commit ea33e5b9cbb7ecc18ec2974245cc75be99c77a22 Author: Candace Gilet Date: Thu Aug 20 14:38:56 2026 -0400 Sync old/new-time state before ComputeDt to fix Boussinesq forcing (#209) use of uninitialized tracer_o on restart and regrid. ComputeDt calls compute_vel_forces_on_level, which uses both the old and new tracer fields for m_use_boussinesq. Previously, immediately after a restart (old-time fields aren't saved to checkpoints) or a regrid (new LevelData arrays start uninitialized) ComputeDt could read bad tracer_o data. Moving the fillpatch + copy-new-to-old block to the top of Advance and InitialIterations ensures old and new are both good before ComputeDt. Note this changes the adaptive dt for boussinesq. However, the dt is now computed with the same velocity forcing that is used to compute the advective velocity. This also ensures that copy_from_*_temperature checks m_use_temperature before trying to copy an mf that might not be defined. src/incflo_advance.cpp src/incflo_utils.cpp src/setup/init.cpp commit 44ba70564dcfc68841270bb6a30353d79903afd2 Author: Candace Gilet Date: Wed Aug 19 15:16:03 2026 -0400 Ensure corner ghost cells where periodic meets a physical bc are (#208) correctly filled in update_velocity/tracer/temperature. Even if corner ghost cells aren't used in the diffusive stencil, not filling periodic cells before call to fillphysbc leads to failure with DEBUG and amrex.fpe_trap_invalid = 1. src/incflo_update_temperature.cpp src/incflo_update_tracer.cpp src/incflo_update_velocity.cpp commit fcfbb96934669829c66e5473c418fc6168455e74 Author: Weiqun Zhang Date: Wed Aug 19 08:38:20 2026 -0700 Enforce nodal in/out solvability on the vel argument, not the state. (#206) The aliases were built from m_leveldata velocity, so a caller passing a different vector had its state rescaled while the projected field kept its influx/outflux imbalance. InitialPressureProjection passes a local gravity field. Fixes #184. src/projection/incflo_apply_nodal_projection.cpp commit 826cb79f337ec5e0fd8d85b5d2da58774a65bf9c Author: Weiqun Zhang Date: Wed Aug 19 08:38:02 2026 -0700 Hoist the eb_flow tracer device vector out of the MFIter loop. (#201) It was constructed per box and destroyed right after the async ParallelFor that captures its data() pointer, so a kernel could read freed device memory. At function scope it outlives the loop, whose MFIter destructor synchronizes every stream used. The values are box-independent, so this also drops a per-box host-to-device copy. Fixes #170. src/boundary_conditions/incflo_set_bcs.cpp commit 4faaacc2603d285e50f63d7c834250afbeffa1ad Author: Weiqun Zhang Date: Wed Aug 19 08:37:44 2026 -0700 Fix inverted direction_dependent sign test in IncfloVelFill LOW K. (#198) The low-z face applied the Dirichlet inflow value when norm_vel <= 0 and copied the interior when norm_vel > 0, reversing inflow and outflow. Its LOW I and LOW J twins, and the low-z branches of the density, tracer and temperature fills, all use >= 0. Fixes #190. src/prob/prob_bc.H commit 002bec23e21c411679b8de2ebe83367354352fa5 Author: Weiqun Zhang Date: Wed Aug 19 08:37:17 2026 -0700 Fix index typo in z-lo direction_dependent MAC velocity BC. (#196) The inflow test read cc_arr(1,j,k-1,2) with a literal x-index 1 instead of the loop index i, so the decision for face (i,j,dlo.z) was made from the ghost w in the x=1 column, and the read went outside the FAB on any box whose grown x-range excludes 1. Use cc_arr(i,j,k-1,2), the same ghost cell that is assigned to wmac_arr(i,j,k), matching the x-lo, y-lo and z-hi blocks. Fixes #195. src/convection/incflo_compute_MAC_projected_velocities.cpp commit f4d756e5ec98d3c8ff1858f7246877123b76baf7 Author: Weiqun Zhang Date: Tue Aug 18 19:11:48 2026 -0700 Use the temperature BCRec when redistributing the temperature term. (#207) The EB redistribution passed the tracer BCRec, so StateRedistribute chose its slope treatment from the tracer's boundary types. The flux computation above and InitialRedistribution already use the temperature BCRec. Fixes #186. src/convection/incflo_compute_advection_term.cpp commit 3c0b79bf6480a593f6f12e2a17fa7b663a7509f4 Author: Weiqun Zhang Date: Tue Aug 18 19:03:57 2026 -0700 Make the ccproj guard in ApplyProjection a real condition. (#205) AMREX_ALWAYS_ASSERT was given a string literal, which is always true, so the guard never fired and a use_cc_proj run reached ApplyNodalProjection and wrote through the undefined p_nd. Fixes #180. src/incflo.cpp commit ac423455745fa806b7f6aecbbd300cf28eca1d7e Author: Weiqun Zhang Date: Tue Aug 18 19:03:37 2026 -0700 Guard particle name list accesses against an empty list. (#204) ErrorEst and the particle_count plot variable both indexed element 0 of particleData.getNames(), which is empty unless use_tracer_particles is set, and operator[] returns nullptr on a miss. m_refine_particles and plt_ccse_regtest reach both sites by default. Fixes #174. src/incflo_tagging.cpp src/utilities/io.cpp commit e71c7832753ed229003a64ddebe0bd30f18b9643 Author: Weiqun Zhang Date: Tue Aug 18 19:03:14 2026 -0700 Accumulate the correct cumulative ref_ratio in ErrorEst. (#203) The particle-count loop multiplied rr by ref_ratio[levc] every iteration, giving ref_ratio[levc]^(lev-levc) rather than the product over levc..lev-1, so average_down used the wrong ratio when per-level ratios differ. Unchanged for uniform amr.ref_ratio. Fixes #173. src/incflo_tagging.cpp commit b5f7a33337aa761b585b753816c3466939ef5e29 Author: Weiqun Zhang Date: Tue Aug 18 19:02:53 2026 -0700 Fix transposed geometry name in the CSG dispatch. (#202) MakeEBGeometry tested geom_type == "cgs", so incflo.geometry = csg fell through to the final else and silently built all-regular geometry. Every other part of the CSG path spells it "csg". Fixes #172. src/embedded_boundaries/embedded_boundaries.cpp commit 747ed00a06475c29c964318013fec744be0641e7 Author: Weiqun Zhang Date: Tue Aug 18 19:02:29 2026 -0700 Guard the cell-volume product by dimension in massDensity. (#200) dxi is a GpuArray with SPACEDIM entries, so dxi[0]*dxi[1]*dxi[2] read past the end in 2D builds. AMREX_D_TERM gives the inverse cell area in 2D and leaves 3D unchanged. Fixes #168. src/particles/incflo_PCUtils.cpp commit ab3f7451e9ede5c12d1677cfdbd34737eb154135 Author: Weiqun Zhang Date: Tue Aug 18 19:01:59 2026 -0700 Add prob_lo to the Taylor-vortex cell coordinates in DiffFromExact. (#199) The probtype 2 branch evaluated the exact solution at (i+0.5)*dx, an offset from the domain corner, while its init_taylor_vortex twin uses problo + (i+0.5)*dx, so error norms were wrong on shifted domains. Probtypes 1 and 16 are left alone: their inits omit problo too, so they already agree. Fixes #167. src/derive/incflo_error.cpp commit 02391cb27dd5ad2424d0a88da58ee8ab4cd459bb Author: Weiqun Zhang Date: Tue Aug 18 19:01:36 2026 -0700 Fix inverted guard in fillcoarsepatch_temperature. (#197) The early return fired when m_use_temperature was true, so a new AMR level's temperature was never filled from the coarse level. Fixes #192. src/boundary_conditions/incflo_fillpatch.cpp commit 7307d8725c2a538f09cafbeacbfeb63e0fb11d22 Author: X.Z. Li <32592710+S-Explorer@users.noreply.github.com> Date: Mon Aug 3 11:37:21 2026 +0800 update cmake configuration for particles (#166) Supplement the `CMake` configuration information for the `Particles` section. CMakeLists.txt Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Particles.rst Docs/sphinx_documentation/source/index.rst src/CMakeLists.txt src/particles/CMakeLists.txt commit d2876747e07a33b61895d48759bfd3cbcc14fabe Author: Candace Gilet Date: Wed Jun 3 12:47:53 2026 -0400 Use updated face_divfree_interp when ref_ratio = 4. (#165) Previously, only ref_ratio=2 supported. Requires amrex PR#5252. src/convection/incflo_compute_advection_term.cpp commit f4642a6bf32ccaae02da37bbb430b2d6ebaeaf42 Author: Candace Gilet Date: Fri May 29 15:44:49 2026 -0400 Add particle Redistribute in MakeNewLevelFromCoarse to ensure (#164) particles are on the finest level. Co-authored-by: Ann Almgren src/incflo_regrid.cpp commit ac3afeec2435b430596dd66e030c2c13603c1fe1 Author: Candace Gilet Date: Fri May 29 14:16:32 2026 -0400 Allow delp or pressure inflow/outflow with orthogonal gravity. (#163) src/setup/set_background_pressure.cpp commit 934e956b2517a936cb0b2bf0cff0b23eb4e8bd56 Author: Candace Gilet Date: Fri May 29 12:17:18 2026 -0400 Add option to specify EB with STL file (#162) src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/Make.package src/embedded_boundaries/eb_csg.cpp src/embedded_boundaries/eb_stl.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit 3a8eb80682bd744665414e7e4461b1f981637735 Author: Ann Almgren Date: Mon May 18 11:25:52 2026 -0700 more precision changes (#161) src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_sphere.cpp src/setup/init.cpp src/utilities/io.cpp commit 74606b70da36b7b42463e12c84dbe7fa251c8c0d Author: Ann Almgren Date: Mon May 18 06:36:57 2026 -0700 wrap constants with Real() (#160) Also update some problem setups to make use of problo src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/derive/incflo_error.cpp src/incflo_compute_forces.cpp src/incflo_tagging.cpp src/incflo_update_temperature.cpp src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp commit fcca5b09dc65576bdd96fc210ff3a9b209a3d955 Author: Bhargav Sriram Siddani <45137944+siddanib@users.noreply.github.com> Date: Wed May 13 17:19:17 2026 -0700 Fix for a minor typo in implicit temperature update. (#159) There was a minor typo in `incflo_update_temperature.cpp` when implicit diffusion is used. src/incflo_update_temperature.cpp commit df7893af63e65b857aa04bff2e1059b0219e1f55 Author: Candace Gilet Date: Wed May 13 20:18:36 2026 -0400 Remove hardcoded m_refine_cutcells = true (#155) src/incflo_tagging.cpp commit a9c149fec91bc794071252703456566a94d849e9 Author: Bhargav Sriram Siddani <45137944+siddanib@users.noreply.github.com> Date: Tue May 12 07:25:07 2026 -0700 Minor changes for Temperature evolution. (#158) The changes were compiled but NOT tested. Co-authored-by: Candace Gilet src/diffusion/incflo_diffusion.cpp src/incflo_update_temperature.cpp commit 8b63d9d999e9a214a56d16e26e4609ef44ef1a33 Author: Candace Gilet Date: Tue May 5 14:39:39 2026 -0400 Get tracer particles working in 2D. Only try to remove particles (#156) outside a cylinder EB if that appears in the inputs. src/particles/incflo_PC.H src/particles/incflo_PCEvolve.cpp src/particles/incflo_PCInit.cpp commit 247b28dc2cc50c64433dd9f9542421331f987a4b Author: Candace Gilet Date: Tue May 5 13:27:54 2026 -0400 Update gcc.yml and .clang-tidy; plus minor clean up (#157) Upgrade C++ standard from 17 to 20, clang-tidy from 14 to 21, checkout@v6 and cache@v5. Update .clang-tidy exclusions and to check incflo files only. .clang-tidy .github/workflows/gcc.yml src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_csg.cpp src/embedded_boundaries/eb_cyl_tuscan.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/eb_spherecube.cpp src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_compute_dt.cpp src/incflo_regrid.cpp src/main.cpp src/rheology/incflo_read_rheology_parameters.cpp src/setup/init.cpp src/utilities/incflo_build_info.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit 13031713f2b53e746c8ca4bce086c63038d5fd7a Author: Candace Gilet Date: Tue Feb 17 17:41:00 2026 -0500 Multilevel particles (#154) Get tagging on particles working during initialization. Also fix compiler error and some warnings. Uses AMReX PR #4951 src/incflo.cpp src/particles/incflo_PCEvolve.cpp src/particles/incflo_PCInit.cpp src/particles/incflo_Tracers.cpp commit 74b1ed2d1876b7f3cc7fea42f42eccc877312778 Author: Candace Gilet Date: Tue Dec 2 16:19:45 2025 -0500 Fix typo in temperature Crank-Nicolson diffusion (#153) src/incflo_update_temperature.cpp commit ca87e6cb87fc62c3a45d08f058f9d32c142f1167 Author: Candace Gilet Date: Thu Oct 30 14:50:28 2025 -0400 Update shear layer benchmark to use scalar velocity diffusion solve (#152) since no other test covers this bit of code test_no_eb_3d/benchmark.double_shear_layer_x commit e5db01c1a406d93c0d31c7801a1c68849a762e24 Author: Candace Gilet Date: Wed Oct 22 13:45:52 2025 -0400 Ensure compute_divtau sees correct component of velocity. Only (#151) correct for vel_x previously. src/diffusion/DiffusionScalarOp.cpp commit aeb668a3f823bc57922db6bc11fe96372a70f4d1 Author: Candace Gilet Date: Wed Sep 3 09:19:07 2025 -0400 Allow refinement ratio != 2 when filling MAC velocity ghost cells (#150) (although amrex still places some restrictions on ref_ratio != 2 for some options). src/convection/incflo_compute_advection_term.cpp commit 1a419b8d424b7816485df38d3120d7c0b7c57809 Author: Candace Gilet Date: Fri Jun 6 18:37:35 2025 +0200 Add option to evolve temperature eqn (#149) Does not yet couple back into fluid or work with MOL advection scheme. Includes updated benchmark.channel_spherecube to include temperature solve with Dirichlet BC on EB in regression tests. Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/InputsAlgorithm.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst src/CMakeLists.txt src/Make.package src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_fillphysbc.cpp src/boundary_conditions/incflo_set_bcs.cpp src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_advance.cpp src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp src/incflo_regrid.cpp src/incflo_specific_heat.cpp src/incflo_update_temperature.cpp src/incflo_utils.cpp src/prob/prob_bc.H src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp test_3d/benchmark.channel_spherecube commit 86badef3d209c9cf5eb6765b2ca5057794bd0513 Author: Candace Gilet Date: Tue Jun 3 19:08:03 2025 +0200 Fix out-of-bounds error in IncfloVelFill when doing u_mac fillpatch (#146) Co-authored-by: Ann Almgren src/prob/prob_bc.H commit 956e948d098bbdff877e9dadd1e52bf9ac7715df Author: Candace Gilet Date: Tue Jun 3 18:27:41 2025 +0200 Ebflow tracer diffusion bc (#148) This PR includes three changes * If using tracer(s) and flow through the EB, the tracer diffusion solve now uses a Dirichlet BC for the EB. * Only define the MFs that hold EB Dirichlet values if they're needed * Updates benchmark.eb_flow_const_vely to evolve a tracer This will require updating the eb_flowy_2d regression test bencchmark src/diffusion/DiffusionScalarOp.cpp src/setup/incflo_arrays.cpp test_2d/benchmark.eb_flow_const_vely commit 5104d1334035a5d1800b28718771989607d00a46 Author: Candace Gilet Date: Mon Jun 2 21:04:25 2025 +0200 Fix memory leak for direction_dependent BCs (#147) src/projection/incflo_apply_nodal_projection.cpp commit 8b4cd342f233708d1e5aa666409e4b57c2e746b3 Author: Andy Nonaka Date: Tue May 13 13:31:24 2025 -0700 CC Projection Outflow Bugfix (#145) Fix bug in cc projection outflow where the ghost velocities were set to zero rather than fillpatching them src/projection/incflo_apply_cc_projection.cpp commit aa70615424eaa55e09cc22a2c1f44fa75bfbdd1d Author: Weiqun Zhang Date: Mon Apr 28 19:07:10 2025 -0700 Use ubuntu-24.04 instead of 20.04 in CIs (#144) Ubuntu-20.04 is no longer supported in GitHub Actions. .github/workflows/cuda.yml .github/workflows/hip.yml commit 2e221e1d271f9e694ba189b0e0a415d3b6cdc11f Author: Candace Gilet Date: Thu Mar 13 10:52:30 2025 +0100 Fix regrid_on_restart (#143) src/utilities/io.cpp commit bdc02b50b5f18afc04f21b6c47c9628f6c80f644 Author: Andy Nonaka Date: Fri Dec 6 10:13:01 2024 -0800 Remove whitespace in plt_p query that was preventing it from working (#142) Remove whitespace in plt_p query that was preventing it from working src/setup/init.cpp commit 5ef9c86cb464436d137ff329bb0ffc3aced46b62 Author: Candace Gilet Date: Tue Dec 3 23:07:10 2024 +0100 Only call setVal on defined p_nd/p_cc (#141) src/incflo_regrid.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp commit 9315bfa0ea364d1610322e7e1e72cd9e6583536f Author: Candace Gilet Date: Tue Dec 3 16:05:16 2024 +0100 Define one p and fix BC for cc_proj (#140) This PR contains * Now only define one pressure MultiFab, p_cc if m_use_cc_proj and p_nd otherwise * For use_cc_proj, use LinOpBCType::Neumann in place of LinOpBCType::inflow (which is for nodal_proj only) * In checkpoint file write, fix MultiFabFileFullPrefix name parameter * In checkpoint file read, if use_cc_proj use p_cc, otherwise use p_nd src/projection/incflo_projection_bc.cpp src/setup/incflo_arrays.cpp src/utilities/io.cpp commit 6066d049d0a747e5f6149fabaeb67694e4f6a7d1 Author: Candace Gilet Date: Mon Dec 2 16:52:58 2024 +0100 If m_use_cc_proj write p_cc to checkpoint; logic was reversed (#139) src/utilities/io.cpp commit 4093772dde5462076b5eb1e583165be1e91a9d56 Author: Weiqun Zhang Date: Wed Oct 30 18:10:33 2024 -0700 Disable Warnings in oneAPI 2025.0 (#138) .github/workflows/sycl.yml commit 4d40f0e8a8a5225c9ed5da6868511d933bd1013e Author: Candace Gilet Date: Wed Oct 9 23:49:16 2024 +0200 Add option to write a smallplotfile as in AmrLevel. A user defined (#136) selection of variables can be written at a different interval than the full plotfile, e.g. amr.smallplot_int = 5 amr.smallplotVariables = density magvel Also add the option to specify plotfile variables as a list, e.g. amr.plotVariables = velx vely velz Docs/sphinx_documentation/source/InputsPlotFiles.rst src/incflo.H src/incflo.cpp src/setup/init.cpp src/utilities/io.cpp test_2d/benchmark.eb_flow_const_velx test_2d/benchmark.eb_flow_const_vely test_2d/benchmark.eb_flow_sphere test_2d/benchmark.inviscid_rotated_planes_x test_2d/benchmark.rotated_planes_x test_2d/benchmark.rotated_planes_y test_2d/benchmark.split test_2d/benchmark.tracer_adv_diff test_2d/benchmark.tracer_adv_diff_cn test_2d/benchmark.tracer_advection test_2d/benchmark.vortex_in_sphere test_3d/benchmark.channel_sphere test_3d/benchmark.double_shear_layer test_3d/benchmark.double_shear_restart test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz test_3d/benchmark.eb_flow_density test_3d/benchmark.rotated_cylinder_x test_3d/benchmark.rotated_cylinder_y test_3d/benchmark.rotated_cylinder_z test_3d/benchmark.slanted_cylinder test_3d/benchmark.tracer_adv_diff test_3d/benchmark.tracer_adv_diff_cn test_3d/benchmark.tracer_advection test_3d/benchmark.upipe test_no_eb_2d/benchmark.bouss_bubble_god test_no_eb_2d/benchmark.bouss_bubble_mol test_no_eb_2d/benchmark.bouss_bubble_plm test_no_eb_2d/benchmark.burggraf test_no_eb_2d/benchmark.double_shear_layer test_no_eb_2d/benchmark.rayleigh_taylor test_no_eb_3d/benchmark.bouss_bubble_god test_no_eb_3d/benchmark.bouss_bubble_mol test_no_eb_3d/benchmark.bouss_bubble_plm test_no_eb_3d/benchmark.burggraf test_no_eb_3d/benchmark.double_shear_layer_x test_no_eb_3d/benchmark.double_shear_layer_y test_no_eb_3d/benchmark.double_shear_layer_z test_no_eb_3d/benchmark.rayleigh_taylor commit 197009548adb258f749f9e9bbc4e4000b7648982 Author: Candace Gilet Date: Tue Oct 8 19:06:11 2024 +0200 For certain 2D EB geometries, fix out of bounds access in Print (#137) statement src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_cyl_tuscan.cpp src/embedded_boundaries/eb_sphere.cpp commit e8f071a027539024116255aca59c7c70204bf091 Author: Ann Almgren Date: Fri Sep 27 13:57:47 2024 -0700 fix for the last commit (#135) Co-authored-by: Weiqun Zhang .github/workflows/codespell.yml .github/workflows/docs.yml Docs/sphinx_documentation/source/InputsAlgorithm.rst src/incflo.H src/incflo.cpp src/setup/init.cpp commit 8796a02022a40f5a57342d6101e4dedc64474dac Author: Ann Almgren Date: Wed Sep 25 13:02:10 2024 -0700 put in basic data structures / operations for cc-projection as altern… (#134) …ative to nodal projection src/boundary_conditions/CMakeLists.txt src/boundary_conditions/Make.package src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_regrid.cpp src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/CMakeLists.txt src/projection/Make.package src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_projection_bc.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit a7f92133863c784924411bdc1fac3b55e465bee1 Author: Candace Gilet Date: Tue Sep 17 16:34:26 2024 +0200 For time-dependent BCs, need to pass the real time when (#133) FillPatching umac. src/convection/incflo_compute_advection_term.cpp commit d792c63027cc2f1ecf74d74a118802e262af1541 Author: Weiqun Zhang Date: Wed Sep 11 10:07:00 2024 -0500 Simplify cache cleanup actions (#129) In our old approach, a workflow file contains a job that uploads the PR number as an artifact. While the PR is still open, the workflow_run triggered by it will download the artifact and use the information to clean up all except the last used cache associated with that original workflow. When a PR is merged or closed, there will be a post-pr workflow that uploads the PR number as an artifact and triggers a workflow_run that clean up all caches associated with the PR. The reason we did it this way was in the cache cleanup workflows, we did not find an easy way to get the number of the PR triggering them. This is not convenient because we have to add jobs uploading artifacts to workflow files. After some experiments, we have found a reliable way to find the PR number without using artifacts. The workflow_run's payload always contains the head SHA of the commit that triggers it, whether the PR comes from a fork or not. We can then use `gh pr list` to search for that head and obtain the PR number. .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/cuda.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/post-pr.yml .github/workflows/sycl.yml commit a007c21a941c5fe959e8f1de1b1d3b08fb970231 Author: Candace Gilet Date: Wed Sep 11 16:57:56 2024 +0200 Fix case of multiple tracers with default initial conditions. Issue (#132) introduced in PR#131 src/setup/init.cpp commit f3f129b9320a5ee84abf1e59fd4597291943e92d Author: Candace Gilet Date: Tue Sep 10 15:58:42 2024 +0200 For wall BCs, fix option for scalar Dirichlet BC (#130) src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H commit d88a1a76c74060199be9dc9f4c87c45c10ac7c7b Author: Candace Gilet Date: Tue Sep 10 15:54:49 2024 +0200 Use incflo::m_ic_t to initialize tracer initial conditions. Also (#131) update m_ic_t to hold multiple tracers. src/incflo.H src/prob/prob_init_fluid.cpp src/setup/init.cpp commit 3db46ad57751624596a7330e04dfcb0014c5a277 Author: Ann Almgren Date: Sat Aug 31 10:03:58 2024 -0700 fix probtype 1102 (#128) src/prob/prob_bc.H commit 1575b68ce5180205ce6e4f1a1f0c2547cb3ed502 Author: Ann Almgren Date: Sat Aug 31 09:07:37 2024 -0700 fix probtype 1101 logic (#127) src/prob/prob_bc.H commit 8643ecc84e2a40007098fccf1abbb82d0012b5eb Author: Ann Almgren Date: Fri Aug 30 20:37:16 2024 -0700 fix typo (#126) src/prob/prob_bc.H commit 56342876d295d00a1d8e20eb2948bea93d2afb95 Author: Ann Almgren Date: Thu Aug 29 20:50:00 2024 -0700 fix logic in IncfloVelFill (#125) src/prob/prob_bc.H commit 60881d3c0e61cc265ecfc365c65d50911072e252 Author: Ann Almgren Date: Thu Aug 29 13:09:08 2024 -0700 enable direction-dependent bcs (#122) src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_fillphysbc.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/prob/prob_bc.H src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_projection_bc.cpp test_no_eb_2d/benchmark.inout test_no_eb_3d/benchmark.inout commit 6e7bb3ebd0194f4f281792cad64535b59b2dbe13 Author: drangara <69211175+drangara@users.noreply.github.com> Date: Wed Aug 28 13:09:20 2024 -0400 fix a typo when printing EB info for cylinder (#123) src/embedded_boundaries/eb_cylinder.cpp commit 6668f123524a56cd7d08295d253a0bb360200dcf Author: Weiqun Zhang Date: Sun Aug 18 20:38:40 2024 -0500 Add runtime parameter tensor_diffusion.use_gauss_seidel (#121) The default is true. One can use Jacobi smoothers for tensor, mac and nodal solves with tensor.use_gauss_seidel = false mac_proj.use_gauss_seidel = false nodal_proj.use_gauss_seidel = false src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp commit 94aa2ba650c5c269abf465d5ff579d9249df6a45 Author: Ann Almgren Date: Thu Aug 15 09:17:37 2024 -0700 Add time dep velocities (#117) commit 78dcbd8d1664dd653c2f8a53968b31e9ce70d2ae Author: Ann Almgren Date: Wed Aug 14 16:38:37 2024 -0700 initialize to 0 so we don't use uninitialized values (#120) src/convection/incflo_compute_MAC_projected_velocities.cpp commit 1fbb115360467c29e38f775a17930ea31c889e5c Author: Ann Almgren Date: Mon Aug 12 15:03:11 2024 -0700 fix ptr (#119) src/convection/incflo_compute_advection_term.cpp commit 402f76cba3f324f0a70797ec5327b15a338757a8 Author: Ann Almgren Date: Sun Aug 11 19:21:08 2024 -0700 Add time dep vels 2 (#118) CMakeLists.txt src/boundary_conditions/incflo_set_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/prob/prob_bc.H src/prob/prob_init_fluid.cpp test_no_eb_2d/benchmark.time_dep_inflow test_no_eb_3d/benchmark.time_dep_inflow commit 6314ddd1ea3e544fd639c251882a9c0cae3975ce Author: Ann Almgren Date: Tue Aug 6 08:36:38 2024 -0700 consolidate test directories (#116) test_bds_2d/GNUmakefile test_bds_3d/GNUmakefile test_no_eb_2d/inputs.circ_traceradect_bds test_no_eb_2d/inputs.gaussian_traceradvect_bds test_no_eb_3d/inputs.gaussian_traceradvect_bds test_no_eb_3d/inputs_circ_traceradvect_bds commit 0457abca39034ed6b8703e38f6ad926eb2c3a5d4 Author: Ann Almgren Date: Sat Aug 3 15:59:34 2024 -0700 fix oops from previous commit (#115) src/convection/incflo_compute_MAC_projected_velocities.cpp commit 45a352140027b2e72adef26a7656d0f1aeb437bc Author: Bhargav Sriram Siddani <45137944+siddanib@users.noreply.github.com> Date: Fri Aug 2 09:21:27 2024 -0700 BCType::foextrap as default for (density, BC::slip_wall) combination when advection_type == "BDS" (#113) Making `BCType::foextrap` as the default type for _density_ and _tracer_ at `BC::slip_wall` boundary only when `advection_type == "BDS"`. Also made a minor change in docs (`src/boundary_conditions/README.org`) for _(scalar/density, sw)_ combination. src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp commit 308c35cd088f41885d4ea1ec284dd4cbda3e780f Author: Ann Almgren Date: Thu Aug 1 14:38:50 2024 -0700 changes to go along with update AMReX-Hydro (#114) src/convection/incflo_compute_advection_term.cpp commit ec86f810a7bd93deb0bceb12290edc33ba14fa81 Author: Weiqun Zhang Date: Mon Jul 8 18:34:21 2024 -0700 CI: Add codespell (#112) .codespell-ignore-words .codespellrc .github/workflows/codespell.yml CODE_OF_CONDUCT.md Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst src/boundary_conditions/incflo_set_bcs.cpp src/convection/incflo_compute_advection_term.cpp src/particles/ParticleData.H src/prob/prob_init_fluid.cpp src/setup/init.cpp test_2d/benchmark.rotated_planes_y test_bds_2d/inputs.circ_traceradvect test_bds_2d/inputs.gaussian_traceradvect test_bds_3d/inputs.circ_traceradvect test_bds_3d/inputs.gaussian_traceradvect commit 2a17da252b2fb1c3cb2ab7ff83bbd61f49fdb795 Author: Ann Almgren Date: Fri Jun 21 18:21:26 2024 -0700 1) initial pressure projection now plays correctly with gp0, 2) the p… (#110) …lotfile variables gpx, gpy, gpz now contain (gp0+gp) instead of just the gp variables src/boundary_conditions/incflo_set_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/derive/incflo_derive.cpp src/derive/incflo_error.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_compute_forces.cpp src/incflo_correct_small_cells.cpp src/incflo_explicit_update.cpp src/incflo_redistribute.cpp src/incflo_tagging.cpp src/incflo_update_velocity.cpp src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_rheology.cpp src/setup/init.cpp src/utilities/io.cpp commit 83d124d9bdc9125409d3702772af503bd5fbe3fb Author: Candace Gilet Date: Thu Jun 20 15:23:07 2024 -0400 Add InitialPressureProjection to enforce hydrostatic equilibrium (#102) in cases where that's not done through the background density and pressure. Right now, this is a runtime option that is off by default. It does not check for any background state; it is up to the user to know when to use it and to ensure that the background density is turned off with incflo.ro_0 = 0 --------- Co-authored-by: Ann Almgren src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp test_no_eb_2d/benchmark.rayleigh_taylor test_no_eb_3d/benchmark.rayleigh_taylor commit a101f71afcba8c6d3bc90c9156180d6e1395a016 Author: Ann Almgren Date: Thu Jun 20 07:40:44 2024 -0700 add magvel as an optional derived quantity (#109) src/derive/incflo_derive.cpp src/derive/incflo_derive_K.H src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit a9a7df4bceba8f03f87dca957203a55aa6a2a1c1 Author: Candace Gilet Date: Wed Jun 19 15:28:48 2024 -0400 Add a second, non-conservative tracer to the BDS benchmarks (#108) test_2d/benchmark.bds_tracer_advection test_3d/benchmark.bds_tracer_advection commit d104f4ef9c40b2ccaf60f790aefad8a6e93d3719 Author: Weiqun Zhang Date: Tue Jun 18 18:20:37 2024 -0700 Bump up actions' version (#107) .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/cuda.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/post-pr.yml .github/workflows/style.yml .github/workflows/sycl.yml commit 117293a150e5bdfcd0dc415d9c4ede1d1a8854b7 Author: Candace Gilet Date: Tue Jun 18 14:36:05 2024 -0400 Pass the this ptr to LevelData constructor to allow for easier (#106) addition of optional components src/incflo.H src/incflo.cpp src/incflo_regrid.cpp src/setup/incflo_arrays.cpp commit 0e232e807353aded1559059ee11ae6fbb50f57da Author: Candace Gilet Date: Mon Jun 17 14:21:29 2024 -0400 Fix indexing error in computing the advective term for (#104) non-conservative tracers. In practice, this makes little difference because it's multiplied by div(Umac) which the MAC projection just enforced to be numerically zero to within its tolerance. Also make the density field non-constant and add a second, non-conservative tracer in the tracer_adv_diff_cn regression test. This will require creating new benchmarks for the 2D and 3D tests. Co-authored-by: Ann Almgren src/convection/incflo_compute_advection_term.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test_2d/benchmark.tracer_adv_diff_cn test_3d/benchmark.tracer_adv_diff_cn commit bc553d11527c0fc5809b5832f225a85e84a5cf84 Author: Ann Almgren Date: Sun Jun 16 18:11:39 2024 -0700 separate routines into separate files so predictor and corrector aren… (#105) …'t so long src/CMakeLists.txt src/Make.package src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_update_density.cpp src/incflo_update_tracer.cpp src/incflo_update_velocity.cpp src/incflo_utils.cpp src/setup/incflo_arrays.cpp commit 844091a9d3265f738188363dc4285a32167d7b05 Author: Candace Gilet Date: Fri Jun 14 18:02:05 2024 -0400 Add regrid on restart (#101) Docs/sphinx_documentation/source/InputsCheckpoint.rst src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit 4a94e63b6a18c1c9697853f6159ca812847c8fee Author: Candace Gilet Date: Fri Jun 14 17:55:35 2024 -0400 Cleanup (#103) 1. Make first call to compute_vel_forces in ApplyPredictor safer for new forms of the forcing term. For the forcing terms currently in incflo, the old way was fine and this code change should not alter results. However, for restart, only old time data is guaranteed to be FillPatched at this point. So, since old and new represent the same data at this point in the code, this is a safer choice for more general forms of the forcing term that users may wish to introduce. 2. Add time step options to Docs 3. Add a comment, fix typo and outdated info in other comments. Docs/sphinx_documentation/source/InputsTimeStepping.rst src/incflo_apply_predictor.cpp src/incflo_compute_dt.cpp commit 0a40f113e7d5850c29c8748d82b90f362d239593 Author: Candace Gilet Date: Mon May 13 09:22:06 2024 -0400 Make the maxiumum dt change between time steps a runtime variable. (#100) src/incflo.H src/incflo_compute_dt.cpp src/setup/init.cpp commit 011b26a4121847b1eb1fcbc1a0c9b73ae9a0717c Author: Ann Almgren Date: Mon Apr 29 10:56:36 2024 -0700 Add particles (#99) src/Make.incflo src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_regrid.cpp src/incflo_tagging.cpp src/particles/Make.package src/particles/ParticleData.H src/particles/incflo_PC.H src/particles/incflo_PCEvolve.cpp src/particles/incflo_PCInit.cpp src/particles/incflo_PCUtils.cpp src/particles/incflo_Tracers.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp src/setup/init.cpp src/utilities/io.cpp commit 9c4695252b4216ab2db33b42bedd25eb17a68fb4 Author: Candace Gilet Date: Mon Apr 15 21:55:35 2024 -0400 Fix for when a new level is created (#98) Also correct incflo.H include guard, a typo and a couple outdated comments. .github/workflows/docs.yml src/incflo.H src/incflo_apply_predictor.cpp src/incflo_regrid.cpp commit dda01f2318d19d14160b242feb91b9e4e99a18af Author: Candace Gilet Date: Tue Apr 9 14:07:57 2024 -0400 Fix for non-conservative tracers (#96) Add updates for non-conserv diffusion that were mistakenly not committed in pr 94. Also update docs to include non-conservative scalar option. Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/InputsAlgorithm.rst Docs/sphinx_documentation/source/index.rst src/diffusion/DiffusionScalarOp.cpp commit 069fd36e36768c40936491f8608f9255fb564697 Author: Candace Gilet Date: Wed Apr 3 15:25:05 2024 -0400 Fix fillpatch tracer (#95) for ntrac>1 src/boundary_conditions/incflo_fillpatch.cpp src/incflo_apply_corrector.cpp commit 3c02cade2a09565bcf90af00246a87d0acc265e8 Author: Candace Gilet Date: Tue Apr 2 13:38:12 2024 -0400 Add nonconservative tracer (#94) src/CMakeLists.txt src/Make.package src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp src/incflo_explicit_update.cpp src/setup/init.cpp commit a732e8437d4981e645569ec814bf5aeaa750c035 Author: Candace Gilet Date: Tue Apr 2 12:31:39 2024 -0400 Fix InitialRedistribution for ntrac >1 (#92) src/setup/init.cpp commit 69f54a702e6d311a1b942cb6480774e66cb57861 Author: Candace Gilet Date: Mon Mar 25 12:16:44 2024 -0400 Use dynamic tiling with OMP when creating BC MFs for mixed BCs (#90) src/boundary_conditions/incflo_set_bcs.cpp commit f9e8dfa5cb435a4dbc99fc3a506b7a4da99c929f Author: Weiqun Zhang Date: Mon Mar 25 08:58:04 2024 -0700 update build and deploy (#91) .github/workflows/docs.yml commit e78cd29b5bf9b92d1eb693356c59934c3c620070 Author: Candace Gilet Date: Fri Mar 15 10:16:24 2024 -0400 Add mixed bc and update docs (#89) This allows inflow and outflow on the same domain face, where the Dirichlet and Neumann regions are separated by an EB. Depends on Hydro pr 126 and AMReX PR 3788 Docs/sphinx_documentation/source/InputsAlgorithm.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_set_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/incflo_apply_predictor.cpp src/incflo_redistribute.cpp src/incflo_regrid.cpp src/prob/CMakeLists.txt src/prob/Make.package src/prob/incflo_prob_I.H src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_projection_bc.cpp src/setup/init.cpp test_2d/benchmark.split test_3d/benchmark.upipe commit ae8f233a23512c9bbabe83985328a64d0e97cd17 Author: Candace Gilet Date: Thu Mar 14 21:36:09 2024 -0400 Consolidate code (#88) * Update make_eb_box() to use amrex::BoxIF. This allows specifying internal or external flow. * Remove incflo::set_velocity_bc functions in favor of using PhysBCFunct, which is needed to set the inflow bcs during FillPatch. Now we only need one function to set the inflow bc. * Rename file to better reflect contents which includes setting density and tracer EB bcs. Renamed: incflo_set_velocity_bcs.cpp -> incflo_set_bcs.cpp src/boundary_conditions/CMakeLists.txt src/boundary_conditions/Make.package src/boundary_conditions/incflo_set_bcs.cpp src/embedded_boundaries/eb_box.cpp src/incflo.H src/prob/CMakeLists.txt src/prob/Make.package src/prob/prob_bc.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_projection_bc.cpp commit 7a525e0a9e0d5fafaff5f839182eca60a5c465ac Author: Candace Gilet Date: Mon Nov 6 14:39:27 2023 -0500 ensure initial_shrink still gets applied. together with pr83, this (#84) ensures the initial timestep is computed as expected. This will require redoing some regression tests due to the change in the initial dt. Co-authored-by: Ann Almgren src/incflo_advance.cpp commit db1c123b9f174265c2b4a48bb927db572a54696b Author: Weiqun Zhang Date: Mon Nov 6 09:44:27 2023 -0800 Update URL (#85) .github/workflows/cuda.yml .github/workflows/docs.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/sycl.yml CMakeLists.txt CONTRIBUTING.md Docs/README.md Docs/sphinx_documentation/source/Debugging.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/index.rst README.md test_3d/README.md commit 58de1d921fee91fc7963a039051099cc0f4e9090 Author: Candace Gilet Date: Thu Nov 2 14:12:46 2023 -0400 Minor fix for initial dt. We need to reset dt at the end of (#83) InitialIterations in order to get the specifed dt. Otherwise, we can end up with dt = initial_dt*change_max. src/setup/init.cpp commit afa2a5c9b0dc9e8e96bf66f43e44715ffdc20003 Author: Weiqun Zhang Date: Wed Oct 4 12:14:23 2023 -0700 Disable Scheduled GitHub Actions on Forks (#82) The default branch on a fork is often out of sync with the main repo, resulting in failures in scheduled actions. This disables scheduled actions on forks. Note that `push` and `pull_request` still trigger GitHub actions on forks. If one wants to disable it entirely in their fork, follow the instruction in the link below. https://docs.github.com/en/actions/using-workflows/disabling-and-enabling-a-workflow?tool=webui#disabling-a-workflow .github/workflows/cuda.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/sycl.yml commit 6a44ae90504222bc786b60e9dca590d2d332112b Author: Weiqun Zhang Date: Mon Sep 18 12:00:05 2023 -0700 Change nghost_eb_basic to 5 due to assertion in amrex #3549 (#81) src/incflo.H commit 62a3b269b795a774d7e2861030b98780937509ad Author: Candace Gilet Date: Fri Sep 1 17:39:57 2023 -0400 Update doc (#80) Docs/sphinx_documentation/source/BuildingCMake.rst Docs/sphinx_documentation/source/BuildingGMake.rst Docs/sphinx_documentation/source/BuildingMacVelocities.rst Docs/sphinx_documentation/source/Debugging.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EBWalls.rst Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/FluidTimeDiscretization.rst Docs/sphinx_documentation/source/Fluids_Chapter.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/InputsAlgorithm.rst Docs/sphinx_documentation/source/InputsInitialization.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst Docs/sphinx_documentation/source/Inputs_Chapter.rst Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst Docs/sphinx_documentation/source/Slopes.rst Docs/sphinx_documentation/source/TimeStep.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/index.rst src/incflo.H src/setup/init.cpp commit 1ee4f1ed79b2496f9ef20f28be2eee27d4228c25 Author: Weiqun Zhang Date: Sat Aug 12 09:48:57 2023 -0700 Use the new nvcc installation script (#79) .github/workflows/cuda.yml commit bb5d37699dae420b5bb8da07ecf88aee11b8e7c3 Author: Yue Sun Date: Fri Aug 4 16:22:18 2023 -0400 fix header again (#78) src/prob/incflo_prob_usr_I.H commit c1588fd6752d7c06350ac895f676ebaca9f7f971 Author: Ann Almgren Date: Sat Jul 8 11:06:02 2023 -0700 update ifndef lines (#75) src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionTensorOp.H src/prob/prob_bc.H commit be7a04ab70e56e4dfdd8913ab517fdb76f518c87 Author: Weiqun Zhang Date: Fri Jul 7 19:29:30 2023 -0700 Increase verbosity of CI jobs (#74) .github/workflows/gcc.yml commit 0e624c8bda996f4ed6c281e7f34b05bcdb219e75 Author: Weiqun Zhang Date: Thu Jul 6 20:21:29 2023 -0700 Add more CIs (#73) * Update CMake for CUDA. * Add support of HIP and SYCL in CMake. * Add more CIs. * Fix style. * Fix clang-tidy warnings. .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/cuda.yml .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_ccache.sh .github/workflows/dependencies/dependencies_clang-tidy.sh .github/workflows/dependencies/dependencies_clang.sh .github/workflows/dependencies/dependencies_codeplay.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_gcc.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_llvm_cuda11_ubuntu22.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/dependencies_nofortran.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc12.sh .github/workflows/dependencies/dependencies_nvhpc.sh .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/post-pr.yml .github/workflows/smoke.yml .github/workflows/style.yml .github/workflows/sycl.yml CMakeLists.txt src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/eb_if.H src/incflo.H src/incflo.cpp src/incflo_compute_forces.cpp src/incflo_redistribute.cpp src/incflo_tagging.cpp src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_projection_bc.cpp src/utilities/incflo_build_info.cpp src/utilities/io.cpp commit 00b1955dd4f2f8e81c52eea09c2d02fff19de176 Author: Weiqun Zhang Date: Mon Jul 3 12:08:21 2023 -0700 Add some files adapted from amrex (#71) .clang-tidy .editorconfig .gitattributes CODE_OF_CONDUCT.md CONTRIBUTING.md README.md commit 90238a0f2780767cccd55e2a5efb6a074fd672ea Merge: 02b596e1 c6c712d3 Author: Weiqun Zhang Date: Sun Jul 2 20:10:40 2023 -0700 Merge pull request #70 from AMReX-Codes/move_redist_into_amrex Modify incflo to work with moving redistribution from AMReX-Hydro into amrex commit 02b596e15553da495393cda4fb9f7f8eb47490ea Author: cgilet Date: Thu Jun 29 02:22:48 2023 -0400 Add check for restart, to ensure we don't take a step if n_step >= max_step; otherwise code always takes at least 1 step. src/incflo.cpp commit c6c712d30bdc9622d25e17c813e9b4e93567d165 Merge: 43a46c29 b6517981 Author: Weiqun Zhang Date: Tue Jun 27 17:16:24 2023 -0700 Merge branch 'development' into move_redist_into_amrex commit b651798176ceaa282788b37cd8e308aa117a6a1e Author: Ishan Srivastava Date: Mon Jun 26 11:15:21 2023 -0600 divide divtau by rho before adding to vel_force in advection step when m_advect_momentum is true (#68) src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp commit fc222d747ec3dbcfa3a20468ece5e7492a58c72f Author: Ann Almgren Date: Sun Jun 25 17:29:52 2023 -0700 adding dependencies*.sh files .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_ccache.sh .github/workflows/dependencies/dependencies_clang-tidy.sh .github/workflows/dependencies/dependencies_clang.sh .github/workflows/dependencies/dependencies_codeplay.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_gcc.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_llvm_cuda11_ubuntu22.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/dependencies_nofortran.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc12.sh .github/workflows/dependencies/dependencies_nvhpc.sh commit e8639112e1f975ec7afef4809ab29871c5b30f57 Author: Ann Almgren Date: Sun Jun 25 17:26:13 2023 -0700 adding smoke test to CI .github/workflows/smoke.yml commit 43a46c2958d39081729387de3461dc22bee17cf0 Author: Ann Almgren Date: Fri Jun 23 12:23:48 2023 -0700 Modify incflo to work with moving redistribution from AMReX-Hydro into amrex .clang-tidy src/Make.incflo src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/incflo_redistribute.cpp src/setup/init.cpp commit 30ad1d7a0104ac403c3cef0c43dd44875acd1705 Author: drangara <69211175+drangara@users.noreply.github.com> Date: Wed Jun 7 14:29:29 2023 -0400 Call FillBoundary when setting EB flow BCs (#67) src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 70c81305909c2c55b73bf2870e99e1eab01dc0fc Author: Ann Almgren Date: Mon Apr 10 11:28:10 2023 -0700 add 3d version of Burggraf problem test_no_eb_3d/benchmark.burggraf test_no_eb_3d/test_convergence_burggraf commit 90ff0c8770afcc04df5f80b11ba72ddd77604ba4 Author: Ann Almgren Date: Fri Apr 7 14:10:10 2023 -0700 add Burggraf problem setup and run script for convergence testing Docs/sphinx_documentation/source/EBWalls.rst src/derive/incflo_error.cpp src/incflo_compute_forces.cpp src/prob/incflo_prob_I.H src/prob/prob_bc.H src/prob/prob_init_fluid.cpp test_no_eb_2d/benchmark.burggraf test_no_eb_2d/test_convergence_burggraf commit 3858b1ec0add3003fd10e3f6570924728d848360 Author: Ann Almgren Date: Wed Mar 29 10:58:48 2023 -0700 fix compile src/incflo.H commit 191adff567eda8ba550a7af96975c44c37e91819 Author: Ann Almgren Date: Tue Mar 28 20:16:30 2023 -0700 make clang-tidy happy src/incflo.H src/incflo.cpp src/incflo_regrid.cpp commit 040b8f744c4f285fc577c317863acd9264c14b32 Author: Ann Almgren Date: Tue Mar 28 18:22:48 2023 -0700 clang-tidy fixes src/convection/incflo_compute_advection_term.cpp src/derive/incflo_derive.cpp src/derive/incflo_error.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/eb_csg.cpp src/embedded_boundaries/eb_if.H src/incflo.H src/incflo.cpp src/incflo_redistribute.cpp src/incflo_regrid.cpp src/incflo_tagging.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 271a0a69a0228f4cfb37231d066aef6f27e36b88 Author: cgilet Date: Fri Mar 17 14:35:47 2023 -0400 Create more general redistribute function. Use in advection only for now. Diffusion still always does FRD, but there's a commented out call to new redistribute function as well. Squashed commit of the following: commit 983e61752adc1fcb2d0f5e5810696a61a16bf574 Author: cgilet Date: Wed Mar 15 21:26:28 2023 -0400 Put back FRD in diffusion for testing. New redistribute fn in convection only. Shouldn't change any results. commit 75eeb5997d382a95685dad6323309d818b7bce2a Author: cgilet Date: Wed Mar 15 13:37:10 2023 -0400 Have advection use general redistribute func. Makes. Needs testing and cleanup. commit dd480e51cc5ec2b9e059dc7aa113b4a7aa0260a9 Author: cgilet Date: Tue Mar 14 14:28:39 2023 -0400 Make sure regular boxes windup unchanged commit 4c31ce936842755f26ce10af97e3a8b484432cd0 Author: cgilet Date: Mon Mar 13 13:57:05 2023 -0400 SRD for explicit diffusive term appears to work src/CMakeLists.txt src/Make.package src/convection/CMakeLists.txt src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/incflo.H src/incflo_redistribute.cpp commit 65abc6e839f8c047397d80e3eb32508562c6a4d2 Author: cgilet Date: Fri Mar 17 14:34:17 2023 -0400 In DiffFromExact(), use m_mu rather than hard-coding src/derive/incflo_error.cpp commit 50bf6936d4c18072e5af58527bf5f7bca07c0ddd Author: cgilet Date: Thu Mar 16 12:56:11 2023 -0400 remove unused variable src/incflo_correct_small_cells.cpp commit eb526d5fb6b9aae5ca9deb17489cd1b7ed69a51a Author: drangara <69211175+drangara@users.noreply.github.com> Date: Wed Mar 8 09:55:46 2023 -0500 Correct code for 2D when computing dt (#66) src/incflo_compute_dt.cpp commit 04965054e337a86a2197f1bf0a55609ed5cca224 Author: cgilet Date: Tue Feb 21 08:25:24 2023 -0500 Fix typo in 523e13b07a6 src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit 523e13b07a6a594933bc1a9db9e135e5332f899b Author: cgilet Date: Mon Feb 20 22:05:39 2023 -0500 Average down scalar solutions for multilevel problems. This shouldn't change the evolution of problems, since fine always overrides coarse. But this does put the correct data in underlying coarse cells for visualization & data analysis. src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit a1bc0d6334993dcf33473f8e9f4cca71c1ccab7c Merge: a96d3dc6 bed1ef1e Author: asalmgren Date: Fri Feb 10 16:46:29 2023 -0800 Merge pull request #58 from etpalmer63/cmake_eb_3d_fix CMake: Changes to files compiled when INCLFLO_DIM=2 commit bed1ef1ecf545af6fcdc3c2ac09c9f96f6dec44e Merge: cb114981 a96d3dc6 Author: asalmgren Date: Fri Feb 10 16:46:17 2023 -0800 Merge branch 'development' into cmake_eb_3d_fix commit a96d3dc69e53523acc25cb6f4819dd19eaa179bb Merge: 2d23f896 32b6a814 Author: asalmgren Date: Fri Feb 10 16:41:10 2023 -0800 Merge pull request #64 from drangara/support_for_csg_eb_library Support for csg eb library commit 32b6a8144f5147057f05ce7424bebbaa4790a1ee Author: Deepak Rangarajan Date: Wed Feb 8 19:39:16 2023 +0000 update EB documentation Docs/sphinx_documentation/source/EBWalls.rst commit ebc31e1fed9be2cab6390abebab860e75a687b32 Author: Deepak Rangarajan Date: Mon Feb 6 01:34:47 2023 +0000 add CSG-EB library support CMakeLists.txt src/Make.package src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/Make.package src/embedded_boundaries/eb_csg.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H test_2d/GNUmakefile test_3d/GNUmakefile test_3d/cylinder.csg test_3d/inputs.test_csg test_no_eb_2d/GNUmakefile test_no_eb_3d/GNUmakefile commit 2d23f8962998965cde05d4049b762f49ff5e64a4 Author: cgilet Date: Tue Feb 7 13:48:46 2023 -0500 Fix flow through EB with momentum advection: need to pass momentum to final div src/convection/incflo_compute_advection_term.cpp commit d93be3ec4550fed99b3cd1635c800e2b85305597 Merge: ecfa447d c159390c Author: asalmgren Date: Mon Feb 6 10:28:19 2023 -0800 Merge pull request #62 from ajnonaka/bds_tests BDS Tests commit ecfa447d5f6b3735a36650d7a053e0d3e4b98093 Merge: 3b58737e bce2a6b9 Author: asalmgren Date: Mon Feb 6 10:27:23 2023 -0800 Merge pull request #65 from drangara/fix_cmake_build fix cmake build commit bce2a6b9e31c55a415d7916e8c79472e259035b5 Author: Deepak Rangarajan Date: Mon Feb 6 18:23:47 2023 +0000 fix cmake build src/CMakeLists.txt commit 3b58737ee31aa39976fe8ac5235b0d38032b5044 Author: drangara <69211175+drangara@users.noreply.github.com> Date: Tue Jan 24 11:03:47 2023 -0500 add special handling inside incflo_correct_small_cells for the case with flow through EB (#63) src/incflo_correct_small_cells.cpp commit c159390c8f30d60a75e8e30f218225f0646d6aa0 Author: Andy Nonaka Date: Wed Dec 14 14:00:43 2022 -0800 bds gaussian advection test from 3d bds paper src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test_bds_2d/inputs.gaussian_traceradvect test_bds_3d/inputs.gaussian_traceradvect commit 48ae7ce9c2afddbd399ff9864a364e18761f8f94 Author: Andy Nonaka Date: Wed Dec 14 13:29:54 2022 -0800 2D version of BDS test 4.1 src/prob/prob_init_fluid.cpp test_bds_2d/GNUmakefile test_bds_2d/inputs.circ_traceradvect test_bds_3d/inputs.circ_traceradvect commit ca0670cc446ba8bdc585c43f9250b4ee61dea496 Author: Andy Nonaka Date: Tue Dec 13 13:52:32 2022 -0800 BDS test 4.1 from the 3D paper advection of discontinuous sphere of tracer src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test_bds_3d/GNUmakefile test_bds_3d/inputs.circ_traceradvect commit 7ea1aeb6a886b94761ea89d6bd15109cc9015643 Author: cgilet Date: Tue Dec 6 12:24:20 2022 -0500 Clean up - remove no longer used umacFill src/convection/incflo_compute_advection_term.cpp commit 145875f227167a6a3b6ec3da0b94341030c0239f Author: cgilet Date: Wed Nov 23 09:42:30 2022 -0500 Complete the option to advect momentum: compute div(rhoUU) and redistribute. src/convection/incflo_compute_advection_term.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit d69b6df4194c47f517a0e65fcf2833b7b97c4570 Author: Ann Almgren Date: Thu Nov 17 19:59:51 2022 -0800 fix typo src/incflo_apply_corrector.cpp commit 6e239671c85d57b8c1c81bd0c685a7b4743d9883 Author: Ann Almgren Date: Thu Nov 17 19:38:35 2022 -0800 start to adding option to update momentum rather than velocity -- this option is not fully functional yet src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/incflo.H src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp commit 2e3de867a639f652086604965ecf32680e0007b5 Author: Ann Almgren Date: Mon Nov 7 16:43:06 2022 -0800 reduce the number of compiler warnings when compiling with PRECISION = FLOAT src/derive/incflo_derive.cpp src/derive/incflo_derive_K.H src/derive/incflo_error.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/embedded_boundaries/eb_annulus.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/incflo_tagging.cpp src/main.cpp src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp src/utilities/io.cpp commit ab586f5675af1d3b1b5a2e928c2891edefc0c32f Author: Ann Almgren Date: Sun Oct 16 12:07:52 2022 -0700 1) remove ccproj, 2) quiet compiler warnings, 3) move test_no_eb to test_no_eb_3d README.md convergence_3d/todo src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp src/derive/incflo_derive.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_regrid.cpp src/prob/prob_init_fluid.cpp src/projection/CMakeLists.txt src/projection/Make.package src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/CMakeLists.txt src/utilities/Make.package src/utilities/diagnostics.cpp src/utilities/io.cpp test_no_eb_3d/GNUmakefile test_no_eb_3d/benchmark.bouss_bubble_god test_no_eb_3d/benchmark.bouss_bubble_mol test_no_eb_3d/benchmark.bouss_bubble_plm test_no_eb_3d/benchmark.double_shear_layer_x test_no_eb_3d/benchmark.double_shear_layer_y test_no_eb_3d/benchmark.double_shear_layer_z test_no_eb_3d/benchmark.poiseuille_halfplane_newtonian_x test_no_eb_3d/benchmark.poiseuille_halfplane_newtonian_y test_no_eb_3d/benchmark.poiseuille_halfplane_newtonian_z test_no_eb_3d/benchmark.poiseuille_plane_newtonian_x test_no_eb_3d/benchmark.poiseuille_plane_newtonian_y test_no_eb_3d/benchmark.poiseuille_plane_newtonian_z test_no_eb_3d/benchmark.rayleigh_taylor test_no_eb_3d/benchmark.slip_wall_test_x test_no_eb_3d/benchmark.taylor_green_vortices commit f95ef5c6ca7136e43ec441c375cea43e928614f5 Author: cgilet Date: Thu Oct 6 13:00:39 2022 -0400 Use HydroUtils::ComputeConvectiveTerm. Shouldn't change anything src/convection/incflo_compute_advection_term.cpp commit b0dce52d3444852e9901cdf23c3601dd81679301 Merge: 8ba34e6b 7f792517 Author: asalmgren Date: Wed Oct 5 12:21:43 2022 -0700 Merge pull request #59 from drangara/eb_restart support for EB checkpoint files commit 8ba34e6bd78f8a5ee90839ab0e359645805830f1 Author: Ann Almgren Date: Mon Sep 26 13:18:53 2022 -0700 now using amrex volumeWeightedSum instead of local incflo version src/Make.package src/incflo_advance.cpp src/incflo_vol_wgt_sum.cpp commit 7f7925178a0fcb5afcf9d02992388e92f01dbf3a Author: Deepak Rangarajan Date: Fri Aug 19 06:19:53 2022 -0700 update call to write checkpoint file src/embedded_boundaries/embedded_boundaries.cpp commit e789208cde97700c73527a4ab22e8c8799e7132e Author: Deepak Rangarajan Date: Wed Jul 20 14:42:22 2022 -0400 support for EB checkpoint files src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/Make.package src/embedded_boundaries/eb_chkptfile.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/setup/init.cpp test_2d/benchmark.eb_chkptfile.read test_2d/benchmark.eb_chkptfile.write test_3d/benchmark.eb_chkptfile.read test_3d/benchmark.eb_chkptfile.write commit ba2bca1e938601f7bd9d0ed3a478ff135e636bee Author: Ann Almgren Date: Thu Jul 14 16:39:42 2022 -0700 fix order of reading input parameters src/setup/init.cpp commit cb114981de4e4d87e16c48989806aadf310dbfc8 Author: Erik Palmer Date: Fri Jun 10 11:26:53 2022 -0700 CMake change: Do no include eb_spherecube.cpp, eb_tuscan.cpp, or eb_twocylinders.cpp when not INCFLO_DIM=3 src/embedded_boundaries/CMakeLists.txt commit e32339f138f64fcfaa6e0a457d490a2551abfb9b Author: cgilet Date: Fri Jun 3 12:28:56 2022 -0400 Add regression test inputs for 2d and 3d BDS test_2d/benchmark.bds_tracer_advection test_3d/benchmark.bds_tracer_advection commit b5b4c65e659553b9bc6c090123e40da3062a5d37 Author: Candace Gilet Date: Thu Jun 2 13:25:24 2022 -0400 Allow incflo to run with advection_type == BDS (#55) * If using BDS, use Godunov during initial velocity extrapolation to determine advective velocity. BDS only currently works for edge state prediction given known advective velocity. * Allow for flexible destination index in IncfloVelFill so that this can also be used to FillPatch Umac. * Update Umac FillPatch to fill all of Umac's ghost cells in accordance with velocity BCs. Previously, only periodic or foextrap BCs were used; and on level 0, only periodic ghost cells got filled. * Add benchmark.2d.bds_tracer_advection src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/prob/prob_bc.H src/setup/init.cpp test_2d/benchmark.bds_tracer_advection commit a540d2d422281263eda4379218e277d3b9e7896a Author: cgilet Date: Wed Jun 1 08:49:35 2022 -0400 Make separate functions to set nodal and mac projection bcs, since only the nodal solver has LinOpBCType::inflow. src/convection/incflo_compute_MAC_projected_velocities.cpp src/incflo.H src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_projection_bc.cpp commit 7161a08d9e7e6dfb9bdfc085e135f191c7cc70cc Author: cgilet Date: Tue May 31 20:56:53 2022 -0400 For projection, use LinOpBCType::inflow at inflow boundaries. src/projection/incflo_projection_bc.cpp commit 353914008f40522f869b4019548f95bc973ee374 Author: cgilet Date: Thu May 26 12:02:24 2022 -0400 Docs: Remove reference to deleted master branch Docs/sphinx_documentation/source/index.rst commit 6d33c664e17129d2fd7cc8af13c1db8626194b6a Author: cgilet Date: Thu May 26 10:18:48 2022 -0400 Use face_divfree_interp in FillPatching Umac. face_linear_interp had been used for comparision to old routine and IAMR, but face_divfree_interp is really the best choice here. src/convection/incflo_compute_advection_term.cpp commit 06dc7eeb5f322c871beef98cfc8442c2f464bf86 Author: Ann Almgren Date: Sun May 15 16:08:47 2022 -0700 add BL_NO_FORT=TRUE to GNUmakefiles test_2d/GNUmakefile test_3d/GNUmakefile test_no_eb/GNUmakefile commit cb1a4c2a0c32a3aeb9995d70119efd83d26029ec Merge: 338b301e 8a92d3d4 Author: asalmgren Date: Tue May 3 06:38:02 2022 -0700 Merge pull request #53 from drangara/fixes_for_eb_flow Fixes for eb flow commit 8a92d3d4d3c88d66c02d3b5435f51a6ff6666b56 Author: Deepak Rangarajan Date: Tue Apr 19 14:32:37 2022 -0400 Fixes for eb flow src/convection/incflo_compute_MAC_projected_velocities.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/incflo.H test_2d/benchmark.eb_flow_const_velx test_2d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz commit 338b301e8cbf8c24c4614a8361201bdb40222cdc Merge: e0566b0f ab7296b1 Author: asalmgren Date: Wed Mar 30 13:31:12 2022 -0700 Merge pull request #51 from drangara/fix_gpu_compilation fix gpu compilation commit ab7296b1dc916767694e7c2096fd87b27f744c76 Author: Deepak Rangarajan Date: Wed Mar 30 15:35:53 2022 -0400 fix gpu compilation src/boundary_conditions/incflo_set_velocity_bcs.cpp commit e0566b0f8041c08737104f5b5889ed0399ce4e4c Merge: 27ae8b11 4e569716 Author: asalmgren Date: Wed Mar 30 09:09:41 2022 -0700 Merge pull request #50 from drangara/eb_flow Eb flow commit 4e56971646d62c3c41f8e995e511b66d6f39e574 Author: Deepak Rangarajan Date: Wed Mar 30 11:05:59 2022 -0400 use density test instead of tracer for scalars src/prob/incflo_prob_I.H src/prob/incflo_prob_usr_I.H src/prob/prob_init_fluid.cpp test_3d/benchmark.eb_flow_density commit 815732b853e17b9b4684581fa52852b8b4bf2037 Author: Deepak Rangarajan Date: Wed Mar 30 10:48:48 2022 -0400 add a new probtype for constant tracer src/convection/incflo_compute_advection_term.cpp src/prob/incflo_prob_I.H src/prob/incflo_prob_usr_I.H src/prob/prob_init_fluid.cpp test_3d/benchmark.eb_flow_tracer commit ff8acf85e0265291942e75b22ee32c49d7d461ee Author: Deepak Rangarajan Date: Wed Mar 30 09:07:13 2022 -0400 fix a bug with scalars src/convection/incflo_compute_advection_term.cpp commit fcf2d582e5dbd9bf02ba1e399766b8ae5be7481d Author: Deepak Rangarajan Date: Fri Mar 25 14:48:48 2022 -0400 new method names src/convection/incflo_compute_MAC_projected_velocities.cpp src/projection/incflo_apply_nodal_projection.cpp commit a15233837b026d639d9ca368cc32ec7c972a6066 Author: Deepak Rangarajan Date: Sun Mar 20 23:07:41 2022 -0400 fix sign src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 93426aa76bae7af5d9a561e4d96ffea1df4f5fd7 Merge: 3640e272 27ae8b11 Author: Deepak Rangarajan Date: Sun Mar 20 22:51:04 2022 -0400 Merge branch 'development' into eb_flow commit 3640e2726576127df4cb5768077ae3c0cd0b4107 Author: Deepak Rangarajan Date: Sun Mar 20 22:50:27 2022 -0400 support for scalar in eb flow src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit d5b7ff563e4192567a9ba4cfbeeb6539ab19bfc0 Author: Deepak Rangarajan Date: Thu Mar 17 11:50:50 2022 -0400 add todo items src/convection/incflo_compute_advection_term.cpp commit 02b5f7de46d301e97bcdbbcdef4515ff40b1d0da Author: Deepak Rangarajan Date: Thu Mar 17 10:38:39 2022 -0400 add call for eb flow src/convection/incflo_compute_advection_term.cpp commit 160ac5b0f9dbea06e5e1dc9b73405033aa91f274 Author: Deepak Rangarajan Date: Wed Mar 16 18:05:23 2022 -0400 fix non EB compilation src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp commit 7bec302935697a9ef09b6e317ec9968b24bcb643 Author: Deepak Rangarajan Date: Tue Mar 15 09:47:00 2022 -0400 fix bug when grid is regular src/convection/incflo_compute_advection_term.cpp commit e9d27d906f0bd1e41c6f3edba05ba835f377485b Author: Deepak Rangarajan Date: Mon Mar 14 17:37:03 2022 -0400 implement support for EB normal src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 89ab7658d031e45799446a909820c3e48c005fa4 Author: Deepak Rangarajan Date: Mon Mar 14 16:00:15 2022 -0400 better inputs handling src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp test_2d/benchmark.eb_flow_const_velx test_2d/benchmark.eb_flow_const_vely test_2d/benchmark.eb_flow_sphere test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz commit 02ab00b758c6e6009fc169d39b78c23c441050db Author: Deepak Rangarajan Date: Sun Mar 13 19:19:29 2022 -0400 switch to getBndryNormal src/convection/incflo_compute_advection_term.cpp commit 654e881cc9d6f8845e6d4ae273ba1b522a0d1284 Author: Deepak Rangarajan Date: Wed Mar 9 09:25:16 2022 -0500 move flux correction to the hydro call src/convection/incflo_compute_advection_term.cpp commit eb6f34dd07493938441a0a63000e21e4b811f458 Author: Deepak Rangarajan Date: Sat Mar 5 22:41:29 2022 -0500 support velocity magnitude input, add 2d sphere test case src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp test_2d/benchmark.eb_flow_const_velx test_2d/benchmark.eb_flow_const_vely test_2d/benchmark.eb_flow_sphere test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz commit 27ae8b119cb6bb47d89eb737c988048bebb01eda Merge: 97e27ced 1c4ee853 Author: Candace Gilet Date: Wed Mar 2 13:32:23 2022 -0500 Merge pull request #47 from etpalmer63/SphinxDocStyleFix Replace 'html_context' with 'html_css_files' command commit 97e27ced70397f76a05fe5e9d24fa06cd445f540 Author: cgilet Date: Wed Mar 2 12:57:17 2022 -0500 Update Make.incflo to include BDS src/Make.incflo commit 06a713225b380516795812ac1b320226ec857f56 Author: Deepak Rangarajan Date: Wed Mar 2 12:22:47 2022 -0500 add singlevalued check, add 2d vely test case, fix tests src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_advection_term.cpp src/incflo_advance.cpp test_2d/benchmark.eb_flow_const_velx test_2d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz commit 6412bb9893c65b46ad5a51a6f3c836b5331a9560 Author: Deepak Rangarajan Date: Tue Mar 1 23:01:01 2022 -0500 fix flux correction, add y, z test cases src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp test_3d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_vely test_3d/benchmark.eb_flow_const_velz commit a5612d1f0f949564623586f4ab8a59e3d27fbf69 Author: Deepak Rangarajan Date: Tue Mar 1 16:53:03 2022 -0500 remove print src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 7a08a52dfa15e70f9f31c01e883d1d13faa8b11d Author: Deepak Rangarajan Date: Tue Mar 1 16:52:22 2022 -0500 fix bug src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 50a8003f509682ef9db6b73bcb9693b0cadce361 Author: Deepak Rangarajan Date: Tue Mar 1 16:14:02 2022 -0500 Support for flow through EBs src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp test_2d/benchmark.eb_flow_const_velx test_3d/benchmark.eb_flow_const_velx commit 3424f125e7d62feabeb9e8fb3336c6b877848c8e Merge: 7ba1bec3 214292a3 Author: Candace Gilet Date: Wed Jan 19 13:34:17 2022 -0500 Merge pull request #49 from AMReX-Codes/fix_tag_region Fix tag_region to work with problo != 0. commit 214292a311d8b54b54fa45a8982d41f9840b6e53 Author: cgilet Date: Mon Jan 10 19:54:32 2022 -0500 Fix tag_region to work with problo != 0. src/incflo_tagging.cpp commit 7ba1bec37fce7ac48edbb4cf3ba9f67dee15fba4 Merge: 91f83054 c433c89d Author: Candace Gilet Date: Sat Jan 8 21:02:42 2022 -0500 Merge pull request #48 from AMReX-Codes/cug_to_FP2L Use FillPatchTwoLevels to fill U_mac ghost cells. commit c433c89d94d22f6eb3e0dadfde4ec27787cd0858 Author: cgilet Date: Fri Jan 7 10:24:28 2022 -0500 Use FillPatchTwoLevels to fill U_mac ghost cells. src/convection/incflo_compute_advection_term.cpp commit 91f830546419ae4c347eb3120209810479265846 Author: Ann Almgren Date: Wed Dec 15 11:03:36 2021 -0800 fix call to EnforcePeriodicity -- previously we were getting buggy behavior at inflow faces with multiple grids touching then inflow and at least one direction periodic src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 6895390e2d629707682945f4cc553b87ced72bd8 Author: Ann Almgren Date: Tue Dec 14 19:40:40 2021 -0800 change call src/convection/incflo_redistribute_convective_term.cpp commit f521ced6400ecb8837d48e2ca2be7c55855a778d Author: Ann Almgren Date: Tue Dec 14 19:08:09 2021 -0800 No more NewStateRedistribute -- it is now just StateRedistribute src/convection/incflo_redistribute_convective_term.cpp src/setup/init.cpp test_3d/benchmark.channel_sphere commit 1c4ee853f993a9462e9026f3129bf32c0b7d25fc Author: etpalmer63 Date: Mon Nov 15 16:27:40 2021 -0500 replace 'html_context' with 'html_css_files' command to fix html style issue Docs/sphinx_documentation/source/conf.py commit f3e660166ee4edc66ac4db481c5c8ad744425374 Author: Ann Almgren Date: Tue Nov 2 09:39:33 2021 -0700 update to work with new Hydro namespace for the projections src/incflo.H src/incflo.cpp src/incflo_regrid.cpp src/projection/incflo_apply_nodal_projection.cpp commit 59a5752987c8c5514505adbe09879a16ecbf461f Author: Ann Almgren Date: Mon Nov 1 10:37:07 2021 -0700 Fix comments src/incflo.H commit 0a8507efc38f4499c8f06195b65931f02286ba4b Author: Ann Almgren Date: Mon Nov 1 10:30:06 2021 -0700 1) Replace AMReX_MacProjector and AMReX_NodalProjector by hydro_MacProjector and hydro_NodalProjector. 2) Remove tabs and trailing white spaces. .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh Docs/sphinx_documentation/source/BuildingGMake.rst Docs/sphinx_documentation/source/BuildingMacVelocities.rst Docs/sphinx_documentation/source/Debugging.rst Docs/sphinx_documentation/source/EBWalls.rst Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/InputsTimeStepping.rst Docs/sphinx_documentation/source/Inputs_Chapter.rst Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst Docs/sphinx_documentation/source/TimeStep.rst Docs/sphinx_documentation/source/index.rst src/Make.incflo src/boundary_conditions/boundary_conditions.