nov 14 16:49:53 2018 -0800 Finished breaking up fhd-particle move function. Code not currently compiling due to error in initCells exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp src_compressible/flux.cpp src_compressible/timeStep.cpp src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 7757b6dc930985f15eacf5b670867047993f0fc8 Author: Daniel Ladiges Date: Tue Nov 13 20:34:33 2018 -0800 Started spinning off different parts of interpolation code into seperate functions. Will avoid future duplication and and make the particle_move function actually readable. exec/immersedParticles/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 9f665696f19b3f4687b6b56aed586f0008620aa2 Author: Daniel Ladiges Date: Tue Nov 13 18:49:19 2018 -0800 Merged latest version of fluct hydro into immersed particles code. Code compiles but is not tested. exec/immersedParticles/GNUmakefile exec/immersedParticles/main_driver.cpp commit 3f58765acffa4df99ae38d1c480f84497fdf6ca6 Author: Daniel Ladiges Date: Tue Nov 13 11:36:12 2018 -0800 fixed difflux code for new ghost cell arrangement src_compressible/src_F90/flux_funcs.F90 commit 7f95d9bf4762f28418dcae96b19231ab824b885e Author: Daniel Ladiges Date: Tue Nov 13 11:27:02 2018 -0800 MOdified code to use vector of ghost cell sizes instead of unecessary cells in all directions exec/compressible/inputs_3d src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 commit 1438fa5bbaa3efbb8439ea3f8f46a5153521b541 Author: Daniel Ladiges Date: Mon Nov 12 18:01:02 2018 -0800 Added alternative version of multifabFillRandom for 1D case which avoids use of OverrideSync. Testing to see if this fixes crashing in compressible code. src_common/MuliFABFillRandom.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_fill_random.F90 src_compressible/flux.cpp src_compressible/src_F90/flux_funcs.F90 src_compressible/timeStep.cpp src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 commit ff2a14ec1752a218d83c05e4430b0486f3c383bf Author: Daniel Ladiges Date: Fri Nov 9 19:13:02 2018 -0800 Bug checking for writePlotFile function in compressible exec/DSMC/inputs_3d exec/DSMC/surfaces.cpp exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp exec/immersedParticles/GNUmakefile src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/timeStep.cpp commit b3a01b7ed0362628bd7dc8128c808a4f092ee079 Author: Daniel Ladiges Date: Fri Nov 2 18:15:32 2018 -0700 Updated main_driver in immersed particles to use multi-component multifab format used by particle functions. Immersed particles code now compiles. exec/immersedParticles/main_driver.cpp commit ab340c460430ccffeb4117986a2f33212a6da00b Author: Daniel Ladiges Date: Fri Nov 2 15:15:20 2018 -0700 Fixed output bug for compressible. Started cleaning up immersed particles and bringing up to date with changes made to DSMC code. exec/DSMC/surfaces.cpp exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/immersedParticles/main_driver.cpp src_compressible/src_F90/stats_funcs.F90 commit 3571be4e2d0a0a0beb0131d680820414b81aa853 Author: Daniel Ladiges Date: Thu Nov 1 16:23:11 2018 -0700 Fixed pressure interpolation causing unphysical oscillation. Note that current version is nerfed to do only 1D exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp exec/compressible/GNUmakefile exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/ssa.cpp src_compressible/stats.cpp src_compressible/timeStep.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit 71b00ca757d40a6c7e737d20abc165e82f1beb08 Author: Daniel Ladiges Date: Thu Oct 25 12:16:28 2018 -0700 Complete version for ssa test cases exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.cpp exec/compressible/inputs_3d exec/compressible/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit bcf1d4247afadefcb36060ecf34b9c6645ba2638 Author: Daniel Ladiges Date: Mon Oct 22 14:23:02 2018 -0700 Added some items to common namelist for membrane related stuff Various membrane related modifications exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/inputs_2d exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp exec/compressible/GNUmakefile exec/compressible/exec_functions.H exec/compressible/inputs_3d exec/compressible/interpAnalysis.nb exec/compressible/main_driver.cpp exec/compressible/stressTensor.nb exec/compressible/writePlotFile.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/membrane.cpp src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/membrane_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/stats.cpp src_compressible/timeStep.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit c4fa041b2d8ffc0f98abcc134da05f16d1bc2b4d Author: Guy Moore Date: Fri Oct 19 13:44:27 2018 -0700 Variable select, improved, cleaned-up, & simplified exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit fb46a4e95359cfb75c3c03c0be7adbaadce8a05f Author: Guy Moore Date: Thu Oct 18 19:17:00 2018 -0700 Added ability to select structure factor pairs: - Error checking - Sort pairs and remove repeats exec/hydro/main_driver.cpp src_analysis/StructFact.H src_analysis/StructFact.cpp commit 32d9d2633959de4ab8955febbaf32139910e5aef Merge: 3291ccae 5baa966e Author: Guy Moore Date: Mon Oct 15 08:41:42 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 5baa966e77deaba606b8aefaf994f962da10c221 Author: Daniel Ladiges Date: Thu Oct 11 18:37:34 2018 -0700 Added stochastic flux and some analysis functions. Compressible (single species) fluctuating hydro code now complete. exec/compressible/exec_functions.H exec/compressible/inputs_3d exec/compressible/main_driver.cpp exec/compressible/writePlotFile.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/stats_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/timeStep.cpp commit 3291ccaec2c17acec7727081284b27684e3e181c Author: Guy Moore Date: Thu Oct 11 15:30:12 2018 -0700 Futher cleanup of initial projection routine src_hydro/MacProj_hydro.cpp commit 9ec4d312ba31c0cf9456a12d378b49050778e692 Author: Guy Moore Date: Thu Oct 11 15:02:01 2018 -0700 Cleaned up projection function and added iteration controls on linear solver exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/main_driver.cpp src_hydro/MacProj_hydro.cpp src_hydro/hydro_functions.H commit 372025b5369faf6cabdb8a0fdcd59fff27d5ef05 Author: Daniel Ladiges Date: Wed Oct 10 16:36:41 2018 -0700 Added hyperbolic flux, boundary conditions, and basic output. Deterministic compressible code now complete with basic testing. exec/compressible/Make.package exec/compressible/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/boundary.cpp src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/bound_funcs.F90 src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/timeStep.cpp commit 1ed84a300e4160f4dbc1bb4d41aa2c069c59d510 Author: Guy Moore Date: Tue Oct 9 16:25:53 2018 -0700 Cleaned up main driver & added separate advance routine exec/hydro/advance.cpp exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/hydro_functions.H commit 65488a78b354cc3633dfddb652ee06792b3d9ea0 Author: Daniel Ladiges Date: Mon Oct 8 14:05:25 2018 -0700 Added multispecies to calcuation of transport coefficients src_compressible/conservedPrimitiveConversions.cpp src_compressible/src_F90/trans_funcs.F90 commit 0612d617e84de5d009d411b6a0e0ecb5b6fed147 Author: Daniel Ladiges Date: Mon Oct 8 13:17:40 2018 -0700 Finished conserved to primitive function including multi species heat capacity. Added boundary filling and visc/heat conduction calcs to RK3 loop. src_compressible/compressible_functions.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/src_F90/conv_funcs.F90 src_compressible/timeStep.cpp commit dacca460c05e0235503814c29f626f4e314f4cd6 Author: Daniel Ladiges Date: Fri Oct 5 17:42:24 2018 -0700 Added to compressible code: -Several compressible physical parameters in common namespace -Function to calculate diff flux -Function to update transport coeffs -RK3 time stepping -Outline of functions for converting between primitive and conserved variables exec/compressible/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/conservedPrimitiveConversions.cpp src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/conv_funcs.F90 src_compressible/src_F90/diff_flux.F90 src_compressible/src_F90/flux_funcs.F90 src_compressible/src_F90/time_step_funcs.F90 src_compressible/src_F90/trans_funcs.F90 src_compressible/timeStep.cpp src_compressible/transCoeffs.cpp commit 44f6633f2a16d71b205c812c58e0c57b8d897a91 Author: Guy Moore Date: Thu Oct 4 16:50:43 2018 -0700 Accounted for changed source directory of StructFact class exec/hydro/GNUmakefile exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/StochMFlux.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/struct_fact.F90 commit 31ac64e54e224322996138af7bbac639173cab66 Author: Guy Moore Date: Thu Oct 4 14:19:37 2018 -0700 Initial projection and added momentum fluctuations appear to be working exec/hydro/inputs_incomp_equil_fluct_2d exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/main_driver.cpp src_hydro/MacProj_hydro.cpp src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp commit fd1a38ae91f88a357c59ac2553249891113b66f7 Author: Guy Moore Date: Wed Oct 3 19:06:26 2018 -0700 First commit of initial projection step capabilities - needs debugging src_hydro/MacProj_hydro.cpp src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/mac_solver_hydro.F90 commit 50cca3d7090d774692a2a21829001aaca7a0877a Author: Daniel Ladiges Date: Tue Oct 2 18:14:41 2018 -0700 Outline of diffusive and hyperbolic flux bits for compressible code exec/compressible/GNUmakefile exec/compressible/Make.package exec/compressible/main_driver.cpp src_compressible/Make.package src_compressible/compressible_functions.H src_compressible/compressible_functions_F.H src_compressible/flux.cpp src_compressible/src_F90/Make.package src_compressible/src_F90/diff_flux.F90 src_compressible/src_F90/flux_funcs.F90 commit feffab84f54eec049d49e4a89bc485d39c903f4a Author: Daniel Ladiges Date: Tue Oct 2 12:49:43 2018 -0700 Added 'diameter' vector to common namespace. Used for storing kinetic diameter for particles and for calculating transport coefficients exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.cpp exec/immersedParticles/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 src_surfaces/src_F90/surface_functions.F90 commit eda8a7cdf8bb15cff81c7fcf533d00aabbe95729 Author: Daniel Ladiges Date: Tue Oct 2 10:49:01 2018 -0700 Removed line break from middle of string in src_analysis/StructFact.cpp src_analysis/Make.package src_analysis/StructFact.cpp commit 1bf06fe29248d52f7ba6ec752aafc974c1da5a8e Author: Guy Moore Date: Mon Oct 1 18:14:11 2018 -0700 Ability to add initial equilibrium momentum fluctuations src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit 9f0006331b59ff97d7bcdc6c443df5b4d2febe0e Author: Daniel Ladiges Date: Mon Oct 1 17:30:32 2018 -0700 Moved files pertaining to structure factors to /src_analysis. These can be used by hydro, compressible, and DSMC. Guy will remove them from their current location in /src_hydro when he has updated the hydro code. Daniel will also move the analysis code he has written for DSMC into this directory, for use with all codes. src_analysis/Make.package src_analysis/StructFact.H src_analysis/StructFact.cpp src_analysis/analysis_functions_F.H src_analysis/src_F90/Make.package src_analysis/src_F90/struct_fact.F90 commit c4caf8e33abca237d2d35856c3c091fffdf1f412 Author: Guy Moore Date: Thu Sep 27 14:40:48 2018 -0700 Cleanup and added error control statements exec/hydro/inputs_incomp_equil_fluct_3d src_hydro/StructFact.H src_hydro/StructFact.cpp commit 2b0f0bcbadf095628ddbb6b68aa891fa60e90458 Author: Guy Moore Date: Thu Sep 27 12:35:51 2018 -0700 Appears to be working in 2D, as well as with non-cubic/square grids exec/hydro/inputs_incomp_equil_fluct_2d commit a21f4498b2f6ef9ac2c92ec3c510fda0537ea3f7 Author: Guy Moore Date: Thu Sep 27 12:19:06 2018 -0700 First commit before adapting for 2D - removed division by pi in structure factor scaling src_hydro/StructFact.cpp commit 94313a53f6fb69de08611351ebff363424846ea3 Author: Guy Moore Date: Tue Sep 25 19:10:55 2018 -0700 FFT on multiple procs appears to work - transpose needed? src_hydro/StructFact.H src_hydro/StructFact.cpp commit b625f63a71a4fddd69d656e7969ed8b9ab5b99a9 Author: Guy Moore Date: Tue Sep 18 11:36:50 2018 -0700 Changed vectors of 1 component MFs to multi-component MFs exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/struct_fact.F90 commit cca16a03dadc15fc8d618d93efd64f04558e3d6d Author: Guy Moore Date: Tue Sep 18 09:18:42 2018 -0700 First commit before changing MF vectors to multi-component multifabs src_hydro/StructFact.cpp commit d6bc664799631a75156ece17313bab98f0b39acc Author: Andy Nonaka Date: Mon Sep 17 17:09:43 2018 -0700 report run time per time step exec/hydro/main_driver.cpp commit d1dda3c1bc45e6bc8e9e0d9ea2a3733b5297870e Author: Guy Moore Date: Mon Sep 17 16:59:57 2018 -0700 second input file commit exec/hydro/inputs_incomp_equil_fluct_3d commit 59bd25e468b962e11e03a1a248047f4d6ffc08aa Author: Guy Moore Date: Mon Sep 17 16:54:48 2018 -0700 inputs file updated for 36 hour long run (serial) exec/hydro/inputs_incomp_equil_fluct_3d commit b300139adbde12ad765e2a682a8009ddd1ccb093 Author: Guy Moore Date: Mon Sep 17 16:06:25 2018 -0700 Removed serial hack to enforce div. free constraint on initial condition exec/hydro/init_funcs.F90 commit 468ba9fe9e8272aec410184f1ee20b1d69b5abce Author: Andy Nonaka Date: Mon Sep 17 15:09:50 2018 -0700 serialized shift routine. FFT stuff should work now in parallel if nproc=ngrid and the grids are cubic src_hydro/StructFact.cpp commit c78726bac85472433a2cc47bbffcbe4cf478e280 Author: Guy Moore Date: Fri Sep 14 17:03:42 2018 -0700 Adapted StructFact for arbitrary number of variables exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit f0bb72249253a471342a8af54df8b92f5659e2a5 Author: Guy Moore Date: Fri Sep 14 14:45:07 2018 -0700 Changed averaging to shifting nodal to cell centered exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit 718dee876dd270ce24ff89330cb5890cd8798a47 Author: Guy Moore Date: Mon Sep 10 19:09:52 2018 -0700 Minor tune-ups + div. free enforcement for vortex initial condition exec/hydro/init_funcs.F90 exec/hydro/inputs_incomp_equil_fluct_3d exec/hydro/main_driver.cpp src_hydro/StochMFlux.cpp commit e8623a45f16c2956962744d5200a9ff1e5883e13 Author: Guy Moore Date: Fri Sep 7 14:29:28 2018 -0700 Added profiling tags to cpp functions exec/hydro/WritePlotFile.cpp exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_common/ConvertStag.cpp src_common/FindCoords.cpp src_common/FindNodalValues.cpp src_common/MuliFABFillRandom.cpp src_common/main.cpp src_common/main_driver.cpp src_gmres/ApplyMatrix.cpp src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/NormInnerProduct.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/StochMFlux.cpp src_hydro/StructFact.cpp commit 210e95220ad94095fea08b4b91d4ac857238dfe6 Author: Andy Nonaka Date: Fri Sep 7 14:18:15 2018 -0700 structure factor test setup exec/hydro/inputs_incomp_equil_fluct_3d commit 4b09c350c447cdf802699c4c9e0179e18581052f Merge: 9e766566 b218fd6a Author: Guy Moore Date: Fri Sep 7 12:59:52 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX Conflicts: exec/hydro/inputs_3d commit 9e766566496d958f93f3fb04e80c176eb2ce1682 Author: Guy Moore Date: Fri Sep 7 12:56:03 2018 -0700 Fixed complex magnitude routine and corrected scaling - appears to be working exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/struct_fact.F90 commit b218fd6a9e2c79cd47c04c62f2ba4d96c0297477 Author: Andy Nonaka Date: Fri Sep 7 10:58:55 2018 -0700 test file for equilibrium structure factors in 3d. still WIP. making a version in the old FluctHydro code that does the same thing. exec/hydro/inputs_incomp_equil_fluct_3d commit bb2f964c5105d0823ec7ad97949117091704f9a0 Author: Andy Nonaka Date: Fri Sep 7 10:58:33 2018 -0700 update these inputs files to use T=273.15 exec/hydro/inputs_2d exec/hydro/inputs_3d commit 1cc231abe0723e4109d4a70c6aa227df180ffb21 Author: Andy Nonaka Date: Fri Sep 7 10:57:03 2018 -0700 use T_init[0] from inputs file. NOTE: the default value for T_init is 1.0 so the inputs files will have to be updated exec/hydro/main_driver.cpp commit 4d02c17cf13dc55d2f6c3fe048482457215e13fe Author: Andy Nonaka Date: Fri Sep 7 10:54:21 2018 -0700 added T_init to the common namelist/namespace. This has two components (similar to u_init) that allows us some control over how to specify temperature. For now our applications will likely use T_init[0] to define the global temperature, so we can set it in the inputs file src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit d632337ff95347995154716c05d66279601969c1 Author: Andy Nonaka Date: Fri Sep 7 10:09:09 2018 -0700 add shifted velocities to cell-centered plotfile exec/hydro/WritePlotFile.cpp commit df338279c3f55e7700f3fec54c6a48e1cd04dd32 Author: Andy Nonaka Date: Fri Sep 7 10:08:39 2018 -0700 bugfix... shift_face_to_cc was calling the average_face_to_cc routine src_common/ConvertStag.cpp commit 2cbe9bd2819f372eabb72bf5ea9f1b23605ab11b Author: Guy Moore Date: Fri Sep 7 09:31:15 2018 -0700 First scaling attempt exec/hydro/GNUmakefile exec/hydro/init_funcs.F90 exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit f5a563ddce6b6cd7948b23e055a38b87da5a386b Author: Guy Moore Date: Wed Sep 5 16:25:20 2018 -0700 Fixed namelist bug & added struct_fact update controls exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_common/src_F90/common_namelist.F90 src_hydro/StructFact.cpp commit a580669a8c65d8bfd50bf4f97c130a7f4fac8a30 Author: Guy Moore Date: Wed Sep 5 14:16:28 2018 -0700 Added WritePlotFile routine - MPI bug exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit 2e7801c9edc68f2bb94b1d3603f122bf93bf6b45 Author: Andy Nonaka Date: Wed Sep 5 10:50:36 2018 -0700 implement a timer src_common/ComputeDivAndGrad.cpp commit 2fd41f9dbe3842748c00645db6694963be101610 Author: Andy Nonaka Date: Wed Sep 5 10:47:46 2018 -0700 comment src_common/common_namespace.H commit 260ec4a7814a3b9db614e4b41cc630bff67c796b Author: Andy Nonaka Date: Wed Sep 5 10:42:36 2018 -0700 put struct_fact_int and n_steps_skip into common namelist and namespace src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 commit 0398fe94b9f6b2f2ec567eabd7a3344f41d3abf6 Author: Guy Moore Date: Tue Sep 4 16:10:34 2018 -0700 Added fft shift routine - not parallel compatible exec/hydro/inputs_2d exec/hydro/inputs_3d src_hydro/StructFact.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/fft_shift.F90 commit 026c446865bc75b436a4a4feabc11348636f326b Author: Guy Moore Date: Tue Sep 4 11:09:23 2018 -0700 computes covariance - needs proper scaling and further testing exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit 19ecf59254e38f0f57acdceaab7e250ab890767c Author: Guy Moore Date: Fri Aug 31 16:27:34 2018 -0700 Added cumulative covariance multifabs exec/hydro/GNUmakefile exec/hydro/compute_convfact_2.sh exec/hydro/init_funcs.F90 exec/hydro/inputs_3d exec/hydro/run_conv_tests_2.sh src_hydro/StructFact.H src_hydro/StructFact.cpp commit 8b25cd6bd870d244ee69c612a3c645e62eaea7cf Author: Andy Nonaka Date: Fri Aug 31 10:28:18 2018 -0700 bug fix for 3d div and grad src_common/src_F90/compute_div_and_grad.F90 commit de492f3953f82f8f1382cc4a7b9c1cc91b7a3aae Author: Andy Nonaka Date: Fri Aug 31 10:17:26 2018 -0700 move function definitions into cpp file src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp commit 44a9fd3b58bdc97647e82f2a19faf61d3e3dd554 Author: Guy Moore Date: Thu Aug 30 18:35:30 2018 -0700 First commit of structure factor class exec/hydro/GNUmakefile exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/StochMFlux.H src_hydro/StochMFlux.cpp src_hydro/StructFact.H src_hydro/StructFact.cpp commit aab52f18c252f05bf97fdd9cae18a05af14533c3 Author: Guy Moore Date: Mon Aug 27 16:43:22 2018 -0700 Added random fluxes to CR scheme exec/hydro/GNUmakefile exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp commit 48595180d16f7e2dae37d4faa2d3bdbaf90ec7d0 Author: Guy Moore Date: Mon Aug 27 10:54:02 2018 -0700 prob_type toggles initial condition choice between vortex, KH(sine), and KH(smooth) exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_hydro/StochMFlux.H commit e2f0d58029a47743940ae1c5014a9a412aebc845 Author: Daniel Ladiges Date: Mon Aug 13 13:46:59 2018 -0700 Changed all references from FParallelMG.mak to FParallelMG2.mak in make files - this avoids conflict with existing LLNS code. If anyone has any untracked cases using the rng code you will need to make the same change. exec/DSMC/GNUmakefile exec/INS/GNUmakefile exec/hydro/GNUmakefile exec/immersedParticles/GNUmakefile src_particles/FhdParticleContainer.cpp commit 13108c8b90922b5bc39d1f9d7bff33dea55021e1 Author: Guy Moore Date: Thu Aug 9 16:30:40 2018 -0700 Added scaling of stoch. fluxes by variance, which is dependent on namespace variable cell_depth exec/hydro/inputs_2d exec/hydro/main_driver.cpp src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/common_namelist.F90 src_hydro/StochMFlux.H src_hydro/hydro_functions_F.H src_hydro/src_F90/stoch_m_force.F90 commit 762707c65fad577206e74002a8885f97d6564bbd Author: Guy Moore Date: Tue Aug 7 17:24:09 2018 -0700 Made changes to StochMFlux class - still need to scale fluxes by variance exec/hydro/main_driver.cpp src_hydro/StochMFlux.H commit bd58fbdfa174a792f389efda62bbb4fcd7b8acdf Author: Guy Moore Date: Tue Aug 7 12:17:03 2018 -0700 Eta & temp set to default constant values src_hydro/StochMFlux.H commit a9fad6e10fcaf31b155294c2fdb9906b8adbd02a Author: Guy Moore Date: Tue Aug 7 12:05:44 2018 -0700 Added functions to StochMFlux class to scale fluxes by sqrt(eta*temperature) exec/hydro/inputs_2d src_hydro/StochMFlux.H src_hydro/hydro_functions_F.H src_hydro/src_F90/stoch_m_force.F90 commit fc2af459100176fd2ecae94c192a3bbb0f32c1f5 Merge: 212e5b0a dda2d5bc Author: Daniel Ladiges Date: Mon Aug 6 17:21:36 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 212e5b0a97cd19ad79890b425052a457c8a056fa Author: Daniel Ladiges Date: Mon Aug 6 17:18:59 2018 -0700 Updated FhdParticleContainer class to use Andrew's changes to ParticleContainer class. Around 25% speed improvement in membrane test case exec/DSMC/GNUmakefile exec/DSMC/main_driver.cpp exec/DSMC/surfaces.