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp src/derive/incflo_derive.cpp src/derive/incflo_derive_K.H src/derive/incflo_error.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_cyl_tuscan.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_if.H src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/eb_spherecube.cpp src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/incflo_correct_small_cells.cpp src/incflo_regrid.cpp src/incflo_tagging.cpp src/incflo_vol_wgt_sum.cpp src/main.cpp src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/prob/prob_init_fluid_usr.cpp src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_compute_MAC_projected_velocities.cpp src/rheology/incflo_read_rheology_parameters.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit a96691c32733db88dbe0c2f68035f7d98867d4a0 Merge: f1658b38 6dba587c Author: asalmgren Date: Wed Oct 20 11:29:43 2021 -0700 Merge pull request #46 from esclapez/fix_ConvectiveAdvEBtests While adding u div(u) piece to velocity advection term, don't commit 6dba587c03c7fc046ff7bee10b8c9e6218ff1212 Author: Lucas Esclapez Date: Mon Oct 18 22:44:21 2021 -0600 While adding u div(u) piece to velocity advection term, don't access fully covered boxes. src/convection/incflo_compute_advection_term.cpp commit f1658b38923b48df446e31a61eed1fc959e3a8e4 Author: Ann Almgren Date: Thu Sep 30 14:35:11 2021 -0700 compile on GPUs... src/projection/incflo_apply_cc_projection.cpp commit 44264711e2303d77d08aaa3bbe538d76fda37b10 Author: Ann Almgren Date: Wed Sep 29 10:49:00 2021 -0700 Add vortex in sphere test case (probtyle = 66) src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test_2d/benchmark.vortex_in_sphere commit f6fa7c4c656891e26d38752d46658cfaed469b84 Author: Ann Almgren Date: Sun Sep 26 16:11:44 2021 -0700 use amrex version of fc-->cc src/projection/incflo_apply_cc_projection.cpp commit f7f246fd07691a7af8899ec86e0958368a84d5b9 Author: Ann Almgren Date: Sun Sep 26 15:46:51 2021 -0700 Adapt CCproj stuff for EB Docs/sphinx_documentation/source/InputsTimeStepping.rst src/projection/incflo_apply_cc_projection.cpp commit d2b8306c5022795e2257db4cd1c43ac63d8feed8 Merge: 55d88346 5eae625b Author: Ann Almgren Date: Sun Sep 26 15:23:52 2021 -0700 Merge branch 'ccproj' into development commit 5eae625b0fd880be79892aba4a7b07a9b8301996 Author: Ann Almgren Date: Sun Sep 26 14:28:00 2021 -0700 match development branch in setting StateRedistribute as the default src/convection/incflo_redistribute_convective_term.cpp src/incflo.H commit f3f0991a8d100edbb519d05b65d43b8fe5b67997 Author: Ann Almgren Date: Sun Sep 26 13:34:27 2021 -0700 This version of incflo allows a run-time option for whether to use a nodal vs a cell-centered end-of-time-step projection (both still use the intermediate-time MAC projection) src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_regrid.cpp src/prob/prob_init_fluid.cpp src/projection/CMakeLists.txt src/projection/Make.package src/projection/incflo_apply_cc_projection.cpp src/projection/incflo_apply_nodal_projection.cpp src/projection/incflo_compute_MAC_projected_velocities.cpp src/projection/incflo_projection_bc.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit 55d88346da689f07c0394497b6786e6d8585043a Merge: 162d8fcd 45ee494b Author: Weiqun Zhang Date: Wed Sep 15 14:27:28 2021 -0700 Merge pull request #44 from esclapez/knownFaceStateFlag Update signature of HydroUtils::ComputeFluxesOnBoxFromState commit 45ee494bcee5dc65ff6e46ab1b2419e65b46a118 Author: Lucas Esclapez Date: Wed Sep 15 11:27:29 2021 -0700 Update signature of HydroUtils::ComputeFluxesOnBoxFromState src/convection/incflo_compute_advection_term.cpp commit 162d8fcd541d62bed48a8d7211f8ca76cee6ba43 Author: Ann Almgren Date: Tue Sep 14 12:52:57 2021 -0700 Just some cleanup ... no change in functionality or solutions src/convection/incflo_compute_advection_term.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp commit 92bc4ce5d5bb0d7acb6523eb8809927c5718e6bb Author: Ann Almgren Date: Fri Aug 27 18:42:27 2021 -0700 Make sure we fill enough ghost cells to do the redistribution src/setup/init.cpp commit 16cf9c1f5276c33c13072155a10b6765c2f08057 Author: Ann Almgren Date: Fri Aug 27 15:05:11 2021 -0700 update Make.incflo to allow for slopes routines now living in AMReX-Hydro src/Make.incflo commit ba14a6468cab4efacf1b9da08b52ec84204e486f Author: cgilet Date: Mon Aug 9 13:57:01 2021 -0400 Docs: fix momentum equation Docs/sphinx_documentation/source/FluidEquations.rst commit 6cb19303fd0d2ae58ae06059a4198fcb97f62a8d Author: cgilet Date: Fri Jul 23 10:43:30 2021 -0400 Docs: get Godunov equations to display correctly Docs/sphinx_documentation/source/TimeStep.rst commit 1c5727c0ac4dbd8b33344d59389c1bf916bde1c4 Author: Ann Almgren Date: Thu Jun 24 13:16:58 2021 -0700 Enforce periodicity of the velocity inflow boundary conditions (just in case the function used to fill them didn't have the right periodicity) src/boundary_conditions/incflo_set_velocity_bcs.cpp commit c2497cadc4cf695c150b8e9054733a5978b95521 Author: Weiqun Zhang Date: Fri Jun 11 16:42:11 2021 -0700 Update cmake to use AMReX-Hydro CMakeLists.txt src/convection/incflo_redistribute_convective_term.cpp src/incflo.cpp src/incflo_correct_small_cells.cpp src/incflo_regrid.cpp commit 1b912588e23e21da44b4f4c5212ac9ff54efcf3a Author: Ann Almgren Date: Wed Jun 9 20:12:54 2021 -0700 Call create_umac_grown before creating advective terms if at lev > 0. src/convection/incflo_compute_advection_term.cpp commit a0c3aa29bf97c491fa5a86e3b67519a81b6af77c Author: Ann Almgren Date: Wed Jun 9 18:28:28 2021 -0700 Protect against divide by 0 -- test on vfrac before doing convective correction src/convection/incflo_compute_advection_term.cpp commit fa120a39635ecb1a8b20506510dc5dce8340e48a Author: Ann Almgren Date: Wed Jun 9 17:23:10 2021 -0700 Remove the lnies setting advection_type from the benchmark.* files ... this will change the EB regression tests since Godunov is now the default test_2d/benchmark.channel_cylinder test_2d/benchmark.couette test_2d/benchmark.double_shear_layer test_2d/benchmark.inviscid_rotated_planes_x test_2d/benchmark.lid_driven_cavity test_2d/benchmark.poiseuille_cylinder_bingham test_2d/benchmark.poiseuille_cylinder_newtonian test_2d/benchmark.poiseuille_plane_bingham test_2d/benchmark.poiseuille_plane_newtonian test_2d/benchmark.rotated_planes_x test_2d/benchmark.rotated_planes_y test_2d/benchmark.taylor_green_vortices test_2d/benchmark.tracer_adv_diff test_2d/benchmark.tracer_adv_diff_cn test_2d/benchmark.tracer_advection test_2d/benchmark.uniform_velocity_sphere test_3d/benchmark.channel_cylinder-x test_3d/benchmark.channel_cylinder-xx test_3d/benchmark.channel_cylinder-y test_3d/benchmark.channel_cylinder-yy test_3d/benchmark.channel_cylinder-z test_3d/benchmark.channel_cylinder-zz test_3d/benchmark.channel_spherecube test_3d/benchmark.couette test_3d/benchmark.couette_poiseuille test_3d/benchmark.double_shear_layer test_3d/benchmark.double_shear_restart test_3d/benchmark.lid_driven_cavity test_3d/benchmark.poiseuille_cylinder_bingham test_3d/benchmark.poiseuille_cylinder_newtonian test_3d/benchmark.poiseuille_halfplane_newtonian test_3d/benchmark.poiseuille_plane_bingham test_3d/benchmark.poiseuille_plane_newtonian test_3d/benchmark.rotated_cylinder_x test_3d/benchmark.rotated_cylinder_y test_3d/benchmark.rotated_cylinder_z test_3d/benchmark.slanted_cylinder test_3d/benchmark.taylor_green_vortices test_3d/benchmark.tracer_adv_diff test_3d/benchmark.tracer_adv_diff_cn test_3d/benchmark.tracer_advection test_3d/benchmark.tuscan test_3d/benchmark.uniform_velocity_sphere commit d94764d3c56b22cdc4b6326978bcfa8dfcde01a9 Author: Ann Almgren Date: Wed Jun 9 17:03:22 2021 -0700 Set default advection type to Godunov rather than MOL src/incflo.H commit ae197b56f224851cc28750b3c94d2f3b3d8f99d5 Author: Ann Almgren Date: Tue Jun 8 18:39:10 2021 -0700 Add link to AMReX-Hydro documentation Docs/sphinx_documentation/source/TimeStep.rst commit d4942c977c12d16fe3b039516be8451049406ff6 Merge: 17b46cfe 00657118 Author: Ann Almgren Date: Tue Jun 8 18:11:17 2021 -0700 Merge branch 'development' of github.com:AMReX-Codes/incflo into development commit 17b46cfe879319820077fcd5023bc92f8d1594db Author: Ann Almgren Date: Tue Jun 8 18:10:05 2021 -0700 update directory name in gmake instructions Docs/sphinx_documentation/source/BuildingGMake.rst commit 006571183bc150da2db9f0726a9d367a1afeb7bf Author: Andrew Myers Date: Tue Jun 8 10:43:35 2021 -0700 turn off pdf for now .github/workflows/docs.yml commit b7d00308374cec3cc683644275c21434400233d0 Author: Andrew Myers Date: Tue Jun 8 10:40:13 2021 -0700 port docs CI from travis to github actions. .github/workflows/dependencies/documentation.sh .github/workflows/docs.yml .travis.yml build_and_deploy.sh deploy_rsa.enc commit 55cef616e1798cfed625c20687f58cdbae094a32 Author: Ann Almgren Date: Mon Jun 7 18:32:34 2021 -0700 update incflo documentation Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst Docs/sphinx_documentation/source/InputsVerbosity.rst Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst Docs/sphinx_documentation/source/index.rst commit 5dd085b49f0b38c379bc30fd13624c5edb9c43c2 Author: Ann Almgren Date: Wed Jun 2 08:45:32 2021 -0700 Should be dividing by 6 not 8 when computing the correction from conservative to convective differencing. src/convection/incflo_compute_advection_term.cpp commit b17c67d45cd562db8b393df64a57a2f393a71383 Author: Ann Almgren Date: Wed May 26 19:53:50 2021 -0700 Move the cylinder slightly so it doesn't sit at a corner -- this eliminates any cut cells with exactly 45 degree cut -- which then doens't trigger the symmetry issue inside the state redistribution. These give essentially identical answers (x vs y vs z) test_3d/benchmark.channel_cylinder-x test_3d/benchmark.channel_cylinder-y test_3d/benchmark.channel_cylinder-z commit 3ea06441be51678efda492f721df15a1e637f365 Author: Ann Almgren Date: Wed May 26 19:47:39 2021 -0700 Don't have constant density = true -- we want the x,y,z versions to be comparable test_3d/benchmark.channel_cylinder-x commit 37f4bdb414a0b40701e9a9335a1ec23d65c4ff74 Author: Ann Almgren Date: Wed May 26 19:38:11 2021 -0700 When deciding whether a particular box is "regular" for the purposes of State Redistribution, we need to check the box grown by 3 or 4, not 2. We choose 4 just to be sure. Here we make this change in the initial redistribution (the previous commit was for the redistribution following computation of the advective terms). src/setup/init.cpp commit 09cbd96ba361cc3eac4cf975616f6cd76882012e Author: Ann Almgren Date: Wed May 26 16:15:08 2021 -0700 When deciding whether a particular box is "regular" for the purposes of State Redistribution, we need to check the box grown by 3 or 4, not 2. Here we choose 4 just to be sure. src/convection/incflo_redistribute_convective_term.cpp commit 0cf74fd99b540a2339c4270bb59486febf2148b5 Author: Ann Almgren Date: Wed May 26 08:24:40 2021 -0700 Fix the construction of (rhotrac) so we have enough ghost cells to construct the fluxes in the same loop src/convection/incflo_compute_advection_term.cpp commit cf97c9da236b9c4499c6c11932915707cfc61663 Author: Ann Almgren Date: Tue May 25 21:42:39 2021 -0700 Don't set dtdt to 0 if advect_tracer = false .. just ignore dtdt in that case src/convection/incflo_redistribute_convective_term.cpp commit 38c478ed2d55a3d9659a58ac2d74e360103f06c5 Author: Ann Almgren Date: Tue May 25 20:59:18 2021 -0700 Define (rhotrac) as a vector of MultiFabs rather than on the fly ... this takes care of the memory issue we were having ... src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp commit 0b224064cf7fbff8599e0d3df75e2999fc8faa81 Author: Ann Almgren Date: Wed May 19 18:59:17 2021 -0700 Make sure to set drdt or dtdt to 0 just so they have 0's not NaNs src/convection/incflo_redistribute_convective_term.cpp commit ccede3e95741cfa7e0915f597784e49bfe4a1465 Author: Ann Almgren Date: Tue May 18 18:56:36 2021 -0700 Default to convective differencing with velocity for EB as well as non-EB src/convection/incflo_compute_advection_term.cpp commit a8c85321d0f6e54c7ec37b963aa7f55adc05093d Author: Ann Almgren Date: Tue May 18 18:40:12 2021 -0700 Change default redistribution scheme from FluxRedist to StateRedist src/incflo.H commit 43c458bc827a0de5c8e541d598e42d0b93a4990e Author: Ann Almgren Date: Tue May 18 18:27:55 2021 -0700 fix typo in EBGodunov convective correction src/convection/incflo_compute_advection_term.cpp commit e0b8d1c59a4329753756d240fae19140322b25f4 Author: Ann Almgren Date: Tue May 18 17:17:56 2021 -0700 Add convective differencing option for u and call new version of AMReX-Hydro routines src/convection/incflo_compute_advection_term.cpp commit 6c3f95a0bc21f4272a9c305f56ecb3ede2536c9d Author: Ann Almgren Date: Tue May 18 16:58:12 2021 -0700 Increase the number of ghost cells for volfrac; we need 5 for StateRedistribution src/incflo.H commit 3a72716a77c5dbe5124541779f8ae8290dfe81e9 Author: Ann Almgren Date: Tue May 18 16:50:08 2021 -0700 clean up new convective differencing stuff src/convection/incflo_compute_advection_term.cpp commit b316f79dc677d0a8f6cde752a33a79580d7fe252 Author: Ann Almgren Date: Tue May 18 16:47:23 2021 -0700 Make benchmark.channel_spherecube use Newtonian not Bingham fluid test_3d/benchmark.channel_spherecube commit 9dc6e714541a466904f0a3699b37e3ecb6186a30 Author: Ann Almgren Date: Tue May 18 13:57:43 2021 -0700 Add code for computing non-conservative update by subtracting q div(u) from div(uq) to get u dot grad(q) src/convection/incflo_compute_advection_term.cpp commit ab9ae80f60142c0e2f91560be8803ed44211cae6 Author: Ann Almgren Date: Sun May 16 18:36:56 2021 -0700 Revert the previous change -- make FluxRedist the default again src/incflo.H commit 7f8be67f65752c61fd4cbdbbf59ef8c16991e272 Author: Ann Almgren Date: Sun May 16 17:40:49 2021 -0700 Change default redistribution type from FluxRedist to StateRedist src/incflo.H commit c195ea0d42d889e2b06c336481cb19a4f6f3a9d2 Author: Ann Almgren Date: Sat May 15 07:18:58 2021 -0700 Need to multiply convective term by -1 *before* we send to redistribution src/convection/incflo_compute_advection_term.cpp commit cad5d2928c28d4d98b133b15123d14a92292182c Author: Ann Almgren Date: Sat May 15 07:18:27 2021 -0700 quiet compiler warning src/convection/incflo_redistribute_convective_term.cpp commit ce0e62251f7e06fe4911f8b788fcfdad2bcf2d71 Author: Ann Almgren Date: Fri May 14 16:45:03 2021 -0700 Remember to initialize scratch to 1 in redistribute src/convection/incflo_redistribute_convective_term.cpp commit 9bd4b9480d735988d2d5d9ec004f121cf79516ad Author: Ann Almgren Date: Fri May 14 14:35:26 2021 -0700 only include redistribute stuff if using EB src/incflo.H commit a573902a189bc3fdfb7fb7cd31fb84a169a69e55 Author: Ann Almgren Date: Fri May 14 14:31:14 2021 -0700 Use redistribution in AMReX-Hydro rather than local version src/Make.incflo src/convection/Convection.H src/convection/Make.package src/convection/Redistribution/Make.package src/convection/Redistribution/Redistribution.H src/convection/Redistribution/incflo_create_itracker_2d.cpp src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_merge_redistribute.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_redistribute_convective_term.cpp src/incflo.H src/setup/init.cpp commit f8d8df413ac6c84f9f6ee8b888252fed721ba702 Author: Ann Almgren Date: Thu May 6 13:31:34 2021 -0700 clean up interface to AMReX-Hydro stuff src/convection/incflo_compute_MAC_projected_velocities.cpp commit b9899242312decfb301caefeb68b9279c5c3b0f3 Author: Ann Almgren Date: Tue May 4 15:46:57 2021 -0700 Now call HydroUtils::ComputeFluxesOnBoxFromState rather than call the MOL/Godunov-specific ComputeEdgeState and ComputeFluxes in AMReX-Hydro src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H commit f7a021402aef82d6f41ab01c84e2cbe844488b32 Author: Weiqun Zhang Date: Tue May 4 10:57:44 2021 -0700 compiles src/convection/incflo_compute_MAC_projected_velocities.cpp src/derive/incflo_error.cpp commit c692dc3c61620e4ce06ab4221f48eea5d2775638 Author: Ann Almgren Date: Tue May 4 10:22:01 2021 -0700 Try to separate out the call for making MAC velocities. src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit 9e081285236c5b51e2b44f8cc21d24d717c5290f Author: Ann Almgren Date: Mon May 3 14:11:21 2021 -0700 Replace "and" by "&&" src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_tagging.cpp src/prob/prob_bc.H src/projection/incflo_apply_nodal_projection.cpp commit 415b4f01e3ddf2420d12793ead1774ac83f9ce1d Merge: 6207bf47 cdfae221 Author: Ann Almgren Date: Mon May 3 13:08:38 2021 -0700 Merge branch 'development' of github.com:AMReX-Codes/incflo into development commit 6207bf4790bc119d72e43ae7c6f4c5e675c178d6 Author: Ann Almgren Date: Mon May 3 13:08:19 2021 -0700 Replace "or" by "||" src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo_advance.cpp src/incflo_tagging.cpp src/prob/prob_init_fluid.cpp src/setup/incflo_arrays.cpp src/utilities/io.cpp commit cdfae2212ec887100978e2329ff96a094a39cefd Author: Ann Almgren Date: Mon May 3 11:38:06 2021 -0700 Update README with more info README.md commit a448d3106784069b5cf7f188a627bb0360e6fe81 Merge: 6352c16b 2507cd94 Author: Ann Almgren Date: Mon May 3 11:36:20 2021 -0700 Merge branch 'development' of github.com:AMReX-Codes/incflo into development commit 6352c16bcbc8b99c0aaf561821d49ae1ec7b6ff4 Author: Ann Almgren Date: Mon May 3 11:36:04 2021 -0700 Update the README README.md commit 2507cd944ef4c80945825b8205cd284361e855c0 Author: Ann Almgren Date: Mon May 3 11:24:52 2021 -0700 Update CMakeLists.txt in src and in src/convection src/CMakeLists.txt src/convection/CMakeLists.txt commit 419dac332f62391dd38c29847fadf8ae3fa57ae0 Author: Ann Almgren Date: Mon May 3 11:21:53 2021 -0700 This version now relies on the routines in AMReX-Hydro rather than having local MOL, Godunov and EBGodunov routines src/Make.incflo src/Make.package src/convection/Convection.H src/convection/EBGodunov/EBGodunov.H src/convection/EBGodunov/Make.package src/convection/EBGodunov/incflo_ebgodunov_corner_couple.H src/convection/EBGodunov/incflo_ebgodunov_fluxes_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_fluxes_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_make_trans_vels.cpp src/convection/EBGodunov/incflo_ebgodunov_plm.cpp src/convection/EBGodunov/incflo_ebgodunov_plm_fpu.cpp src/convection/EBGodunov/incflo_ebgodunov_predict.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_transverse_2D_K.H src/convection/EBGodunov/incflo_ebgodunov_transverse_3D_K.H src/convection/Godunov/Godunov.H src/convection/Godunov/Make.package src/convection/Godunov/incflo_godunov_corner_couple.H src/convection/Godunov/incflo_godunov_fluxes_2D.cpp src/convection/Godunov/incflo_godunov_fluxes_3D.cpp src/convection/Godunov/incflo_godunov_plm.H src/convection/Godunov/incflo_godunov_plm.cpp src/convection/Godunov/incflo_godunov_ppm.H src/convection/Godunov/incflo_godunov_ppm.cpp src/convection/Godunov/incflo_godunov_predict_2D.cpp src/convection/Godunov/incflo_godunov_predict_3D.cpp src/convection/Godunov/incflo_godunov_trans_bc.H src/convection/MOL/MOL.H src/convection/MOL/MOL_constants.H src/convection/MOL/MOL_eb_predict_vel_on_faces.cpp src/convection/MOL/MOL_extrap_vel_to_faces.cpp src/convection/MOL/MOL_predict_vel_on_faces.cpp src/convection/MOL/Make.package src/convection/MOL/incflo_mol_fluxes.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/Make.package src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_compute_update.cpp src/incflo_correct_small_cells.cpp test_2d/GNUmakefile test_3d/GNUmakefile test_no_eb/GNUmakefile test_no_eb_2d/GNUmakefile commit 8761f67bf97b4a20f09119f09ef91f537bc0f940 Author: Ann Almgren Date: Sun May 2 20:12:54 2021 -0700 fix typo src/convection/incflo_compute_advection_term.cpp commit 37b2e30537af290715649b591f324f2811a0892b Author: Ann Almgren Date: Sun May 2 20:10:19 2021 -0700 We need to average down the MAC velocity as well as the fluxes to do consistent convective differencing src/convection/incflo_compute_advection_term.cpp commit 9e8b867e9d1605df61e8cdf8334204d28b62b7ef Author: Ann Almgren Date: Fri Apr 30 17:23:07 2021 -0700 fix for 2d prob init src/prob/prob_init_fluid.cpp commit 78c15618107863949c99c8dc9f956f98cd01a6ec Author: Ann Almgren Date: Thu Apr 29 15:10:38 2021 -0700 Fix typos in MOL (3d only) src/convection/MOL/MOL_eb_predict_vel_on_faces.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp commit ce7a45946779bb59e0b1554860a686a26b1ff493 Author: Ann Almgren Date: Mon Apr 26 19:50:03 2021 -0700 make compile again for non-EB src/convection/MOL/Make.package commit d1d1064ea85c8193220d2d1b0721db525ac9d9f5 Author: Ann Almgren Date: Mon Apr 26 19:27:27 2021 -0700 Adjust the MOL in incflo to use the routines from IAMR ... as part of migrating towards a shared hydro code base src/convection/MOL/MOL.H src/convection/MOL/MOL_constants.H src/convection/MOL/MOL_eb_predict_vel_on_faces.cpp src/convection/MOL/MOL_extrap_vel_to_faces.cpp src/convection/MOL/MOL_predict_vel_on_faces.cpp src/convection/MOL/Make.package src/convection/MOL/incflo_mol_fluxes.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_fluxes.cpp commit b4b49d65962129e9d6bc03cc1eb6a1fff96036ed Author: Ann Almgren Date: Thu Apr 22 20:25:46 2021 -0700 1) Fix the calls to slope routines to now pass vfrac and order 2) Add additional limiting in the EBGodunov post-MAC tracing to match that in the pre-MAC tracing. src/convection/EBGodunov/incflo_ebgodunov_plm.cpp src/convection/EBGodunov/incflo_ebgodunov_plm_fpu.cpp src/convection/MOL/MOL.H src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/MOL/incflo_mol_predict.cpp src/convection/MOL/incflo_mol_predict_eb.cpp src/convection/Redistribution/incflo_state_redistribute.cpp src/convection/incflo_compute_fluxes.cpp commit 8ee8a3d0e4eb7f6642daef50345621ae762148ec Author: Ann Almgren Date: Fri Apr 16 16:50:31 2021 -0700 fix the setDomainBC calls so they see the correct domain bc's for each velocity component when doing the components separately (i.e. not a tensor solve) src/diffusion/DiffusionScalarOp.cpp commit f5be0c16a18ff01ae17a743019268042758df13a Author: Ann Almgren Date: Sun Mar 28 10:04:16 2021 -0700 Re-write logic in need_divtau to make it easier to parse src/incflo.H commit b26e337b8a7861a2eeb991bcf0e8d1aaf9fcb139 Author: Ann Almgren Date: Sat Mar 27 14:45:57 2021 -0700 Fix print statement in 2d src/embedded_boundaries/eb_cylinder.cpp commit b3dc18a3b0e32171fe0cb0d1e1f31c61a465cfdc Author: Ann Almgren Date: Sat Mar 27 14:44:59 2021 -0700 Make sure we get all the ghost cells filled properly before the initial redistribute README.md src/setup/init.cpp commit 49d51ccc4d054a502ba4720bdfe6539a0b60086e Author: Ann Almgren Date: Tue Mar 23 11:31:16 2021 -0700 recode isects loop to quiet compiler warning src/incflo_vol_wgt_sum.cpp commit 41b6252a39afb9445718579244ca50ff5d11dc90 Author: Ann Almgren Date: Mon Mar 22 19:49:33 2021 -0700 Initialize the temporaries dvdt_tmp, etc, to zero src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/incflo_compute_advection_term.cpp commit 39278e3cdb576df76cc6d124d007fbb5151e4644 Author: Ann Almgren Date: Mon Mar 22 19:21:02 2021 -0700 Get rid of at least some compiler warnings src/convection/Convection.H src/convection/Godunov/incflo_godunov_fluxes_2D.cpp src/convection/Godunov/incflo_godunov_fluxes_3D.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_compute_update.cpp src/convection/incflo_redistribute_convective_term.cpp src/incflo_tagging.cpp commit 82b7c0080a2180e619754f55f5f262a075aa7192 Author: Ann Almgren Date: Sat Mar 20 15:35:21 2021 -0700 when 4 nbors isnt' enough to be volfrac > 0.5 in 3d, go ahead and use the whole 2x2x2 block src/convection/Redistribution/incflo_create_itracker_3d.cpp commit d96303d27d6f034b7b91b0b7cacede06a5ffaae4 Author: Ann Almgren Date: Tue Mar 16 19:54:04 2021 -0700 Needed one more Atomic::Add in state redistribute src/convection/Redistribution/incflo_state_redistribute.cpp commit 681235ee1d0764aa56c4966c4e97e4de2849c9c3 Author: Ann Almgren Date: Tue Mar 16 16:07:23 2021 -0700 Two fixes for state redistribution: 1) use scratch array instead of modifying dUdt_in -- this was a bug when tiling was used 2) use Atomic::Add instead state redistribution when we add to nbors of (i,j,k) instead of to (i,j,k) src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp src/convection/incflo_redistribute_convective_term.cpp commit e93aca6eb1f8a742e055d5ab4eea65bdf20f74e3 Author: Ann Almgren Date: Tue Mar 16 11:22:23 2021 -0700 fix just-introduced bugs in 2d and 3d EBGodunov flux routines src/convection/EBGodunov/incflo_ebgodunov_fluxes_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_fluxes_3D.cpp commit 40f7178f5eb306f39eadb598df03328f287bba43 Author: Ann Almgren Date: Mon Mar 15 18:02:22 2021 -0700 Now that we don't do the convective update all the way through we can get away with fewer ghost cells. src/incflo.H commit 52959d020fb313640b906e1b040bfb9bf7d5cc60 Author: Ann Almgren Date: Mon Mar 15 16:56:15 2021 -0700 Add elixirs for temporaries created in state redistribution src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp commit 5bd689872cc3e0186bf86fca52359b2e4e213f61 Author: Ann Almgren Date: Mon Mar 15 16:25:06 2021 -0700 Remove print statement src/convection/incflo_compute_update.cpp commit 30fe15785f33402c404dc6b817db0ee4d4a50277 Author: Ann Almgren Date: Mon Mar 15 15:13:24 2021 -0700 Refactor the computation of the advective terms so we can average down the fluxes before computing the convective update. This will break previous non-EB MOL tests because we were actually using conservative not convective differencing for the velocity update; now we default to convective (if no EB) src/convection/CMakeLists.txt src/convection/Convection.H src/convection/EBGodunov/EBGodunov.H src/convection/EBGodunov/Make.package src/convection/EBGodunov/incflo_ebgodunov_fluxes_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_fluxes_3D.cpp src/convection/Godunov/Godunov.H src/convection/Godunov/Make.package src/convection/Godunov/incflo_godunov_fluxes_2D.cpp src/convection/Godunov/incflo_godunov_fluxes_3D.cpp src/convection/MOL/MOL.H src/convection/MOL/Make.package src/convection/MOL/incflo_mol_divergence.cpp src/convection/MOL/incflo_mol_fluxes.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_compute_update.cpp src/convection/incflo_redistribute_convective_term.cpp src/incflo.H commit 30dabb83c4ff03403c54fdc6f7b508a2d34ef539 Author: Ann Almgren Date: Sun Mar 14 17:07:32 2021 -0700 fix typo src/incflo_vol_wgt_sum.cpp commit 86c84781a79d323ed1861205ea94224521ee9d27 Author: Ann Almgren Date: Sat Mar 13 15:03:13 2021 -0800 Add a routine for doing a volume-weighted sum across multiple levels. src/CMakeLists.txt src/Make.package src/incflo.H src/incflo_advance.cpp src/incflo_vol_wgt_sum.cpp commit 329e1dcf83cc9d4fb25cb4b958e792fb3cc1a6f9 Author: Ann Almgren Date: Wed Mar 10 19:23:17 2021 -0800 Fix 3d offset so we always reduce abs of ny,nz (i.e. don't just subtract, instead subtract if positive and add if negative) src/convection/Redistribution/incflo_create_itracker_3d.cpp commit f6822e2d67167cc44e0a19ce35da081ef171ac87 Author: Ann Almgren Date: Mon Mar 8 10:44:23 2021 -0800 Comment out heated ground so we can compile again src/prob/prob_init_fluid.cpp src/setup/init.cpp commit f152768661deb43139c2b9b4b8797d703ecbf178 Author: Ann Almgren Date: Fri Mar 5 13:00:56 2021 -0800 Add more generality src/boundary_conditions/boundary_conditions.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_tagging.cpp src/prob/CMakeLists.txt src/prob/Make.package src/prob/incflo_prob_usr_I.H src/prob/prob_bc.H src/prob/prob_init_fluid.cpp src/prob/prob_init_fluid_usr.cpp src/setup/init.cpp src/setup/set_background_pressure.cpp commit 67109fe9c21e96192e4f8ce1ef02c334ff4ac620 Author: Ann Almgren Date: Thu Feb 18 18:33:21 2021 -0800 comment out Print () src/convection/Redistribution/incflo_create_itracker_2d.cpp commit c9c3cd75efa21a2827ad2b768b316750a953e2b1 Author: Ann Almgren Date: Thu Feb 18 17:29:01 2021 -0800 Don't have redistribution type without USE_EB src/incflo.H commit 65958ba6321d4f190dfc0de682e77cfceab60f01 Author: Ann Almgren Date: Thu Feb 18 17:25:27 2021 -0800 fix typo src/convection/Redistribution/incflo_create_itracker_2d.cpp commit ee58caec17ceeb3bbe246f0437d2f4d83c9ffcb4 Author: Ann Almgren Date: Thu Feb 18 17:15:38 2021 -0800 Need to pass separate U_in and U_out to redistribute_initial_data routine src/setup/init.cpp commit 1147123c5ae780909b759414429909c4b30ff246 Author: Ann Almgren Date: Thu Feb 18 17:14:14 2021 -0800 We need to grow certain arrays more when using both Godunov and state redistribute -- I believe this makes them big enough (possibly some are too big?) src/incflo.H commit 0a59be303c757abac5ec7ce54689fe395fe3293a Author: Ann Almgren Date: Thu Feb 18 17:01:12 2021 -0800 Add test_redistributions, a directory with a lot of convenient benchmark problems and scripts to compare single grid vs tiled vs multiple grids and compare max/min between x-, y-, and z-rotations of the "same" problem test_3d/test_redistribution/benchmark.inviscid_rotated_cylinder_x test_3d/test_redistribution/benchmark.inviscid_rotated_cylinder_y test_3d/test_redistribution/benchmark.inviscid_rotated_cylinder_z test_3d/test_redistribution/benchmark.periodic_box_x test_3d/test_redistribution/benchmark.periodic_box_y test_3d/test_redistribution/benchmark.periodic_box_z test_3d/test_redistribution/benchmark.rotated_cylinder_x test_3d/test_redistribution/benchmark.rotated_cylinder_y test_3d/test_redistribution/benchmark.rotated_cylinder_z test_3d/test_redistribution/test_inviscid_godunov test_3d/test_redistribution/test_inviscid_mol test_3d/test_redistribution/test_periodic_godunov test_3d/test_redistribution/test_periodic_mol test_3d/test_redistribution/test_viscous_godunov test_3d/test_redistribution/test_viscous_mol commit ed15a585bba007e378eeb2261b313ebfffcafbfa Author: Ann Almgren Date: Thu Feb 18 16:12:34 2021 -0800 Make the temporaries big enough when doing state redistribution src/convection/incflo_compute_advection_term.cpp commit 6b593bbefd32a76cc5ca4b01292a33826b0c85ca Author: Ann Almgren Date: Thu Feb 18 15:33:54 2021 -0800 updated redistribution stuff src/convection/Redistribution/Redistribution.H src/convection/Redistribution/incflo_create_itracker_2d.cpp src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp commit 484c02500669fb93a0aabbc03926f685aa2834e4 Author: Ann Almgren Date: Thu Feb 18 15:01:04 2021 -0800 Add forcing terms to updates of regular cells in EBGodunov prediction -- they were missing ... src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_3D.cpp commit 93b99a5215a165c8f3e1b0dbfe6fcf6ddcb95fb8 Author: Ann Almgren Date: Thu Feb 18 12:57:50 2021 -0800 get rid of errant comment src/convection/EBGodunov/incflo_ebgodunov_advection_3D.cpp commit 8f092034d58a759ea00ea250966ffc22457dea43 Author: Ann Almgren Date: Wed Feb 17 11:30:37 2021 -0800 Only zero dUdt on the bx, not the entire FAB, or it breaks for tiling src/convection/Redistribution/incflo_redistribute.cpp commit 95e7b367edcce3f9e44f2d51151674b5625d4348 Author: Ann Almgren Date: Wed Feb 17 07:41:00 2021 -0800 Only include redistribution stuff with USE_EB src/convection/Redistribution/incflo_redistribute.cpp src/incflo.H src/setup/init.cpp commit e16a03cef58665341caefdf085e243fbb6cf5249 Author: Ann Almgren Date: Tue Feb 16 19:14:55 2021 -0800 more fixes from testing in 3d src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_state_redistribute.cpp commit 9ff350d0aab726cc5270cf95d7b0b5930d4ca8ea Author: Ann Almgren Date: Tue Feb 16 17:31:41 2021 -0800 Update the state redistribution code src/convection/Redistribution/Make.package src/convection/Redistribution/Redistribution.H src/convection/Redistribution/incflo_create_itracker_2d.cpp src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_flux_redistribute.cpp src/convection/Redistribution/incflo_merge_redistribute.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp commit b68a0f38ba3078126a07989959a779481ade72f1 Author: Ann Almgren Date: Sun Feb 14 19:33:24 2021 -0800 Change small_vel from 1e-10 to 1-e8 to be consistent with EBGodunov and less touchy for problems with small volfracs. src/convection/MOL/incflo_mol_fluxes.