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 commit dda2d5bc540522b4237a759a54cafe39bc245d67 Author: Guy Moore Date: Mon Aug 6 16:11:59 2018 -0700 StochMflux functions appear to be working - more functions needed exec/hydro/main_driver.cpp src_hydro/StochMFlux.H commit 8be9daa315611db670e69d24ad2ce110936c4575 Author: Andy Nonaka Date: Mon Aug 6 15:19:11 2018 -0700 build multifab bugfix src_hydro/StochMFlux.H commit eb4c2eb17b69ceea5666eb9b7e7aafcc1f43dc1b Author: Guy Moore Date: Mon Aug 6 15:13:24 2018 -0700 Added compute div. functions to StochMFlux class - needs debugging exec/hydro/main_driver.cpp src_hydro/StochMFlux.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/stoch_m_force.F90 commit 6f67c686e049031c2535ee6f1da33454001eeeda Author: Guy Moore Date: Fri Aug 3 16:29:59 2018 -0700 Added StochFill routine to StochMFlux class - needs testing exec/hydro/main_driver.cpp src_hydro/StochMFlux.H commit f527a11cbe643efd8335cd6dc8b42b322ebf5a4d Merge: 98282a19 fa083a8e Author: Guy Moore Date: Thu Aug 2 17:58:47 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 98282a1917bc7f9f1e366f9ce5596a7d24807e99 Author: Guy Moore Date: Thu Aug 2 17:56:54 2018 -0700 Initial commit of new StochMFlux class exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/StochMFlux.H commit fa083a8e9395c91827ad7f67277c2272ca5aab6d Merge: aa3d0031 ee675fd5 Author: Daniel Ladiges Date: Thu Aug 2 16:24:52 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit aa3d003158de688d6ce20da1c25a62f48c71043a Author: Daniel Ladiges Date: Thu Aug 2 16:22:43 2018 -0700 Added compiler option to select DSMC or immersed particle simulation Added boundary interactions for immersed particles exec/DSMC/inputs_2d exec/DSMC/inputs_3d exec/DSMC/main_driver.cpp exec/immersedParticles/GNUmakefile exec/immersedParticles/INS_functions.H exec/immersedParticles/Make.package exec/immersedParticles/Make_precheck.package exec/immersedParticles/Make_surface.package exec/immersedParticles/TimeStep.cpp exec/immersedParticles/WritePlotFile.cpp exec/immersedParticles/inputs_2d exec/immersedParticles/inputs_3d exec/immersedParticles/main_driver.cpp exec/immersedParticles/precheck.F90 exec/immersedParticles/surfaces.cpp python/convertSeries src_common/species.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 commit ee675fd5858c61b8a601d4c0fee84c391d0c1c3e Author: Guy Moore Date: Wed Aug 1 17:23:52 2018 -0700 Added Crank-Nicolson to predictor step in exec/hydro/main_driver Declared nested MultiFab random flux arrays in main_driver Tested & fixed component bug in ...FillRandom... exec/hydro/main_driver.cpp src_common/MuliFABFillRandom.cpp src_common/common_functions_F.H src_common/src_F90/multifab_fill_random.F90 commit b43ad89014b1fd5046ddc9a8847c6d7f2749992e Author: Guy Moore Date: Wed Aug 1 14:13:52 2018 -0700 Added component input and scale by standard deviation - sqrt(variance) exec/hydro/GNUmakefile exec/hydro/inputs_2d exec/hydro/main_driver.cpp src_common/MuliFABFillRandom.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/multifab_fill_random.F90 commit 0ad205d089b885ec0f4fde5a1f77ce5d18df1da6 Author: Guy Moore Date: Tue Jul 31 17:56:07 2018 -0700 Fixed bug in 3D multifab random fill functions exec/hydro/GNUmakefile exec/hydro/inputs_2d exec/hydro/inputs_3d exec/hydro/main_driver.cpp src_common/src_F90/multifab_fill_random.F90 src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 1ff141762e83a3d4c1f294aade4fc702dce54e12 Author: Guy Moore Date: Tue Jul 31 17:38:20 2018 -0700 Added multifab random fill functions exec/hydro/GNUmakefile exec/hydro/main_driver.cpp src_common/Make.package src_common/MuliFABFillRandom.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/multifab_fill_random.F90 commit 3379e5a287aac8c0b2d37a62017db81cf7ef885c Merge: 490d438e 500cffd5 Author: Guy Moore Date: Tue Jul 31 13:11:36 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 500cffd595a64982f1038a8ad6e06649ae91e1f3 Author: Daniel Ladiges Date: Tue Jul 31 13:08:37 2018 -0700 Added ability to pass seeds to rng_init exec/DSMC/main_driver.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 src_rng/rng_functions_F.H src_rng/src_F90/rng_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit 490d438e4bf12ad01a331da527774e1540e23eb8 Merge: 8967f083 fbb976b1 Author: Guy Moore Date: Mon Jul 30 16:12:40 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit fbb976b1b4409a21bfbdec5d4281d2ceadc08b0e Author: Daniel Ladiges Date: Mon Jul 30 15:53:08 2018 -0700 Added rng function for fhd src_rng/src_F90/rng_functions.F90 commit 8967f083f85082c424ff1af02ab64c37a2b5d837 Merge: d20590df 0eb56c99 Author: Guy Moore Date: Mon Jul 30 09:32:01 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d20590df47f1abc6b21812c54be213d792c53730 Author: Guy Moore Date: Mon Jul 30 09:29:14 2018 -0700 Added viscous term to tracer advection (commented out) src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 0eb56c9979c485be1767b2956cc15a8c8c3a7f84 Author: Daniel Ladiges Date: Fri Jul 27 10:26:47 2018 -0700 Added momentum conservation parameter to particle boundaries Moved collision precheck function to compilation directory to allow changing between individual runs exec/DSMC/GNUmakefile exec/DSMC/Make_precheck.package exec/DSMC/Make_surface.package exec/DSMC/main_driver.cpp exec/DSMC/precheck.F90 exec/DSMC/surfaces.H exec/DSMC/surfaces.cpp exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/Make.package exec/INS/Make_precheck.package exec/INS/Make_surface.package exec/INS/WritePlotFile.cpp exec/INS/inputs_2d exec/INS/inputs_3d exec/INS/main_driver.cpp exec/INS/precheck.F90 exec/INS/surfaces.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/collision_functions.F90 src_rng/src_F90/rng_functions.F90 src_surfaces/Make.package src_surfaces/src_F90/Make.package src_surfaces/src_F90/surface_functions.F90 src_surfaces/src_F90/surface_type.F90 src_surfaces/surfaces.H commit bcb9fd555207f1f4fc42189cfefabe7c80b37297 Author: Daniel Ladiges Date: Wed Jul 25 16:17:53 2018 -0700 Optimised surface collision checking and application of particle boundary conditions. Added makefile option to seperate particle moving code into pure DSMC case, and case where particles are interacting with a fluid. exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/surfaces.H exec/DSMC/surfaces.cpp exec/DiffuisonTest/GNUmakefile exec/INS/GNUmakefile exec/INS/main_driver.cpp exec/gmres/GNUmakefile exec/hydro/GNUmakefile src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_surfaces/src_F90/surface_functions.F90 commit eba4e8e63710dc59a4f5d7920879777b60521d44 Author: guymoore13 Date: Tue Jul 24 11:17:59 2018 -0700 "Step 5" labeled as "Step 4" Minor comment typo src_gmres/ApplyPrecon.cpp commit 28522d2a09e2d67819cf2c615efce9c2488eca7b Author: Guy Moore Date: Mon Jul 23 19:44:40 2018 -0700 Added diffusive term for updating tracer to reduce cell Reynolds number - adjusted for KH instability exec/hydro/WritePlotFile.cpp exec/hydro/hydro_test_functions.H exec/hydro/init_funcs.F90 exec/hydro/init_s_funcs.F90 exec/hydro/inputs_2d exec/hydro/main_driver.cpp src_hydro/MkAdvSFluxdiv.cpp src_hydro/hydro_functions_F.H src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit ff0c66189d972d91cebe3e3c0afdaa985b472729 Author: Guy Moore Date: Mon Jul 23 09:25:56 2018 -0700 Files for tracer that I forgot to add to GIT exec/hydro/hydro_test_functions_F.H exec/hydro/init_s_funcs.F90 src_hydro/MkAdvSFluxdiv.cpp src_hydro/src_F90/mk_advective_s_fluxdiv.F90 commit 81f990d01f797f0c11571384b9454053e7a1e0ca Author: guymoore13 Date: Sun Jul 22 09:39:40 2018 -0700 Fixed/cleaned-up initial conditions for velocity field in exec/hydro/ exec/hydro/init_funcs.F90 commit 97b760b3b56429c9bd83cb0ce233f1d39233471e Author: Guy Moore Date: Fri Jul 20 17:01:05 2018 -0700 Added tracer and analytically "div free" initial condition exec/hydro/Make.package exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package commit 238e95876abaddc19ca22457478ac20b8c73a2ee Author: Daniel Ladiges Date: Fri Jul 20 13:51:52 2018 -0700 Fixed numerical precision issue when detecting particle-boundary collisions. Moved surface definition files to build directory exec/DSMC/GNUmakefile exec/DSMC/INS_functions.H exec/DSMC/Make.package exec/DSMC/Make_surface.package exec/DSMC/TimeStep.cpp exec/DSMC/WritePlotFile.cpp exec/DSMC/main_driver.cpp exec/DSMC/surfaces.H exec/DSMC/surfaces.cpp exec/DSMCTestThermal/inputs_3d exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_particles/src_F90/particle_type.F90 src_surfaces/src_F90/surface_functions.