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/MOL/incflo_mol_predict.cpp src/convection/MOL/incflo_mol_predict_eb.cpp commit 05a80cf7e65bba9168f5e8864e423ca7332c3890 Author: Ann Almgren Date: Sun Feb 14 19:11:14 2021 -0800 remove setVal from gpu code src/convection/Redistribution/incflo_redistribute.cpp commit 9f2d1bbdcc3dbee1d544c35fb5a30cedbbaef54d Author: Ann Almgren Date: Sun Feb 14 19:08:18 2021 -0800 remove Prints src/convection/Redistribution/incflo_state_redistribute.cpp commit 10fb29f662c8002ea369bc2db98e11abf15645f9 Author: Ann Almgren Date: Sun Feb 14 19:07:11 2021 -0800 Remove Print from merge redistribute src/convection/Redistribution/incflo_merge_redistribute.cpp commit 37f388a5164ffea967998e2b3238cc21586c6d15 Author: Ann Almgren Date: Sun Feb 14 19:05:50 2021 -0800 oops -- missing line (for gpus) src/convection/EBGodunov/incflo_ebgodunov_transverse_2D_K.H commit 01fc6a632446300cf4a4b82ea63fd4e7fc5484e5 Author: Ann Almgren Date: Sun Feb 14 18:54:25 2021 -0800 make this gpu-portable again src/prob/prob_bc.cpp commit 2148efff8f5d22b653709e1b2e1d17a926b0edd1 Author: Ann Almgren Date: Sun Feb 14 18:50:10 2021 -0800 Revert the change in small_vel -- just for now to check the regression tests src/convection/MOL/incflo_mol_predict.cpp src/convection/MOL/incflo_mol_predict_eb.cpp commit bc4a8e5d7783066c414bdca2653a10093bb27437 Author: Ann Almgren Date: Sun Feb 14 18:41:16 2021 -0800 Need these to be up to date to compile src/convection/Redistribution/Redistribution.H src/convection/Redistribution/incflo_merge_redistribute.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp commit f2dcbd1c1d540f640df46c1e248a35d9f9abf53c Author: Ann Almgren Date: Sun Feb 14 17:36:53 2021 -0800 wrap with ifdef src/prob/prob_init_fluid.cpp commit 4339226b3518699ab467b9d6f3c2088747e93364 Author: Ann Almgren Date: Sun Feb 14 17:30:35 2021 -0800 moving test --> test_3d test_3d/GNUmakefile test_3d/README.md test_3d/benchmark.channel_cylinder-x test_3d/benchmark.channel_cylinder-xx test_3d/benchmark.channel_cylinder-y test_3d/benchmark.channel_cylinder-yy test_3d/benchmark.channel_cylinder-z test_3d/benchmark.channel_cylinder-zz test_3d/benchmark.channel_spherecube test_3d/benchmark.couette test_3d/benchmark.couette_poiseuille test_3d/benchmark.double_shear_layer test_3d/benchmark.double_shear_restart test_3d/benchmark.lid_driven_cavity test_3d/benchmark.poiseuille_cylinder_bingham test_3d/benchmark.poiseuille_cylinder_newtonian test_3d/benchmark.poiseuille_halfplane_newtonian test_3d/benchmark.poiseuille_plane_bingham test_3d/benchmark.poiseuille_plane_newtonian test_3d/benchmark.rotated_cylinder_x test_3d/benchmark.rotated_cylinder_y test_3d/benchmark.rotated_cylinder_z test_3d/benchmark.slanted_cylinder test_3d/benchmark.taylor_green_vortices test_3d/benchmark.tracer_adv_diff test_3d/benchmark.tracer_adv_diff_cn test_3d/benchmark.tracer_advection test_3d/benchmark.tuscan test_3d/benchmark.uniform_velocity_sphere test_3d/incflo-tests.ini test_3d/inputs.channel_sphere test_3d/inputs.couette_cylinder test_3d/inputs.couette_twocylinders test_3d/inputs.poiseuille_annulus test_3d/inputs.rotating_cylinder test_3d/inputs.taylor_couette commit 4af00adf8f3573682d0f5cd54b941b1c9a825a77 Author: Ann Almgren Date: Sun Feb 14 17:24:19 2021 -0800 The files in this commit pass the following consistency check: When run in 2D or 3D, with either MOL or Godunov, with either NoRedist or FluxRedist a. The answers are within O(1e-12) when run with single grid vs multiple grids vs tiled b. The answers are "identical" (to within the precision of amrvis), when appropriately rotated, between the channels oriented in the x- vs y- vs z-directions The test problems used for this are tests/benchmark.rotated_cylinder_* and test_2d/benchmark.rotated_planes_* in this commit. src/convection/EBGodunov/EBGodunov.H src/convection/EBGodunov/Make.package src/convection/EBGodunov/incflo_ebgodunov_advection_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_advection_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_corner_couple.H src/convection/EBGodunov/incflo_ebgodunov_make_trans_vels.cpp src/convection/EBGodunov/incflo_ebgodunov_plm.cpp src/convection/EBGodunov/incflo_ebgodunov_plm_fpu.cpp src/convection/EBGodunov/incflo_ebgodunov_predict.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_transverse_2D_K.H src/convection/EBGodunov/incflo_ebgodunov_transverse_3D_K.H src/convection/Godunov/incflo_godunov_plm.cpp src/convection/Godunov/incflo_godunov_predict_2D.cpp src/convection/Godunov/incflo_godunov_predict_3D.cpp src/convection/MOL/incflo_mol_predict_eb.cpp src/convection/incflo_compute_advection_term.cpp src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp test/benchmark.rotated_cylinder_x test/benchmark.rotated_cylinder_y test/benchmark.rotated_cylinder_z test_2d/benchmark.rotated_planes_x test_2d/benchmark.rotated_planes_y commit 275dd21f0c613bbd487bc4c4671794bf318139d6 Author: Ann Almgren Date: Sat Feb 13 10:09:26 2021 -0800 make tracer in channel_slant also have the right symmetries src/prob/prob_init_fluid.cpp commit a55800615a99ca388fa40bb75cd64cccb8ede7f3 Author: Ann Almgren Date: Sat Feb 13 09:59:00 2021 -0800 get right symmetries for 2d channel_slant problem src/convection/MOL/Make.package src/convection/MOL/incflo_mol_predict.cpp src/convection/MOL/incflo_mol_predict_eb.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/prob/prob_init_fluid.cpp test/benchmark.rotated_cylinder_x test/benchmark.rotated_cylinder_y test/benchmark.rotated_cylinder_z commit b6dca567138abd9b781349df729849826b018e7e Author: Ann Almgren Date: Thu Feb 11 09:31:41 2021 -0800 do the correct test on bc's when in MOL predict for EB src/convection/MOL/incflo_mol_predict_eb.cpp commit 6b0f9b41f7ab8865e31efc4f442fd45938f43142 Author: Ann Almgren Date: Wed Feb 3 19:18:59 2021 -0800 set soln_hat to zero at start src/convection/Redistribution/incflo_state_redistribute.cpp commit bde3d553c6c8311f8d683c75de6647dfe9bbdaad Author: Ann Almgren Date: Wed Feb 3 13:37:32 2021 -0800 comment out print statements src/convection/Redistribution/incflo_create_itracker_2d.cpp commit 06f96c5376d75579637271c8b73e52e514552dc6 Author: Ann Almgren Date: Wed Feb 3 13:28:00 2021 -0800 update to work on GPU and remove unused variables src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_transverse_2D_K.H commit f9705e0badb0183a5f93544b78cda6022b790e5c Author: Ann Almgren Date: Wed Feb 3 11:45:28 2021 -0800 Compile with GPUs... src/convection/Redistribution/incflo_create_itracker_2d.cpp src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_merge_redistribute.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp commit d6771cae585501790246610fd77292aa79a815ed Author: Ann Almgren Date: Wed Feb 3 10:14:02 2021 -0800 Fix typo src/setup/init.cpp commit da401cb6b745598769ffd05edaaba88d40a67834 Author: Ann Almgren Date: Tue Feb 2 16:59:11 2021 -0800 Turn off options other than FluxRedist for redistribution_type src/setup/init.cpp commit 3286c706cfaff1eddc68e3209bd240c1dcad5fa3 Author: Ann Almgren Date: Tue Feb 2 16:57:17 2021 -0800 1) Add EBGodunov 2) Add more redistribution options -- determined by a runtime flag src/Make.incflo src/convection/EBGodunov/EBGodunov.H src/convection/EBGodunov/Make.package src/convection/EBGodunov/incflo_ebgodunov_advection_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_advection_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_corner_couple.H src/convection/EBGodunov/incflo_ebgodunov_plm.cpp src/convection/EBGodunov/incflo_ebgodunov_plm_fpu.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_2D.cpp src/convection/EBGodunov/incflo_ebgodunov_predict_3D.cpp src/convection/EBGodunov/incflo_ebgodunov_transverse_2D_K.H src/convection/EBGodunov/incflo_ebgodunov_transverse_3D_K.H src/convection/Make.package src/convection/Redistribution/Make.package src/convection/Redistribution/Redistribution.H src/convection/Redistribution/incflo_create_itracker_2d.cpp src/convection/Redistribution/incflo_create_itracker_3d.cpp src/convection/Redistribution/incflo_flux_redistribute.cpp src/convection/Redistribution/incflo_merge_redistribute.cpp src/convection/Redistribution/incflo_redistribute.cpp src/convection/Redistribution/incflo_state_redistribute.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/setup/init.cpp commit 54ded2fa3c55d13cb1693aee91f16d087d7c607f Author: Ann Almgren Date: Sat Jan 30 19:01:00 2021 -0800 Replace un-limited slopes for EB by limited slopes in MOL routines src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/MOL/incflo_mol_predict_eb.cpp commit 8d4f4f315985503104f5612451422aea9547ece3 Author: Ann Almgren Date: Thu Jan 28 18:07:40 2021 -0800 Add missing elixir (for "rhotrac") when using MOL src/convection/incflo_compute_advection_term.cpp src/incflo.cpp src/setup/init.cpp commit 6a7a4f6a8dab1461220135f8b1aedc994152a3d5 Author: Ann Almgren Date: Wed Jan 27 15:37:59 2021 -0800 Comment out itracker for now src/convection/incflo_redistribute.cpp commit 19e1216f88ea6c0d4493279d385481ada8dbbd7a Author: Ann Almgren Date: Wed Jan 27 14:09:59 2021 -0800 Explicitly choose advection_type in the inputs files src/convection/incflo_compute_MAC_projected_velocities.cpp test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-xx test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-yy test/benchmark.channel_cylinder-z test/benchmark.channel_cylinder-zz test/benchmark.channel_spherecube test/benchmark.couette test/benchmark.couette_poiseuille test/benchmark.double_shear_layer test/benchmark.double_shear_restart test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_halfplane_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian test/benchmark.rotated_cylinder_x test/benchmark.rotated_cylinder_y test/benchmark.rotated_cylinder_z test/benchmark.slanted_cylinder test/benchmark.taylor_green_vortices test/benchmark.tracer_adv_diff test/benchmark.tracer_adv_diff_cn test/benchmark.tracer_advection test/benchmark.tuscan test/benchmark.uniform_velocity_sphere test_2d/benchmark.channel_cylinder test_2d/benchmark.couette test_2d/benchmark.double_shear_layer test_2d/benchmark.inviscid_rotated_planes_x test_2d/benchmark.lid_driven_cavity test_2d/benchmark.poiseuille_cylinder_bingham test_2d/benchmark.poiseuille_cylinder_newtonian test_2d/benchmark.poiseuille_plane_bingham test_2d/benchmark.poiseuille_plane_newtonian test_2d/benchmark.rotated_planes_x test_2d/benchmark.rotated_planes_y test_2d/benchmark.taylor_green_vortices test_2d/benchmark.tracer_adv_diff test_2d/benchmark.tracer_adv_diff_cn test_2d/benchmark.tracer_advection test_2d/benchmark.uniform_velocity_sphere test_no_eb/benchmark.bouss_bubble_god test_no_eb/benchmark.bouss_bubble_mol test_no_eb/benchmark.bouss_bubble_plm test_no_eb/benchmark.double_shear_layer_x test_no_eb/benchmark.double_shear_layer_y test_no_eb/benchmark.double_shear_layer_z test_no_eb/benchmark.poiseuille_halfplane_newtonian_x test_no_eb/benchmark.poiseuille_halfplane_newtonian_y test_no_eb/benchmark.poiseuille_halfplane_newtonian_z test_no_eb/benchmark.poiseuille_plane_newtonian_x test_no_eb/benchmark.poiseuille_plane_newtonian_y test_no_eb/benchmark.poiseuille_plane_newtonian_z test_no_eb/benchmark.rayleigh_taylor test_no_eb/benchmark.slip_wall_test_x test_no_eb/benchmark.taylor_green_vortices test_no_eb_2d/benchmark.bouss_bubble_god test_no_eb_2d/benchmark.bouss_bubble_mol test_no_eb_2d/benchmark.bouss_bubble_plm test_no_eb_2d/benchmark.double_shear_layer test_no_eb_2d/benchmark.rayleigh_taylor test_no_eb_2d/benchmark.taylor_green_vortices commit 0d2581a267f801fdf39b191f2829598c4cb9f0d7 Author: Ann Almgren Date: Wed Jan 27 12:57:47 2021 -0800 1) clean-up 2) new box geometry 3) re-factoring of convection stuff in preparation for EBGoudnov No change in any existing functionality expected src/Make.incflo src/convection/Godunov/Godunov.H src/convection/Godunov/Make.package src/convection/Godunov/incflo_godunov_advection_2D.cpp src/convection/Godunov/incflo_godunov_advection_3D.cpp src/convection/Godunov/incflo_godunov_corner_couple.H src/convection/Godunov/incflo_godunov_plm.H src/convection/Godunov/incflo_godunov_plm.cpp src/convection/Godunov/incflo_godunov_ppm.H src/convection/Godunov/incflo_godunov_ppm.cpp src/convection/Godunov/incflo_godunov_predict_2D.cpp src/convection/Godunov/incflo_godunov_predict_3D.cpp src/convection/Godunov/incflo_godunov_trans_bc.H src/convection/MOL/MOL.H src/convection/MOL/Make.package src/convection/MOL/incflo_correct_small_cells.cpp src/convection/MOL/incflo_mol_divergence.cpp src/convection/MOL/incflo_mol_fluxes.cpp src/convection/MOL/incflo_mol_fluxes_eb.cpp src/convection/MOL/incflo_mol_predict.cpp src/convection/MOL/incflo_mol_predict_eb.cpp src/convection/Make.package src/convection/Redistribution.H src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_flux_redistribute.cpp src/convection/incflo_redistribute.cpp src/derive/incflo_derive.cpp src/derive/incflo_derive_K.H src/derive/incflo_error.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/incflo_regrid.cpp src/incflo_tagging.cpp src/main.cpp src/prob/incflo_prob_I.H src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit a341196b82a2de5c5de6e454206b6587e42ef2da Author: Oscar Antepara Date: Fri Dec 18 10:10:48 2020 -0800 Adding explanation comments about the changes introduced in 53205ae5ef78c93d90bada8a269824ddcb7ed498 about the declaration of number of components for 2D/3D src/convection/incflo_compute_advection_term.cpp commit 53205ae5ef78c93d90bada8a269824ddcb7ed498 Author: Oscar Antepara Date: Thu Dec 17 17:57:51 2020 -0800 Fixing the number of components needed for the temporal arrays in 2D src/convection/incflo_compute_advection_term.cpp commit 65870a3428578d4bc7efe64bb4c1a070932f9537 Author: Ann Almgren Date: Mon Dec 14 11:58:16 2020 -0800 writeEBSurface is only relevant in 2D src/embedded_boundaries/writeEBsurface.cpp src/incflo.cpp commit 19f2aef93fe74faf6e072943ed584d5d5e909e37 Merge: 14950cd1 da61e362 Author: Weiqun Zhang Date: Mon Dec 14 10:21:57 2020 -0800 For constant density, use the constant-coefficient version of MacProjector. (#43) commit da61e362bd1d0c9b8d766cea58543252786bf88b Author: Weiqun Zhang Date: Mon Dec 14 09:12:51 2020 -0800 For constant density, use the constant-coefficient version of MacProjector src/convection/incflo_compute_MAC_projected_velocities.cpp commit 14950cd167ee868b65ed49e4697086963ac51f90 Author: Ann Almgren Date: Sat Dec 12 18:01:48 2020 -0800 1) fix the computation of dt when we start the simulation with no-flow and no-body-forces 2) set sig = dt / rho (not dt * rho) when we use the constant density projection src/incflo_compute_dt.cpp src/projection/incflo_apply_nodal_projection.cpp commit e12701315b8ebd022f6e994ab45ff0648ab913d2 Author: Ann Almgren Date: Sat Dec 12 11:36:42 2020 -0800 1) if incflo.constant_density == true, use the constant-coefficient version of the nodal projector 2) set up test problems with constant_density = true in test, test_2d, test_no_eb and test_no_eb_2d src/projection/incflo_apply_nodal_projection.cpp test/benchmark.channel_cylinder-x test_2d/benchmark.channel_cylinder test_no_eb/benchmark.double_shear_layer_x test_no_eb_2d/benchmark.double_shear_layer commit c96126fc7261ae355a29d42322efe82b2f0263db Author: Ann Almgren Date: Sat Dec 5 10:26:23 2020 -0800 For the option use_mac_phi_in_godunov, this correctly gets (1/rho) G^MAC phi from a getFluxes call rather than computing the gradient locally src/convection/Godunov.H src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp commit d7e61191e844c57a65df79843d151a8a0fc1b4e0 Author: Ann Almgren Date: Sat Dec 5 10:15:10 2020 -0800 Hold on to the results that the current code gives for the convergence tests in 2d and 3d convergence_2d/results_2d convergence_3d/results_3d commit 287902a15bdc7fbf25466e77b47272e56edab693 Author: Ann Almgren Date: Tue Dec 1 17:33:57 2020 -0800 Remove assertion that we can't use godunov with EB src/convection/incflo_compute_advection_term.cpp commit 1f60b43f42fd357aaeb8f74c63a6a400fd1dd041 Author: Ann Almgren Date: Tue Dec 1 17:15:35 2020 -0800 Move construction of MacProjector to initialization and regrid rather than creating the object every time we call it. src/convection/incflo_compute_MAC_projected_velocities.cpp src/incflo.H src/incflo.cpp src/incflo_regrid.cpp commit 66d6a2ff74f522e9acc376e7b34794161978c082 Author: Ann Almgren Date: Tue Dec 1 16:10:52 2020 -0800 Use new interfaces to MACProjector src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp commit b93c41eda2ce08efb3cc25deb81c39d17aaf684b Author: Ann Almgren Date: Sun Nov 29 19:29:19 2020 -0800 An earlier change to redistribution got over-written with the last commit. This commit reverses just that change. src/convection/incflo_compute_advection_term.cpp commit 90454612a1ad922161ec5e546c5940a80ea2e844 Author: Ann Almgren Date: Sat Nov 28 10:44:58 2020 -0800 Add the option to use G(phi^MAC) in predition of the velocities to be MAC-projected -- this should not change default behavior. Currently the use_mac_phi_in_godunov option is only good for periodic boundaries. convergence_2d/benchmark.taylor_vortex_decaying convergence_2d/todo convergence_2d/todo_print convergence_3d/benchmark.taylor_vortex_decaying convergence_3d/todo convergence_3d/todo_print src/convection/Godunov.H src/convection/Make.package src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_MAC_projected_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp src/incflo.H commit 0bd3e7511a10c421ab88fc3d87c2aa2a13532a26 Author: Ann Almgren Date: Sat Nov 21 08:58:06 2020 -0800 Merge Candace's fix in fillpatch_gradp: 3 --> AMREX_SPACEDIM src/boundary_conditions/incflo_fillpatch.cpp commit afe29625d08e20ea21646f013036127a6f153692 Author: Michele Rosso Date: Thu Nov 5 12:17:44 2020 -0800 CMake: check for Fortran component CMakeLists.txt commit 62eaf6787f02afffc0e3e18bdee42a0711a9bb28 Author: Michele Rosso Date: Thu Nov 5 12:17:22 2020 -0800 CMake: bump up minimum amrex required version CMakeLists.txt commit 93c9287e86719f3f37ecfa4d1fa98bbd5416ebf5 Author: Michele Rosso Date: Tue Nov 3 13:30:48 2020 -0800 CMake: overhaul options CMakeLists.txt Docs/sphinx_documentation/source/BuildingCMake.rst src/CMakeLists.txt commit d789185f22de9d86322c2c55eff896bdac1c5fd1 Author: Oscar Antepara Date: Tue Oct 27 09:56:52 2020 -0700 Revert "Including the cell itself in the non-conservative flux computation" This reverts commit 7c3e1e5b4fff8ec2474f6559bf5e8f9f3e4bbd6c. src/convection/incflo_compute_advection_term.cpp commit bad00add733f92b18dbcd77200bc4213370a0760 Author: Ann Almgren Date: Mon Oct 26 17:22:38 2020 -0700 add decaying vortex problem for convergence testing test_no_eb_2d/benchmark.taylor_vortex_decaying commit 822f235d45aa1d12b8b421192671c3801540d270 Author: Ann Almgren Date: Mon Oct 26 17:21:05 2020 -0700 Subtract off mean of p and mac_phi before computing error -- affects output only src/derive/incflo_error.cpp src/incflo.H src/incflo_compute_forces.cpp src/utilities/io.cpp commit 7c3e1e5b4fff8ec2474f6559bf5e8f9f3e4bbd6c Author: Oscar Antepara Date: Thu Oct 22 10:08:01 2020 -0700 Including the cell itself in the non-conservative flux computation src/convection/incflo_compute_advection_term.cpp commit 4800ff763d262442e8dffc8981ab838ef1e6a138 Author: Oscar Antepara Date: Thu Oct 22 10:02:52 2020 -0700 Adding test where redistribution fails src/prob/prob_init_fluid.cpp test_2d/benchmark.inviscid_rotated_planes_x commit 4f350288d198d35fa12d550b2f44f059b0519954 Author: Ann Almgren Date: Fri Oct 16 09:00:37 2020 -0700 Don't pass mac_phi into MAC projector if not use_mac_phi_in_godunov src/convection/incflo_MAC_projection.cpp commit f0511bbf9ba4ec9832a936df0f41f9ceb52f787a Author: Ann Almgren Date: Thu Oct 15 19:00:38 2020 -0700 Add the translating vortex problem src/convection/incflo_compute_advection_term.cpp src/derive/incflo_error.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp src/utilities/io.cpp commit ecdfc9c3cee8e9081ad3c0e23f0efe3c74fefadc Author: Ann Almgren Date: Thu Oct 15 14:39:02 2020 -0700 More movement towards getting Gphi^MAC stuff to work. src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict_2D.cpp src/incflo.H src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp src/utilities/io.cpp commit 5a1f2624cb418e88f6eb5612140fc77931e809d1 Author: Ann Almgren Date: Wed Oct 14 16:52:00 2020 -0700 Continued move towards measuring error and enabling use of MAC grad phi src/convection/Godunov.H src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp src/derive/incflo_derive.cpp src/derive/incflo_error.cpp src/incflo.H src/rheology/incflo_rheology.cpp commit 37ac9968911ea5575c1b1936a850d884f23af5a3 Author: Ann Almgren Date: Wed Oct 14 15:52:37 2020 -0700 first pass at 1) adding MAC phi stuff 2) adding error plotting stuff (only for Taylor-Green vortices at this point) src/convection/Godunov.H src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp src/derive/CMakeLists.txt src/derive/Make.package src/derive/incflo_derive.cpp src/derive/incflo_derive_K.H src/derive/incflo_error.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit 693728066424966af9a66a607875df553ea76411 Author: Ann Almgren Date: Mon Oct 12 17:36:25 2020 -0700 Use the "use_forces_in_trans" flag in the post-MAC as well as the pre-MAC part of the construction of face values in the Godunov algorithm. This is now more consistent with the algorithm in IAMR. src/convection/Godunov.H src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection_2D.cpp src/convection/incflo_godunov_advection_3D.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp commit 92ddfd5b0442015bca7a0a62bfe701756e245cc8 Author: Ann Almgren Date: Sat Sep 26 12:42:29 2020 -0700 fix oops src/diffusion/DiffusionScalarOp.cpp commit 7a904b00796c4247ece8c0cc40941d70ea9a8b4f Author: Ann Almgren Date: Sat Sep 26 11:59:48 2020 -0700 Remove duplicated variable src/diffusion/DiffusionScalarOp.H commit d4a8f139cf872203e90e71189fb1f0cab3fbfa3a Author: Ann Almgren Date: Sat Sep 26 11:51:32 2020 -0700 "cg" --> "bottom" in flags and calls to MLMG src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/incflo.H src/setup/init.cpp commit 1bedb9c1cc309df129b4cb5c4abb9a3b272af483 Author: Ann Almgren Date: Wed Sep 23 09:58:41 2020 -0700 Add comments to 4th order slope calls to make sure we remember why we call the extdir version. src/convection/incflo_godunov_plm.H commit 58a6c322a6f1cefa294d3b3671dc23af74ebb5c0 Author: Ann Almgren Date: Wed Sep 23 09:55:03 2020 -0700 Revert the previous change src/convection/incflo_godunov_plm.H commit b39f42958d36d1eb429ee47e35e28c941ed17308 Author: Ann Almgren Date: Wed Sep 23 09:29:39 2020 -0700 call the non-extdir slope routine once we've already tested that this cell doesn't touch a wall ... src/convection/incflo_godunov_plm.H commit be2fb4fc0dda9207dc0209dcf195bfc809728f24 Author: Ann Almgren Date: Thu Sep 10 08:34:15 2020 -0700 Return tracer bc's to be foextrap at pressure outflow and no-slip-wall src/boundary_conditions/boundary_conditions.cpp commit c1ebed641d313ae3b80e23efbab29ec4d1288108 Author: Ann Almgren Date: Wed Sep 9 13:53:53 2020 -0700 Migrate incflo to use the slopes now in amrex src/boundary_conditions/boundary_conditions.cpp src/convection/Make.package src/convection/incflo_godunov_advection_2D.cpp src/convection/incflo_godunov_advection_3D.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H src/rheology/incflo_rheology.cpp src/utilities/incflo_build_info.cpp test/benchmark.rotated_cylinder_x test/benchmark.rotated_cylinder_y test/benchmark.rotated_cylinder_z commit d416d70b2ab544a4c5a0fe1407e693e799bd5378 Author: Ann Almgren Date: Mon Sep 7 11:03:55 2020 -0700 Add rotated channel tests where the channel intersects either the x-faces or y-faces test_2d/benchmark.rotated_planes_x test_2d/benchmark.rotated_planes_y commit 34ff8b59d4fdeedcc318720a2a1429373ced29b4 Author: Ann Almgren Date: Sun Sep 6 11:46:31 2020 -0700 Make annulus ok in 2d src/embedded_boundaries/eb_annulus.cpp commit d10bded825ccc99e5353196b320cf60876593d94 Author: Ann Almgren Date: Fri Sep 4 18:39:12 2020 -0700 Don't include EB files if not building with EB src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict_eb.cpp commit 8a0141a8097c5092ae32d1ca89a96092bbb7a1d4 Author: Ann Almgren Date: Fri Sep 4 18:24:35 2020 -0700 Move the EB-aware slope routines into AMReX src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H commit 176a7336a781d3789fd8f07bed74cd347590ce99 Author: Oscar Antepara Date: Fri Aug 14 10:16:17 2020 -0700 Adding uniform initial values for rotated geometries src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test/benchmark.slanted_cylinder test_2d/benchmark.channel_planes-x test_2d/benchmark.channel_planes_rotated-x commit 31bdff081080d86903504ff249ee30ee14a17fd0 Author: Oscar Antepara Date: Wed Aug 12 12:13:21 2020 -0700 Fix to the parmparse for the eb2 extend_domain_face flag src/main.cpp commit be976b13c6b1b206e04c25984b1e3599509e8183 Author: Oscar Antepara Date: Wed Aug 12 11:58:59 2020 -0700 Adding 3d slanted cylinder test test/benchmark.slanted_cylinder commit 6355a7e6d46b0442218e3f6b08484f81c24672ab Author: Michele Rosso Date: Mon Aug 10 15:18:04 2020 -0700 CMake: add option to control dimensionality of the build CMakeLists.txt Docs/sphinx_documentation/source/BuildingCMake.rst src/convection/CMakeLists.txt commit f25d5ad8ec3980d4360e5edd0b5b2f47a0cc5f8d Merge: 56369098 546a71f3 Author: asalmgren Date: Fri Aug 7 15:36:39 2020 -0700 Merge pull request #42 from drangara/small_volfrac_2d Modify test so it fails to converge commit 546a71f3bb62ca4e20e4aa775af4b30f2ab9bfa8 Author: Deepak Rangarajan Date: Fri Aug 7 17:37:03 2020 -0400 Modify test so it fails to converge test_2d/benchmark.channel_planes_rotated-x commit 5636909873ace27dc869869c7c4d25038b6ea379 Author: Oscar Antepara Date: Fri Aug 7 12:42:38 2020 -0700 Adding additional 2d benchmarks tests (parallel planes and rotated planes) src/embedded_boundaries/eb_cylinder.cpp test_2d/benchmark.channel_planes-x test_2d/benchmark.channel_planes_rotated-x commit 16fce07eda7fb3560f7d87c0cbfbf8212001ca4d Author: Oscar Antepara Date: Mon Jul 13 14:59:16 2020 -0700 Adding more benchmark tests to test_2d src/derive/derive.cpp src/derive/derive_K.H src/rheology/incflo_rheology.cpp test_2d/benchmark.poiseuille_cylinder_bingham test_2d/benchmark.poiseuille_cylinder_newtonian test_2d/benchmark.poiseuille_plane_bingham test_2d/benchmark.poiseuille_plane_newtonian test_2d/benchmark.tracer_adv_diff test_2d/benchmark.tracer_adv_diff_cn test_2d/benchmark.tracer_advection commit 757eb1157670c93b77c97aa3119dc6141cddbd79 Author: Ann Almgren Date: Fri Jul 10 18:40:09 2020 -0700 make this sphere not cylidner test_2d/benchmark.channel_cylinder commit c6d03cea40488674cc1d9f6b17aac40b6f7a4b0e Author: Ann Almgren Date: Fri Jul 10 18:29:42 2020 -0700 rename test_2d/benchmark.channel_cylinder commit 9048219b175930795fe559fc70613a2ee2e179d4 Author: Ann Almgren Date: Fri Jul 10 18:28:33 2020 -0700 update files in test_2d test_2d/GNUmakefile test_2d/benchmark.channel_cylinder-x test_2d/benchmark.couette test_2d/benchmark.double_shear_layer test_2d/benchmark.lid_driven_cavity test_2d/benchmark.taylor_green_vortices test_2d/benchmark.uniform_velocity_sphere commit 54df3477aff1ee3ff7da574d029c4859d8fa1fad Merge: 14444d43 d495578a Author: Oscar Antepara Date: Fri Jul 10 17:43:57 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 14444d43ce9c902a6188a146c9f26bdfda1a5e94 Author: Oscar Antepara Date: Fri Jul 10 17:43:35 2020 -0700 Fixing a 3d/2d problem in plm src/convection/incflo_godunov_plm.cpp commit d495578a2684fd35522b7cfbf9cdb194a4a0856c Merge: 5e0ce715 050ddd8f Author: Ann Almgren Date: Fri Jul 10 17:35:43 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 5e0ce715e0abe69aad4c4157a0efb3e1384da62b Author: Ann Almgren Date: Fri Jul 10 17:35:27 2020 -0700 fix oops -- forgot to change direction of gravity to be in y-direction (not z) test_no_eb_2d/benchmark.rayleigh_taylor commit 050ddd8fa36c1a3c6254d4e3c73be3b01a1d166c Author: Oscar Antepara Date: Fri Jul 10 17:26:10 2020 -0700 Fixing bug with 2d EB src/derive/derive.cpp commit 89aced834f179c435e7ea6556f24e15b1f384635 Author: Ann Almgren Date: Fri Jul 10 17:12:26 2020 -0700 Fix location of bubble for 2D Boussinesq tests src/prob/prob_init_fluid.cpp commit b554076392ce889849c88490f8be5a267e5e2ba4 Author: Ann Almgren Date: Fri Jul 10 16:53:27 2020 -0700 2d vorticity routine src/derive/derive.cpp commit 43f59c2bfbabdb34b2e76a67d3bca2cbd125979c Merge: 3681f5c6 f48e3cc0 Author: Oscar Antepara Date: Fri Jul 10 16:44:17 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 3681f5c61c11bd731125b49856bbc08a44d5dbf0 Author: Oscar Antepara Date: Fri Jul 10 16:43:30 2020 -0700 Adding test_2d src/prob/prob_init_fluid.cpp test_2d/GNUmakefile test_2d/benchmark.channel_cylinder-x test_2d/benchmark.couette test_2d/benchmark.double_shear_layer test_2d/benchmark.lid_driven_cavity test_2d/benchmark.taylor_green_vortices test_2d/benchmark.uniform_velocity_sphere commit f48e3cc05a465c987ee95388d3314101636a5391 Author: Ann Almgren Date: Fri Jul 10 16:41:41 2020 -0700 don't take z gradients when running in 2d src/incflo_tagging.cpp commit 6a80d1421acb952043276fbaf03a451cd62a5972 Author: Ann Almgren Date: Fri Jul 10 16:36:50 2020 -0700 this now compiles src/prob/prob_init_fluid.cpp commit 149382c4e35cd8d83447a0d672d67c20859c44d4 Author: Ann Almgren Date: Fri Jul 10 16:30:10 2020 -0700 Add 2D no-EB test problems src/prob/prob_init_fluid.cpp test_no_eb_2d/GNUmakefile test_no_eb_2d/benchmark.bouss_bubble_god test_no_eb_2d/benchmark.bouss_bubble_mol test_no_eb_2d/benchmark.bouss_bubble_plm test_no_eb_2d/benchmark.double_shear_layer test_no_eb_2d/benchmark.rayleigh_taylor test_no_eb_2d/benchmark.taylor_green_vortices commit 9ad7729230c386df3fe57084b29bdaea5fdf3b54 Author: Oscar Antepara Date: Fri Jul 10 16:23:26 2020 -0700 Adding flag forbc in 2D files src/convection/incflo_godunov_advection_2D.cpp src/convection/incflo_godunov_predict_2D.cpp commit a2ea3ca511483f03dd448b4341a725f27272fbe8 Author: Michele Rosso Date: Fri Jul 10 15:53:32 2020 -0700 CMake: fix bug src/CMakeLists.txt commit 7cdc7463da7e1323488fc0e543192eb16ed6ba78 Merge: ab750717 584ec6ca Author: Michele Rosso Date: Fri Jul 10 15:53:16 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit ab750717bff969a82543c26ba71afb8dca8e9126 Author: Michele Rosso Date: Fri Jul 10 15:20:13 2020 -0700 Godunov: remove superfluous BCs src/convection/incflo_godunov_plm.cpp commit 7f3920fde1d43ec69e7def72f4e69de8ed57a318 Author: Michele Rosso Date: Fri Jul 10 15:18:55 2020 -0700 Godunov: make is_velocity non-optional for safety src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H commit 584ec6cab67e983a34d22b6dd10d6a7b77fcc016 Author: Oscar Antepara Date: Fri Jul 10 10:22:09 2020 -0700 Fix for gpu compilation error src/convection/incflo_slopes_K.H commit d761f5debd0c84414d1dce626caf9630770ae91b Merge: ebbc415e 65684ab9 Author: Oscar Antepara Date: Thu Jul 9 21:06:26 2020 -0700 Merging development into this branch commit ebbc415e244ab958c822728152dccf91a0bff85f Author: Oscar Antepara Date: Thu Jul 9 20:52:59 2020 -0700 Fixing bug with mol src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict_eb.cpp src/incflo_apply_predictor.cpp commit 65684ab918689e85a8a36975af484a978775f6f3 Author: Ann Almgren Date: Thu Jul 9 19:21:10 2020 -0700 wrap with AMREX_USE_EB src/diffusion/incflo_diffusion.cpp commit 6130e4dc7aad63cff5a6dc81f9e64af381537742 Author: Michele Rosso Date: Thu Jul 9 18:37:57 2020 -0700 Godunov: pass flag to specify wheter variable is a velocity component src/convection/Godunov.H src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit 6854c35f4279a652285ee660269fc6b732cbf7e3 Author: Ann Almgren Date: Thu Jul 9 18:15:55 2020 -0700 Update to tensor_correction src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_regrid.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit d60787a792fdfbfb152da3d899015b45363b264d Author: jbb Date: Wed Jul 8 19:14:28 2020 -0700 modification for plm boundary conditions src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit b30a2ebdfe83f7999018bb2d79ed654b98dab57c Author: Michele Rosso Date: Wed Jul 8 16:06:25 2020 -0700 Godunov: fix BCs in Godunov_plm_fpu_* routines src/convection/incflo_godunov_plm.H commit 1062e82487e95e9decbc12a2fff774e6ce452531 Author: Oscar Antepara Date: Wed Jul 8 10:41:04 2020 -0700 Enabling mol 2D/3D with EB src/convection/MOL.H src/convection/incflo_compute_advection_term.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H commit 1c4077dcf78e5e461856539e31c8c856e1e23d4f Author: Oscar Antepara Date: Tue Jul 7 12:27:15 2020 -0700 Enabling mol 2D/3D without EB src/convection/MOL.H src/convection/incflo_compute_advection_term.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_predict.cpp commit 58ce6bce45ad04d2001bb101f839c660ee699895 Merge: 3f005218 5f7f927c Author: Michele Rosso Date: Tue Jul 7 12:20:08 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into mr/godunov-bug-fixes commit c3131020ff7bafab34bd178b0ef4936d1247ce43 Author: Oscar Antepara Date: Tue Jul 7 09:41:36 2020 -0700 Enabling 2D/3D with just one convection folder src/Make.incflo src/boundary_conditions/boundary_conditions.cpp src/convection/CMakeLists.txt src/convection/Godunov.H src/convection/MOL.H src/convection/Make.package src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_correct_small_cells.cpp src/convection/incflo_godunov_advection_2D.cpp src/convection/incflo_godunov_advection_3D.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict_2D.cpp src/convection/incflo_godunov_predict_3D.