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit f5c95acf1e94179a7e6c96953e07efa18370b409 Author: Andy Nonaka Date: Thu Jul 19 11:25:04 2018 -0700 bugfix caught by John... StagInnerProd and CCInnerProd weren't using comp2 properly. code appears to be working now! src_gmres/NormInnerProduct.cpp commit 64f690f7a15e292f2693c915823cb4e82ebf0e81 Author: Andy Nonaka Date: Thu Jul 19 10:29:02 2018 -0700 add divergence to plotfile (just to make sure things are working) exec/hydro/WritePlotFile.cpp exec/hydro/hydro_test_functions.H commit 3291691f97c18d7628de414a3788492091e2aabd Author: Andy Nonaka Date: Thu Jul 19 09:52:58 2018 -0700 fixed a bug in plotfile routine where I was obtaining the boxarray for the plotfile from a staggered multifab. Using a cell-centered MF instead. exec/hydro/WritePlotFile.cpp commit bb6ee504b11bbc427da92d5674ae4a08a7b7435f Author: Guy Moore Date: Wed Jul 18 16:42:56 2018 -0700 Added new initial condition: "stream" exec/hydro/init_funcs.F90 exec/hydro/inputs_2d commit 14d514c4e672e26c9925f3caf86ec27e1ac704b7 Author: Guy Moore Date: Wed Jul 18 11:03:42 2018 -0700 Modified WritePlotFile to write pressure and velocities to a single plotfile exec/hydro/WritePlotFile.cpp exec/hydro/compute_convfact_2.sh exec/hydro/hydro_test_functions.H exec/hydro/inputs_2d exec/hydro/main_driver.cpp commit dba83b195cedd7c351e0ee52a0ca674dc38693e3 Author: Andy Nonaka Date: Wed Jul 18 10:10:22 2018 -0700 fixed an index bug in LeastSquares GMRES still has a bug in it somewhere... src_gmres/GMRES.cpp commit c39669ea0b76caad3c40341c520a4d0d48cfb239 Author: Guy Moore Date: Tue Jul 17 19:15:11 2018 -0700 Fixed ghost cell mult() bug - visc_type=1, 2D -> second order convergence w/ CR exec/hydro/compute_convfact_2.sh exec/hydro/inputs_3d exec/hydro/main_driver.cpp exec/hydro/run_conv_tests_2.sh commit 8b687e8cc451c2c7ab9e235e994cff4f288e9d47 Author: Guy Moore Date: Tue Jul 17 16:45:12 2018 -0700 Tried to multiply both sides of equation by 1/dt - bug needs fixing exec/hydro/inputs_2d exec/hydro/main_driver.cpp exec/hydro/run_conv_tests_2.sh commit 34b06a06a3af7129210d106cf547f062d6dcf77e Merge: 59a7a5b1 1f1d1d48 Author: Andy Nonaka Date: Tue Jul 17 16:28:28 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 59a7a5b1feae1d0243b8cd629e5e64d8e4541ff9 Author: Andy Nonaka Date: Tue Jul 17 16:28:05 2018 -0700 require that norm_pre_rhs be passed in to GMRES (cleans up code so there aren't overloaded functions) src_gmres/GMRES.cpp src_gmres/gmres_functions.H commit 1f1d1d48528563978d263a93a3cfa08d318d95e3 Author: Daniel Ladiges Date: Tue Jul 17 16:21:54 2018 -0700 Parallelised functions for computing spatial correlations exec/DSMCTestThermal/main_driver.cpp src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 commit b9f92bc6260ff063d57f7b8b583a4191eed4083a Merge: c795e2f4 f6dbeaeb Author: Guy Moore Date: Tue Jul 17 14:10:12 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit c795e2f4447f1c3c2974584d0cfc5a243521522d Author: Guy Moore Date: Tue Jul 17 14:08:59 2018 -0700 Crank-nicolson implemented - needs more testing exec/hydro/compute_convfact_2.sh exec/hydro/inputs_2d exec/hydro/main_driver.cpp exec/hydro/run_conv_tests_2.sh commit f6dbeaeb5e3151fe5645dc84c422188ecd6ebd5b Author: Daniel Ladiges Date: Tue Jul 17 14:07:16 2018 -0700 Removed circular dependency Added temperature spatial cross correlation test case exec/DSMCTestThermal/main_driver.cpp exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_surfaces/src_F90/surface_functions.F90 commit 5631b5455136a8cb1b790c9db85478301127a3f9 Merge: 8f5a3763 6b77d19e Author: Guy Moore Date: Tue Jul 17 10:47:52 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8f5a37636607be57a20f69c608267c10a762345a Author: Guy Moore Date: Tue Jul 17 10:47:03 2018 -0700 fixed initial guess for second GMRES call exec/hydro/compute_convfact_2.sh exec/hydro/inputs_2d exec/hydro/main_driver.cpp commit 6b77d19e2a70c2bed7431be384a275d10d23520c Merge: b8b2ea71 0362b369 Author: Daniel Ladiges Date: Mon Jul 16 16:38:54 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit b8b2ea71c5b7fe8c56ab28346b1819230980b97b Author: Daniel Ladiges Date: Mon Jul 16 16:36:24 2018 -0700 Added test case for momentum-density fluctuations in presence of thermal gradient. exec/DSMCTestThermal/GNUmakefile exec/DSMCTestThermal/INS_functions.H exec/DSMCTestThermal/Make.package exec/DSMCTestThermal/WritePlotFile.cpp exec/DSMCTestThermal/inputs_3d exec/DSMCTestThermal/main_driver.cpp exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_surfaces/surfaces.cpp commit 0362b3696b8acb1cbc630046999a6f2ef21018ef Author: Guy Moore Date: Mon Jul 16 15:22:28 2018 -0700 Trapezoidal rule implemented - more convergence testing required exec/hydro/compute_convfact_2.sh exec/hydro/main_driver.cpp exec/hydro/run_conv_tests_2.sh commit 17e94bec30fc2d1be12a5a080f5d6522f2a6d28b Author: Daniel Ladiges Date: Fri Jul 13 17:27:56 2018 -0700 Completed particle interactions with arbitrary planar boundaries. exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_rng/src_F90/rng_functions.F90 src_surfaces/src_F90/Make.package src_surfaces/src_F90/surface_functions.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit 32fdfddabd16eb767307a33fa0f482423c9fdb67 Author: Guy Moore Date: Fri Jul 13 17:08:57 2018 -0700 advection functions fixed - need more testing exec/hydro/GNUmakefile exec/hydro/main_driver.cpp src_hydro/MkAdvMFluxdiv.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit 2affdabe4a474cd169604753d3319c16396ed98e Author: Andy Nonaka Date: Fri Jul 13 14:24:46 2018 -0700 add C binding src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit d0261e099b5330029287f69418cd3f0d569252ac Author: Guy Moore Date: Fri Jul 13 14:18:53 2018 -0700 second commit of advection implementation src_hydro/Make.package src_hydro/hydro_functions.H commit 08b6e73703153212806a43c01a8efceac33a559b Author: Guy Moore Date: Fri Jul 13 13:55:33 2018 -0700 first attempt at adding advective terms - makefile needs correcting exec/hydro/GNUmakefile exec/hydro/Make.package exec/hydro/WritePlotFile.cpp exec/hydro/hydro_test_functions.H exec/hydro/main_driver.cpp src_hydro/Make.package src_hydro/MkAdvMFluxdiv.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/mk_advective_m_fluxdiv.F90 commit d9d631b2d0a60b1b3ba224fc39380d1bde3aed85 Author: Andy Nonaka Date: Thu Jul 12 16:56:44 2018 -0700 tweak problem setup exec/hydro/GNUmakefile exec/hydro/inputs_2d commit a72210f60a8f5c5a77c01356892976a780336e62 Author: Andy Nonaka Date: Thu Jul 12 16:39:32 2018 -0700 replace abs() with std::abs(). For some reason the former doesn't work with the amrex::Real type src_gmres/GMRES.cpp commit 540726ff5b647e1472dd4565bc2dc5a16519d27c Author: Andy Nonaka Date: Thu Jul 12 15:48:48 2018 -0700 set mac projection verbosity with mg_verbose src_gmres/MacProj.cpp commit c121e4693cd164f9017df1736838c6a339f9ca3c Author: Andy Nonaka Date: Thu Jul 12 15:25:51 2018 -0700 vector size allocation bugfix src_gmres/GMRES.cpp commit c11db6320c651a7190353c9e7f6edcf381123aa2 Author: Andy Nonaka Date: Thu Jul 12 14:40:25 2018 -0700 index bugfix src_gmres/GMRES.cpp commit d3148157aa69e80da656c1be3448bb123346f2bc Merge: da725911 db5e83a8 Author: Andy Nonaka Date: Thu Jul 12 14:27:48 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit da7259112c9fe90eb08a4d898e5676ff265c453d Author: Andy Nonaka Date: Thu Jul 12 14:27:37 2018 -0700 comments and verbosity src_gmres/GMRES.cpp commit db5e83a8a9fbcc5df13e922ce25bacc56fa81e4e Author: Guy Moore Date: Thu Jul 12 14:20:23 2018 -0700 added mk_advective_m_fluxdiv.f90 with c++ interface - needs testing src_gmres/StagMGSolver.cpp src_hydro/Make.package src_hydro/MkAdvMFluxdiv.cpp src_hydro/hydro_functions.H src_hydro/hydro_functions_F.H src_hydro/src_F90/Make.package src_hydro/src_F90/mk_advective_m_fluxdiv.f90 commit 3258379afd4a29abfba0347c6e5763a77b3e9bb7 Author: Andy Nonaka Date: Thu Jul 12 12:50:49 2018 -0700 verbosity output src_gmres/StagMGSolver.cpp commit 241f624799b02fa641d14c190470c4feb98c0154 Author: Andy Nonaka Date: Thu Jul 12 10:16:24 2018 -0700 index order bug fixes on Add Subtract and Copy src_gmres/GMRES.cpp commit 10957de8c4858f2522408f969aeb3981642877a4 Author: Andy Nonaka Date: Thu Jul 12 10:01:14 2018 -0700 bugfix - need to initialize guess for new solution exec/hydro/main_driver.cpp commit 0401eba0503ecfc62422ccc97b573a84ab694712 Author: Andy Nonaka Date: Thu Jul 12 09:46:13 2018 -0700 bugfix; forgot to compute l2 norm of rhs src_gmres/GMRES.cpp commit 58a79e7b1d405eb5fea196818cb620f559d0f7de Author: Andy Nonaka Date: Thu Jul 12 09:45:52 2018 -0700 bugfix: pass in umacNew for storage of new solution exec/hydro/main_driver.cpp commit aba8c878042fda43cb42fcdc2f7a90a282111f5a Author: Daniel Ladiges Date: Wed Jul 11 16:44:30 2018 -0700 Added functions for detecting intersection of particles with boundaries exec/INS/GNUmakefile exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit d205090e26bdd5b42c0ae391b5c3695e9c669c13 Author: Guy Moore Date: Wed Jul 11 16:32:08 2018 -0700 changed initial conditions to cylindrical vortex exec/hydro/init_funcs.F90 commit 3b3d905e974b4cbc1f13a9ceae6e39e60f03c811 Author: Andy Nonaka Date: Wed Jul 11 14:41:55 2018 -0700 test case for GMRES solver. implicit stokes system exec/hydro/inputs_2d exec/hydro/main_driver.cpp commit 26de0a9e3b67518df6c3a11493d285d116dbf273 Author: Andy Nonaka Date: Wed Jul 11 14:26:41 2018 -0700 add norm and inner product calls to GMRES src_gmres/GMRES.cpp commit c92f3bd45c7d19469838e41915228d2026944c25 Author: Andy Nonaka Date: Wed Jul 11 14:04:35 2018 -0700 finish STEP 4 in ApplyPrecon src_gmres/ApplyPrecon.cpp commit a7d824690ff1d6d27738575288f6aab14e41c900 Author: Andy Nonaka Date: Wed Jul 11 13:55:26 2018 -0700 modified StagL2Norm so the output is a single real number equal to the sqrt(sum(xvals^2) + sum(yvals^2) + sum(zvals^2)) instead of the previous way where the output was a vector of real numbers holding sum(xvals^2), sum(yvals^2), and sum(zvals^2) src_gmres/GMRES.cpp src_gmres/NormInnerProduct.cpp src_gmres/gmres_functions.H commit e2ae494d2d19c1e6dbf8f4c89ebf313b1a045ba0 Author: Guy Moore Date: Wed Jul 11 12:49:58 2018 -0700 modified/cleaned-up inner product routines in NormInnerProduct.cpp src_gmres/NormInnerProduct.cpp commit 56210c39d3fb4f0dae7c6ee31d03395c56f7db50 Author: Guy Moore Date: Wed Jul 11 10:46:33 2018 -0700 minor adjustments to staggered and cell-centered inner product routines src_gmres/NormInnerProduct.cpp src_gmres/StagMGSolver.cpp commit c480fc5539d0666dc8e6902a003bafb0aded8feb Merge: 2dc4a4c6 b0ecba08 Author: Andy Nonaka Date: Wed Jul 11 10:26:58 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 2dc4a4c6c341da75303f7c177f45400e5b2799ef Author: Andy Nonaka Date: Wed Jul 11 10:26:44 2018 -0700 set up a driver to call GMRES exec/hydro/GNUmakefile exec/hydro/Make.package exec/hydro/WritePlotFile.cpp exec/hydro/hydro_functions.H exec/hydro/init_funcs.F90 exec/hydro/inputs_2d exec/hydro/main_driver.cpp commit b0ecba08594719b9bc2125a6eedbc36915a05dca Author: Guy Moore Date: Tue Jul 10 20:06:13 2018 -0700 cell-centered and nodal inner product functions implemented and appear to be working src_gmres/NormInnerProduct.