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H src/convection_2d/Make.package src/convection_2d/incflo_MAC_projection.cpp src/convection_2d/incflo_correct_small_cells.cpp src/convection_2d/incflo_godunov_plm.H src/convection_2d/incflo_godunov_plm.cpp src/convection_2d/incflo_godunov_ppm.cpp src/convection_3d/CMakeLists.txt src/convection_3d/Godunov.H src/convection_3d/MOL.H src/convection_3d/incflo_compute_advection_term.cpp src/convection_3d/incflo_correct_small_cells.cpp src/convection_3d/incflo_godunov_ppm.H src/convection_3d/incflo_godunov_ppm.cpp src/convection_3d/incflo_mol_fluxes.cpp src/convection_3d/incflo_mol_fluxes_eb.cpp src/convection_3d/incflo_mol_predict.cpp src/convection_3d/incflo_mol_predict_eb.cpp src/convection_3d/incflo_slopes_K.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp commit e1f22b09042dfad0a32e9ed315ab1d03361fa018 Author: Oscar Antepara Date: Thu Jul 2 18:00:37 2020 -0700 Incflo works 2d and 3d but with two different convection folders src/boundary_conditions/incflo_fillpatch.cpp src/convection_2d/incflo_MAC_projection.cpp src/convection_2d/incflo_godunov_advection.cpp src/convection_2d/incflo_godunov_plm.cpp src/convection_2d/incflo_godunov_ppm.cpp src/convection_2d/incflo_godunov_predict.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/prob/prob_bc.H src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp commit 3f00521867af3e7c4f5876e965bf075a9b43e81c Author: Michele Rosso Date: Thu Jul 2 17:11:44 2020 -0700 Godunov: fix BCs routines by following IAMR implentation + John's prescriptions src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit 5f7f927cb9b12f2fb0f27c7fe8e848a6b32d19c2 Author: Ann Almgren Date: Thu Jul 2 12:20:20 2020 -0700 Some clean-up and making sure we can pass through run-time options to multigrid solvers src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/incflo.H src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp commit 12d4e57c47c087c45e115fda7e2f8b5ed761c47c Author: Oscar Antepara Date: Thu Jul 2 11:02:16 2020 -0700 Final steps to enable 2d src/convection_2d/Godunov.H src/convection_2d/incflo_MAC_projection.cpp src/convection_2d/incflo_compute_advection_term.cpp src/convection_2d/incflo_godunov_advection.cpp src/convection_2d/incflo_godunov_ppm.cpp src/convection_2d/incflo_godunov_predict.cpp src/incflo_apply_predictor.cpp src/prob/prob_init_fluid.cpp test/inputs.2dgodunov_eb test_no_eb/inputs.2dgodunov commit c3b4ce43cd9aedb3965c91e00eede548784c1705 Author: Oscar Antepara Date: Wed Jul 1 09:54:05 2020 -0700 More changes for 2d src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.cpp src/incflo_compute_dt.cpp src/incflo_compute_forces.cpp src/prob/prob_bc.H src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/utilities/io.cpp test/inputs.2dgodunov_eb commit 759279e41af492c7ca0f73362cb37bab39da3f66 Author: Oscar Antepara Date: Tue Jun 30 17:23:11 2020 -0700 More steps for 2D src/boundary_conditions/boundary_conditions.cpp src/convection_2d/incflo_compute_advection_term.cpp src/convection_2d/incflo_godunov_plm.cpp src/convection_2d/incflo_godunov_predict.cpp src/convection_2d/incflo_mol_fluxes.cpp src/convection_2d/incflo_mol_fluxes_eb.cpp src/convection_2d/incflo_mol_predict.cpp src/convection_2d/incflo_mol_predict_eb.cpp src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cyl_tuscan.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/embedded_boundaries.cpp src/prob/prob_bc.H src/setup/set_background_pressure.cpp commit 3d2e5900f84f1e36297cc94c421bca654f40db27 Author: Oscar Antepara Date: Tue Jun 30 15:54:15 2020 -0700 First steps to have 2d incflo src/CMakeLists.txt src/Make.incflo src/convection_2d/CMakeLists.txt src/convection_2d/Godunov.H src/convection_2d/MOL.H src/convection_2d/Make.package src/convection_2d/incflo_MAC_projection.cpp src/convection_2d/incflo_compute_advection_term.cpp src/convection_2d/incflo_correct_small_cells.cpp src/convection_2d/incflo_godunov_advection.cpp src/convection_2d/incflo_godunov_plm.H src/convection_2d/incflo_godunov_plm.cpp src/convection_2d/incflo_godunov_ppm.H src/convection_2d/incflo_godunov_ppm.cpp src/convection_2d/incflo_godunov_predict.cpp src/convection_2d/incflo_mol_fluxes.cpp src/convection_2d/incflo_mol_fluxes_eb.cpp src/convection_2d/incflo_mol_predict.cpp src/convection_2d/incflo_mol_predict_eb.cpp src/convection_2d/incflo_slopes_K.H src/convection_3d/CMakeLists.txt src/convection_3d/Godunov.H src/convection_3d/MOL.H src/convection_3d/Make.package src/convection_3d/incflo_MAC_projection.cpp src/convection_3d/incflo_compute_advection_term.cpp src/convection_3d/incflo_correct_small_cells.cpp src/convection_3d/incflo_godunov_advection.cpp src/convection_3d/incflo_godunov_plm.H src/convection_3d/incflo_godunov_plm.cpp src/convection_3d/incflo_godunov_ppm.H src/convection_3d/incflo_godunov_ppm.cpp src/convection_3d/incflo_godunov_predict.cpp src/convection_3d/incflo_mol_fluxes.cpp src/convection_3d/incflo_mol_fluxes_eb.cpp src/convection_3d/incflo_mol_predict.cpp src/convection_3d/incflo_mol_predict_eb.cpp src/convection_3d/incflo_slopes_K.H commit fa9d3d86a22dc8588749dcfdb444246f418ceefd Author: Ann Almgren Date: Mon Jun 29 15:30:57 2020 -0700 bottom_solver_type --> bottom_solver as input for diffusion solves src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/incflo.H commit 33f2c6230e69b0e46e523731b232003c7e710428 Author: Ann Almgren Date: Mon Jun 29 12:52:48 2020 -0700 We need to call the right routine for diffusing the velocity components separately src/diffusion/incflo_diffusion.cpp commit 020cba0f2a6d13e88eb5c8d2e8610dd80dd31846 Author: Ann Almgren Date: Tue Jun 23 13:59:50 2020 -0700 Fix the tracer diffusion src/diffusion/DiffusionScalarOp.cpp commit 4d6008e5c748fb5fd0fc2c3beccca14fbcba72f3 Author: Ann Almgren Date: Tue Jun 23 12:11:24 2020 -0700 Separate scalar apply/solve from velocty component apply/solve so we don't have cross-contamination of boundary conditions src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H commit 9b614631001a05952ceefbc2b7bd7e7e34177324 Author: Ann Almgren Date: Mon Jun 22 13:33:46 2020 -0700 Need to explicitly set the EB BC's for the component-by-component velocity diffusion solve to be homogeneous Dirichlet src/diffusion/DiffusionScalarOp.cpp commit 5884066eecbd9ac192f33c09f015cc9cfe42b2bc Author: Ann Almgren Date: Sun Jun 21 20:24:01 2020 -0700 Fix component bugs for diffusion of velocity components -- this now runs without errors but does not give the correct solution for incflo.use_tensor_solve = false src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H commit b49349a0ff71a485956b28106f2569dc71706793 Author: Ann Almgren Date: Sun Jun 21 19:11:27 2020 -0700 fix more typos in asserts src/diffusion/DiffusionScalarOp.cpp commit 71674c43dad0eac6315df69da597be9462da1032 Author: Ann Almgren Date: Sun Jun 21 19:06:31 2020 -0700 Fix typo in assertion src/diffusion/DiffusionScalarOp.cpp commit 1804fac14c6da31c324644f7e34174d0f6eaecee Merge: 558a5ab2 28ac73fc Author: Ann Almgren Date: Sun Jun 21 18:56:22 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 558a5ab21833cedcda68359ce858837ced42f005 Author: Ann Almgren Date: Sun Jun 21 18:55:47 2020 -0700 Add the option to diffuse the velocity components separately using a single-component operator rather than doing a tensor solve -- determined by flag use_tensor_solver which defaults to true. src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/setup/init.cpp commit 28ac73fc73bd9e080c58d4d8098fe1d9fb53bc9b Author: Ann Almgren Date: Sat Jun 20 18:43:06 2020 -0700 Prevent backflow when predicting face velocities with Godunov src/convection/incflo_godunov_predict.cpp commit 45e3ae9bce209d63c2932ad304fc2491b68bd625 Author: Ann Almgren Date: Sat Jun 20 16:42:39 2020 -0700 Merge fixes from mr/godunov-bug-fixes and distinguish between (extdir or hoextrap) -- i.e. value is on face not cell center -- and (extdir) which means impose ghost cell value src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp commit 6b46ce1b4fe29355dd98a6c3b2768fa10c4bebba Author: Michele Rosso Date: Fri Jun 19 17:24:18 2020 -0700 Godunov: remove locally defined small_vel (follow-up to commit ef7114cf30da091bde513ef) src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit 49a091e413025156f2c77c5afad1cd19318c96e9 Author: Michele Rosso Date: Fri Jun 19 17:03:18 2020 -0700 Godunov: add logic to prevent backflow src/convection/incflo_godunov_predict.cpp commit e87a98aeac2d57b113c064e376817e53ff12fb65 Author: Michele Rosso Date: Fri Jun 19 16:56:28 2020 -0700 Godunov: fix BCs at extdir boundary src/convection/incflo_godunov_plm.cpp commit e37876534f2a001836ed9416ab2a86eb45f46540 Author: cgilet Date: Tue Jun 9 21:35:09 2020 -0400 In mol::predict_vels_on_faces(), need to check for EB regular on the box grown by 2. src/convection/incflo_mol_predict.cpp commit ef7114cf30da091bde513ef4a58e9fa119d8e692 Author: Michele Rosso Date: Tue Jun 2 15:53:48 2020 -0700 Godunov: redefine constant small_vel. Define small_vel only once inside namepsace Godunov. Set small_vel to 1.e-8. src/convection/Godunov.H src/convection/incflo_godunov_advection.cpp commit 62dedaf5c403ba1cd5c81354be6eacc2efd74f00 Author: Michele Rosso Date: Tue Jun 2 15:29:29 2020 -0700 Godunov: fix bugs in slopes computations src/convection/incflo_slopes_K.H commit cdd0a076a93eb9ae796461d020193a60e0afe53a Author: cgilet Date: Fri May 22 11:20:38 2020 -0400 In compute_convection_term, need to check for EB regular on the box with 2 ghost cells. src/convection/incflo_compute_advection_term.cpp commit 948297ee9ff20e52ab8093a8209f5e6947be615b Merge: 09d6ec20 473caed6 Author: Weiqun Zhang Date: Thu May 21 23:39:07 2020 +0000 Merge branch 'development' into dpcpp Conflicts: src/prob/prob_init_fluid.cpp commit 473caed629a5835b1b9334db75fcc5d83b1b8334 Author: cgilet Date: Tue May 12 22:04:01 2020 -0400 For EB DiffusionScalarOp, specify location of BCoeffs as FaceCentroid src/diffusion/DiffusionScalarOp.cpp commit 37fe3d73e615fa2361469a673beb9ecfb768ea03 Author: Ann Almgren Date: Wed May 6 17:40:31 2020 -0700 1) separate out parm-parsing for scalar vs tensor diffusion 2) add run-time parameters to control number of smooths in diffusive solves src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-xx test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-yy test/benchmark.channel_cylinder-z test/benchmark.channel_cylinder-zz test/benchmark.channel_spherecube test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_halfplane_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian test/benchmark.tracer_adv_diff test/inputs.channel_sphere test_no_eb/GNUmakefile test_no_eb/benchmark.bouss_bubble_god test_no_eb/benchmark.bouss_bubble_mol test_no_eb/benchmark.bouss_bubble_plm test_no_eb/benchmark.double_shear_layer_x test_no_eb/benchmark.double_shear_layer_y test_no_eb/benchmark.double_shear_layer_z test_no_eb/benchmark.poiseuille_halfplane_newtonian_x test_no_eb/benchmark.poiseuille_halfplane_newtonian_y test_no_eb/benchmark.poiseuille_halfplane_newtonian_z test_no_eb/benchmark.poiseuille_plane_newtonian_x test_no_eb/benchmark.poiseuille_plane_newtonian_y test_no_eb/benchmark.poiseuille_plane_newtonian_z test_no_eb/benchmark.rayleigh_taylor test_no_eb/benchmark.slip_wall_test_x commit c12958c0acacb2efafc98db8899ce0ed002092ee Author: Ann Almgren Date: Wed May 6 14:22:15 2020 -0700 remove include of incflo_set_MAC_bcs.H src/convection/incflo_godunov_predict.cpp src/convection/incflo_mol_predict.cpp commit b8bcfe1a77f0b90ed675f78eaff05ecae89dc8bf Author: Ann Almgren Date: Wed May 6 14:09:50 2020 -0700 Remove incflo_MAC_bcs.* from the Make.package and CMakeLits.txt src/convection/CMakeLists.txt src/convection/Make.package commit 43db66176d77d29c0780d3e2d148f59f356a5f3a Author: Ann Almgren Date: Wed May 6 14:04:50 2020 -0700 Remove calls to set_mac_bcs ... that is actually handled in the predict routines already src/convection/incflo_MAC_bcs.H src/convection/incflo_MAC_bcs.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_mol_predict.cpp commit ce2c947e154f51c9e1678e5c02cea7aa33e343a3 Author: Ann Almgren Date: Mon May 4 10:34:49 2020 -0700 Re-enable plt_eta and plt_strainrate (though both default to off). This required separating out some exisitng functionality into level-by-level calls. src/derive/derive.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/rheology/incflo_rheology.cpp src/utilities/io.cpp commit 09d6ec206c42cc61b433a62baccc44e169e09a44 Author: Weiqun Zhang Date: Thu Apr 30 00:33:09 2020 +0000 new std:: -> amrex::Math:: src/convection/incflo_slopes_K.H commit dc79e75dbf5a6348a185961b1ba78caf4d69b175 Author: Weiqun Zhang Date: Wed Apr 29 23:24:58 2020 +0000 add std:: src/prob/prob_init_fluid.cpp commit cb0786f04e00b0f582950c983fb412540ad83094 Merge: 000b0c05 3384fb35 Author: Weiqun Zhang Date: Wed Apr 29 23:22:50 2020 +0000 Merge branch 'development' into dpcpp Conflicts: src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp src/incflo_compute_dt.cpp commit 3384fb354f7d50ec311ff9e446409dc7da183aa5 Author: Ann Almgren Date: Wed Apr 29 13:31:00 2020 -0700 Just adding lines in preparation for when we sent phi on centroid into solvers src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp commit ab90b5849eb13f25437d4be82ab4d45a56aac8aa Merge: be03cff8 101990e2 Author: Ann Almgren Date: Tue Apr 28 09:07:48 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit be03cff8ae8b7f6c283833d5643b272b717c39e9 Author: Ann Almgren Date: Tue Apr 28 08:49:56 2020 -0700 Oops -- mac_phi is on CellCenter not FaceCenter src/convection/incflo_MAC_projection.cpp commit 101990e24510776b525ef234f72b5d79a3ee860e Merge: bafab1ee f7555a1a Author: Michele Rosso Date: Mon Apr 27 21:40:14 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into mr/add-cmake-support commit bafab1eead7ddc2dca7333f66049c7ee591435f7 Author: Michele Rosso Date: Mon Apr 27 21:40:02 2020 -0700 CMake: fix variable to pass to amrex in superbuild mode CMakeLists.txt commit c1e5f36c6aa148a8d716c9b0e53bf41a7cfe1560 Author: Michele Rosso Date: Mon Apr 27 21:20:47 2020 -0700 CMake: add documentation on how to build with CMake Docs/sphinx_documentation/source/BuildingCMake.rst commit f7555a1a374d32782999acca26bfb23045a8037d Merge: 9c7113e6 692ff80d Author: Ann Almgren Date: Mon Apr 27 20:55:36 2020 -0700 Merge branch 'development' into amrex_pr_810 commit 41f630dc3f7d7c32821e7148d050b54414124154 Author: Michele Rosso Date: Mon Apr 27 20:07:46 2020 -0700 CMake: increase AMReX minimum version required (standalone mode only) CMakeLists.txt commit 1b7ec295f6afe675968d314e12ee83aeef15132f Author: Michele Rosso Date: Mon Apr 27 20:05:27 2020 -0700 CMake: build amrex with xSDK defaults in superbuild mode CMakeLists.txt commit 692ff80d169200ab4368d51a48a5e3ed75f76f6a Author: Ann Almgren Date: Mon Apr 27 17:06:04 2020 -0700 Remove unused "AverageDown" in incflo class src/incflo.H src/incflo.cpp commit e7f754131f5213e1bf3b3dadbe11ad66b0773872 Author: Michele Rosso Date: Mon Apr 27 16:42:37 2020 -0700 CMake: update convection/CMakelists.txt to reflect changes in development branch src/convection/CMakeLists.txt commit e0ae03b4ae6db79f16931635f54823e8276b56d5 Merge: 72eb07dd 85ea5cff Author: Michele Rosso Date: Mon Apr 27 16:30:59 2020 -0700 Merge remote-tracking branch 'origin/development' into mr/add-cmake-support commit 9c7113e69d04eb63e2d599817200060e818034b8 Merge: f8c211e7 85ea5cff Author: Ann Almgren Date: Mon Apr 27 08:35:47 2020 -0700 Merge branch 'development' into amrex_pr_810 commit 85ea5cff23042574bcc3dde47bcf034acf2f653b Author: Ann Almgren Date: Mon Apr 27 08:35:15 2020 -0700 Update to match change in amrex single_level_redistribute interface src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp commit f8c211e7d7e68ef74daceb35ad6dcc88115473f7 Author: Ann Almgren Date: Sun Apr 26 16:12:56 2020 -0700 These changes will be required when amrex PR 810 is merged into amrex development. src/convection/incflo_MAC_projection.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp commit 61ba93dbca9a065afffc6bc266bc283eb18b82b4 Author: Ann Almgren Date: Tue Apr 21 21:00:25 2020 -0700 Fix box indices in PLM advection. src/convection/incflo_godunov_advection.cpp commit 72eb07dd8ceea0af92bb67be2041680bd243b7d7 Author: Michele Rosso Date: Tue Apr 21 14:23:00 2020 -0700 CMake: setup CUDA before including AMReX directory (SUPERBUILD MODE) CMakeLists.txt commit e22128f4d8e59f0c54a9bfc13a255030cc47eab7 Author: Michele Rosso Date: Tue Apr 21 11:30:14 2020 -0700 CMake: add CUDA support CMakeLists.txt commit c6e5fda648d72bd74230b6ce1e58a912cad59224 Author: Michele Rosso Date: Tue Apr 21 11:29:42 2020 -0700 CMake: some modifications to the handling of AMReX CMakeLists.txt commit ebb8d0bedcb0a976362fbd9033c20e77a86b3042 Author: Michele Rosso Date: Tue Apr 21 11:08:35 2020 -0700 CMake: add superbuild option CMakeLists.txt commit 887d34f956d3f9a13a2a72e5402e0233b281a810 Author: Michele Rosso Date: Tue Apr 21 10:28:21 2020 -0700 CMake: update MReX build info capabilities CMakeLists.txt commit 2427fd9c393e46581571bcdd26d1ad68f9c313a2 Author: Ann Almgren Date: Mon Apr 20 18:21:35 2020 -0700 Make sure to test on hoextrap as well as ext_dir when deciding to use a special stencil that uses the boundary value as living at the face not a cell center src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H commit 0b55bbe4c0f324d7691fe92907a2975ab42e88a1 Author: Ann Almgren Date: Sun Apr 19 18:05:37 2020 -0700 Call compute_vel_forces within ComputeDt so we use the real forcing term, not an approximation (which used only gp0 and gravity) src/incflo_compute_dt.cpp commit dea073a865c85d9294a52c55b0048938d8bb5960 Author: Ann Almgren Date: Sun Apr 19 15:12:19 2020 -0700 Forgot to include a file in MOL.H src/convection/MOL.H commit 1e0b60829b646b23765a8fd1c1dc6ebe57c565a4 Author: Ann Almgren Date: Sun Apr 19 14:52:56 2020 -0700 Create MOL class and move MOL-files only out of incflo and into MOL. src/convection/MOL.H src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_slopes_K.H src/incflo.H commit 69fd74097f31c4e8f7e65370a6806ca8688770da Author: Ann Almgren Date: Sun Apr 19 12:47:27 2020 -0700 Fix bc's for MOL so they use the "mathematical" ones (e.g. ext_dir) rather than the "physical" ones (e.g. inflow) src/convection/Godunov.H src/convection/incflo_compute_advection_term.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/incflo.H commit 797e0dda2c91218e405337438b65992380e20e51 Author: Ann Almgren Date: Sat Apr 18 20:31:14 2020 -0700 Interpolate the coefficients from cell centroids to face centroids for the MAC projection. src/convection/incflo_MAC_projection.cpp commit 7ed1c07d299913dbbab0126716099bb0bb0dfb7a Author: Ann Almgren Date: Sat Apr 18 20:18:53 2020 -0700 Add a Crank-Nicolson regression test test/benchmark.tracer_adv_diff_cn commit 7b288566830cd248fbc48d1a18662dab6c9e4634 Author: Ann Almgren Date: Sat Apr 18 20:06:04 2020 -0700 Add test using Godunov PLM (as opposed to Godunov PPM) test_no_eb/benchmark.bouss_bubble_plm commit 16670546b0b6338e76bb60f883f1348b8ee5e21e Author: Ann Almgren Date: Sat Apr 18 18:23:21 2020 -0700 remove print statement src/convection/incflo_godunov_advection.cpp commit 5fd9be1dc381bac1093808a7619a6f765fd4ee3c Author: Ann Almgren Date: Sat Apr 18 18:22:33 2020 -0700 We can now run PLM with 3 ghost cells by using the correct boxes on PLM loops src/convection/Godunov.H src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_predict.cpp commit 54629360c306712c01f130207273314bfce03749 Author: Ann Almgren Date: Sat Apr 18 18:21:37 2020 -0700 Fix indexing bug in slopes near boundaries for Godunov PLM only src/convection/incflo_convection_K.H commit b819f26205eb3a7bf35585b69d238a2ffd20ecfd Author: Ann Almgren Date: Sat Apr 18 17:10:02 2020 -0700 get this to compile with EB again src/incflo.H commit c9d4fe2889af7472472f8ba819b9c88b82e260bf Author: Ann Almgren Date: Sat Apr 18 16:50:31 2020 -0700 slight clean-up of godunov stuff. Note that this does fix a problem with the bc's for PLM when using slip wall src/convection/Godunov.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp commit 4f2262153d61b22811914894cdd8b3d28c44642b Author: Ann Almgren Date: Sat Apr 18 16:38:13 2020 -0700 Move Godunov files into a separate class (Godunov)...no change in results expected src/convection/Godunov.H src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp commit 6d7cff6fc572fab81a24fe45aa3304f8ba32b4c8 Author: Ann Almgren Date: Sat Apr 18 11:32:22 2020 -0700 remove unused rho_nph ... src/incflo_apply_corrector.cpp commit f813e9632243c3730489d5b5c14042673154affa Author: Ann Almgren Date: Sat Apr 18 11:29:02 2020 -0700 We were missing a factor of 0.5 in the C-N velocity diffusion case ... src/incflo_apply_corrector.cpp commit 85a0470cc96a5f630fca41036af5245811b107d7 Author: Michele Rosso Date: Wed Apr 15 10:23:59 2020 -0700 CMake: bare bone initial implementation CMakeLists.txt src/CMakeLists.txt src/boundary_conditions/CMakeLists.txt src/convection/CMakeLists.txt src/derive/CMakeLists.txt src/diffusion/CMakeLists.txt src/embedded_boundaries/CMakeLists.txt src/prob/CMakeLists.txt src/projection/CMakeLists.txt src/rheology/CMakeLists.txt src/setup/CMakeLists.txt src/utilities/CMakeLists.txt commit c033d412d3bc46684fa7fdce9f6745c3e5fd1667 Author: Michele Rosso Date: Tue Apr 14 17:40:34 2020 -0700 GNUMake: add forgotten header file src/embedded_boundaries/Make.package commit 84c441eb46012038feae6845b85d87b533c4da5b Merge: 42847f38 887ac894 Author: Ann Almgren Date: Sun Apr 12 12:26:49 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 42847f38d838c23ceac5820148a9cb5795d4f574 Author: Ann Almgren Date: Sun Apr 12 12:25:32 2020 -0700 fix the construction of gp0 -- we had the sign backwards src/incflo.cpp src/setup/set_background_pressure.cpp commit 000b0c05bb8d8bee4033db42a3921031fac2c2d9 Author: Weiqun Zhang Date: Sun Mar 29 17:52:07 2020 +0000 Revert "Revert "some cmath functions are fixed now" because dpc++ beta4 broke" This reverts commit 2bdf926439b0acf509fe44fe296d7949d586bc0a. src/derive/derive.cpp src/derive/derive_K.H src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp commit 2bdf926439b0acf509fe44fe296d7949d586bc0a Author: Weiqun Zhang Date: Sun Mar 29 02:06:03 2020 +0000 Revert "some cmath functions are fixed now" because dpc++ beta4 broke them again. This reverts commit 21ca2c7a07861ab8220486a5929ef6f2ce1a4162. src/derive/derive.cpp src/derive/derive_K.H src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp commit 887ac894c2e4d552361e6f74e7bb249c77531f09 Author: cgilet Date: Sat Mar 28 21:41:38 2020 -0400 Remove unused variable src/convection/incflo_compute_advection_term.cpp commit 62aeaf74d8a2206e5b2cd243347886aa4885476b Author: Roberto Porcu Date: Fri Mar 27 18:31:01 2020 -0400 Fixed bugs in previous commit src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp commit 0d6beedb59bac6bb39509ffdb08f00e78ac8070a Author: Roberto Porcu Date: Fri Mar 27 18:11:22 2020 -0400 Push same changes made in MFIX-Exa src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit f3257798ae31578ed3395fca516b721fe38b2556 Author: Ann Almgren Date: Fri Mar 27 09:08:08 2020 -0700 make bool tag_region static src/incflo_tagging.cpp commit 05c868059bf659425b5bbee86a1a97d30b55fbd5 Author: Ann Almgren Date: Sun Mar 22 17:47:40 2020 -0700 update Docs/sphinx_documentation/source/FluidTimeDiscretization.rst Docs/sphinx_documentation/source/TimeStep.rst commit 1ab910391f4946cdc7a5b4d50d41717c5739c9ec Author: Ann Almgren Date: Sun Mar 22 17:39:33 2020 -0700 Add CUDA to gmake Docs/sphinx_documentation/source/BuildingGMake.rst commit 3a9e654a1116e97e0a3f60d961296f4adcd54f8a Author: Ann Almgren Date: Sun Mar 22 17:31:35 2020 -0700 Remove reference to SIMPLE Docs/sphinx_documentation/source/BuildingGMake.rst commit 9b519ad4987f3a1830e288a9d4ca5254a81b9345 Author: Ann Almgren Date: Sun Mar 22 17:29:07 2020 -0700 get this to build with USE_OMP=TRUE again src/diffusion/DiffusionTensorOp.cpp src/rheology/incflo_rheology.cpp commit cc37627ec13895dd761075d1c87b3065212cebb4 Author: Ann Almgren Date: Sun Mar 22 17:21:41 2020 -0700 1) remove plotting of stress (we weren't using it) 2) add amr.plotfile_on_restart flag src/incflo.H src/incflo.cpp src/setup/init.cpp src/utilities/io.cpp commit 7363a43acb0845772b2d2e6427da8559ef39960d Author: Ann Almgren Date: Sun Mar 22 17:06:44 2020 -0700 updating ... Docs/sphinx_documentation/source/BuildingCMake.rst Docs/sphinx_documentation/source/BuildingMacVelocities.rst Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/FluidTimeStep.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/InputsPlotFiles.rst Docs/sphinx_documentation/source/Structure.rst Docs/sphinx_documentation/source/index.rst summit_script.sh commit b467cf813967408c9bb0466465704c346081f753 Author: Ann Almgren Date: Sun Mar 22 15:56:06 2020 -0700 more mfix-->incflo ... 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Docs/sphinx_documentation/source/BuildingCMake.rst Docs/sphinx_documentation/source/CITests.rst Docs/sphinx_documentation/source/FluidEquations.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/InputsDrag.rst Docs/sphinx_documentation/source/InputsInitialization.rst Docs/sphinx_documentation/source/InputsPlotFiles.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst Docs/sphinx_documentation/source/InputsTimeStepping.rst Docs/sphinx_documentation/source/InputsVerbosity.rst Docs/sphinx_documentation/source/NightlyTests.rst Docs/sphinx_documentation/source/RegressionTesting.rst Docs/sphinx_documentation/source/RunningTestSuite.rst Docs/sphinx_documentation/source/index.rst commit 1493c24583c313d17d9fed46f99f03a99a098b08 Author: Ann Almgren Date: Sun Mar 22 15:10:36 2020 -0700 update mfix-->incflo for gmake Docs/sphinx_documentation/source/BuildingGMake.rst commit 88b4b4428b19663b811b3abbf2f6a6ca4396ee47 Author: atmyers Date: Sun Mar 22 14:56:28 2020 -0700 path build_and_deploy.sh commit af05861e4c3cdd57d7f1e5055e5c15d5f88b5ebc Author: atmyers Date: Sun Mar 22 14:49:37 2020 -0700 deploy to gh-pages build_and_deploy.sh commit 802faa56f9a1f26882211abe747ca6bddb29ae62 Author: atmyers Date: Sun Mar 22 14:26:25 2020 -0700 maybe it will work if I do this in .travis.yml instead of build_and_deploy.sh .travis.yml build_and_deploy.sh commit 2f5f9bad355c6d724717a220550d5f76f201c124 Author: atmyers Date: Sun Mar 22 14:19:53 2020 -0700 still need to change permissions and add ssh key build_and_deploy.sh commit 0e1a3a6cadaeb5549e0fc6cbaf3a233edfbadb8d Author: atmyers Date: Sun Mar 22 14:17:11 2020 -0700 trying again with the encrypted file deploy_rsa.enc commit 326fb010cf866eb9174e77dcf80e47329752efa0 Author: atmyers Date: Sun Mar 22 14:03:30 2020 -0700 adding encrypted deploy jey .travis.yml build_and_deploy.sh deploy_key.enc deploy_rsa.enc commit bbfcc185ecfd16a2ba8fd46490ed4dc46be1364c Merge: 7ea17e9d d5432b24 Author: atmyers Date: Sun Mar 22 13:05:04 2020 -0700 Merge branch 'development' of github.com:AMReX-Codes/incflo into development commit 7ea17e9db71176cc6891589edeea689b0c81a654 Author: atmyers Date: Sun Mar 22 13:04:51 2020 -0700 amrex -> incflo Docs/sphinx_documentation/source/conf.py commit d5432b24e6a890a4f8f8f8012028c8e743b48335 Author: Ann Almgren Date: Sun Mar 22 12:57:57 2020 -0700 Replace amrex .rst files by mfix.rst files as start to incflo documentation Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst Docs/sphinx_documentation/source/AMReX_Profiling_Tools_Chapter.rst Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv1.png Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv2.png Docs/sphinx_documentation/source/AmrCore/figs/Adv3.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv3.png 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src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionTensorOp.H src/incflo.H src/projection/incflo_apply_nodal_projection.cpp commit 1e6454164c32e7b8a6dabd9c4ff468cc12ac1d32 Author: Ann Almgren Date: Sat Mar 21 18:39:34 2020 -0700 replace two by 2.0_rt src/incflo_compute_dt.cpp commit 35de3bf348b74c98db0924e5590c004166a4b156 Author: Ann Almgren Date: Sat Mar 21 15:00:58 2020 -0700 This now compiles with single precision src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp commit 0b8f5bdc6f79437699b7714b0a2bb2124a9f59f8 Author: Ann Almgren Date: Sat Mar 21 14:07:31 2020 -0700 fix typo src/incflo_apply_corrector.cpp commit f8b41608997faf7627047aca790de8168894c131 Author: Ann Almgren Date: Sat Mar 21 14:04:29 2020 -0700 need to fillpatch density before viscous solve src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp test_no_eb/benchmark.rayleigh_taylor commit 83fdb0105a43922e1f9f5939dc85f3d5c96832c6 Author: Ann Almgren Date: Sat Mar 21 13:34:47 2020 -0700 Add tracer to the RT problem src/prob/prob_init_fluid.cpp commit 598d07c9f97959ae0db1ee0a70be2eaef4098f31 Author: Ann Almgren Date: Wed Mar 18 13:19:26 2020 -0700 Protect the vanLeer slopes against tiny eps vs -tiny eps ... this makes it somewhat more robust src/convection/incflo_godunov_ppm.H commit 8a3b6322d416a69ceb1073f8d1924f4dbbbd5cfa Author: Ann Almgren Date: Tue Mar 17 18:06:08 2020 -0700 use q(i,j,k,n) instead of q(i,j,k) in 4th order slopes src/convection/incflo_convection_K.H commit 8ac4cf2b06839d83693ad79ad87b862c38e79cfe Author: Ann Almgren Date: Tue Mar 17 14:36:45 2020 -0700 Make sure to use (i,j,k,n) instead of (i,j,k) when indexing the tracer array src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp commit e4d1d4386e08e5c2f3fa6ee42cfd93d61da930dc Author: Ann Almgren Date: Sun Mar 15 16:42:05 2020 -0700 Adding the ability to tag at level 0 in a region specified by low and high values in physical space src/incflo.H src/incflo_tagging.cpp commit c37188e448654ffffc3617cc27018d1775abe7df Author: Ann Almgren Date: Sun Mar 15 15:28:55 2020 -0700 Use the density that is passed in, not the new state density src/projection/incflo_apply_nodal_projection.cpp commit c2ea1ad4bea54ea8153a7809d36825e45fe6c0f4 Author: Ann Almgren Date: Sun Mar 15 15:26:06 2020 -0700 need to test on m_probtype *outside* the kernel call src/prob/prob_init_fluid.cpp commit 29a6ca2e47c80fa3fc8eba479c3bf6fc2461a356 Author: Ann Almgren Date: Sun Mar 15 15:20:58 2020 -0700 "denisty" --> "density" src/prob/incflo_prob_I.H commit afee8567213152d096d57930776268c66746841c Author: Ann Almgren Date: Sun Mar 15 13:25:10 2020 -0700 Add a tracer to the non-EB double_shear_layer test src/prob/prob_init_fluid.cpp commit 1d9f4250ccd6c955ea05e2a0d4b91e1fb8366350 Author: Ann Almgren Date: Sun Mar 15 13:03:19 2020 -0700 Make sure that the tracer advects identically if rho is different constant value src/diffusion/DiffusionScalarOp.cpp src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp commit 2681290ceb41ba382fa2b733c459cb91cbfd695b Author: Ann Almgren Date: Sun Mar 15 10:54:41 2020 -0700 Update flags in the benchmark files to use bool (not ints) for advect_tracer and constant_density test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-xx test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-yy test/benchmark.channel_cylinder-z test/benchmark.channel_cylinder-zz test/benchmark.tracer_adv_diff test/benchmark.tracer_advection test/benchmark.tuscan commit b1ec2dedd11b904b004f27ff9664b7b3dd217a8d Author: Ann Almgren Date: Sun Mar 15 10:01:33 2020 -0700 Make sure Godunov updates (rho * tracer) instead of (tracer) since we want to do the update conservatively. src/convection/incflo_compute_advection_term.cpp commit 8dd126203b87015cf97eddd2e0ee5cb8d229570a Author: Ann Almgren Date: Sun Mar 15 08:55:29 2020 -0700 Move scalar diffusion before computation of velocity forcing term. src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp commit 76a291c7614b94ed0a6c359cb75fed84cf0a6f65 Author: Ann Almgren Date: Sat Mar 14 20:01:04 2020 -0700 Add Boussinesq bubble tests for regression testing -- one Godunov and one MOL test_no_eb/benchmark.bouss_bubble_god test_no_eb/benchmark.bouss_bubble_mol commit 1c6ffe4e50e9768f0aaf37ffd91df9cf1ea6c968 Author: Ann Almgren Date: Sat Mar 14 19:41:14 2020 -0700 use time-centered density and tracer in computing the velocity forcing terms -- this should change the answer for Boussinesq flows src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/incflo_compute_forces.cpp src/utilities/io.cpp commit 76f742d2ac52d662d34950503b1e3070ce64bf2b Author: Ann Almgren Date: Sat Mar 14 18:44:41 2020 -0700 Separate tracer update from velocity update src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/setup/incflo_arrays.cpp commit 29a79dad44edb62f54c93b0247db3f6431e7684f Author: Ann Almgren Date: Sat Mar 14 16:49:55 2020 -0700 Part of migration to getting all terms at the right time level src/incflo.H src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp commit 4b57d04faaafd41451c042940d5ce6bf50a193e7 Author: Ann Almgren Date: Fri Mar 13 14:10:04 2020 -0700 1) split predictor and corrector out into separate files 2) rename m_ppm --> m_godunov_ppm 3) rename m_use_forces_in_trans --> m_goduonv_use_forces_in_trans 4) add new flag m_godunov_include_diff_in_forcing -- this one is not being used yet 5) remove time variable from calling sequence of diffusion/viscous calls src/Make.package src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_predict.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/incflo.H src/incflo_advance.cpp src/incflo_apply_corrector.cpp src/incflo_apply_predictor.cpp src/main.