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/Make.package src_gmres/src_F90/norm_inner_prod.F90 src_gmres/src_F90/stag_inner_prod.F90 commit dfd83705f71e0edcb938cc795cbba66257ecd1a5 Author: Daniel Ladiges Date: Tue Jul 10 14:42:06 2018 -0700 Added 'surface' type to handle particle interactions with boundaries exec/INS/GNUmakefile exec/INS/main_driver.cpp src_surfaces/Make.package src_surfaces/surfaces.H src_surfaces/surfaces.cpp commit a4c520ba01e9c89dcf7b278d96df48dfa2170e2a Author: Daniel Ladiges Date: Tue Jul 10 12:47:26 2018 -0700 Completed framework for statistical analysis of flows. Fixed rng seeding bug (note that rngs currently have fixed seeds) exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_rng/src_F90/rng_functions.F90 commit a6977be691f666e3957544965ab6cc9ca99783f6 Author: Andy Nonaka Date: Tue Jul 10 12:45:28 2018 -0700 theta_alpha=1 exec/INS/TimeStep.cpp commit 4ff4bc8684062a602e41acf2c9a3f05f9a89e37f Author: Guy Moore Date: Tue Jul 10 10:11:29 2018 -0700 rename StagInnerProd.cpp -> NormInnerProd.cpp src_gmres/Make.package src_gmres/NormInnerProduct.cpp src_gmres/src_F90/stag_inner_prod.F90 commit a4f103733c66ee5e889934b30f67080ca85681c2 Author: Andy Nonaka Date: Mon Jul 9 18:50:52 2018 -0700 more progress with GMRES solver... almost done src_gmres/GMRES.cpp src_gmres/gmres_functions.H commit 1d1efa9dc316e886867ea5513712794276aca9a5 Merge: d45d6ad6 b7d0c185 Author: Guy Moore Date: Mon Jul 9 17:27:45 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit d45d6ad623251d5c63d76d6694596fe6278bf517 Author: Guy Moore Date: Mon Jul 9 17:26:50 2018 -0700 staggered inner product appears to be working in 2D and 3D src_gmres/StagMGSolver.cpp src_gmres/src_F90/stag_inner_prod.F90 commit b7d0c185b64543b12f09e6fdadd3bef3b8d11e6f Author: Andy Nonaka Date: Mon Jul 9 14:45:39 2018 -0700 complete ApplyMatrix function src_gmres/ApplyMatrix.cpp commit 6944f3e07cf74a0b97cf7ee529147f755a18d9e5 Author: Andy Nonaka Date: Mon Jul 9 14:21:33 2018 -0700 StagApplyOp now takes in theta_alpha as an argument exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/main_driver.cpp src_gmres/ApplyMatrix.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit ff33b270be1d0259e2034f30e3a4dddbd288229b Author: Andy Nonaka Date: Mon Jul 9 14:12:19 2018 -0700 more GMRES progress. Starting an ApplyMatrix function src_gmres/ApplyMatrix.cpp src_gmres/GMRES.cpp src_gmres/Make.package src_gmres/gmres_functions.H commit c75c81a402c438c30dd2ccd3d0bdd8aeed1203ba Author: Guy Moore Date: Mon Jul 9 13:52:39 2018 -0700 fixed pointer reference in stag_inner_prod.F90 src_gmres/StagInnerProduct.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_inner_prod.F90 commit 73f2a294eab9bf96986ef31f528f6fcdadbf5f94 Author: Andy Nonaka Date: Mon Jul 9 11:12:55 2018 -0700 fixed the parallel reduce sum over a vector initialized the sum to zero in C++ and removed the setval in the F90 src_gmres/StagInnerProduct.cpp src_gmres/src_F90/stag_inner_prod.F90 commit 415e01bbfe381f97fc4b26bd7726b526488468c7 Author: Andy Nonaka Date: Mon Jul 9 11:03:54 2018 -0700 added linear solvers exec/INS/GNUmakefile commit 1e824ffde9d0b16165755002dfe7eaef046b711e Author: Andy Nonaka Date: Mon Jul 9 10:58:34 2018 -0700 add stag_inner_prod.F90 src_gmres/src_F90/Make.package commit d2482edcd5f528425f9471f868f4e8797aee616d Author: Guy Moore Date: Mon Jul 9 10:56:40 2018 -0700 L2 test commit src_gmres/StagMGSolver.cpp commit 67fa27483e9205b6aa5a2aa0f00188bb5b34b33c Merge: cd11c8ba f1112450 Author: Guy Moore Date: Mon Jul 9 10:50:17 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX Conflicts: exec/DiffuisonTest/inputs_debug_multigrid_2d src_gmres/Make.package commit cd11c8ba45ee58f9882b4adef5c8660d8e08ada4 Author: Guy Moore Date: Mon Jul 9 10:15:21 2018 -0700 L2 inner product Makefile commit exec/DiffuisonTest/GNUmakefile exec/DiffuisonTest/inputs_debug_multigrid_2d src_gmres/Make.package commit 70eee59a634849a08e341893d4d62b452c0575aa Author: Guy Moore Date: Mon Jul 9 10:12:43 2018 -0700 L2 inner product needs more debugging exec/DiffuisonTest/compute_convfact_2.sh exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/run_conv_tests_2.sh src_gmres/NormInnerProduct.cpp src_gmres/StagInnerProduct.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_inner_prod.F90 commit f1112450e5a4e1422e99f4865edf5b84288c78ac Author: Andy Nonaka Date: Fri Jul 6 16:48:21 2018 -0700 starting on GMRES. clean up some other interfaces src_gmres/ApplyPrecon.cpp src_gmres/GMRES.cpp src_gmres/MacProj.cpp src_gmres/Make.package src_gmres/gmres_functions.H commit 797d977ef94b9deaa070c84376861b4ff6b44a41 Author: Andy Nonaka Date: Fri Jul 6 15:18:07 2018 -0700 more preconditioner progress src_gmres/ApplyPrecon.cpp commit 07fcf45f3dcfa11c60ab3630e9984ea748fd7a35 Author: Andy Nonaka Date: Fri Jul 6 14:58:34 2018 -0700 interface to perform mac projection src_gmres/ApplyPrecon.cpp src_gmres/MacProj.cpp src_gmres/gmres_functions.H commit 33cd47639549a6b2dfcbdbfbffd84d967fbecb90 Author: Andy Nonaka Date: Fri Jul 6 09:57:50 2018 -0700 wrote a CCApplyOp interface exec/DiffuisonTest/GNUmakefile src_gmres/ApplyPrecon.cpp src_gmres/MacProj.cpp src_gmres/gmres_functions.H commit cc2510fcaabd94736e209bb34463a2970eff2465 Author: Andy Nonaka Date: Thu Jul 5 17:19:53 2018 -0700 more preconditioner progress - WIP src_gmres/ApplyPrecon.cpp src_gmres/gmres_functions.H commit 2a47c611c0b9cf35c1f587119820411e4b90117e Author: Andy Nonaka Date: Thu Jul 5 16:39:00 2018 -0700 wrote SubtractWeightedGradP function src_gmres/MacProj.cpp src_gmres/Make.package src_gmres/gmres_functions.H commit 70b67f69ce8e9fea2bd7bfbc1169fa4005fbd4fa Author: Andy Nonaka Date: Tue Jul 3 16:49:27 2018 -0700 more preconditioner progress src_gmres/ApplyPrecon.cpp src_gmres/gmres_functions.H commit 3505df4b47f59ff414f9ff164ba1f77c79c85581 Author: Andy Nonaka Date: Tue Jul 3 16:37:36 2018 -0700 generalize ComputeGrad to take in start_incomp, start_outcomp, and ncomp as arguments src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_common/src_F90/compute_div_and_grad.F90 commit ee1e59c323a6b6d218e6c273f4e204989370c74f Author: Andy Nonaka Date: Tue Jul 3 16:16:10 2018 -0700 generalize ComputeDiv to take in start_incomp, start_outcomp, and ncomp. also fixed a bug in the 3d increment divergence function src_common/ComputeDivAndGrad.cpp src_common/common_functions.H src_common/src_F90/compute_div_and_grad.F90 commit a565e3644a60d826bcc53e2c20ef40486a8c35d4 Author: Andy Nonaka Date: Tue Jul 3 14:41:13 2018 -0700 set up outline for ApplyPrecon exec/DiffuisonTest/inputs_debug_multigrid_2d src_gmres/ApplyPrecon.cpp src_gmres/Make.package src_gmres/gmres_functions.H commit d5f860f08c926e032cadf4cab17529532500a2b0 Merge: 20e00d2d e0163dd2 Author: Andy Nonaka Date: Tue Jul 3 13:47:18 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 20e00d2da84561ff539d3115a7a9f96639cf16e3 Author: Andy Nonaka Date: Tue Jul 3 13:46:51 2018 -0700 outline for staginnerprod src_gmres/Make.package src_gmres/NormInnerProduct.cpp src_gmres/gmres_functions.H commit e0163dd2a3133b8786739636afed8c9f173b5716 Author: Guy Moore Date: Mon Jul 2 18:02:33 2018 -0700 changed ICs & added .sh scripts for convergence testing exec/DiffuisonTest/compute_convfact_2.sh exec/DiffuisonTest/init_funcs.F90 exec/DiffuisonTest/run_conv_tests_2.sh commit b489fad6b6a94784d1cfb877a9bcae0c16ddcf15 Author: Andy Nonaka Date: Mon Jul 2 13:08:17 2018 -0700 fix uninitizlied variables src_gmres/src_F90/stag_apply_op.F90 commit 447bbf2282760a55743c8f379b218485f4d77df2 Author: Guy Moore Date: Mon Jul 2 11:44:23 2018 -0700 implemented Crank-Nicolson (needs more testing) and fixed bug in StagMGSolver.cpp ("return" used in place of "break") exec/DiffuisonTest/main_driver.cpp src_gmres/StagMGSolver.cpp commit 23f8fe091e05ed1b826e4d99839aed5a7a0fb8b1 Author: Daniel Ladiges Date: Mon Jul 2 11:32:58 2018 -0700 Fixed 2d bug in particle advection Changed domian boundary def in inputs_3d to 3d vector exec/INS/inputs_3d exec/INS/main_driver.cpp src_particles/src_F90/particle_functions.F90 commit e3594d9a8688800742d11a5f05ada89e31017708 Merge: 527d9e92 76f244e4 Author: Daniel Ladiges Date: Fri Jun 29 18:34:39 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 527d9e927eb3a6c84b783d41b76c73799b5198c0 Author: Daniel Ladiges Date: Fri Jun 29 18:31:34 2018 -0700 Moved particle code over to 'cell sorted particle container' framework provided by Andrew. Some 2D debugging still required. exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_common/src_F90/common_namelist.F90 src_common/src_F90/find_nodal_values.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 commit 76f244e41e8541fc19331bd964212508077aa046 Author: Guy Moore Date: Wed Jun 27 12:38:43 2018 -0700 corrected gaussian ICs exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/init_funcs.F90 exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/main_driver.cpp commit 1bc925c23a1bdf3ef2046327d06398735d3beb7e Author: Andy Nonaka Date: Tue Jun 26 18:38:36 2018 -0700 fixed periodic bug in multigrid jacobi sweep multigrid appears to be working. thorough testing required exec/DiffuisonTest/inputs_debug_multigrid_2d src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 665bd29a8396bd46e659fd40ad74bbd971938bf8 Author: Andy Nonaka Date: Mon Jun 25 16:13:08 2018 -0700 turn on 3 levels (2 levels seems to work) exec/DiffuisonTest/inputs_debug_multigrid_2d commit 150a9f31b314d69797402f08667e53e6e332e37b Author: Andy Nonaka Date: Mon Jun 25 16:11:44 2018 -0700 set to use backward euler exec/DiffuisonTest/inputs_debug_multigrid_2d commit 0e3b2a974de12851b7e1fa2c08b3a6f002363066 Author: Guy Moore Date: Mon Jun 25 14:46:22 2018 -0700 added algorithm_type for DiffusionTest: 0 - explicit trapezoidal, 1 - implicit backward Euler exec/DiffuisonTest/Make.package exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/main_driver.cpp commit ca3fb763a81d49e851064e22c13c7d430a0f6df1 Author: Guy Moore Date: Mon Jun 25 13:46:16 2018 -0700 moved/removed unnecessary files from src_gmres exec/DiffuisonTest/DiffusionTest_functions.H exec/DiffuisonTest/Make.package exec/DiffuisonTest/StagExpSolver.cpp exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/main_driver.cpp src_gmres/Make.package src_gmres/StagApplyOpWeighted.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/Make.package src_gmres/src_F90/stag_apply_op_weighted.F90 commit 3fe196fb7690ae993b598e86104b8676ba2f148c Author: Andy Nonaka Date: Mon Jun 25 12:49:53 2018 -0700 use "-1" for periodic to match all other AMReX codes exec/INS/inputs_2d exec/INS/main_driver.cpp exec/gmres/inputs_2d exec/gmres/main_driver.cpp exec/hydro/inputs_2d commit 3aa195cec7d00ce7689b92ba15da8b781de680e9 Author: Andy Nonaka Date: Mon Jun 25 12:42:33 2018 -0700 revert StagApplyOp.cpp and StagMGSolver.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp commit d3c38231e9e674d421d04357c8bec7576b546308 Author: Guy Moore Date: Mon Jun 25 11:25:19 2018 -0700 trapezoidal progress exec/DiffuisonTest/main_driver.cpp src_gmres/StagExpSolver.cpp commit fcc42c34c647dc23fb4c13116f5204e83991c306 Merge: 68abe34d c9115980 Author: Guy Moore Date: Mon Jun 25 09:07:52 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 68abe34d26017ae47d3e5f024ecbc6d4d2792508 Author: Guy Moore Date: Mon Jun 25 09:06:15 2018 -0700 first modified files commit exec/DiffuisonTest/init_funcs.F90 exec/DiffuisonTest/main_driver.cpp src_common/src_F90/init_funcs.F90 src_gmres/Make.package src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/Make.package src_gmres/src_F90/stag_apply_op.F90 commit 9a55c69ccac9c5bfa498b95ddc2fcb75c53332ce Author: Guy Moore Date: Mon Jun 25 09:04:01 2018 -0700 first attempt at trapezoidal rule & crank nicolson src_gmres/StagApplyOpWeighted.cpp src_gmres/StagExpSolver.cpp src_gmres/src_F90/stag_apply_op_weighted.F90 commit c9115980fe95fcb3a8f7bc6bad99c2ead625bbe2 Author: Andy Nonaka Date: Fri Jun 22 16:53:56 2018 -0700 2-level MG failure exec/DiffuisonTest/inputs_debug_multigrid_2d commit 6f88627031adaac4b57bee1ce87cfbfd3ded85b3 Author: Andy Nonaka Date: Fri Jun 22 16:52:31 2018 -0700 print out residual after each relaxation src_gmres/StagMGSolver.cpp commit 1e9ec97c63a46695c9b7395314f99237eb2d521d Author: Daniel Ladiges Date: Tue Jun 19 17:07:59 2018 -0700 Basic DSMC program complete. Started adding framework to measure and validate fluctuations. exec/INS/main_driver.cpp src_common/species.