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp commit 5b683a087eac357d70e77aea95a7ab5b6d1221d0 Author: Ann Almgren Date: Fri Mar 13 11:40:26 2020 -0700 Make plt_forcing default to 0 not 1 src/incflo.H commit 75099d6d68ebf16cfecc6afd153bfe25543b7621 Author: Ann Almgren Date: Fri Mar 13 09:27:22 2020 -0700 Need to let BL_NO_FORT be FALSE so we can use amrex/Src/EB/writeMyEBSurface test/GNUmakefile commit 8cba31c554915a3a63f616fc18a1c542e6db936d Author: Ann Almgren Date: Thu Mar 12 13:32:06 2020 -0700 1) Separate the compute_forces routines into compute_vel_forces and compute_tra_forces 2) Move these into a separate file: incflo_compute_forces.cpp 3) Add the option to include the forcing terms in the plotfile -- to do so set amr.plt_forcing = 1 to the inputs file 4) Added a new geometry which is two pipes of different diameters attached end to end -- it's "eb_cyl_tuscan" src/Make.package src/embedded_boundaries/Make.package src/embedded_boundaries/eb_cyl_tuscan.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_compute_forces.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit ae7fead7953c0d6e928333fce17a517d50fff6f7 Author: jbb Date: Wed Mar 11 11:21:42 2020 -0700 put in fourth order slopes for plm. at present it's only option src/convection/incflo_convection_K.H src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp commit 3306c00c501af0ab84bef1063138753115882d2c Author: Ann Almgren Date: Tue Mar 10 18:45:56 2020 -0700 fix boundary conditions at hi sides. This commit passes the x/y/z lo/hi symmetry tests for the Boussinesq bubble using plm. src/convection/incflo_godunov_plm.H commit 5848de629082497c7b2a6d4ef15dfb47647a55b8 Author: Ann Almgren Date: Tue Mar 10 18:24:45 2020 -0700 remove commented out line src/convection/incflo_godunov_predict.cpp commit 7695ad0856e058d36cb15f9af4db5bfdeedb0404 Author: Ann Almgren Date: Tue Mar 10 18:24:09 2020 -0700 fix typo in z-part of plm src/convection/incflo_godunov_plm.H commit f3679e0ca44c21101523cf9f780f55ab9bff2ce8 Author: Ann Almgren Date: Tue Mar 10 18:21:15 2020 -0700 fix sign error in plm src/convection/incflo_godunov_plm.H commit 73594344e8355d987b00bd28674a5d72f07db293 Merge: 1e69da43 64c8dccf Author: jbb Date: Tue Mar 10 17:42:06 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 64c8dccf2e7fa96b8125e3042ca77543787d589f Author: Ann Almgren Date: Tue Mar 10 17:16:21 2020 -0700 More cleanup -- removing restrictions which were wrong when periodic. This commit retains the full x/y/z lo/hi symmetry for the Boussinesq bubble cases. src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit 7ac3fda41cc6a1b12c5e155cdbd7cbb8a33463fd Author: Ann Almgren Date: Tue Mar 10 16:51:07 2020 -0700 Combine the trans_bc_lo and trans_bc_hi routines into trans_bc routines src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp commit b77cc1cf42c8e12fce88d4cb26e3f1f4ef7ba7c1 Author: Ann Almgren Date: Tue Mar 10 16:32:44 2020 -0700 Change in the transverse bc -- instead of doing it the way it was in IAMR we do something simpler which preserves the right symmetries. src/convection/incflo_godunov_ppm.H commit 1e69da4390de38f66dce6971b1eb41599973d196 Merge: 9e91468e d918b141 Author: jbb Date: Tue Mar 10 12:33:57 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 9e91468e49384697a01a948d42689a8e9e3c5e57 Author: jbb Date: Tue Mar 10 12:33:39 2020 -0700 made plm do all components src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H commit d918b14131f43029140ffbe8834c253181ee1023 Author: Ann Almgren Date: Tue Mar 10 12:04:33 2020 -0700 catch a few more typos ... src/convection/incflo_godunov_ppm.H commit 97fc27ac0eaf7ebb4db758858758366fe5ce3a31 Author: Ann Almgren Date: Tue Mar 10 11:48:51 2020 -0700 fix bug in sedge1 vs sedge2 typos src/convection/incflo_godunov_ppm.H commit c617fafafb58165590ee7bc87e7e03e962649d8c Author: Ann Almgren Date: Tue Mar 10 11:16:22 2020 -0700 fix setting of bc's -- we were setting tracer where we should have been setting density src/boundary_conditions/boundary_conditions.cpp commit 599e159226c3e8e3aca7e4ff04fb4edf2019720d Author: Ann Almgren Date: Tue Mar 10 10:29:20 2020 -0700 just formatting src/convection/incflo_godunov_ppm.H commit c00aa810abec5239f20d34559866ab11cba79bee Author: Ann Almgren Date: Mon Mar 9 19:40:39 2020 -0700 1) Add Boussinesq bubble problem in x/y/z directions 2) Fix Godunov PPM to the point that it gives the correct symmetries when we run Boussinesq in x-/y-/z-directions src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp src/setup/set_background_pressure.cpp commit a244395c72e850adbe12f205aca518c670d015ab Author: Ann Almgren Date: Thu Mar 5 19:48:56 2020 -0800 Initialize old density as well as new density so that we don't have uninitialized values in the ghost cells. src/prob/prob_init_fluid.cpp commit 5d9bee5704d0dd87eade4e314c110a690e4aacaf Author: Weiqun Zhang Date: Wed Mar 4 09:10:59 2020 -0800 fix for gpu src/convection/incflo_godunov_plm.H src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict_eb.cpp commit f167f4cecffb076190f018ee44a0d37819b1ffc9 Author: Weiqun Zhang Date: Wed Mar 4 08:49:49 2020 -0800 get around gcc bug src/convection/incflo_mol_predict_eb.cpp commit ba22ec8a047d28e5f261968bc836f30d07b8cced Author: Ann Almgren Date: Tue Mar 3 20:35:11 2020 -0800 a lot of clean-up and fix one major oops which caused the asymmetry src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp commit 5ab60a7da93d3e1eae2323721ea6415f909623dc Author: Ann Almgren Date: Tue Mar 3 16:10:55 2020 -0800 This one actually compiles src/boundary_conditions/boundary_conditions.cpp commit a771dd6255154b92e5e8ac3fce10b6afdc4a56bd Author: Ann Almgren Date: Tue Mar 3 16:10:01 2020 -0800 Making scalars be hoextrap not foextrap at slip walls. src/boundary_conditions/boundary_conditions.cpp commit cb0cc02ebc2b0f73a9379c0273875552846005c8 Author: Ann Almgren Date: Tue Mar 3 15:52:30 2020 -0800 1) replace hard-wired 1e-6 by "small_vel" set to 1e-10 2) use conservative vs convective differencing instead of just convective src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H commit 161f164943c98c89a0f51505b4910bb0f6e4b1b3 Author: Ann Almgren Date: Tue Mar 3 14:24:29 2020 -0800 Use small_vel = 1e-10 instead of eps = 1e-6 in order to be consistent with MOL. src/convection/incflo_godunov_ppm.H commit 2822b866cdc3037d742b7eaf14e84dbbb5eea3a4 Author: Ann Almgren Date: Tue Mar 3 14:23:28 2020 -0800 Use small_vel = 1e-10 instead of eps = 1e-6 in order to be consistent with MOL. src/convection/incflo_godunov_predict.cpp commit 9a295582f2a9ea93be95dea4def535f52b15f037 Author: Ann Almgren Date: Sun Mar 1 18:30:45 2020 -0800 Trying to get Godunov PLM working but it's not right yet -- however this compiles and runs -- flags that control are "incflo.use_godunov = true/false" and "incflo.use_ppm = true/false" -- note Godunov only relevant for no EB src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_plm.H src/convection/incflo_godunov_plm.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_mol_fluxes.cpp src/convection/incflo_mol_fluxes_eb.cpp src/convection/incflo_mol_predict.cpp src/convection/incflo_mol_predict_eb.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp test_no_eb/benchmark.slip_wall_test_x commit 392dd4d0bb977d633cff8a3075b2a1bf87f64539 Author: Ann Almgren Date: Mon Feb 24 12:46:03 2020 -0800 Array --> GpuArray src/convection/incflo_convection_K.H commit 2c284ea9e0da548b77af3574a860c8c1f268be7b Author: Ann Almgren Date: Mon Feb 24 12:40:26 2020 -0800 Oops -- forgot to uncomment some lines src/convection/incflo_compute_eb_fluxes.cpp commit 716d897c37d085018bff7290002b41440689391d Author: Ann Almgren Date: Sun Feb 23 10:18:06 2020 -0800 Add a few tests to capture different orientations test/benchmark.channel_cylinder-xx test/benchmark.channel_cylinder-yy test/benchmark.channel_cylinder-zz commit 00f040e6bb9dd750d38d6f0977bac2a3a793b287 Author: Ann Almgren Date: Sun Feb 23 10:08:33 2020 -0800 Make the inflow velocities consistent for probtype = 31*, 32*, 33* src/prob/prob_bc.H commit 96d079c4921f95930dcc172ce81d5560029041c8 Author: Ann Almgren Date: Sun Feb 23 09:29:48 2020 -0800 removed commented out lines src/convection/incflo_compute_advection_term.cpp commit dcab704a737d3b7113a801bef255d1f34139ab61 Author: Ann Almgren Date: Sun Feb 23 09:22:24 2020 -0800 Add more problem types so that we can compare different orientations and boundry types src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp commit b4b2010b612efdb67c8411e26742609dc0725f6b Author: Ann Almgren Date: Sun Feb 23 09:18:34 2020 -0800 fix typo in testing on extdir and domain hi (domain_jhi instead of domain_ihi) src/convection/incflo_eb_convection_K.cpp commit 13358f60588900c402dc9ae128af88185846611a Author: Ann Almgren Date: Sat Feb 22 15:03:04 2020 -0800 Fix bc test src/convection/incflo_convection_K.H commit ff2151912ae406cc27cd0562a4e856134c0bb62a Merge: 87929bab ffe79395 Author: Ann Almgren Date: Fri Feb 21 13:50:57 2020 -0800 Merge branch 'least-sq' of https://github.com/AMReX-Codes/incflo into least-sq commit ffe79395045b3903f124968db70c9d0df42ee08a Author: Weiqun Zhang Date: Fri Feb 21 13:53:23 2020 -0800 fix #if src/convection/incflo_convection_K.H commit 87929bab3582f5a1c8ac76ff5dcbe09375df457a Merge: 6b1be893 6a717520 Author: Ann Almgren Date: Fri Feb 21 12:54:50 2020 -0800 Merge branch 'development' into least-sq commit 21ca2c7a07861ab8220486a5929ef6f2ce1a4162 Author: Weiqun Zhang Date: Thu Feb 20 17:35:20 2020 -0800 some cmath functions are fixed now src/derive/derive.cpp src/derive/derive_K.H src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp commit 6a717520575fc85c9019ca5ee712577649501aa8 Merge: b01f951e bfffd457 Author: WeiqunZhang Date: Tue Feb 18 17:16:53 2020 -0800 Merge pull request #37 from michaeljbrazell/mjb/nonEB_lap_fix nonEB Laplacian bug fix when using Godunov and advect tracer commit bfffd457afc7091a6bc8fc5290efc0135266dc19 Author: michael brazell Date: Tue Feb 18 15:58:35 2020 -0700 Thank you Weiqun for finding this bug, the boundary conditions are stored in tracer_comp not a_laps src/diffusion/DiffusionScalarOp.cpp commit 281f8820e91b9d8a597ed2124832103e2e543e22 Author: michael brazell Date: Mon Feb 17 14:40:25 2020 -0700 bug fix for nonEB when Godunov and advect tracer are true src/diffusion/DiffusionScalarOp.cpp commit 77f01e3ff3561c289a203602e3be3b5f1364e5a2 Author: Weiqun Zhang Date: Sun Feb 16 08:45:05 2020 -0800 amrex::Math src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp src/derive/derive.cpp src/derive/derive_K.H src/incflo.H src/incflo_compute_dt.cpp src/incflo_tagging.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_rheology.cpp commit bd7d0b082e59d7b307f4bfe1b9dc2e87d1cc1f70 Author: Weiqun Zhang Date: Fri Feb 14 19:25:34 2020 -0800 compile with dpcpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp src/incflo_compute_dt.cpp src/incflo_tagging.cpp src/prob/prob_init_fluid.cpp commit 6b1be893effdbdc51cdeb767153856122c84197e Merge: c95d9065 b01f951e Author: Ann Almgren Date: Mon Feb 10 09:06:45 2020 -0800 Merge branch 'development' into least-sq commit c95d906531c2f726eed8130dfe0b36309d69c788 Author: Ann Almgren Date: Mon Feb 10 09:06:19 2020 -0800 Array --> GpuArray src/convection/incflo_convection_K.H commit b01f951ef4a647d61a4cc17db16de1479b7927d4 Author: Weiqun Zhang Date: Mon Feb 10 08:38:26 2020 -0800 set m_nstep to 0 properly src/incflo.cpp src/setup/init.cpp commit 6f35e6c0539f555c91b71e75dcead7951c4c74d6 Author: Ann Almgren Date: Mon Feb 10 08:24:55 2020 -0800 This version uses the new "least-squares-slopes" to calculate the slopes both when we predict velocity and when we compute the fluxes. It captures EB effects and ext_dir effects separately, but when there is both EB and ext_dir, it will only capture the EB-ness (i.e. it will treat the ext_dir value as living on the cell centroid outside the domain, not on the face). This could be fixed in future. src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_eb_fluxes.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_eb_convection_K.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit 6ed8ed098d58d54e2a4c47ba0b568e13feb17aac Author: Ann Almgren Date: Sat Feb 8 15:17:18 2020 -0800 Add incflo_correct_small_cells ... to do this we needed to create the MAC velocities in incflo_advance, not in compute_advection_term ... src/convection/Make.package src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_correct_small_cells.cpp src/incflo.H src/incflo_advance.cpp commit 4bb6be8b553e2c61c17bf27c29d49336b05d1ead Author: Weiqun Zhang Date: Wed Feb 5 11:07:12 2020 -0800 fix comments test_no_eb/benchmark.double_shear_layer_x test_no_eb/benchmark.double_shear_layer_y test_no_eb/benchmark.double_shear_layer_z test_no_eb/benchmark.rayleigh_taylor commit fbbb2207edf0ac66edf6bb3e26f1293d2529cc20 Author: Ann Almgren Date: Wed Feb 5 09:24:10 2020 -0800 Let us set a constant inflow velocity without needing to specify a probtype src/prob/prob_bc.cpp commit a36bc09fa625921f1ccc6fcc03bebe64cdd6979f Author: Regression Tester Date: Wed Feb 5 07:55:41 2020 -0800 add missing header src/incflo_tagging.cpp commit 1897f2f0b531148b354aa148a3bb441866e91608 Author: Weiqun Zhang Date: Wed Feb 5 07:51:41 2020 -0800 around gcc bug src/incflo_tagging.cpp commit dd76fbc5404e53afb07a2db0116ab64d94b0ed0e Author: Weiqun Zhang Date: Tue Feb 4 19:19:49 2020 -0800 index bug in ppm src/convection/incflo_godunov_ppm.H test_no_eb/benchmark.rayleigh_taylor commit a4cbf9720767eb573877d099d9b433d02cc2d39c Author: Weiqun Zhang Date: Tue Feb 4 18:12:21 2020 -0800 make the Rayleigh-Taylor interface sharper src/prob/prob_init_fluid.cpp commit 5b92d33ebbf73203189892dd568622f0ad64d699 Author: Weiqun Zhang Date: Mon Feb 3 15:25:12 2020 -0800 regrid and Rayleigh-Taylor test src/Make.package src/boundary_conditions/incflo_fillpatch.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_regrid.cpp src/incflo_tagging.cpp src/prob/incflo_prob_I.H src/prob/prob_init_fluid.cpp test_no_eb/benchmark.rayleigh_taylor commit 5e76543ed0743af63e7f4f2c0abcf9ea8980777a Author: Weiqun Zhang Date: Mon Feb 3 09:40:54 2020 -0800 set BL_NO_FORT to TRUE test/GNUmakefile test_no_eb/GNUmakefile commit 2d1c40a6dba419c1c683ca062f6140380bf2f4a5 Author: Weiqun Zhang Date: Tue Jan 28 12:47:14 2020 -0800 no longer need to average down velocity after projection because of changes in amrex nodal projector src/projection/incflo_apply_nodal_projection.cpp commit b76e84f63531b330914788bc895018277202d3b5 Author: Weiqun Zhang Date: Mon Jan 27 18:59:04 2020 -0800 fillpatch forces src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/incflo.H src/incflo_advance.cpp src/prob/prob_bc.H commit 1ec3c3b330f25a3c5a28f46b184e9431043a6d42 Merge: a4bf5d68 012d6283 Author: WeiqunZhang Date: Mon Jan 27 11:54:10 2020 -0800 Merge pull request #36 from AMReX-Codes/cgilet_dev Update compute_convective_fluxes_eb() to work with general ncomp commit 012d6283ae5c437683378498847c8b2a7e9af933 Author: cgilet Date: Mon Jan 27 11:29:58 2020 -0800 Update compute_convective_fluxes_eb() to work with general ncomp src/convection/incflo_compute_fluxes.cpp commit a4bf5d683dd1cb7ab7752dd99f66349c9103ad22 Author: Ann Almgren Date: Sun Jan 26 11:29:24 2020 -0800 Set default value of vel_force to 1e20 just to prove to ourselves it's not actually used (but it needs to not be undefined) src/convection/incflo_MAC_projection.cpp src/incflo_advance.cpp commit 7edf56e7675d71dfe3e6eb85d63514ad28f6a75d Author: Ann Almgren Date: Sun Jan 26 07:58:06 2020 -0800 1) Print warning but keep going if running with godunov and not fully periodic - for now we are setting the forces to zero outside the domain, need to think if we want to do something different 2) Add benchmark.poiseuille_plane_newtonian_* and benchmark.poiseuille_halfplane_newtonian* in all three coordinate directions. src/incflo_advance.cpp test_no_eb/benchmark.poiseuille_halfplane_newtonian_x test_no_eb/benchmark.poiseuille_halfplane_newtonian_y test_no_eb/benchmark.poiseuille_halfplane_newtonian_z test_no_eb/benchmark.poiseuille_plane_newtonian_x test_no_eb/benchmark.poiseuille_plane_newtonian_y test_no_eb/benchmark.poiseuille_plane_newtonian_z commit 9d13e1e005464c2bbe096b20b59647a755857ad7 Merge: bf63bed3 9ba1b3ea Author: Weiqun Zhang Date: Sat Jan 25 20:32:33 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/incflo into development commit bf63bed364d9720a2f36236c7262754ca1af2c3a Author: Weiqun Zhang Date: Sat Jan 25 20:31:16 2020 -0800 use hoextrap for tangential velocity at slip wall src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp commit 9ba1b3eafb2d35422c91aa8ee0a7676954255277 Author: Ann Almgren Date: Sat Jan 25 20:23:10 2020 -0800 Only print MAC Projection if m_verbose > 1 (not > 0) src/convection/incflo_MAC_projection.cpp commit 605f1dfe23bc4165b640dd88dbad511d4ba93f54 Author: Weiqun Zhang Date: Sat Jan 25 19:52:31 2020 -0800 Fix fillpatch for velocity and tracers. Need to test each component separately for ext_dir. src/prob/prob_bc.H commit bdff91102dc487d3adea4ef401a3f0c02337e977 Author: Ann Almgren Date: Sat Jan 25 16:50:04 2020 -0800 We now set tensor bcs correctly for the case of slip walls. src/diffusion/incflo_diffusion.cpp commit db0a57d872297b10912c92a2adcf001cf3742af5 Author: Ann Almgren Date: Sat Jan 25 16:45:32 2020 -0800 When query-ing values of velocity at mass inflow, only use them if queryarr finds them src/boundary_conditions/boundary_conditions.cpp commit 301c8ac10eafa80724d98f820d440512433f841e Author: Ann Almgren Date: Sat Jan 25 15:29:28 2020 -0800 Add test case that uses slip-wall... test/benchmark.poiseuille_halfplane_newtonian commit 27f4db5282c979a60cca2494f8ffdb0015b57aa2 Author: Ann Almgren Date: Sat Jan 25 14:59:56 2020 -0800 Add slip wall as an option src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/diffusion/incflo_diffusion.cpp commit 2575e23a05b6f475495d67f2a94b04cdd39293bb Author: Ann Almgren Date: Sat Jan 25 13:49:33 2020 -0800 Set bc's for pressure in projection to be Neumann for slip_wall (as for no_slip_wall) src/projection/incflo_apply_nodal_projection.cpp commit eb614d2ef6c94d242b90374b5d4649d6c782a99e Author: Weiqun Zhang Date: Sat Jan 25 12:14:26 2020 -0800 set mac velocity bcs src/convection/Make.package src/convection/incflo_MAC_bcs.H src/convection/incflo_MAC_bcs.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_predict_vels_on_faces.cpp commit f9497d58ac8bf8730758db9484473ac92056a22c Author: Weiqun Zhang Date: Sat Jan 25 08:01:42 2020 -0800 add BC::slip_wall src/boundary_conditions/README.org src/boundary_conditions/boundary_conditions.cpp src/incflo.H commit 1aab110e147e82ee3b664608ca7c8bb4d2cdd545 Author: Weiqun Zhang Date: Sat Jan 25 06:59:37 2020 -0800 remove m_bc_location src/boundary_conditions/boundary_conditions.cpp src/incflo.H commit c3e9d4170e0e9386e2e2b45d87efb4d30c4d46e0 Author: Weiqun Zhang Date: Sat Jan 25 06:20:45 2020 -0800 update README README.md commit df8d155abd97bcfec19cd16c526cf742a0e57032 Author: Weiqun Zhang Date: Fri Jan 24 21:37:50 2020 -0800 use expm1 src/rheology/incflo_rheology.cpp commit a83ebe0a824e3592fa47fa59249bf90188a089c0 Author: Weiqun Zhang Date: Fri Jan 24 21:07:24 2020 -0800 Revert "Merge branch 'new_dev2' into new_dev" This reverts commit 8c2495137a8132dd9afbdb77f15c896be62674dc. src/rheology/incflo_rheology.cpp commit 67102394c738ce3ec88e00fde086443c86b42afd Author: Weiqun Zhang Date: Fri Jan 24 21:02:20 2020 -0800 minor cleanup src/incflo.cpp commit 8c2495137a8132dd9afbdb77f15c896be62674dc Author: Weiqun Zhang Date: Fri Jan 24 20:45:57 2020 -0800 Merge branch 'new_dev2' into new_dev src/rheology/incflo_rheology.cpp commit 34fb5be83809c9ab38880fc05c427ced5ea8a2a5 Author: Weiqun Zhang Date: Fri Jan 24 20:45:10 2020 -0800 simplification src/convection/incflo_godunov_predict.cpp commit 8118246524aef233a2cdf4429b0eefe3d853b127 Author: Weiqun Zhang Date: Fri Jan 24 20:31:41 2020 -0800 fix bug for non-Newtonian model src/diffusion/DiffusionTensorOp.cpp commit cae8b673a4d9ba13b13923d91da7b05720d7b4b2 Author: Weiqun Zhang Date: Fri Jan 24 19:32:32 2020 -0800 add new file src/derive/derive_K.H src/rheology/incflo_rheology.cpp commit 3aabb6849ebea4f3b7b15db7eaf3a093304f73be Author: Weiqun Zhang Date: Fri Jan 24 19:05:19 2020 -0800 non-Newtonian src/derive/Make.package src/incflo.H src/rheology/incflo_read_rheology_parameters.cpp src/rheology/incflo_rheology.cpp commit 3e357f5a0533bbc973ec2573ff1e78c47457a7b2 Author: Weiqun Zhang Date: Fri Jan 24 15:31:58 2020 -0800 fix up eta on domain faces src/diffusion/incflo_diffusion.cpp src/incflo.H commit c17d226d2bc0bd12dbfac8bde1c0342f6f1dd0a0 Author: Weiqun Zhang Date: Fri Jan 24 14:40:05 2020 -0800 support for variable diffusion coefficient src/convection/incflo_compute_advection_term.cpp src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_advance.cpp src/rheology/incflo_rheology.cpp commit 3d0368a7dfe111f7c00fc137170cfc104e405d10 Author: Weiqun Zhang Date: Fri Jan 24 12:52:15 2020 -0800 make force multifabs to be temporary src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/incflo_arrays.cpp commit 878f466adac66757e402b064164c10712fd4ee1f Author: Weiqun Zhang Date: Fri Jan 24 10:54:17 2020 -0800 fix a gpu bug src/convection/incflo_godunov_predict.cpp commit e0f2097c91e749cca8157652be243d4eb742b5e4 Author: Weiqun Zhang Date: Fri Jan 24 09:40:10 2020 -0800 let's not worry about minor optimization in InitialIterations src/setup/init.cpp commit c4f23c8e684d92ff844e81cad62f11b00bba0aaa Author: Weiqun Zhang Date: Thu Jan 23 20:48:22 2020 -0800 averagedown after projection src/projection/incflo_apply_nodal_projection.cpp commit 720ed5967d06a56f8c6fea3a3a7548e63c8e86ff Author: Weiqun Zhang Date: Wed Jan 22 20:11:18 2020 -0800 fillpatchtwolevels src/boundary_conditions/incflo_fillpatch.cpp commit 1a049393a21824be5c924ed897226415323a52ff Author: Weiqun Zhang Date: Wed Jan 22 16:27:16 2020 -0800 refine on cut cells src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo.cpp src/rheology/incflo_rheology.cpp commit 4b9408ddb6a6b130c3bebc2d889588058a9e36d2 Author: Weiqun Zhang Date: Wed Jan 22 15:59:49 2020 -0800 checkpoint and restart src/incflo.cpp src/utilities/io.cpp commit 042c7981bc6852f088ad7e8db270896fb9643814 Author: Weiqun Zhang Date: Wed Jan 22 14:31:19 2020 -0800 fix bug src/convection/incflo_convection_K.H commit 9af7bcb34f2c7df3f360edd1f9cff36f329ab202 Author: Weiqun Zhang Date: Wed Jan 22 12:52:20 2020 -0800 fix inflow for probtype 31 and 33 src/prob/prob_bc.H commit 530e39b8bb17e31c6672c25e358720aa691a53b7 Author: Weiqun Zhang Date: Wed Jan 22 11:56:40 2020 -0800 fix sign of gp0 src/setup/set_background_pressure.cpp commit 3dae8ff6113a634ab2f294dc682fe350a528dbd7 Author: Weiqun Zhang Date: Wed Jan 22 10:46:12 2020 -0800 fix src/utilities/io.cpp commit cc62dc23584be29daa411929c67843bfda2be2e0 Author: Weiqun Zhang Date: Wed Jan 22 10:42:46 2020 -0800 zero out covered cells in plotfile src/utilities/io.cpp commit be9e5f97a34e7b3d3192358eddf2834b57015e2b Author: Weiqun Zhang Date: Wed Jan 22 10:03:32 2020 -0800 fix bug src/convection/incflo_compute_advection_term.cpp commit 20a6453a3dd671a4e61afc0deb0bc4d84064e286 Author: Weiqun Zhang Date: Wed Jan 22 09:58:00 2020 -0800 fix probtype test src/prob/prob_init_fluid.cpp commit 75c346cc0f063933aef527e436a24cc3293b2ce8 Author: Weiqun Zhang Date: Wed Jan 22 09:21:51 2020 -0800 new file src/prob/incflo_prob_I.H commit 6525fd49b2b9b4dc0d690d4bf4092d97fe26ef8a Author: Weiqun Zhang Date: Wed Jan 22 09:05:59 2020 -0800 more probtypes src/incflo.H src/prob/Make.package src/prob/prob_bc.H src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp commit 1461465692685e404a74f4889bf16e1b898ce721 Author: Weiqun Zhang Date: Tue Jan 21 21:14:17 2020 -0800 probtype 0 src/prob/prob_init_fluid.cpp commit cd2c8d4e56bac33d65ab964d870590dbd1488021 Author: Weiqun Zhang Date: Tue Jan 21 20:47:09 2020 -0800 update message src/embedded_boundaries/embedded_boundaries.cpp commit eada579d0982539a721db87b3714abf104a549a3 Author: Weiqun Zhang Date: Tue Jan 21 20:16:59 2020 -0800 taylor green src/incflo.H src/prob/prob_init_fluid.cpp commit c40d9d0f1ffb701281cc81548c378e2d4e54fd8e Author: Weiqun Zhang Date: Tue Jan 21 16:20:39 2020 -0800 trying to help gcc src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.cpp commit 4f483cbc045130cd2b900d55d72df6256d055ec2 Author: Weiqun Zhang Date: Tue Jan 21 15:54:08 2020 -0800 trying to help gcc src/convection/incflo_compute_fluxes.cpp src/derive/derive.cpp commit 8f2cb1d07a91ba0291a8c7008d407fd30321c336 Author: Weiqun Zhang Date: Tue Jan 21 15:29:24 2020 -0800 plotfile and computevorticity src/derive/derive.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/init.cpp src/utilities/io.cpp commit 9195a95fe988848f2392a250d90c7471894acbaf Author: Weiqun Zhang Date: Tue Jan 21 13:30:23 2020 -0800 godunov: at the end of first step src/incflo.H src/incflo_advance.cpp src/setup/init.cpp commit 8e49abadb2fd1e10aa62182494d9db032df4006d Author: Weiqun Zhang Date: Tue Jan 21 12:28:09 2020 -0800 godunov advection of rho and tracer src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp commit bd1adf00b9d5e5b9ce19497a3f995bfbb39be897 Author: Weiqun Zhang Date: Tue Jan 21 10:51:05 2020 -0800 godunov advection for velocity src/convection/Make.package src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_advection.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo.cpp commit d6bf04b2ef466044f9cb386cffbf81596b3f5c8f Author: Weiqun Zhang Date: Sat Jan 18 07:01:05 2020 -0800 predict w_mac src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict.cpp commit 0af0761172a74759eeeb24b4f69f3b7a2a45caba Author: Weiqun Zhang Date: Sat Jan 18 06:39:19 2020 -0800 cleanup src/convection/incflo_godunov_predict.cpp commit dc82581ed1b4450e1610bf9de3441b76f02c259b Author: Weiqun Zhang Date: Sat Jan 18 06:16:47 2020 -0800 predict v_mac src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict.cpp commit be7e9d8f40f3bc277b9f2581fb20c34289fc2aac Author: Weiqun Zhang Date: Fri Jan 17 22:22:25 2020 -0800 add div tau to force src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/incflo_arrays.cpp commit cbcd6fadfc6a88530e9968d21317360e320b11d8 Author: Weiqun Zhang Date: Fri Jan 17 20:01:12 2020 -0800 compute div tau src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/incflo.H commit ea90793cdfe935100d74185fc965ec7eeb3d6278 Author: Weiqun Zhang Date: Fri Jan 17 18:31:28 2020 -0800 allocate divtau and laps in LevelData if necessary src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp commit b60284a530e37dbdb2d84f49d24730d1f0033b62 Author: Weiqun Zhang Date: Fri Jan 17 14:48:24 2020 -0800 add m_ src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_fillphysbc.cpp src/convection/incflo_compute_advection_term.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/init.cpp commit 888f3bd4644a596dc19257d33c097ed6db13b8b9 Author: Weiqun Zhang Date: Fri Jan 17 14:40:58 2020 -0800 add m_ src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict.cpp src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp src/rheology/incflo_read_rheology_parameters.cpp src/setup/init.cpp src/setup/set_background_pressure.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit 075c5d115ddd5413b98d51e1707847177ea49c52 Author: Weiqun Zhang Date: Fri Jan 17 14:01:08 2020 -0800 add m_ src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_fillphysbc.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/incflo_compute_dt.cpp src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_background_pressure.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit 543a4ca48869d82293da089c60ae971e5f916174 Author: Weiqun Zhang Date: Fri Jan 17 13:18:31 2020 -0800 minor src/convection/incflo_compute_advection_term.cpp src/convection/incflo_predict_vels_on_faces.cpp src/diffusion/DiffusionTensorOp.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/writeEBsurface.cpp src/utilities/diagnostics.cpp commit 311b2c7e249dbe528d1027a9c4bcecad977fd88c Author: Weiqun Zhang Date: Fri Jan 17 12:19:56 2020 -0800 more cleanups src/derive/derive.cpp src/incflo.H src/rheology/incflo_rheology.cpp src/setup/init.cpp commit 0e99cd17b8cf4c0e81c3e1671a9c202f0663d4f3 Author: Weiqun Zhang Date: Fri Jan 17 11:17:50 2020 -0800 more cleanups src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/rheology/incflo_rheology.cpp src/utilities/io.cpp commit c0e38bc1672d1b6816fb512344d618723123b3c1 Author: Weiqun Zhang Date: Fri Jan 17 10:59:19 2020 -0800 more cleanups src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/eb_tuscan.cpp src/embedded_boundaries/eb_twocylinders.cpp src/incflo.H src/setup/Make.package src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit ddd5a9319f63b8afae57eb0162455fb9556c810c Author: Weiqun Zhang Date: Fri Jan 17 10:27:44 2020 -0800 clean up convection/ src/convection/Make.package src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_MAC_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/incflo.H commit 0d1f89e61a9f11d975ab1217d23e0e3d505f8eef Author: Weiqun Zhang Date: Fri Jan 17 09:44:38 2020 -0800 clean up utilities/ src/incflo.H src/utilities/diagnostics.cpp commit e291a300f8abb59163f0e670bd072f54d5d60538 Author: Weiqun Zhang Date: Fri Jan 17 09:39:09 2020 -0800 clean up setup/ src/incflo.H src/incflo.cpp src/setup/Make.package src/setup/incflo_arrays.cpp commit 11e87993e902262f3de36913c2fc384f67bbaebe Author: Weiqun Zhang Date: Fri Jan 17 09:32:45 2020 -0800 clean up embedded_boundaries/ src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit 481c52a84a04e8d52994342536b83b76d775ccb7 Author: Weiqun Zhang Date: Fri Jan 17 09:29:33 2020 -0800 clean up diffusion/ src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/diffusion/Make.package src/incflo.H commit 99c991fd3e1cee0d6247e35a0dce9ee5f8ab7bde Author: Weiqun Zhang Date: Fri Jan 17 09:23:08 2020 -0800 clean up boundary_conditions/ src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/setup/init.cpp src/utilities/incflo_steady_state.cpp commit a7051ad57a7f5a3311827d102d454749c32cba1f Author: Weiqun Zhang Date: Fri Jan 17 09:09:10 2020 -0800 fix a bug and clean up src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.cpp commit 37fdbd1cb90a0b38e79af1dbd9dcb85603e46eef Author: Weiqun Zhang Date: Thu Jan 16 16:26:58 2020 -0800 remove fortran src/Make.package src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/bc_mod_F.H src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/fill_bc0.f90 src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/derive/Make.package src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_mod.f90 src/diffusion/DiffusionOp.cpp src/diffusion/Make.package src/diffusion/diffusion_F.H src/diffusion/set_scal_diff_bcs.f90 src/diffusion/set_vel_diff_bcs.f90 src/incflo.H src/incflo.cpp src/incflo_bclist.H src/projection/incflo_apply_nodal_projection.cpp src/rheology/Make.package src/rheology/incflo_rheology.cpp src/rheology/incflo_rheology_mod.f90 src/rheology/rheology_F.H src/setup/Make.package src/setup/incflo_proj_F.H src/setup/incflo_setup_solvers.cpp src/setup/incflo_to_fortran.F90 src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc_type.f90 src/setup/set_delp_dir.f90 src/setup/set_p0.f90 src/setup/set_ppe_bcs.f90 src/setup/setup_F.H src/utilities/Make.package src/utilities/constant_mod.f90 commit 31946c20d28897812141687b74f2065f4123738f Author: Weiqun Zhang Date: Thu Jan 16 13:48:40 2020 -0800 number of ghost cells src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_fillphysbc.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_MAC_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_convection_K.cpp src/derive/derive.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit 1850d601c5a4fb181d04067ec45d724e6a3f9b02 Merge: f6ab9190 2bbb29f0 Author: Weiqun Zhang Date: Thu Jan 16 11:13:23 2020 -0800 Merge branch 'development' into new_dev commit f6ab91902e7becc114ac49f090bdb5f83b19d8a6 Author: Weiqun Zhang Date: Thu Jan 16 10:12:32 2020 -0800 add forces src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 2bbb29f0455aa87a7a09ac719a09306c4fe0ae46 Author: Ann Almgren Date: Wed Jan 15 16:01:08 2020 -0800 Fix indexing bug caught by Weiqun src/convection/incflo_godunov_predict.cpp commit 8aabe555c3ed9eb85117d95913e2c4b709625b08 Author: Weiqun Zhang Date: Wed Jan 15 15:15:14 2020 -0800 first pass of predict godunov for x faces src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp commit bf9175855f4513ae8a2e78f175bf16affb5a835e Author: Weiqun Zhang Date: Wed Jan 15 09:45:49 2020 -0800 refactor src/boundary_conditions/boundary_conditions.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/incflo_advance.cpp src/prob/prob_init_fluid.cpp src/setup/init.cpp commit f6edffed789fdd1e7dee51c71003d60baa0384c0 Merge: e28c27b6 a2d13c36 Author: Weiqun Zhang Date: Tue Jan 14 09:49:52 2020 -0800 Merge branch 'development' into new_dev commit a2d13c3657538b0dc2f69692aac8fe8b0ae00058 Author: Ann Almgren Date: Tue Jan 14 08:57:05 2020 -0800 Add set_ppe_bcs call to the MAC Projection -- this gets restart working again. src/convection/incflo_MAC_projection.cpp commit 6f666e05f76d6297690a3aeeae4f6ecec417108d Merge: eeadfe97 e10dac18 Author: Ann Almgren Date: Tue Jan 14 08:42:30 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit eeadfe971b2d48fa7a6deb9e4afae2c50617e18b Author: Ann Almgren Date: Tue Jan 14 08:41:59 2020 -0800 Add restart test. test/benchmark.double_shear_restart commit e28c27b6d4c6332b127fd61535e5af41de6d1636 Merge: 72b31655 e10dac18 Author: Weiqun Zhang Date: Mon Jan 13 16:20:51 2020 -0800 update nodal projector commit e10dac181bc19e1dbba6f04b54c5a38cdca7927b Merge: 7e14ec6f f45e1378 Author: Michele Rosso Date: Mon Jan 13 15:44:26 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 72b31655efb93cf0d5b725d39eff7576545aef72 Author: Weiqun Zhang Date: Mon Jan 13 15:43:18 2020 -0800 finish one step src/incflo_advance.cpp commit b5975c1f53c7da8172dc642695ad1a6acfe83ad7 Author: Weiqun Zhang Date: Mon Jan 13 14:47:11 2020 -0800 fillpatch before apply corrector src/convection/incflo_compute_advection_term.cpp src/incflo_advance.cpp commit 7e14ec6fdb9a88736349987d356eb06b5531f955 Author: Michele Rosso Date: Mon Jan 13 14:02:19 2020 -0800 Some clean up src/projection/incflo_apply_nodal_projection.cpp commit 024cf76f56f9bfa435807d1d799c8a6e64523d3c Author: Michele Rosso Date: Mon Jan 13 13:56:34 2020 -0800 Deply AMReX new NodalProjector class src/derive/derive.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_setup_solvers.cpp commit 4013cf916d634c734be3ce7e74f5686e70f09b0e Author: Weiqun Zhang Date: Mon Jan 13 12:58:02 2020 -0800 do not set inflow velocity for incremental projection src/projection/incflo_apply_nodal_projection.cpp commit f45e13780f871aa9046063d85b20a33b9db88e73 Author: Ann Almgren Date: Mon Jan 13 12:50:05 2020 -0800 Get working on GPUs -- must remember to make local copies of variables such dt and use_forces_on_trans that are members of the incflo class src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H commit f6a3da3c217a54bed54af02d04aea3a906a2b0d5 Author: Weiqun Zhang Date: Mon Jan 13 12:14:36 2020 -0800 add amrex:: src/incflo.H commit 86c091e58e09354ee3816d9bc720d598ae7485bd Merge: 21ee2576 d86a573e Author: Weiqun Zhang Date: Mon Jan 13 11:25:31 2020 -0800 Merge branch 'development' into new_dev commit d86a573eede19d285cd3c63250d092a780ae424a Author: Ann Almgren Date: Mon Jan 13 06:34:18 2020 -0800 GpuArray --> amrex::GpuArray in .H file src/convection/incflo_godunov_ppm.H commit 0dee20305048a9327f2b7f39926caf5e5a3e945f Author: Weiqun Zhang Date: Sat Jan 11 20:54:51 2020 -0800 USE_CUDA compiles src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H commit c2d7d61e55be12556d2520ed568a891a3298cf19 Author: Ann Almgren Date: Sat Jan 11 19:43:17 2020 -0800 Don't use godunov when built with EB test/benchmark.double_shear_layer commit 7ef85451f906636a00664f8381f0069811c3d052 Author: Ann Almgren Date: Sat Jan 11 19:06:36 2020 -0800 Fix the split of computing the MAC velocities and using them. src/convection/incflo_compute_MAC_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/incflo_advance.cpp commit 11d4086d3d9d60d26a1163eeaa4bfb487040e509 Author: Ann Almgren Date: Sat Jan 11 14:12:29 2020 -0800 Renamed compute_convective ... --> amrex_compute_convective ... src/convection/incflo_compute_advection_term.cpp commit 8b173a4819dafbcbae79d2b40215de324939279f Author: Ann Almgren Date: Sat Jan 11 14:07:02 2020 -0800 Have default for use_godunov = true to do the convective differencing of velocity. Have double shear layer tests now use Godunov and cfl = 0.9 src/convection/incflo_compute_advection_term.cpp src/convection/incflo_godunov_ppm.H test_no_eb/benchmark.double_shear_layer_x test_no_eb/benchmark.double_shear_layer_y test_no_eb/benchmark.double_shear_layer_z commit a96ad2da38ff212a5b2bdbf26977cce51579772f Author: Ann Almgren Date: Sat Jan 11 13:51:12 2020 -0800 Add the option to use (u dot grad u) instead of div(u u) when using Godunov with no EB. src/convection/Make.package src/convection/incflo_compute_MAC_velocities.cpp src/convection/incflo_compute_advection_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/incflo.H src/incflo_advance.cpp src/setup/init_fluid.f90 test/benchmark.double_shear_layer test_no_eb/benchmark.double_shear_layer test_no_eb/benchmark.double_shear_layer_x test_no_eb/benchmark.double_shear_layer_y test_no_eb/benchmark.double_shear_layer_z commit 2365a630db278a2befcfa7b00c732cda7c923e8d Author: Ann Almgren Date: Sat Jan 11 11:37:39 2020 -0800 Remove leftover print statements src/convection/incflo_godunov_predict.cpp src/incflo_advance.cpp commit edc05ed306f53c6fbd02559ec4bedde272fec8d5 Author: Ann Almgren Date: Sat Jan 11 11:24:03 2020 -0800 1) set the iconserv flag correctly pass through to the routines 2) use scal_forces now as well as vel_forces src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo_advance.cpp commit 8057cb5d70777c081ee042da7468aa7f1be2e145 Author: Ann Almgren Date: Sat Jan 11 07:46:51 2020 -0800 Make sure to pass domain bounds not box bounds to bc routines. src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp commit 21ee2576250bba688cabb414458cfd2238763991 Author: Weiqun Zhang Date: Fri Jan 10 15:04:20 2020 -0800 In the initial iterations we now project (U^* - U^n) rather than U^* src/projection/incflo_apply_nodal_projection.cpp commit cb0d71663e9e68f40fc87c331119b3f156bb68e8 Merge: e7a218b5 781fb647 Author: Weiqun Zhang Date: Fri Jan 10 14:48:57 2020 -0800 Merge branch 'development' into new_dev commit e7a218b5a132b5e62c6bf281ccb0a47eeaa62274 Author: Weiqun Zhang Date: Fri Jan 10 14:32:39 2020 -0800 move on to ApplyCorrector src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/init.cpp commit 781fb6479d0ca2e93d224362ba46a415ff7818c3 Author: Ann Almgren Date: Fri Jan 10 12:39:20 2020 -0800 Combine all the vel and scal forcing terms before using them to update vel and scal. src/incflo_advance.cpp commit 26d1062173b79fd36acedda701338c050b3779b5 Author: Weiqun Zhang Date: Fri Jan 10 11:37:03 2020 -0800 no need to advect tracers in initial pressure iterations src/convection/incflo_compute_convective_term.cpp src/incflo_advance.cpp src/setup/init.cpp commit a50488dc3ed5563f3a419585d6e248598c9e7cf3 Author: Weiqun Zhang Date: Fri Jan 10 11:18:55 2020 -0800 fillphysbc src/boundary_conditions/Make.package src/boundary_conditions/incflo_fillphysbc.cpp src/incflo.H src/incflo_advance.cpp src/setup/init.cpp commit d7c8b3171b9c47279b12d871651a2c915c98ff59 Author: Ann Almgren Date: Fri Jan 10 10:21:52 2020 -0800 Update with force arrays, etc -- shouldn't chnage the answers. src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/incflo.H src/incflo_advance.cpp src/setup/incflo_arrays.cpp commit 3403ca0e53e538c505f67f79b9b2ea1ef36f5e54 Author: Weiqun Zhang Date: Fri Jan 10 09:35:19 2020 -0800 copy pressure back from projector src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp commit fb65caa422f41a4471b617111634de0f14bde79a Author: Ann Almgren Date: Fri Jan 10 09:33:37 2020 -0800 Enable us to set the diffusion type (Explicit vs C-N vs Implicit) in the inputs file. src/incflo.H src/setup/init.cpp commit c8d61fd04d3b6d8298f77aa0cfcec90dcf1c858a Author: Ann Almgren Date: Fri Jan 10 09:24:57 2020 -0800 Oops -- diffusion_type is int not bool src/incflo.H commit b02d7b64344c6b2024f8fbfd2f1b03ba3cd9cbbb Author: Ann Almgren Date: Fri Jan 10 09:22:34 2020 -0800 Add "init_shrink" variable and have it default to 0.1 for now -- this should not change any results. src/incflo.H src/incflo_compute_dt.cpp src/setup/init.cpp commit f0a781b84f30d0379d656303d4c2402419221aa9 Author: Weiqun Zhang Date: Fri Jan 10 09:10:10 2020 -0800 fix domain bc for tracer src/diffusion/DiffusionScalarOp.cpp src/diffusion/incflo_diffusion.cpp commit 7727e38f1e15c53441ad869cf92f642a7a094b4a Merge: 7d157bea 0b83f3ae Author: Ann Almgren Date: Fri Jan 10 08:03:05 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 7d157bea12a5300b204171f69c4e2fdb3e7ba47e Author: Ann Almgren Date: Fri Jan 10 08:02:45 2020 -0800 In the initial iterations we now project (U^* - U^n) rather than U^* src/projection/incflo_apply_nodal_projection.cpp commit 47f5c1900da3fac3df2e8824f989536e069763e5 Author: Weiqun Zhang Date: Thu Jan 9 16:29:38 2020 -0800 diffuse scalar src/diffusion/DiffusionScalarOp.H src/diffusion/DiffusionScalarOp.cpp src/diffusion/DiffusionTensorOp.cpp src/diffusion/Make.package src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp commit 0b83f3ae9bcf98a3ce79fa3224de0690c034057c Author: Ann Almgren Date: Thu Jan 9 15:26:56 2020 -0800 Oops -- we weren't including the explicit viscous term when USE_EB was FALSE src/diffusion/DiffusionOp.cpp commit 90cf7d4ae3704a01165d353bf1bd670dbe65969f Author: Weiqun Zhang Date: Thu Jan 9 14:26:32 2020 -0800 diffuse velocity src/diffusion/DiffusionTensorOp.cpp src/incflo_advance.cpp src/setup/init.cpp commit 7f9bce36fa60fa4973aca3a3eca411e2d2ac9f6f Author: Weiqun Zhang Date: Thu Jan 9 13:33:24 2020 -0800 set solver's diffusion coefficients src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/incflo_diffusion.cpp src/incflo.H src/incflo_advance.cpp src/incflo_compute_dt.cpp src/prob/prob_init_fluid.cpp src/setup/incflo_arrays.cpp commit 3253f75eee8332ac4224f2bc5adfb7f6bd458a88 Merge: ce1420b1 ea447635 Author: Weiqun Zhang Date: Thu Jan 9 11:13:15 2020 -0800 Merge branch 'development' into new_dev commit ce1420b17511f05bfbf71ebef8ee6cb2d6a72400 Author: Weiqun Zhang Date: Thu Jan 9 11:12:46 2020 -0800 setup diffusion bc src/convection/incflo_MAC_projection.cpp src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/Make.package src/diffusion/incflo_diffusion.cpp src/incflo.H src/projection/incflo_apply_nodal_projection.cpp commit ea4476356f2ff003baa9bc2419bc6ebde4335031 Author: Ann Almgren Date: Thu Jan 9 10:12:50 2020 -0800 This is now "correct" but not as good a result as MOL ... something still not quite right ... src/convection/incflo_godunov_predict.cpp commit 8025d1358a89bfb5e4bf02bcb7530163436b88f4 Author: Ann Almgren Date: Thu Jan 9 09:57:08 2020 -0800 remove unused variables src/convection/incflo_godunov_ppm.cpp commit 3c20229d1a9d9c80e371219b108ef27e7d7bf389 Author: Ann Almgren Date: Thu Jan 9 09:56:55 2020 -0800 remove unused variables src/convection/incflo_godunov_ppm.H commit 062b21e60bf74a8f13da513dd9eeb3372de2205c Merge: 21b714aa 42ff0231 Author: Weiqun Zhang Date: Thu Jan 9 09:43:17 2020 -0800 Merge branch 'development' into new_dev commit 42ff02315c901e75c196b4373b28285b8e4057ce Author: Ann Almgren Date: Thu Jan 9 07:11:11 2020 -0800 1) slight clean-up of ebfactory usage 2) getting closer on Godunov ... still a WIP src/convection/incflo_compute_convective_term.cpp src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit 21b714aa1f09acf24973a99510279ee117c227e2 Author: Weiqun Zhang Date: Wed Jan 8 20:52:19 2020 -0800 WIP: tensor solver src/diffusion/DiffusionTensorOp.H src/diffusion/DiffusionTensorOp.cpp src/diffusion/Make.package src/incflo.H src/incflo_advance.cpp commit 66f30fd913bfada45918ee1aa29cf7aac1560843 Author: Weiqun Zhang Date: Wed Jan 8 19:52:10 2020 -0800 bug fix and comments src/incflo_advance.cpp commit af71683b26e19a590a3e2c2047d7a39f4ce86de4 Author: Weiqun Zhang Date: Wed Jan 8 16:32:28 2020 -0800 ApplyPredictor: WIP src/incflo.H src/incflo_advance.cpp commit a27a6f148151157d71348ddaf8dab99aa6dbe011 Author: Weiqun Zhang Date: Wed Jan 8 14:31:06 2020 -0800 convective terms for density and tracer src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/setup/init.cpp commit f45ec7c3970b6ef454463e4c6cb006a0f03dda70 Author: Ann Almgren Date: Wed Jan 8 14:00:56 2020 -0800 Godunov is still a WIP but I want to make sure not to lose what I've got. src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/convection/incflo_godunov_predict.cpp commit 6a954ab4f84cf0c0ccff09dbcdc23b8c6ec1e6a1 Author: Weiqun Zhang Date: Wed Jan 8 09:53:01 2020 -0800 bug fixes src/boundary_conditions/boundary_conditions.cpp src/convection/incflo_convection_K.cpp commit 21bcf0c1f0d458340248b7b03bee9edfd42e38d0 Author: Weiqun Zhang Date: Tue Jan 7 10:21:55 2020 -0800 convective terms for velocity src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_convection_K.cpp src/incflo.H src/setup/init.cpp commit c7ff33a8c9eb57aa29b2214751fc052ce0c28b48 Merge: a6c7ae7e f470d87a Author: Weiqun Zhang Date: Wed Jan 1 21:13:43 2020 -0800 Merge branch 'development' into new_dev commit a6c7ae7ec31556b4fa17be9e64a495c07ad07141 Author: Weiqun Zhang Date: Wed Jan 1 20:45:32 2020 -0800 convective terms WIP src/boundary_conditions/boundary_conditions.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/incflo.H src/incflo_advance.cpp commit f470d87a4cd4fe44bcad7ca2fd41663d8f7ba162 Author: Ann Almgren Date: Thu Dec 26 15:26:43 2019 -0800 Remove namespace amrex from incflo.H and put it in the various .cpp files src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_slopes.cpp src/incflo.H src/incflo_advance.cpp src/incflo_compute_dt.cpp src/main.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_read_rheology_parameters.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/incflo_build_info.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit f187d556b3a7bc5106dad411f81eaac828fc6caf Author: Ann Almgren Date: Fri Dec 20 19:38:24 2019 -0800 Adding more of the Godunov functionality but most of it is still commented out -- don't try to use it! src/convection/Make.package src/convection/incflo_compute_convective_term.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_predict.cpp src/incflo.H commit 91147fb274a00809751ff79dfa76e77524846de2 Author: Ann Almgren Date: Fri Dec 20 17:50:30 2019 -0800 Add version of ppm for pre-MAC and rename existing post-MAC routine as ppm_fpu src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp commit dcc2d205dc10a23515d8aae1b49ad58b0f375303 Author: Ann Almgren Date: Fri Dec 20 17:35:42 2019 -0800 More cleanup using amrex namespace src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_godunov_ppm.cpp src/convection/incflo_set_mac_velocity_bcs.cpp commit c703e9a48bf171e7d194d80bad72394eaa8bd4fc Author: Ann Almgren Date: Fri Dec 20 17:30:03 2019 -0800 more clean-up src/Make.package src/convection/incflo_MAC_projection.cpp src/setup/Make.package src/setup/incflo_proj_F.H commit 23020378ae9a5faca9b3615527ae3f21a86ae229 Author: Ann Almgren Date: Fri Dec 20 17:28:02 2019 -0800 remove unneeded dependency src/derive/derive.cpp commit 2f84f5c9636891968ecadeb08c0c4b301303a50b Author: Ann Almgren Date: Fri Dec 20 16:32:20 2019 -0800 More clean-up src/convection/incflo_predict_vels_on_faces.cpp src/derive/derive.cpp src/diffusion/DiffusionOp.cpp src/incflo.H src/incflo.cpp src/utilities/constants.H commit 6c4877856958dd0c667a0ef1fce44e40e80ee02f Author: Ann Almgren Date: Fri Dec 20 16:06:17 2019 -0800 Remove nlev (replace using finest_level), prepare incflo.H to remove namespace amrex, and update density and tracer bc's so they use first-order extrap value -- not external value -- at nsw src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_godunov_ppm.H src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp commit a6854d6a7e07caa3bb157633432142b7bbd5dc69 Author: Weiqun Zhang Date: Fri Dec 20 10:17:02 2019 -0800 fillpatch for tracer src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/prob/prob_bc.H src/setup/init.cpp commit af5680bfccd2e8aaacdb662ef7f681ec47bc2d01 Author: Weiqun Zhang Date: Fri Dec 20 09:09:51 2019 -0800 fix merge issues src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_godunov_ppm.H src/incflo.H commit 5c49817258edab8b136ed7245832d04108320689 Merge: 4e12e1bd 12ea4764 Author: Weiqun Zhang Date: Fri Dec 20 09:01:36 2019 -0800 Merge branch 'development' into new_dev commit 12ea47645f2cee156866cd4d9e14e5f395a3ad13 Author: Ann Almgren Date: Fri Dec 20 07:02:34 2019 -0800 Add godunov files -- but this is not ready for use yet. src/convection/Make.package src/convection/incflo_compute_fluxes.cpp src/convection/incflo_godunov_ppm.H src/convection/incflo_godunov_ppm.cpp src/incflo.H commit b6b5baa806ee73b2ef6a0f96e957f6e6e43e5afd Author: Ann Almgren Date: Thu Dec 19 19:18:55 2019 -0800 Simplify nghost (just one now -- not nghost_for_this and nghost_for_that) src/convection/incflo_compute_convective_term.cpp src/incflo.H src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit d1ff93b2007a9ab6a6fba80feb80c50d0f734d4f Author: Ann Almgren Date: Thu Dec 19 17:03:07 2019 -0800 Remove extrap_dir flag for bc routines src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/derive/derive.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp src/utilities/incflo_steady_state.cpp commit 4e12e1bd09d3c4ab68868fbfdbd5c974a4dc3f3a Author: Weiqun Zhang Date: Thu Dec 19 15:59:36 2019 -0800 fix bugs src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_compute_convective_term.cpp commit 98ce5372a9f647fcf12c7314670e66e0c389ed19 Author: Weiqun Zhang Date: Thu Dec 19 14:16:13 2019 -0800 first mac projection src/boundary_conditions/boundary_conditions.cpp src/convection/incflo_MAC_projection.cpp src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp commit 69fecfa09a931786ae9635f635604bd65d538367 Author: Weiqun Zhang Date: Thu Dec 19 13:02:47 2019 -0800 fillpatch density src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/prob/prob_bc.H commit 91baffc946274361be932365034b54faae9869b6 Author: Ann Almgren Date: Thu Dec 19 12:08:27 2019 -0800 Update derive routines to test on isConnected rather than isCovered src/derive/derive.cpp commit 0cb97b490ae9b0a5bd780618a46d76e9deeb9916 Author: Ann Almgren Date: Thu Dec 19 10:15:49 2019 -0800 Revert "Update derive routines to test on isConnected rather than isCovered" This reverts commit aae46b44b95955a6724312cf0035c126ba64dc03. src/derive/derive.cpp commit 93256ddd97bd7e7c612c55914b99e9d10a22732a Author: Ann Almgren Date: Thu Dec 19 10:07:18 2019 -0800 In slopes, test on nsw as well as minf to decide whether to use special stencil src/convection/incflo_slopes.cpp commit aae46b44b95955a6724312cf0035c126ba64dc03 Author: Ann Almgren Date: Thu Dec 19 10:04:32 2019 -0800 Update derive routines to test on isConnected rather than isCovered src/derive/derive.cpp commit c2adc98e56846e476001c6176e41e52e8d4cd148 Author: Weiqun Zhang Date: Thu Dec 19 09:54:45 2019 -0800 for comparison with current development branch src/convection/incflo_convection_K.H commit e024345cc1a4ebdf9813da7111b07c5d034bfa07 Author: Ann Almgren Date: Thu Dec 19 09:28:01 2019 -0800 Update slopes to test on isConnected rather than isCovered src/convection/incflo_slopes.cpp commit 35185c3a83639481e2377be7ff861c8b01fee663 Author: Weiqun Zhang Date: Wed Dec 18 21:40:59 2019 -0800 fix ext_dir for predict_vels_on_faces src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp commit 71190b80e1c05b24847e2fa3f85f43be2915256c Author: Weiqun Zhang Date: Wed Dec 18 19:08:09 2019 -0800 move predict_vels_on_faces into incflo class so that it has access to its members src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit fb287a0f106a759d31f73233d45f171374ec7bb0 Author: Weiqun Zhang Date: Wed Dec 18 14:46:03 2019 -0800 fix bugs src/convection/incflo_convection_K.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/setup/init.cpp commit 30ad3eac1c51382f48336c5217d50d29405cf989 Author: Weiqun Zhang Date: Wed Dec 18 12:22:37 2019 -0800 fillpatch velocity src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H src/prob/Make.package src/prob/prob_bc.H commit c822e735817cfbf6e4458be8a565ed5b900bec3f Author: Weiqun Zhang Date: Tue Dec 17 11:38:54 2019 -0800 predict vels on faces for eb src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit 9c09a5dab9d700c1065a355c7fb9e1e99b3ba8e7 Author: Weiqun Zhang Date: Tue Dec 17 09:55:39 2019 -0800 predict vels on faces for regular fab src/convection/Make.package src/convection/incflo_compute_convective_term.cpp src/convection/incflo_convection_K.H src/convection/incflo_convection_K.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit a2b5e910ca64ba8178710ec87417f7e440e88157 Author: Weiqun Zhang Date: Mon Dec 16 10:03:31 2019 -0800 start compute_convective_term src/convection/incflo_compute_convective_term.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 50ff35bad24c439541239855a0154b47de0685d8 Author: Weiqun Zhang Date: Sat Dec 14 19:56:55 2019 -0800 remove using namespace amrex from headers src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_if.H src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/eb_spherecube.cpp src/embedded_boundaries/eb_tuscan.cpp src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/incflo_advance.cpp src/main.cpp src/projection/incflo_apply_nodal_projection.cpp src/rheology/incflo_read_rheology_parameters.cpp src/rheology/incflo_rheology.cpp src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/incflo_build_info.cpp src/utilities/incflo_steady_state.cpp src/utilities/io.cpp commit dbd007d2b6ee61be7d6a5b77b208b964cc12c3ee Author: Weiqun Zhang Date: Sat Dec 14 19:37:32 2019 -0800 compute dt src/incflo.H src/incflo.cpp src/incflo_compute_dt.cpp src/setup/init.cpp commit 02d01671203205648f3a2d26223c8243e00d36df Author: Weiqun Zhang Date: Sat Dec 14 10:33:43 2019 -0800 finish initial velocity projection src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo.cpp src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp commit f5374e7a3b3c85ccef6c0e7262db3582da3f3788 Author: Weiqun Zhang Date: Fri Dec 13 15:43:45 2019 -0800 put probtype specific stuff inot src/prob src/Make.incflo src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo.cpp src/prob/Make.package src/prob/prob_bc.cpp src/prob/prob_init_fluid.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/Make.package commit 74f47f5dadd890d301c8c2a9349ed3046cc49c34 Author: Weiqun Zhang Date: Fri Dec 13 14:39:38 2019 -0800 start initial projection src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_prob_fluid.cpp src/utilities/diagnostics.cpp commit 95b25b550fd9603f12edf6e4b0fe848cc1e5a007 Merge: b5f54c60 b7a0e381 Author: Weiqun Zhang Date: Thu Dec 12 20:50:51 2019 -0800 Merge branch 'development' into weiqun/dev commit b5f54c60f983183c0880c4d608f304e94226d6c1 Author: Weiqun Zhang Date: Thu Dec 12 20:45:28 2019 -0800 start initial projection src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp src/setup/init_prob_fluid.cpp src/setup/set_background_pressure.cpp commit b7a0e381762214d82a70e673db3593fe0460c2e8 Author: Ann Almgren Date: Thu Dec 12 18:21:10 2019 -0800 more clean-up of bc stuff src/boundary_conditions/bc_mod.f90 src/boundary_conditions/bc_mod_F.H test/benchmark.eb_lid_driven_cavity commit 8a74eae29f28ec46ac78f8e09fbdf01e31086617 Author: Ann Almgren Date: Thu Dec 12 17:58:41 2019 -0800 clean up the way we impose boundary conditions src/boundary_conditions/bc_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/embedded_boundaries_F.H src/embedded_boundaries/get_eb_walls.f90 src/embedded_boundaries/get_walls.cpp src/incflo.H src/setup/init.cpp src/setup/set_bc_type.f90 commit fb13991fff48d7516fa6d029c9fd8c533894e641 Author: Weiqun Zhang Date: Thu Dec 12 15:36:54 2019 -0800 set gp0 src/incflo.H src/setup/incflo_arrays.cpp src/setup/set_background_pressure.cpp commit 61d740aafab7514b2f8a9ddb856ff0f6545cae3d Author: Weiqun Zhang Date: Thu Dec 12 13:34:00 2019 -0800 add bc type, location, density etc. src/boundary_conditions/boundary_conditions.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp commit 949298312448f2064fea768129ad0fc25cc13851 Author: Weiqun Zhang Date: Thu Dec 12 12:00:37 2019 -0800 add set_background_pressure.cpp src/incflo.H src/incflo.cpp src/setup/Make.package src/setup/set_background_pressure.cpp commit bf24091ce575f97e21278f852e06be876d677a3d Author: Weiqun Zhang Date: Thu Dec 12 11:18:30 2019 -0800 add C++ init_prob_fluid src/incflo.H src/incflo.cpp src/setup/Make.package src/setup/incflo_arrays.cpp src/setup/init_prob_fluid.cpp src/setup/setup_F.H commit dd571db8ed35c9a167ef8f1b8bbadfc089a0fb3c Author: Weiqun Zhang Date: Thu Dec 12 09:56:28 2019 -0800 define new level data src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp commit ca3f79e839d6018b46a1e787f2bb080131e86b48 Author: Ann Almgren Date: Thu Dec 12 09:49:28 2019 -0800 Shorten the benchmark.channel_cylinder-* cases. test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit 30123b5f94458454dae9b3565189d672512e5c2c Author: Ann Almgren Date: Thu Dec 12 09:47:03 2019 -0800 Fix the growth rate of dt after using a small time step due to plot_per_exact src/incflo.H src/incflo_compute_dt.cpp commit 37c3092cdcfc4f976be9edf0a79eda1a1813582a Author: Weiqun Zhang Date: Thu Dec 12 09:08:25 2019 -0800 add LevelData src/incflo.H src/setup/incflo_arrays.cpp commit e23cd6f7a4af09fe7bce0d3e7fc9570c45925d7d Author: Ann Almgren Date: Thu Dec 12 09:03:24 2019 -0800 Remove un-needed bc fill before predictor src/incflo_advance.cpp commit 4b885abec99157237925648b5e4353cd4428ae82 Author: Weiqun Zhang Date: Thu Dec 12 08:53:23 2019 -0800 add amrex:: src/incflo.H commit de78cf4ea52f1c403a23c6a133ba93740d6974a5 Author: Ann Almgren Date: Thu Dec 12 08:12:57 2019 -0800 Change radius in benchmark.channel_cylinder-* so that the regression test is more robust test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit eca0f499bc2582b5812eda369d800f062fb49e3e Author: Weiqun Zhang Date: Thu Dec 12 05:45:09 2019 -0800 incflo ctor src/incflo.H src/incflo.cpp src/main.cpp src/setup/incflo_arrays.cpp commit 1c7f55797b6440683a8e9ce96c6856dd0628aaf6 Author: Weiqun Zhang Date: Wed Dec 11 16:31:25 2019 -0800 make files exec/GNUmakefile src/Make.incflo test/GNUmakefile test_no_eb/GNUmakefile commit dc5ff735f3f8e56519124c484c2ce9ef2b24ff81 Author: Ann Almgren Date: Wed Dec 11 16:14:46 2019 -0800 Fix blocking factor in inputs files test/inputs.couette_cylinder test/inputs.couette_twocylinders test/inputs.rotating_cylinder test/inputs.taylor_couette commit d78cbff480f19090dfc78533a3f93ee6c8701998 Author: Weiqun Zhang Date: Wed Dec 11 16:09:34 2019 -0800 rm clang-format .clang-format commit 59f49082f48c13c18b5c1808f7104e6b5a713b32 Merge: ccfdf7df 47949e18 Author: Weiqun Zhang Date: Wed Dec 11 16:00:19 2019 -0800 Merge branch 'development' into weiqun/dev commit d830a147bb67597fa7bb6192e451e0be14e9f6ee Author: Ann Almgren Date: Wed Dec 11 15:48:51 2019 -0800 Added inputs files from exec since we are getting rid of exec directory exec/GNUmakefile exec/inputs.channel_cylinder exec/inputs.channel_cylinder_bingham exec/inputs.channel_spherecube exec/inputs.couette exec/inputs.couette_poiseuille exec/inputs.double_shear_layer exec/inputs.lid_driven_cavity exec/inputs.poiseuille_cylinder exec/inputs.poiseuille_plane_bingham exec/inputs.poiseuille_plane_newtonian exec/inputs.taylor_green_vortices exec/inputs.taylor_green_vortices3d exec/inputs.uniform_velocity_sphere src/setup/init.cpp test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z test/inputs.channel_sphere test/inputs.couette_cylinder test/inputs.couette_twocylinders test/inputs.poiseuille_annulus test/inputs.rotating_cylinder test/inputs.taylor_couette commit 47949e18e912bf5a58ac9cf77bbb94e9085aff9b Author: Ann Almgren Date: Tue Dec 10 13:17:42 2019 -0800 Need to drop absolute tolerance for nodal projection to 1-e11 test_no_eb/benchmark.poiseuille_plane_newtonian commit 5939a577ef894861d4c294cf8151f90bf29fe77f Author: Ann Almgren Date: Tue Dec 10 13:13:43 2019 -0800 Add nodal_proj.atol to poiseuille_plane_newtonian test_no_eb/benchmark.poiseuille_plane_newtonian commit d5b76cbeecb04d126cc144b5f854042f96b44deb Author: Ann Almgren Date: Tue Dec 10 13:12:33 2019 -0800 Update projection-related inputs test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z test/benchmark.couette test/benchmark.eb_lid_driven_cavity test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian test/benchmark.tracer_adv_diff test/benchmark.tracer_advection test/benchmark.tuscan test/benchmark.uniform_velocity_sphere commit c59e3a512094611613eea8fcb2cda6adc4a71691 Author: Ann Almgren Date: Tue Dec 10 10:17:05 2019 -0800 Pass nghost_for_bcs not nghost when used for size of bc_ilo, etc, arrays src/rheology/incflo_rheology.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit bb8fd992ed487ef577a6db222aed01a4c770b963 Author: Ann Almgren Date: Tue Dec 10 09:48:33 2019 -0800 Fix how we pass the input variables relevant to the MAC projection src/convection/incflo_MAC_projection.cpp commit 5b1df67d6d5256fce9c4ee1ae8522e2537aa3feb Author: Ann Almgren Date: Mon Dec 9 14:38:00 2019 -0800 add this to no_eb case test_no_eb/benchmark.poiseuille_plane_newtonian commit 28dc4933f0ac121fea539dce68692c9420b9b8e5 Author: Ann Almgren Date: Mon Dec 9 14:34:04 2019 -0800 Fix size of bc_ilo, etc, for case with no EB. src/convection/incflo_compute_convective_term.cpp src/incflo.H src/setup/incflo_arrays.cpp src/setup/init.cpp commit 3a332a37c6430463f1d1e291e245f09f15c8dd19 Author: Ann Almgren Date: Mon Dec 9 11:51:48 2019 -0800 Re-commit the change that means we apply the 10% limit on dt growth even at nstep = 0; before we weren't imposing that constraint at nstep = 0. src/incflo_compute_dt.cpp commit 9d41b854b4cbb4e05496ec0d01684a846d43d298 Author: Ann Almgren Date: Mon Dec 9 11:45:55 2019 -0800 Sync exec/GNUmakefile with test/GNUmakefile exec/GNUmakefile commit 4a82998632630ef4277a159a2c603847725e5796 Author: Ann Almgren Date: Mon Dec 9 11:45:23 2019 -0800 sync test_no_eb/GNUmakefile with that in test test_no_eb/GNUmakefile commit cdd2631759ffdf950f0f5cbee216a28560624280 Author: Ann Almgren Date: Mon Dec 9 11:38:23 2019 -0800 plot_per --> plot_per_exact for no_eb cases test_no_eb/benchmark.double_shear_layer test_no_eb/benchmark.taylor_green_vortices commit 2a26449ee6a9d0bc438f9248ea0268b2519996ae Author: Ann Almgren Date: Mon Dec 9 11:19:26 2019 -0800 plot_per --> plot_per_exact test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z test/benchmark.channel_spherecube test/benchmark.couette test/benchmark.double_shear_layer test/benchmark.eb_lid_driven_cavity test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.taylor_green_vortices test/benchmark.tracer_adv_diff test/benchmark.tracer_advection test/benchmark.tuscan test/benchmark.uniform_velocity_sphere commit e624b967b8afe2fb1fbd083d925438d13d03ed95 Author: Ann Almgren Date: Mon Dec 9 10:17:39 2019 -0800 Revert the change in dt -- just to be sure the reg tests still pass src/incflo_compute_dt.cpp commit 0f4ef07e2a5d2ce7bb5f41569f3b4c2f6d153e52 Author: Ann Almgren Date: Fri Dec 6 14:05:49 2019 -0800 Add plot_per_exact and plot_per_approx options instead of just plot_per. Also change the type of projection we do when we're taking a smaller dt (project U*-Un rather than U*). mfix_tracker src/convection/incflo_MAC_projection.cpp src/incflo.H src/incflo.cpp src/incflo_compute_dt.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp commit 69bcc5883970693ea0bb6b42ff35d7a8c0ed4ce1 Author: Ann Almgren Date: Tue Dec 3 12:43:05 2019 -0800 Need 2 ghost cells not 1 for computing strain rate and vorticity in presence of EB src/derive/derive.cpp commit 75244929865f868e7e42d1de33719570fc319cf3 Author: Ann Almgren Date: Tue Dec 3 10:13:39 2019 -0800 1) set nghost = 1 for non-EB case 2) a bit of clean-up ... 3) nghost for mac_phi = 1 regardless of EB src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/incflo.H src/incflo.cpp commit aefe162559f3dde49c41491e0c25e33360dd1132 Author: Ann Almgren Date: Tue Dec 3 09:43:47 2019 -0800 minor clean-up src/setup/init.cpp src/setup/init_fluid.f90 commit 9862b915446441e9466019175ad5d8ded510634d Author: Ann Almgren Date: Tue Dec 3 09:39:49 2019 -0800 I don't think we need nghost ghost cells for the temporaries used for derived quantities -- replace nghost by 1. src/derive/derive.cpp commit 393b8258cc412d63ea4d45e616166b30fb4bfc15 Author: Michele Rosso Date: Mon Dec 2 14:44:51 2019 -0800 Set nstep to 0 after performing initial iterations src/setup/init.cpp commit 2cc18ab256d932f36593a04410682140079fa6c3 Author: Michele Rosso Date: Mon Dec 2 11:25:47 2019 -0800 ApplyProjection(): pass bool to select how to set p and gradp src/incflo.H src/incflo_advance.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp commit eafe3f6fd73871ede429a902b51ed356de2fdb8d Author: Michele Rosso Date: Wed Nov 27 14:24:30 2019 -0800 Set nstep to 0 AFTER initial pressure iterations. nstep was set to 0 after initial projection. By doing so, ApplyProjection() never updated the pressure and the pressure gradient, AKA proj2 was never performed. As a result, it as like perfoming a single pressure iteration. src/setup/init.cpp commit acb1be0b44cee453fa0c210c65550f42281fe30f Author: Ann Almgren Date: Mon Nov 25 17:07:40 2019 -0800 Add new benchmark test for tracer advection and diffusion... test/benchmark.tracer_adv_diff commit edf601aa5e625f3bcf8f9211e04336379cbe5f8e Author: Ann Almgren Date: Mon Nov 25 07:35:26 2019 -0800 add file for tracer advection test/benchmark.tracer_advection commit 9886c55d0a97b699da4312d15889b58f686469b4 Author: Ann Almgren Date: Mon Nov 25 07:19:39 2019 -0800 Add tracer advection test ( on conservation ) -- src/incflo.H src/incflo_advance.