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/collision_functions.F90 src_rng/src_F90/rng_functions.F90 commit 91b2f1d68660f9ee4aa2205c62d492019e2a25dd Author: Andy Nonaka Date: Tue Jun 19 12:08:06 2018 -0700 write out mac velocities to separate staggered plotfiles exec/DiffuisonTest/WritePlotFile.cpp commit cd3a5cf761967264b302139624d676d3955f7317 Author: Daniel Ladiges Date: Mon Jun 18 18:02:24 2018 -0700 Fixed bug calculating domain volume in 2D exec/INS/main_driver.cpp commit 56b383828a5f2453ca82bcb62472a4f338b9b7ef Merge: de0cb882 04a27a54 Author: Daniel Ladiges Date: Mon Jun 18 17:52:22 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit de0cb882242b521cf91c9fc87a71b695aadb4300 Author: Daniel Ladiges Date: Mon Jun 18 17:48:55 2018 -0700 Implemented collision cell initialization, pair selection and ntc tracking. Added type 'species' to store kinetic properties of particle species exec/INS/main_driver.cpp src_common/Make.package src_common/species.H src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/collision_functions.F90 src_particles/src_F90/particle_functions.F90 src_rng/src_F90/rng_functions.F90 commit 04a27a543a7072ebe34a4d034a4b883341d7a080 Author: Andy Nonaka Date: Mon Jun 18 13:05:37 2018 -0700 more MG verbosity for debugging exec/DiffuisonTest/init_funcs.F90 src_gmres/StagMGSolver.cpp commit a504a902060b8016d0f2b11500e9bc6f166e50d7 Author: Andy Nonaka Date: Mon Jun 18 12:32:34 2018 -0700 some cleanup, fixed a scaling but in coefficient exec/DiffuisonTest/main_driver.cpp src_common/src_F90/init_funcs.F90 src_gmres/StagMGSolver.cpp commit 7fac1dbc71d2ca7e7c867bd4c60fe65ec64d861b Merge: 20f1f01b aa19a8d9 Author: Andy Nonaka Date: Mon Jun 18 11:22:46 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 20f1f01bc413aca8a2ca7adc3a950c1a679298df Author: Andy Nonaka Date: Mon Jun 18 11:22:36 2018 -0700 cleanup src_gmres/StagMGSolver.cpp commit c8a3c371aa39a22cbaa4426d04782b254ecb4e9c Author: Andy Nonaka Date: Mon Jun 18 11:22:11 2018 -0700 clean up diffusion test driver exec/DiffuisonTest/DiffusionTest_functions.H exec/DiffuisonTest/WritePlotFile.cpp exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/main_driver.cpp commit aa19a8d9d3f086a202b5bfcf17d2cd7f913d3f59 Author: Daniel Ladiges Date: Fri Jun 15 16:47:10 2018 -0700 Finished particle cell tracking. Started implementing collision routines. exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 9300bb09cde845e69a29412035b2950d83484019 Author: Daniel Ladiges Date: Thu Jun 14 18:29:42 2018 -0700 Added collision cell framework for particles, which is seperate from the underlying fluid grid. Added plotfile output for collision cell information. exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_common/src_F90/init_funcs.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 3366dc040ff823c2136243b12bacf8c7a1ea0b30 Author: Andy Nonaka Date: Wed Jun 13 11:18:03 2018 -0700 new problem setup to test multigrid diffusion solver only exec/DiffuisonTest/DiffusionTest_functions.H exec/DiffuisonTest/GNUmakefile exec/DiffuisonTest/Make.package exec/DiffuisonTest/WritePlotFile.cpp exec/DiffuisonTest/inputs_2d exec/DiffuisonTest/main_driver.cpp commit 6bef3e93ea8b8705479decb32a6429564594ed19 Author: Andy Nonaka Date: Wed Jun 13 11:17:41 2018 -0700 don't include INS_function.H src_common/ComputeDivAndGrad.cpp commit 1d64713af0d5e0792cbababfebc31f4a1e6442ba Author: Andy Nonaka Date: Tue Jun 12 16:59:15 2018 -0700 test commit 2 README.md commit ee4371a8b7a2a0c94dfb67c8a5bae77308766bfb Author: Andy Nonaka Date: Tue Jun 12 16:56:32 2018 -0700 test commit README.md commit d6f63151addaefe21e28397bb58cb2cf901f9833 Merge: 8a2bad5b f6353d38 Author: Daniel Ladiges Date: Tue Jun 12 16:51:41 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit 8a2bad5b99b47221a43a454dc1f5c6e1b07dbfa7 Author: Daniel Ladiges Date: Tue Jun 12 16:42:14 2018 -0700 Added particle Brownian motion exec/INS/main_driver.cpp src_common/src_F90/init_funcs.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit f6353d38d560a8b158edfd3402aa3e15b7944e82 Author: Andy Nonaka Date: Tue Jun 12 14:25:48 2018 -0700 update README README.md commit 594432861a18de2ae8f217cb5657407eb45b843a Merge: cdfa6bf6 5fdc2c31 Author: Andy Nonaka Date: Tue Jun 12 13:20:19 2018 -0700 Merge branch 'master' of https://github.com/AMReX-FHD/FHDeX commit cdfa6bf65a634c7c0bf925d7040e50b1873722d7 Author: Andy Nonaka Date: Tue Jun 12 13:19:34 2018 -0700 test commit README.md commit 5fdc2c313b16c45db41ff49b67113063d4114519 Author: Daniel Ladiges Date: Mon Jun 11 17:47:54 2018 -0700 Setup normal random number generating functions from BboxLib for calling in fortran Bug fix in init_funcs.F90 exec/INS/GNUmakefile exec/INS/main_driver.cpp python/convertSeries src_common/src_F90/find_nodal_values.F90 src_common/src_F90/init_funcs.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 src_rng/Make.package src_rng/rng_functions_F.H src_rng/src_F90/Make.package src_rng/src_F90/rng_functions.F90 commit 589bfa15f7f24b53d443562a2a55c61514ae89a1 Author: Daniel Ladiges Date: Fri Jun 8 18:00:27 2018 -0700 Added correct ghost cell handling for fluid forcing Started framework for Brownian motion exec/INS/GNUmakefile exec/INS/main_driver.cpp src_common/common_functions_F.H src_common/src_F90/init_funcs.F90 src_gmres/src_F90/stag_apply_op.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit b6ef592e66957d10fe5dbed047767d99330be957 Merge: c5e4cb4f 4dcb3bf0 Author: Andy Nonaka Date: Tue Jun 5 17:43:39 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Codes/FHDeX commit c5e4cb4fe78e0c93bd53fe22e9acde5877130a0a Author: Andy Nonaka Date: Tue Jun 5 17:43:04 2018 -0700 added a missing ghost cell fill routine src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 4dcb3bf0b9f0ba35e1d357941d45805aed96c5f2 Author: Daniel Ladiges Date: Tue Jun 5 17:30:54 2018 -0700 Added forcing of fluid by particle motion. Momentum change values are output to a face centred multifab. Still have to implement correct updating of ghost cells before FillBoundary call. exec/INS/main_driver.cpp src_common/FindCoords.cpp src_common/src_F90/find_nodal_values.F90 src_particles/FhdParticleContainer.cpp src_particles/src_F90/particle_functions.F90 commit 79cda895d3fe0284b89c01a1492a0f0abbbe1935 Author: Daniel Ladiges Date: Mon Jun 4 17:39:38 2018 -0700 Added a range of functions for the interpolation of fields, acceleration and advection of particles, and calculating resulting force on fluid. exec/INS/inputs_2d exec/INS/main_driver.cpp src_common/FindCoords.cpp src_common/FindNodalValues.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/find_nodal_values.F90 src_common/src_F90/init_funcs.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 0116302786bff8ae7826cd8c0930a463da835fcc Author: Daniel Ladiges Date: Fri May 25 16:05:30 2018 -0700 Added multifabs and functions to store real coordinates of cell faces. For use in interpolating velocity for particle forcing. exec/INS/main_driver.cpp src_common/FindCoords.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/find_coords.F90 src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 31911606a96d852b7f2ae705f5ecbbe5317edade Author: Daniel Ladiges Date: Thu May 24 16:25:03 2018 -0700 Added source multifabs. Outline for functions accelerating and moving particles, and forcing fluid. exec/INS/GNUmakefile exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions_F.H src_particles/src_F90/particle_functions.F90 commit 2533ad7225b6a3c2855abb0bd4faf1cfbce1368b Author: Daniel Ladiges Date: Tue May 22 14:01:02 2018 -0700 Fixed/verified stag_apply_op(..) for visc_type 1,-1,2,-2 in 2d & 3d src_gmres/src_F90/stag_apply_op.F90 commit 10c641a7d6890cd21242d8abb34520214e5e8e6f Author: Daniel Ladiges Date: Mon May 21 18:48:04 2018 -0700 Added functions for particle intialization, movement, and visualization exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp python/amrex_to_vtp.py python/write_pview_file.py python/write_pview_file.pyc src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp src_particles/particle_functions.H src_particles/particle_functions_F.H src_particles/src_F90/Make.package src_particles/src_F90/particle_functions.F90 commit e5f61d6652ff5a9416fe450e070a2da90bb62608 Author: Andy Nonaka Date: Mon May 21 17:17:06 2018 -0700 index bug fix in viscous operator src_gmres/src_F90/stag_apply_op.F90 commit fc4ad489cdd4cd03f6e46e6154c95cf7bb004e18 Author: Andy Nonaka Date: Mon May 21 17:09:47 2018 -0700 clean up print statements src_gmres/StagMGSolver.cpp commit 71d917d67fe4c1936aaebbb0fca109209e7fd4e2 Author: Andy Nonaka Date: Mon May 21 16:36:18 2018 -0700 StagApplyOp now takes in dx as an argument rather than a Geometry object. This was needed for the multigrid algorithm where I have to pass in different dx's not associated with the actual simulation data exec/INS/TimeStep.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 6666f442cffa0fac304d79ec034f4e02440ec1d5 Author: Andy Nonaka Date: Mon May 21 16:32:11 2018 -0700 bugfix in multigrid coarsening src_gmres/StagMGSolver.cpp commit 802fb0f0742abb1ad0cf911f472aad6878feb577 Author: Andy Nonaka Date: Mon May 21 15:59:12 2018 -0700 another indexing bug fix src_gmres/src_F90/stag_mg_solver.F90 commit 825c7a6e67085f16893610a48cec99b6478975d4 Author: Andy Nonaka Date: Mon May 21 15:58:42 2018 -0700 temporarily commented out the L2 norm diagnostics (the default L2 norm in AMReX does not support nodal data - need to write a custom routine for this) src_gmres/StagMGSolver.cpp commit 4ef804b693a1645e913992492fe019cb291125c8 Author: Andy Nonaka Date: Mon May 21 15:47:08 2018 -0700 an assortment of bug fixes for the staggered multigrid stuff. fixed one type on stag_applyop.F90 also src_gmres/StagMGSolver.cpp src_gmres/src_F90/stag_apply_op.F90 src_gmres/src_F90/stag_mg_solver.F90 commit 3bd37cf44bf6f4a3da001b6409b4f13f6d69a1f0 Author: Andy Nonaka Date: Mon May 21 14:50:12 2018 -0700 first attempt (it compiles but not tested yet) at an implicit staggered-grid velocity solver for the system "(theta*alpha*I - L) phi = rhs" using multigrid with Jacobi relaxation if abs(visc_type) = 1, L = div beta grad if abs(visc_type) = 2, L = div [ beta (grad + grad^T) ] if abs(visc_type) = 3, L = div [ beta (grad + grad^T) + I (gamma - (2/3)*beta) div ] if visc_type > 1 we assume constant coefficients if visc_type < 1 we assume variable coefficients beta_cc, and gamma_cc are cell-centered alpha_fc, phi_fc, and rhs_fc are face-centered beta_ed is nodal (2d) or edge-centered (3d) phi_fc must come in initialized to some value, preferably a reasonable guess src_gmres/StagMGSolver.cpp commit 8262761a387483d8c698c939d2bcc2017b3d2b7c Author: Andy Nonaka Date: Fri May 18 18:34:25 2018 -0700 updates to staggered multigrid src_gmres/StagMGSolver.cpp commit 92423952e017c2252bb9bb09f074319684632322 Author: Daniel Ladiges Date: Fri May 18 18:33:00 2018 -0700 Passing particle container to WritePlotFile.cpp exec/INS/WritePlotFile.cpp commit 3f366f2d54a7297f8b181f0557585bc6dc8d5b81 Author: Daniel Ladiges Date: Fri May 18 18:30:24 2018 -0700 Added make package for src_particles directory src_particles/Make.package commit 93e90550b15c8e78a7a92081142a057ecb24ecfa Author: Daniel Ladiges Date: Fri May 18 18:13:58 2018 -0700 Added particle container class with initialization function exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/main_driver.cpp src_particles/FhdParticleContainer.H src_particles/FhdParticleContainer.cpp commit e02bbfe10809f26ee974578bba739a2678270ec1 Merge: 782361a3 d9939123 Author: Daniel Ladiges Date: Fri May 18 15:59:31 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Codes/FHDeX commit 782361a33da037baa57107d2578d7d34f702c8a9 Author: Daniel Ladiges Date: Fri May 18 15:56:48 2018 -0700 Commit update to GNUmakefile before pulling Andy's changes exec/INS/GNUmakefile exec/INS/main_driver.cpp src_common/common_functions.H commit d9939123f719c17d11115b9c9abe59a8d3a15a90 Author: Andy Nonaka Date: Fri May 18 15:49:18 2018 -0700 replace betaEdge and betaNodal with an array of MultiFabs, betaEdge that contains only the nodal beta for 2d, and the xy/xy/yz edge betas in 3d exec/INS/INS_functions.H exec/INS/TimeStep.cpp exec/INS/main_driver.cpp src_gmres/StagApplyOp.cpp src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit dff0906b860ff2777a586aef27e36fac51be1b7a Author: Andy Nonaka Date: Fri May 18 15:14:16 2018 -0700 added coloring option to stag_applyop for multigrid algorithm src_gmres/src_F90/stag_apply_op.F90 commit ff6df02a5579604c19e6981b8b5c6ff47a1b9bcc Author: Daniel Ladiges Date: Fri May 18 13:16:29 2018 -0700 Moved TimeStep.cpp to INS directory and updated make files exec/INS/INS_functions.H exec/INS/Make.package exec/INS/TimeStep.cpp exec/INS/main_driver.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/time_step.F90 commit 04d8d4ca7362d6601ca3e87ac3b4cffbd2f7407c Merge: d4d0f462 030dd596 Author: Daniel Ladiges Date: Fri May 18 12:54:13 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Codes/FHDeX commit d4d0f4627844310093320b04b642b5967f06729b Author: Daniel Ladiges Date: Fri May 18 12:53:44 2018 -0700 Minor edit exec/INS/main_driver.cpp commit 030dd5967aeeda810e18bd83e8c64db0be28793d Author: Andy Nonaka Date: Fri May 18 12:24:35 2018 -0700 A few changes: don't need to pass in gamma on nodes or edges (only gamma at cell-centers is ever needed) fixed a bug in StagApplyOp for 3D where the wrong component for betayz was passed in passed in an optional color argument to StagApplyOp to prepare for use in multigrid src_common/TimeStep.cpp src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_apply_op.F90 commit a1a3f9beb4561e98a333221c576d66aced5cafc8 Author: Andy Nonaka Date: Fri May 18 11:52:43 2018 -0700 remove visc_type from the 3d version of stag_applyop src_gmres/src_F90/stag_apply_op.F90 commit a1da3d51c190fcbe1fbe25315c37f5e3cb0b090b Author: Andy Nonaka Date: Fri May 18 11:39:14 2018 -0700 Don't pass visc_type through C++ routines nor into Fortran routines; use the namelist and namespaces instead. exec/INS/main_driver.cpp src_common/TimeStep.cpp src_common/common_functions.H src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_apply_op.F90 commit 251350a8a0b236cc5ac6e0757aee5864b2c221f8 Author: Daniel Ladiges Date: Thu May 17 18:09:10 2018 -0700 Headers etc. for adding particles exec/INS/GNUmakefile exec/INS/main_driver.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/init_funcs.F90 src_common/src_F90/time_step.F90 src_gmres/src_F90/stag_apply_op.F90 commit ebe5c9485f525ee2ab92f7cb99e379cebeb105ca Author: Andy Nonaka Date: Wed May 16 18:59:43 2018 -0700 saving progress on staggered multigrid solver src_gmres/StagMGSolver.cpp commit c2fcd1c0cba84add376b8994ee14778d90d7ea8b Author: Andy Nonaka Date: Wed May 16 18:57:10 2018 -0700 fix the function definition for StagMGSolver src_gmres/gmres_functions.H commit 3975fa6e69dbffa52e71db6bfca65e04e6a47b68 Author: Daniel Ladiges Date: Tue May 15 17:41:21 2018 -0700 Added 3D viscous operators type -1 and -2 exec/INS/main_driver.cpp src_common/TimeStep.cpp src_common/common_functions.H src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_apply_op.F90 commit e0fcdfcf5ccefe00f69bc50313c486140034e6c4 Author: Daniel Ladiges Date: Mon May 14 17:07:42 2018 -0700 2D viscous operator types 2 and -2 added. Alpha changed to a multifab to match approach used in fortran FHD exec/INS/inputs_2d exec/INS/main_driver.cpp src_common/Make.package src_common/TimeStep.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/init_funcs.F90 src_common/src_F90/time_step.F90 src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_apply_op.F90 commit e6757db22f398fe0a85034a4ef729a8cda4dea70 Author: Daniel Ladiges Date: Fri May 11 17:48:07 2018 -0700 Implemented simplest 2D version of diffusion operator in StagApplyOp.cpp and stag_apply_op.F90 Added basic Euler timestep functions in TimeStep.cpp and time_step.F90 src_common/TimeStep.cpp src_common/src_F90/time_step.F90 commit aebcdcf077217d14d2ac451eea9e30a960ecf7b3 Author: Andy Nonaka Date: Fri May 11 10:58:17 2018 -0700 fix a 3d compilation error src_common/src_F90/compute_div_and_grad.F90 commit 669188fa472058cdd0d70c648fbbef74d17842a7 Author: Daniel Ladiges Date: Thu May 10 18:00:28 2018 -0700 Added outlines for StagApplyOP stag_apply_op cpp and F90 functions src_gmres/Make.package src_gmres/StagApplyOp.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/Make.package src_gmres/src_F90/stag_apply_op.F90 commit dd87469be971af5bb76a657841c2add934b62353 Author: Andy Nonaka Date: Thu May 10 10:33:56 2018 -0700 wrote a stag_mg_update function for staggered velocity multigrid src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit 010fe1555df158e5e725cfe75e1062639c4d9845 Author: Andy Nonaka Date: Thu May 10 08:56:03 2018 -0700 wrote staggered (face) prolongation for multigrid algorithm src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit be4d7eda34429245f7d6e5efa6a6b1c434ff3c0a Author: Daniel Ladiges Date: Wed May 9 17:28:41 2018 -0700 git added missing files src_common/ComputeDivAndGrad.cpp src_common/src_F90/compute_div_and_grad.F90 commit e7a45a06be6525e6c2c0b9dc655e2cac2536a6ae Author: Daniel Ladiges Date: Wed May 9 16:30:05 2018 -0700 Added grad function Added cpp functions for div and grad mfi loops Moved fortran div and grad to file compute_div_and_grad.F90 Changed 2D/3D checking for div and grad to convention used in existing code More efficient fortran loop for div function Added increment option for div function exec/INS/inputs_2d exec/INS/main_driver.cpp src_common/ConvertStag.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/convert_stag.F90 src_common/src_F90/init_funcs.F90 commit fc90aaa792852f1c9405698b142576dae074a364 Author: Andy Nonaka Date: Wed May 9 16:23:32 2018 -0700 test git commit/push src_gmres/gmres_functions.H commit 48bf866a190a1afc86b1b7cb80e7f75e0d597eee Author: Andy Nonaka Date: Wed May 9 16:18:40 2018 -0700 wrote face, edge, and nodal restriction operators src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit 0f8a5334835aea140bf767431fb4a275a049cb0c Author: Daniel Ladiges Date: Wed May 9 09:32:17 2018 -0700 Initialised velocity field Function to calculate divergence Added divergence to plot function exec/INS/INS_functions.H exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_common/common_functions_F.H src_common/src_F90/Make.package src_common/src_F90/init_funcs.F90 commit f4b2b19642fdc4f74fbe9fa31e8a9a890e587452 Author: Andy Nonaka Date: Wed May 9 09:17:36 2018 -0700 get this compiling again exec/INS/GNUmakefile src_common/ConvertStag.cpp src_common/common_functions.H src_gmres/src_F90/stag_mg_solver.F90 commit ed7bf9955ddd84611e0ba3f6427e9495b7fcd4e4 Author: Andy Nonaka Date: Tue May 8 16:56:23 2018 -0700 more staggered MG progress src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/stag_mg_solver.F90 commit 17b39dcc0ff8ff5b0f5bf2525082284ea97bdb09 Author: Andy Nonaka Date: Tue May 8 15:47:11 2018 -0700 added cc restriction code exec/gmres/GNUmakefile src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H src_gmres/gmres_functions_F.H src_gmres/src_F90/Make.package src_gmres/src_F90/stag_mg_solver.F90 commit e5165889611cdc6178c440799c11868d8ceb0137 Author: Andy Nonaka Date: Mon May 7 15:56:36 2018 -0700 more progress in staggered mg solver src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 66c95f63e6ca5313b8569b47de77d083bb8b25f1 Author: Andy Nonaka Date: Mon May 7 13:57:20 2018 -0700 starting to write a staggered velocity multigrid solver src_gmres/Make.package src_gmres/StagMGSolver.cpp src_gmres/gmres_functions.H commit 90c1b8d9262adcdaeaba1ca6b3c24e4761bb7ed0 Author: Andy Nonaka Date: Mon May 7 09:33:16 2018 -0700 plotfile routine written. switch to 0-based components in F90 (for now...) exec/INS/WritePlotFile.cpp exec/INS/main_driver.cpp src_common/common_functions.H src_common/src_F90/convert_stag.F90 commit 009f640e45d60789664f25aebfbfa16413677831 Author: Andy Nonaka Date: Fri May 4 18:19:56 2018 -0700 minor exec/INS/main_driver.cpp commit 9c07609d84c3d78ac0059c21f7b94e41e00d781e Author: Andy Nonaka Date: Fri May 4 17:59:29 2018 -0700 template for writing a plotfile exec/INS/GNUmakefile exec/INS/INS_functions.H exec/INS/Make.package exec/INS/WritePlotFile.cpp exec/INS/inputs_2d exec/INS/main_driver.cpp commit d74179036a7a104744a513c0e3591b9e36554db6 Author: Andy Nonaka Date: Thu May 3 14:45:28 2018 -0700 average_face_to_cc src_common/ConvertStag.cpp src_common/common_functions.H src_common/common_functions_F.H src_common/src_F90/convert_stag.F90 commit 44e31c64715f72625d943f77cc36565f2b64fc6a Author: Andy Nonaka Date: Thu May 3 14:21:30 2018 -0700 sample average_face_to_cc function exec/gmres/GNUmakefile exec/gmres/main_driver.cpp src_common/ConvertStag.cpp src_common/Make.package src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/src_F90/Make.package src_common/src_F90/common_namelist.F90 src_common/src_F90/convert_stag.F90 commit fe05ba3c0254873a952578ca90d43aca5f620129 Author: Andy Nonaka Date: Wed May 2 17:08:36 2018 -0700 nodal flags exec/gmres/main_driver.cpp src_common/common_functions.cpp src_common/common_namespace.H src_common/common_namespace_declarations.H commit c932cb091fd3ce81618426f1df084fc71c16f273 Author: Andy Nonaka Date: Wed May 2 15:13:00 2018 -0700 clean up include statements src_common/common_functions.H src_gmres/gmres_functions.H src_gmres/gmres_functions.cpp commit bbe7fc8c1eabbb9b0a8cf95cb4b988fab8976895 Author: Andy Nonaka Date: Wed May 2 14:47:49 2018 -0700 putting together a gmres main driver exec/gmres/GNUmakefile exec/gmres/inputs_2d exec/gmres/main_driver.cpp src_common/main_driver.cpp commit 876245d23df0b9dc594e411b2c8112cef61086f7 Author: Andy Nonaka Date: Wed May 2 14:35:14 2018 -0700 re-order src_common/common_namespace.H commit 31b7ec4f4b68237c758d38f86fa652bf0c964cf6 Author: Andy Nonaka Date: Wed May 2 14:28:41 2018 -0700 setting up inputs file, comments exec/hydro/inputs_2d src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namelist.F90 src_gmres/Make.package src_gmres/gmres_namelist.F90 commit 301cccf73487123178f13bdc1a2e15f0a09cfa5d Author: Andy Nonaka Date: Wed May 2 12:37:00 2018 -0700 convenction - C++ functions have capital letters. F90 functions have lowercase with underscores separating words src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namelist.F90 src_gmres/gmres_functions.H src_gmres/gmres_functions.cpp src_gmres/gmres_functions_F.H src_gmres/gmres_namelist.F90 src_hydro/main_driver.cpp commit 14a4de092a1c6864ea9f033041be9dac4fa9f973 Author: Andy Nonaka Date: Wed May 2 09:45:42 2018 -0700 more code re-org exec/hydro/inputs_2d src_gmres/Make.package src_gmres/gmres_functions.cpp src_gmres/gmres_functions_F.H src_gmres/gmres_namelist.F90 src_gmres/gmres_namespace.H src_gmres/gmres_namespace_declarations.H src_gmres/gmres_params_F.H src_hydro/main_driver.cpp commit f59650bbef8bf13dbbc31c4e42e1445645473df2 Author: Andy Nonaka Date: Wed May 2 09:36:03 2018 -0700 code re-org src_common/Make.package src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_namelist.F90 src_common/common_namespace.H src_common/common_namespace_declarations.H src_common/common_params_F.H src_hydro/advance_timestep_inertial.cpp src_hydro/main_driver.cpp commit b9ea1beada6af6e2729643cf20a91661ce944cc0 Author: Andy Nonaka Date: Wed May 2 08:56:30 2018 -0700 gmres namespace initialization src_common/common_params_F.H src_gmres/gmres_functions.cpp src_gmres/gmres_params.f90 src_gmres/gmres_params_F.H src_hydro/main_driver.cpp commit 2a17a187cdf1566e74562c40246d3964bc8cceba Author: Andy Nonaka Date: Wed May 2 08:22:15 2018 -0700 gmres namelist WIP exec/hydro/inputs_2d src_common/common_functions.H src_common/common_functions.cpp src_common/common_params.F90 src_gmres/Make.package src_gmres/gmres_functions.H src_gmres/gmres_functions.cpp src_gmres/gmres_functions_F.H src_gmres/gmres_params.f90 src_gmres/gmres_params_F.H src_gmres/gmres_params_declarations.H src_gmres/gmres_params_defaults.H src_gmres/gmres_params_queries.H src_hydro/main_driver.cpp commit 880798c89aeb04bca734cd8e602be69d71f659c5 Author: Andy Nonaka Date: Tue May 1 13:50:31 2018 -0700 more cleanup src_common/Make.package src_common/common_functions.H src_common/common_functions.cpp src_common/common_params_F.H src_common/main.cpp src_common/main_driver.cpp src_hydro/advance_timestep_inertial.cpp src_hydro/main_driver.cpp commit 6f41e3db4905338500c506f21103ed1755ff9031 Author: Andy Nonaka Date: Tue May 1 13:42:34 2018 -0700 code cleanup src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_params.F90 commit 390709d317063eae882f07e6128b4fe8894e5500 Author: Andy Nonaka Date: Tue May 1 12:33:09 2018 -0700 read in namelist from inputs file only exec/hydro/inputs_2d exec/hydro/probin_2d src_common/common_functions.H src_common/common_functions_F.H src_common/common_params.F90 src_common/main.cpp src_hydro/main_driver.cpp commit 1bf605837fe1f12e59b255d8ebec61b5e472e7b6 Author: Andy Nonaka Date: Tue May 1 11:27:04 2018 -0700 read in plot and check base name from probin src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_params.F90 commit d6e4ab587b451fe9951619a813a19f250181fff3 Author: Andy Nonaka Date: Tue May 1 10:58:15 2018 -0700 more namelist progress exec/hydro/probin_2d src_common/Make.package src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_params.F90 src_common/common_params.H src_common/common_params_declarations.H src_common/common_params_queries.H commit 88bfc9f6aaae89c56a5b75e2a44640fcb12ea2ea Author: Andy Nonaka Date: Mon Apr 30 18:58:33 2018 -0700 framework for loading fortran module contents into namelist src_common/Make.package src_common/common_functions.H src_common/common_functions.cpp src_common/common_functions_F.H src_common/common_params.F90 src_common/common_params.H src_common/common_params_declarations.H src_common/common_params_defaults.H src_hydro/main_driver.cpp commit 73e83eaa440be5b24da16ed50366a0151d9a0c43 Author: Andy Nonaka Date: Mon Apr 30 14:29:26 2018 -0700 toward reading in namelists exec/hydro/inputs_2d exec/hydro/probin_2d src_common/common_functions_F.H src_common/common_params.H src_common/common_params.f90 src_hydro/main_driver.cpp commit 72a5c07b51b95f35c5f2659a7d1b73c77246a090 Author: Andy Nonaka Date: Mon Apr 30 10:54:47 2018 -0700 example showing how to read in multi-d array from namelist exec/hydro/probin_2d src_common/common_params.f90 commit edc3ceadbdaa820d08be0ca25e6d6c4450196c44 Author: Andy Nonaka Date: Fri Apr 27 15:44:06 2018 -0700 implement gmres parameter read-in src_common/common_params.f90 src_gmres/Make.package src_gmres/gmres_functions_F.H src_gmres/gmres_params.f90 src_gmres/gmres_params_defaults.H src_gmres/gmres_params_queries.H src_hydro/main_driver.cpp commit 274563f6539c9b5b6adc648347e92e3069d2539e Author: Andy Nonaka Date: Fri Apr 27 15:22:28 2018 -0700 new file src_hydro/advance_timestep_inertial.cpp commit 9429aeba804f97ee8d1e63347b4eba6799935324 Author: Andy Nonaka Date: Fri Apr 27 15:21:00 2018 -0700 new stuff src_gmres/Make.package src_gmres/gmres_params.H src_gmres/gmres_params.f90 src_gmres/gmres_params_defaults.H src_gmres/gmres_params_queries.H commit a6c3df1ac03a4c3e43748875de7c67dbb0d956b0 Author: Andy Nonaka Date: Fri Apr 27 13:59:56 2018 -0700 starting on gmres parameters exec/hydro/GNUmakefile src_hydro/Make.package src_hydro/hydro_functions.H src_hydro/main_driver.cpp commit 830ba7959459727b13931ac3bfc8e84d36d19590 Author: Andy Nonaka Date: Fri Apr 27 13:04:18 2018 -0700 header guards src_common/common_functions.H src_common/common_functions_F.H src_hydro/Make.package src_hydro/hydro.H src_hydro/hydro_functions.H src_reactDiff/Make.package src_reactDiff/main_driver.cpp src_reactDiff/reactDiff.H commit 50960a8f5465a2a5a1b864ef9438baa580017c8f Author: Andy Nonaka Date: Fri Apr 27 12:52:33 2018 -0700 code re-org src_common/Make.package src_common/common_functions.H src_common/common_functions_F.H src_common/common_params.H src_common/common_params_defaults.H src_common/common_params_queries.H src_common/main.cpp src_common/main_driver.cpp src_hydro/main_driver.cpp commit aa642b7703baefaadcff50272442f7100bdca4ad Author: Andy Nonaka Date: Fri Apr 27 11:23:45 2018 -0700 not needed exec/reactDiff/GNUmakefile commit 60eb1ee6b3a241d368d3805ad4dae0653cb893ae Author: Andy Nonaka Date: Fri Apr 27 10:43:21 2018 -0700 memory management src_common/common_F.H src_common/common_params.f90 src_hydro/main_driver.cpp commit 04488b9bb4c6db2874502a67dbb9214358654bc5 Author: Andy Nonaka Date: Fri Apr 27 08:44:35 2018 -0700 fortran module with common parameters src_common/Make.package src_common/common_F.H src_common/common_params.f90 src_hydro/main_driver.cpp commit cc8c632ceffe1f121122b34ba6606e15e387d045 Author: Andy Nonaka Date: Thu Apr 26 18:23:50 2018 -0700 read in common parameters exec/hydro/inputs_2d src_common/Make.package src_common/common.H src_common/common_defaults.H src_common/common_queries.H src_hydro/main_driver.cpp commit 3ed90b02b6d8e9977edef147fafd65be2df32de9 Author: Andy Nonaka Date: Thu Apr 26 17:55:08 2018 -0700 more code re-org src_common/Make.package src_common/common.H src_common/common_defaults.H src_common/functions.H src_common/main.cpp src_common/parameters_defaults.H src_hydro/main_driver.cpp commit e8a25809eeaf03c9f1e517e5b791d0325975033e Author: Andy Nonaka Date: Thu Apr 26 17:48:25 2018 -0700 re-org exec/hydro/inputs exec/hydro/inputs_2d src_common/Make.package src_common/common.H src_common/main.cpp src_common/parameters.H src_common/parameters_defaults.H src_hydro/main_driver.cpp commit 0f36297decd31794fd4abf7ec19607e4b9decbac Author: Andy Nonaka Date: Tue Apr 3 17:36:43 2018 -0700 use the parameters in the namespace when appropriate src_common/parameters.H src_common/parameters_defaults.H src_hydro/hydro.H src_hydro/main_driver.cpp commit 84d284fc9c2996d6f6fe3bfdb3a43ca41899ea80 Author: Andy Nonaka Date: Tue Apr 3 16:53:40 2018 -0700 fix variable type compilation bug src_common/parameters_defaults.H commit 102d5259aa6646e28b4ae86ae2a3f4d1240a667d Author: Andy Nonaka Date: Tue Apr 3 15:02:06 2018 -0700 setting up parameter exec/hydro/GNUmakefile exec/hydro/inputs src_common/Make.package src_common/common.H src_common/parameters.H src_common/parameters_defaults.H src_hydro/hydro.H src_hydro/main_driver.cpp src_reactDiff/reactDiff.H commit dfcf53039cfdd671dd14317294108f4967702ec1 Author: Andy Nonaka Date: Tue Apr 3 10:08:50 2018 -0700 set up directory structure exec/hydro/GNUmakefile exec/reactDiff/GNUmakefile src_common/common.H src_common/main.cpp src_hydro/Make.package src_hydro/hydro.H src_hydro/main_driver.cpp src_reactDiff/Make.package src_reactDiff/main_driver.cpp src_reactDiff/reactDiff.H commit 31b76d1b8e57827b919c5fef90394e429c0dfd45 Author: Andy Nonaka Date: Tue Apr 3 09:30:28 2018 -0700 setup directory exec/hydro/GNUmakefile src_common/FHD.H src_common/FHD.cpp src_common/Make.package src_common/common.H src_common/main.cpp src_common/main_driver.cpp commit fbece778c28fcf6790f3a1388f66a3c3c8783bf0 Author: Andy Nonaka Date: Mon Apr 2 19:26:07 2018 -0700 initial commit exec/GNUmakefile src_common/FHD.H src_common/FHD.cpp src_common/Make.package src_common/main.cpp commit 011cb77c38e89c550f890e25a67d0f4825335df3 Author: Andy Nonaka Date: Mon Apr 2 18:12:33 2018 -0700 updates README.md commit 9eba3511881cffdc2ea1f7edf09338904ae23d9a Author: Andy Nonaka Date: Mon Apr 2 18:09:45 2018 -0700 update README README.md commit bc4039ea2ca077b6f0fee448e85271256645506d Author: Andy Nonaka Date: Mon Apr 2 17:57:58 2018 -0700 README README.md