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/utilities/diagnostics.cpp test/benchmark.tracer_advection commit 350ef7e72e7a81ed1f32b1debe2dc9ba8a0c9aaa Author: Ann Almgren Date: Tue Nov 19 17:18:30 2019 -0800 Make this GNUMakefile USE_EB-aware ... test/GNUmakefile commit 83301fd3eec957e657007c8c9f738a36472ab365 Author: Ann Almgren Date: Tue Nov 19 15:28:15 2019 -0800 Get rid of duplicate code in RegridArrays as well. src/setup/incflo_arrays.cpp commit 5fee216c82f34dad66f855975198d7fe1953c0a9 Author: Ann Almgren Date: Tue Nov 19 15:14:02 2019 -0800 Don't have completely separate section for non-EB array creation src/setup/incflo_arrays.cpp commit af5b4f6429a26087f5e9bbbba1de9f105f7df7c2 Author: Ann Almgren Date: Tue Nov 19 09:34:43 2019 -0800 Sync the test_no_eb/benchmark* with the test versions of these inputs files. test_no_eb/benchmark.double_shear_layer test_no_eb/benchmark.taylor_green_vortices commit 9962e4659ff91f7771039ef717ae55453ea7f10f Author: Ann Almgren Date: Mon Nov 18 10:17:52 2019 -0800 1) get this compiling with USE_EB = FALSE again 2) change the effect of plt_ccse_regtest = true -- this now resets the defaults but we can use plt_vort = 0 for example to over-ride those defaults src/convection/incflo_slopes.cpp src/diffusion/DiffusionOp.H src/setup/init.cpp commit 420bb826bd04830c49e23678490fad266a759241 Author: Ann Almgren Date: Thu Nov 14 16:00:50 2019 -0800 plt_vel --> (plt_velx,plt_vely,plt_velz) and plt_gradp --> (plt_gpx,plt_gpy,plt_gpz) src/convection/incflo_set_mac_velocity_bcs.cpp src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit 0966cbcba3f2107e9aa945139aaeb2f00a0355b0 Author: Ann Almgren Date: Wed Nov 13 16:24:06 2019 -0800 fix typo src/convection/incflo_compute_fluxes.cpp commit de00e5dfd789ae066cc8044026187dd73b8386b3 Author: Roberto Porcu Date: Wed Nov 13 14:24:07 2019 -0800 FabArray::BuildMask method is used now src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp commit 4c74f1fab5619e22e3b113c83d50641365d1e0ba Merge: 91576f7c f2bf6808 Author: Ann Almgren Date: Wed Nov 13 13:29:37 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 91576f7cdedff5e06b944c16363abe6b0784d4c0 Author: Ann Almgren Date: Wed Nov 13 13:28:55 2019 -0800 Replace AMREX_FOR_3D and AMREX_FOR_4D with ParallelFor where we explicitly list the arguments being passed to the GPU -- benefit is more checking at compile time and hopefully less crashing. src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp commit f2bf68083972f8c8e3cd432f881872b3627184ae Author: Weiqun Zhang Date: Wed Nov 13 12:31:47 2019 -0800 remove some Gpu::synchronize src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_predict_vels_on_faces.cpp src/projection/incflo_apply_nodal_projection.cpp commit 68415fdbc1071279961cdaf808e4ae6f83fbb169 Author: Weiqun Zhang Date: Wed Nov 13 11:36:28 2019 -0800 fix gpu bug src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/incflo.H commit defe06249920ed02bf5777644b2afd8b265b5618 Author: Michele Rosso Date: Tue Nov 12 11:05:08 2019 -0800 incflo_compute_fluxes: use only one ghost cell when testing if the box is regular. There is no need to test if a box + 4 ghost nodes is regular. src/convection/incflo_compute_fluxes.cpp commit f2fe23be1254195f7e1ed9b233a68fc4912fb279 Author: Michele Rosso Date: Tue Nov 12 10:26:21 2019 -0800 Replace namespace Cuda with Gpu to reflect changes in amrex src/incflo.H commit 298e47007f8db8308b48bcabfe626a2d32844b37 Author: Ann Almgren Date: Sun Nov 10 11:15:39 2019 -0800 use finest_level not max_level in diffusion solves src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/setup/init.cpp commit e02b466351b78d3bbb899b0104d490c1d22dc360 Author: Ann Almgren Date: Sun Nov 10 07:58:42 2019 -0800 More clean up and get rid of param* src/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/incflo.cpp src/param_mod.f90 src/param_mod_F.H src/setup/set_bc_type.f90 src/setup/set_p0.f90 src/setup/set_ppe_bcs.f90 src/utilities/constant_mod.f90 commit 36f83ba596ef9b309d766bc1818afbd7efb76daa Author: Ann Almgren Date: Sat Nov 9 18:16:48 2019 -0800 1) code cleanup 2) reset all cfl in test to 0.45 so don't violate stability limit of MOL 3) some re-naming src/Make.package src/incflo.H src/incflo_advance.cpp src/rheology/Make.package src/rheology/incflo_read_rheology_parameters.cpp src/rheology/incflo_rheology.cpp src/rheology/incflo_rheology_mod.f90 src/setup/init.cpp src/utilities/Make.package src/utilities/incflo_steady_state.cpp test/GNUmakefile test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z test/benchmark.channel_spherecube test/benchmark.couette test/benchmark.couette_poiseuille test/benchmark.double_shear_layer test/benchmark.eb_lid_driven_cavity test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_newtonian test/benchmark.taylor_green_vortices test/benchmark.tuscan test/benchmark.uniform_velocity_sphere commit fa52449cccef588213b2431e3812cc586b79fb93 Author: Ann Almgren Date: Fri Nov 8 12:23:28 2019 -0800 1+ntrac --> 1 (bug fix) src/convection/incflo_compute_convective_term.cpp commit e0a9309db8eee5b50df37a7fc5e6343f0395f316 Author: Ann Almgren Date: Fri Nov 8 12:11:03 2019 -0800 1) Abort if cfl > 0.5 is specified 2) Don't use diffusive constraint on time step unless doing explicit diffusion src/advance.cpp src/incflo.H src/incflo_compute_dt.cpp src/setup/init.cpp commit 44eb1c1e382f3f9659f80c7843bc71ff14cb7981 Author: Ann Almgren Date: Fri Nov 8 11:51:46 2019 -0800 We go ahead and fillpatch density even if constant_density to be sure that the ghost cells are filled. We can optimize this away later. src/convection/incflo_compute_convective_term.cpp commit 0dbda375eb478a43f26889975778c906be975cc6 Author: Ann Almgren Date: Thu Nov 7 18:25:20 2019 -0800 Fix the scalar advection so it uses mu_s *not* the velocity viscous coefficient src/advance.cpp src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/setup/init_fluid.f90 commit 223a06768edeee32806de47190d0b01c8ae77d30 Merge: f39ce889 69f63c7a Author: Ann Almgren Date: Thu Nov 7 10:07:32 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit f39ce8892e22977d6261b3148ba3d836f75d7f3d Author: Ann Almgren Date: Thu Nov 7 10:06:18 2019 -0800 This version fixes a problem with the previous commit in which the huge values in the slopes were getting seen at both inflow and outflow. src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/incflo.H commit 69f63c7a07bf0c6cb10c2df127eee03d6fe0ea4d Author: Roberto Porcu Date: Thu Nov 7 10:04:40 2019 -0800 Introduced some further host-device synchronization and elixirs to be consistent with MFIX-Exa src/boundary_conditions/incflo_fillpatch.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/projection/incflo_apply_nodal_projection.cpp commit 837db2f2bd0f1a4e0574270fa358550081201e1e Author: Ann Almgren Date: Wed Nov 6 15:34:41 2019 -0800 Currently the FAB setVal doesn't play well with CUDA -- for now we work around it ... also some code cleanup src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/incflo.H commit 8ae7608ea10a391367a7f72d2f8cf15e0c4591d2 Author: Ann Almgren Date: Wed Nov 6 12:51:25 2019 -0800 1) Abort if ntrac set to 0 -- that will break some things 2) add max tracer to output diagnostics src/setup/init.cpp src/utilities/diagnostics.cpp commit 4731c82dc756f7832d79f30123ce2ac974986dec Author: Ann Almgren Date: Sun Nov 3 00:16:47 2019 -0700 Pass info to nodal projector src/setup/incflo_setup_solvers.cpp commit 431d12a143d1e251009b15fb377415e118c4153d Author: Ann Almgren Date: Fri Nov 1 12:46:56 2019 -0700 slight tweaks src/convection/incflo_predict_vels_on_faces.cpp src/incflo.H commit 90f080a6464d09fdf6c48136b318f85ec2659503 Merge: 7848846d 0781cf30 Author: Ann Almgren Date: Fri Nov 1 07:15:29 2019 -0700 Merge branch 'development' into aa/no_eb commit 7848846d4e5205da3c40cca24dc74e16b02e3177 Author: Ann Almgren Date: Fri Nov 1 07:04:27 2019 -0700 This enables us to run with USE_EB = FALSE src/advance.cpp src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/diffusion/set_scal_diff_bcs.f90 src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp src/setup/set_bc_type.f90 src/utilities/io.cpp test_no_eb/GNUmakefile test_no_eb/benchmark.double_shear_layer test_no_eb/benchmark.taylor_green_vortices commit 0781cf30134dda044317cb58d578ee2a4252fd1c Merge: 383c8483 04cc3e70 Author: WeiqunZhang Date: Thu Oct 31 14:54:50 2019 -0700 Merge pull request #35 from michaeljbrazell/mjb/level_mask moved makeFineMask outside of AllocateArrays commit 04cc3e7087c523a61dbf94261c5ed8cdda98fcda Author: michael brazell Date: Thu Oct 31 14:08:48 2019 -0700 moved the level_mask outside of AllocateArrays function because when that function is called the finer level has not been set up yet src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 383c8483aed9896d18acce90d26372bbfe6ea83a Author: Roberto Porcu Date: Thu Oct 31 13:58:37 2019 -0700 removed some unnecessary host-device synchronization src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp commit c9b991d2c8e4fc3aa6ec0197f1f3942419d24cbc Author: Michael J. Brazell Date: Thu Oct 31 13:30:31 2019 -0700 Added function to sum Kinetic Energy (#34) * added function that computes kinetic energy and an input to control frequency. Added 3D Taylor-Green Vortex initial condition and input file * moved a FAB based volmask to an iMultiFab level_mask. Level mask does not have to perform box intersection everytime kinetic energy is called but instead only when regrid is called. * cleaned up a bit and now compiles with latest AMReX development branch * updated ComputeKineticEnergy to use the three MultiFab version of ReduceSum and divided by freestream density ro_0. Use latest version of AMReX development to compile. * Removed level_mask setup function since it already exists in AMReX as makeFineMask, thanks Weiqun. * moved the ComputeKineticEnergy to public for CUDA lambdas to work, and flipped the masking number (0,1)->(1,0), thanks Weiqun exec/inputs.taylor_green_vortices3d src/derive/derive.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_fluid.f90 commit 23967384a7898d65dccce6c955adf95ed5dc27ff Author: Michele Rosso Date: Mon Oct 28 18:06:57 2019 -0700 Nodal projection: update calls to NodalProjector methods src/derive/derive.cpp src/projection/incflo_apply_nodal_projection.cpp commit ccfdf7df4e7b6dacd4804c92dd55216b41b32fda Author: Weiqun Zhang Date: Sat Oct 26 07:40:59 2019 -0700 only pass up to finest level to NodalProjector src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit 6ef3d72753e79af910fb79d70a631528e6ae6496 Author: Weiqun Zhang Date: Sat Oct 26 07:15:28 2019 -0700 remove use Fortran module entity conflicts src/setup/set_ppe_bcs.f90 commit 6f8debd5f6bf1a951abb2641910e912caca8c5d1 Author: Weiqun Zhang Date: Fri Oct 25 16:26:09 2019 -0700 move SetBCTypes to the beginning of InitData so that they are ready for InitFromScratch. Only allocate tracer MultiFabs if ntrac > 0. src/embedded_boundaries/embedded_boundaries.cpp src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 40bad93bf0dc6c118af467ab695d77b7df1fa188 Author: Weiqun Zhang Date: Fri Oct 25 15:34:42 2019 -0700 move the call to GetInputBCs to incflo constructor src/boundary_conditions/boundary_conditions.cpp src/incflo.cpp src/main.cpp commit 67d13a0542f7f8a022bde781602977f258b5cdbb Author: Weiqun Zhang Date: Fri Oct 25 15:28:58 2019 -0700 no need to inflo::eb_level src/incflo.H commit e8a4d8c43b0122bce8579695da192242c91167ac Author: Weiqun Zhang Date: Fri Oct 25 15:23:09 2019 -0700 remove a bunch of new EBFArrayBoxFactory before valid grids exist src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/eb_spherecube.cpp src/embedded_boundaries/eb_tuscan.cpp src/embedded_boundaries/eb_twocylinders.cpp commit d10479120e566e09a876183ab7846485cf550cc1 Author: Weiqun Zhang Date: Fri Oct 25 15:15:16 2019 -0700 fix a bug introduced in 7a5a35df5a43bf7d0edc5b1 src/convection/incflo_predict_vels_on_faces.cpp commit 99465d752e75fe64a558e4aaa38755444fbe795f Author: Weiqun Zhang Date: Fri Oct 25 14:54:12 2019 -0700 indentation src/embedded_boundaries/embedded_boundaries.cpp src/setup/init.cpp commit 5523a4762cebb40a7ae011081407821d9cc596d5 Author: Weiqun Zhang Date: Fri Oct 25 14:09:34 2019 -0700 no reason for diffusion_op to be static either src/incflo.H src/incflo.cpp commit 7a5a35df5a43bf7d0edc5b161c1f885cc0ccbf99 Author: Weiqun Zhang Date: Fri Oct 25 14:06:06 2019 -0700 no need for e_x, e_y and e_z src/convection/incflo_predict_vels_on_faces.cpp src/diffusion/DiffusionOp.cpp src/incflo.H src/incflo.cpp src/utilities/constants.H commit 456cc66ae156ae21b1c9daa2c9b411468cff8e76 Author: Weiqun Zhang Date: Fri Oct 25 14:00:00 2019 -0700 no reason for ntrac to be static src/incflo.H src/incflo.cpp commit 718d72a04615b853ac0e87502552e7b23c7ca0dc Author: Weiqun Zhang Date: Fri Oct 25 13:34:51 2019 -0700 remove nlev and max_level from many places because they are not safe when finest_level != max_level src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/incflo.H src/incflo.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/init.cpp src/utilities/io.cpp commit b41a264542754c463e12b68be9f8629c93342e68 Author: Weiqun Zhang Date: Fri Oct 25 13:00:00 2019 -0700 remove unused (by inclfo) MakeBaseGrids and ChopGrids functions src/incflo.H src/incflo.cpp commit 2ae279e98cd676b2c27c5bd5fdab8881d9abb2dd Author: Weiqun Zhang Date: Fri Oct 25 12:43:04 2019 -0700 remove set_ptr_to_incflo src/boundary_conditions/incflo_fillpatch.cpp src/incflo.H src/main.cpp commit d84445d9e4f67e642c8ca5c18c2e1a4528a7f218 Author: Weiqun Zhang Date: Fri Oct 25 11:38:34 2019 -0700 explicitly add virtual to some incflo functions src/incflo.H commit f69d4f3d6834533b6de3f8e680764b395041dd8c Author: Weiqun Zhang Date: Fri Oct 25 11:34:25 2019 -0700 make DiffusionType enum struct src/incflo.H commit d27f3c0ef2cb7e79babe280eb69324c6bb915bd3 Author: Weiqun Zhang Date: Fri Oct 25 11:31:05 2019 -0700 indentation in main src/main.cpp commit 656fcf7e1bf55d3c98fc895447526701b69d4103 Author: Weiqun Zhang Date: Fri Oct 25 11:24:11 2019 -0700 clean up GNUmakefile exec/GNUmakefile commit b5b05c9ed61e75c8751b4f3fa35847ba12879646 Author: Weiqun Zhang Date: Fri Oct 25 10:15:06 2019 -0700 USE_MG is not being used exec/GNUmakefile test/GNUmakefile commit f579f61ac8fd594e40f22a1fcf43f414128214f4 Author: Ann Almgren Date: Thu Oct 24 22:30:33 2019 -0700 Update incflo to use NodalProjctor object that now lives in amrex src/derive/derive.cpp src/incflo.H src/incflo.cpp src/projection/Make.package src/projection/NodalProjector.H src/projection/NodalProjector.cpp src/projection/incflo_apply_nodal_projection.cpp src/setup/incflo_setup_solvers.cpp commit b006328b1419129acf56b319ee681027838260b1 Merge: 76689a47 600d88a2 Author: Michele Rosso Date: Thu Oct 24 20:13:46 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 76689a470d024c49067e165775dfd0b131f55cc6 Author: Michele Rosso Date: Thu Oct 24 20:10:12 2019 -0700 Nodal projection: rename class to be consistent with MacProjector src/derive/derive.cpp src/incflo.H src/incflo.cpp src/projection/Make.package src/projection/NodalProjector.H src/projection/NodalProjector.cpp src/projection/projection.cpp src/setup/incflo_setup_solvers.cpp src/utilities/diagnostics.cpp commit 61a3546a9a058113e7eb041ba69274989d014590 Author: Michele Rosso Date: Thu Oct 24 19:36:58 2019 -0700 Nodal projection: provide computeRHS method to user src/derive/derive.cpp src/projection/NodalProjection.H src/projection/NodalProjection.cpp commit 7f3a71204c91cbbf6e1f63fb4d485d386cd6d215 Author: Michele Rosso Date: Thu Oct 24 19:13:32 2019 -0700 Nodal projection: make NodalProjecion independent from incflo src/incflo.H src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/setup/incflo_setup_solvers.cpp commit 600d88a28b7857d6a210e1a2f2085ae52f06e2e1 Author: Ann Almgren Date: Thu Oct 24 18:48:31 2019 -0700 add a little more verbosity to the output test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit 7a22cd64f906151ddb70d9f2022b3e8027718297 Author: Ann Almgren Date: Thu Oct 24 18:47:05 2019 -0700 remove print statements src/diffusion/set_scal_diff_bcs.f90 commit 29a322652aab3a2df6809f3a3e5218bd30bed82b Merge: 5883461b 40cb343c Author: Ann Almgren Date: Thu Oct 24 18:32:58 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 5883461b6786bf50f625eaf80601e623e32731a0 Author: Ann Almgren Date: Thu Oct 24 18:32:30 2019 -0700 1) Add scalar diffusion 2) Modify test/benchmark.channel_cylinder-* to include scalar advection and diffusion src/advance.cpp src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/diffusion/Make.package src/diffusion/diffusion_F.H src/diffusion/set_scal_diff_bcs.f90 src/diffusion/set_vel_diff_bcs.f90 src/incflo.H src/setup/incflo_arrays.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp src/setup/init_fluid.f90 test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit 40cb343c51d94a591f5f7d0f42ef990623481f27 Author: Roberto Porcu Date: Thu Oct 24 17:51:22 2019 -0700 Bugs fixed for CUDA compilation src/derive/derive.cpp src/incflo.H src/rheology/rheology.cpp src/rheology/rheology_F.H commit de8654acb952f849796ded81fa6214ec303eafe1 Author: Michele Rosso Date: Thu Oct 24 16:14:52 2019 -0700 Nodal projection: pass sigma instead of computing it inside NodalProjection src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/projection/projection.cpp commit f516951591ff95794abd6291aa26f9f05f3bc0fc Author: Michele Rosso Date: Thu Oct 24 15:42:33 2019 -0700 Nodal projection: include scale factor in matrix coefficient. Perform setup at each projection to account for changes in matrix coefficients. This changes the benchmarks. src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/setup/incflo_setup_solvers.cpp commit cb584a630e6eb9e474a61adcb1aea7c2fbf3a05c Author: Michele Rosso Date: Thu Oct 24 14:53:27 2019 -0700 Nodal projection: set velocity BCs before calling projection object src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/projection/projection.cpp commit fbd7e51c38ed8b6bfc75a4174be9fecf66107542 Author: Ann Almgren Date: Thu Oct 24 08:54:01 2019 -0700 Fix computation of divu for plotfile. src/derive/derive.cpp src/incflo.H src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit bf1847196fff33423b249ee7f14ca66db1d74a54 Author: Ann Almgren Date: Wed Oct 23 21:35:14 2019 -0700 Make probtype = {31,32,33} work in periodic as well src/convection/incflo_set_mac_velocity_bcs.cpp src/setup/init.cpp commit 7b59141cc75ec78a94c6effa0e4b05c22a912e65 Author: Ann Almgren Date: Wed Oct 23 20:44:01 2019 -0700 ComputeRHS --> computeRHS src/utilities/diagnostics.cpp commit d107af0f18b1e5bd12761ea0b0d84847e1b690b5 Author: Ann Almgren Date: Wed Oct 23 20:42:57 2019 -0700 Get rid of incflo::ComputeDivU since it is the same as nodal_projector->ComputeRHS src/derive/derive.cpp src/incflo.H src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit ab6a10ff6f469cc831cd19ad412adef3553fe9ac Author: Ann Almgren Date: Wed Oct 23 20:31:26 2019 -0700 This commit has the new diffusion and nodal projection classes now working in the form that we want. src/incflo.H src/incflo.cpp src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/projection/projection.cpp src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit 922757f32ede9527d1f20d816fd68d0dfec69f0c Author: Ann Almgren Date: Wed Oct 23 19:34:10 2019 -0700 This has the new DiffusionOp class to handle diffusion -- this is in preparation for regridding. src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/incflo.H src/incflo.cpp src/setup/Make.package src/setup/incflo_setup_solvers.cpp src/setup/init.cpp commit 62cd539ddfa1732f4a90bb09d5fcf5facd5f975a Author: Ann Almgren Date: Mon Oct 21 19:08:21 2019 -0700 Just minor clean-up src/diffusion/DiffusionOp.cpp src/diffusion/diffusion_F.H src/diffusion/set_diff_bcs.f90 commit 3d8fb518f91797d0176d96eff9ff6458adc7ea48 Author: Ann Almgren Date: Mon Oct 21 15:42:52 2019 -0700 Move redistribution code into amrex. src/convection/incflo_compute_convective_term.cpp src/diffusion/DiffusionOp.cpp src/utilities/Make.package src/utilities/incflo_redistribute.cpp commit aef65108c9bc7170b935bedeeb0cbc8dfb77530b Author: Ann Almgren Date: Mon Oct 21 14:02:11 2019 -0700 Update diffusion stuff to 1) make ComputeDivTau part of the DiffusionOp class instead of part of incflo 2) move the redistribute routine out of incflo as well (it will end up in amrex soon) src/advance.cpp src/convection/incflo_compute_convective_term.cpp src/diffusion/DiffusionOp.H src/diffusion/DiffusionOp.cpp src/diffusion/Make.package src/diffusion/incflo_compute_divtau.cpp src/incflo.H src/setup/init.cpp src/utilities/incflo_redistribute.cpp commit cca2e2f72199d0c63427373da5de82a509ddf01f Author: Ann Almgren Date: Mon Oct 21 08:01:46 2019 -0700 Don't add gp0 if use_boussinesq is true. src/advance.cpp commit 84a1b40cd6be69bb0eae54704c1688de26c99569 Author: Ann Almgren Date: Sun Oct 20 22:42:00 2019 -0700 Use new-time (instead of old-time) eta in the implicit/semi-implicit solve in the corrector. src/advance.cpp commit ffe5797dd117df07757f4b696c952a1be7968e34 Author: Ann Almgren Date: Sun Oct 20 20:57:51 2019 -0700 Add choices for the time-centering of the viscous terms. src/advance.cpp src/derive/derive.cpp src/incflo.H src/incflo.cpp src/rheology/rheology.cpp src/utilities/io.cpp commit 7a2fe318081dde6660bffd7e037af5255661afd1 Author: Weiqun Zhang Date: Sun Oct 20 16:45:35 2019 -0700 fix the call to amrex::TagCutCells: volfrac's fabs are not eb fabs src/incflo.cpp commit 0233462f442ea65ab3612764c2d9ad730734ae72 Author: Ann Almgren Date: Sun Oct 20 15:01:03 2019 -0700 Oops -- need ComputeViscosity at start of predictor, not start of corrector src/advance.cpp commit 8a9da7bd3740a56c3310d3ae6deaa50a27c542ed Author: Ann Almgren Date: Sun Oct 20 13:12:35 2019 -0700 More clean-up and removing unnecessary work wrt derived quantities src/advance.cpp src/convection/incflo_compute_convective_term.cpp src/derive/derive.cpp src/incflo.H src/incflo.cpp src/rheology/rheology.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/utilities/diagnostics.cpp src/utilities/io.cpp commit df9aa9eb940a9352dcf29d90f45ea7e1afe59a12 Author: Ann Almgren Date: Fri Oct 18 12:55:46 2019 -0700 Need to keep the ghost cell filling routines for eta for the cases where we have non-constant viscosity. src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/fill_bc0.f90 src/rheology/rheology.cpp commit d185c5dfa9c7767134ee06af61a85d3bd8e650b8 Author: Ann Almgren Date: Thu Oct 17 19:57:22 2019 -0700 fix number of components src/setup/incflo_arrays.cpp commit 8f523d7f94ea4c5811baaba92fb56a3ced5b9cff Author: Ann Almgren Date: Thu Oct 17 19:22:42 2019 -0700 add use_boussinesq flatg src/advance.cpp src/incflo.H src/setup/init.cpp commit d261a689d0a265801e7a67edde150bb9433cbcb9 Author: Ann Almgren Date: Thu Oct 17 18:59:46 2019 -0700 don't force us to have 3 tracers for probtype = 31 src/setup/init_fluid.f90 commit 90cd8f72854d65b115aa90d57cabd86a63ca5e33 Author: Ann Almgren Date: Thu Oct 17 18:55:58 2019 -0700 default number of tracers should be 1 src/incflo.cpp commit 8ec7b15a09e1ceb52e908805de15f6c8f34d7ebe Author: Ann Almgren Date: Thu Oct 17 18:55:07 2019 -0700 Enable multiple tracers -- clean this up by separating density and tracer more completely. src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/fill_bc0.f90 src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_density_bcs.cpp src/boundary_conditions/incflo_set_tracer_bcs.cpp src/boundary_conditions/set_density_bcs.f90 src/boundary_conditions/set_tracer_bcs.f90 src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/diffusion/incflo_compute_divtau.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/incflo_to_fortran.F90 src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc_type.f90 src/setup/setup_F.H src/utilities/constant_mod.f90 src/utilities/incflo_build_info.cpp src/utilities/incflo_redistribute.cpp src/utilities/io.cpp commit 06f6093ba03820eae479e61f90eb08c2353c8a4f Author: Michele Rosso Date: Thu Oct 17 12:44:17 2019 -0700 Fix redistribution src/utilities/incflo_redistribute.cpp commit e4b7dbea6a5069f22e7b6cb84e7560ac3c327879 Author: Michele Rosso Date: Thu Oct 17 12:37:47 2019 -0700 Revert "Revert to older version of diffusion" This reverts commit c28d0e95878c082b1c7a67e7c218c592b8be9d9b. src/diffusion/Make.package src/diffusion/incflo_compute_divtau.cpp src/diffusion/incflo_redist_diff.cpp src/diffusion/incflo_redist_diff.hpp commit e7628c1b39256c12c76112f21905918078563a1b Author: Michele Rosso Date: Thu Oct 17 12:37:23 2019 -0700 Revert "Revert "Sync redistribution code with mfix'"" This reverts commit e4f4acc926e212acdbd32af2f6cdd8a8a8700b9b. src/convection/Make.package src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/incflo.H src/utilities/Make.package src/utilities/divop_mod.f90 src/utilities/incflo_redistribute.cpp commit fd9321a0c28297a99eaa3ee742d76b0c2985bed6 Author: Michele Rosso Date: Thu Oct 17 12:37:05 2019 -0700 Revert "Enable new redistribution for convective term only" This reverts commit e87ca9f175361663cd13e6757e8a6f8d18f31ef1. src/convection/incflo_compute_convective_term.cpp src/incflo.H src/utilities/Make.package src/utilities/incflo_redistribute.cpp commit e87ca9f175361663cd13e6757e8a6f8d18f31ef1 Author: Michele Rosso Date: Thu Oct 17 11:20:28 2019 -0700 Enable new redistribution for convective term only src/convection/incflo_compute_convective_term.cpp src/incflo.H src/utilities/Make.package src/utilities/incflo_redistribute.cpp commit 129c03c18aca644c2953529a8faae46ea010b449 Merge: ad3f3745 535958d3 Author: Michele Rosso Date: Thu Oct 17 11:11:09 2019 -0700 Merge branch 'development' into mr/redistribution commit 535958d303432556b744696adf2f4a44e3c2c2f3 Author: Michele Rosso Date: Thu Oct 17 11:10:46 2019 -0700 Update GNUmakefile in exec directory exec/GNUmakefile commit ad3f3745adbb665a01d05c7f3e65d5cd41089d3b Merge: e4f4acc9 94be7c23 Author: Michele Rosso Date: Thu Oct 17 10:39:49 2019 -0700 Merge branch 'development' into mr/redistribution commit e4f4acc926e212acdbd32af2f6cdd8a8a8700b9b Author: Michele Rosso Date: Thu Oct 17 10:31:32 2019 -0700 Revert "Sync redistribution code with mfix'" This reverts commit f986c1f4ace1d0815d62523d1a656f840abede11. src/convection/Make.package src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/incflo.H src/utilities/Make.package src/utilities/divop_mod.f90 src/utilities/incflo_redistribute.cpp commit 94be7c23d24a32cc8c10ad9fb00dd149e469ac3d Author: Ann Almgren Date: Thu Oct 17 10:21:38 2019 -0700 We now see amrex/Src/LinearSolvers/Projections (and definitely do not need C_CellMG) test/GNUmakefile commit c28d0e95878c082b1c7a67e7c218c592b8be9d9b Author: Michele Rosso Date: Thu Oct 17 09:57:02 2019 -0700 Revert to older version of diffusion src/diffusion/Make.package src/diffusion/incflo_compute_divtau.cpp src/diffusion/incflo_redist_diff.cpp src/diffusion/incflo_redist_diff.hpp commit 402a8f15a708bb13c3849290553aeac80f5be31e Author: Ann Almgren Date: Wed Oct 16 18:19:08 2019 -0700 change the default variables in the incflo plotfiles. src/incflo.H commit f986c1f4ace1d0815d62523d1a656f840abede11 Author: Michele Rosso Date: Wed Oct 16 18:18:27 2019 -0700 Sync redistribution code with mfix' src/convection/Make.package src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/diffusion/Make.package src/diffusion/incflo_compute_divtau.cpp src/diffusion/incflo_redist_diff.cpp src/diffusion/incflo_redist_diff.hpp src/incflo.H src/utilities/Make.package src/utilities/divop_mod.f90 src/utilities/incflo_redistribute.cpp commit e93f2b8c466c36b70a049e4962224beef8784ad3 Author: Michele Rosso Date: Mon Oct 14 15:01:26 2019 -0700 Use AMReX native EB-aware norm routines src/utilities/diagnostics.cpp commit 3ce2f8d433a8a7314d2231b538145dc3c475b413 Author: Michele Rosso Date: Mon Oct 14 14:52:23 2019 -0700 Clean up src/incflo.H src/projection/Make.package src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp src/projection/projection.cpp src/setup/init.cpp commit 1f75475b6549e0b41b0232cebb790e8c6727539c Author: Michele Rosso Date: Mon Oct 14 12:36:22 2019 -0700 Start porting nodal projection class from mfix src/boundary_conditions/incflo_set_velocity_bcs.cpp src/incflo.H src/incflo.cpp src/projection/Make.package src/projection/NodalProjection.H src/projection/NodalProjection.cpp src/projection/projection.cpp commit cbbad22d45c0c28bb46599a020d70a533ab3e21a Author: Jordan Musser Date: Fri Oct 11 13:50:58 2019 -0400 Fix IO for divu - convert from nodal to cell-center src/utilities/io.cpp commit c96bdcc17c26951dcfa70c8d55b795977c1cd995 Author: Ann Almgren Date: Wed Oct 9 16:20:27 2019 -0700 oops -- didn't set up the z-case correctly src/convection/incflo_set_mac_velocity_bcs.cpp commit a5a0ac89f74387499dea14f932bc9b5715c5be6b Author: Ann Almgren Date: Wed Oct 9 14:33:37 2019 -0700 fix the copy to only act on the valid box not the whole array src/convection/incflo_compute_convective_term.cpp commit 4683e1f012462289b71866f456571627027b4839 Author: Ann Almgren Date: Wed Oct 9 13:31:13 2019 -0700 Need this to avoid "erroneous operations" src/convection/incflo_predict_vels_on_faces.cpp commit f0a78418c5b7e656eec7dfb98c2ab732a8e7aed7 Author: Ann Almgren Date: Wed Oct 9 13:21:42 2019 -0700 "diveu" --> "divu" src/convection/incflo_MAC_projection.cpp commit 8e3ae5e098329deb94e9ece032acdea1d55db76a Author: Ann Almgren Date: Wed Oct 9 10:32:03 2019 -0700 Fix convection bug -- needed the FlilBoundary to include periodic wraparound. src/convection/incflo_MAC_projection.cpp src/convection/incflo_predict_vels_on_faces.cpp commit 02dcb459e5e7c2d89f734bd536ebe0b4d6c7856f Author: Ann Almgren Date: Wed Oct 9 08:57:42 2019 -0700 Fix some convection stuff ... this should work ... src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection_old/Make.package commit d9671e840cef54857b4bbcbeed8972fab5ba603c Merge: aff02f8e 64de1dc0 Author: Ann Almgren Date: Wed Oct 9 07:16:39 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit aff02f8eb7f8457b86ef533a1439c2fb0c7e73b4 Author: Ann Almgren Date: Wed Oct 9 07:16:29 2019 -0700 Fix oops in setting scalar bcs. src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/incflo_set_scalar_bcs.cpp commit 64de1dc01f1a4632f8e928f90dd72b3f300ba642 Author: Roberto Porcu Date: Wed Oct 9 00:52:17 2019 -0700 Gpu::synchronize uniformized with MFIX-Exa src/boundary_conditions/incflo_set_scalar_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/diffusion/incflo_redist_diff.cpp commit a7aad4692129ac7c1c5d537374b2b94bded0d579 Author: Ann Almgren Date: Tue Oct 8 14:58:17 2019 -0700 Update incflo to use new AMReX functionality and new way of doing convection so we correctly put things on centroids... src/Make.package src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/bc_mod_F.H src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_scalar_bcs.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/boundary_conditions/set_mac_velocity_bcs.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/Make.package src/convection/convection.cpp src/convection/convection_F.H src/convection/incflo_MAC_projection.cpp src/convection/incflo_compute_convective_term.cpp src/convection/incflo_compute_fluxes.cpp src/convection/incflo_compute_velocity_at_faces.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/convection/incflo_predict_vels_on_faces.cpp src/convection/incflo_set_mac_velocity_bcs.cpp src/convection/incflo_slopes.cpp src/convection/mac_F.H src/convection_old/Make.package src/derive/derive.cpp src/diffusion/DiffusionEquation.cpp src/incflo.H src/incflo.cpp src/incflo_proj_F.H src/projection/Make.package src/projection/PoissonEquation.cpp src/projection/projection.cpp src/projection/projection_F.H src/setup/Make.package src/setup/init.cpp src/setup/set_ppe_bcs.f90 commit 9624dfde1f986d145c77211a457c51161e4638af Author: Roberto Porcu Date: Mon Oct 7 14:53:41 2019 -0700 Gpu::synchronize() calls have been uniformized to improve consistency src/boundary_conditions/incflo_set_velocity_bcs.cpp src/convection/convection.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_slopes.cpp src/diffusion/incflo_redist_diff.cpp commit 0de9c1f7e55cdec9bc3fff1403367e6b669ff0ec Author: Ann Almgren Date: Wed Sep 25 11:51:09 2019 -0700 Adding test case which should replicate behavior of benchmark.lid_driven_cavity but with inhomog bc on EB boundary instead of on nsw test/benchmark.eb_lid_driven_cavity commit cb9f6f7173507f472e266dde3a66ba275bd1eaf1 Author: Ann Almgren Date: Tue Sep 24 17:24:48 2019 -0700 Replace "copy" by MultiFab::Copy where appropriate src/diffusion/DiffusionEquation.cpp src/utilities/io.cpp commit ef9d2d2c476cf8c1d7822ddbf1cc879b333170b4 Author: Ann Almgren Date: Mon Sep 23 09:12:29 2019 -0700 THe version I committed earlier had several things commented out which shouldn't have been. This is much better. src/advance.cpp commit 5e89b68948f5900c909411178723ab517e203757 Author: Ann Almgren Date: Sun Sep 22 16:16:35 2019 -0700 Remove print statement src/diffusion/set_diff_bcs.f90 commit d4ac64d995a6d63ada812dce6a8eb72ff963b152 Author: Ann Almgren Date: Sun Sep 22 14:31:33 2019 -0700 Update to use tensor solve for diffusion -- note that this still won't pass some regression test because of a bug in the tensor solve at inflow/nsw corner. Also for tests that have non-zero cross terms, there will be a difference due to no longer lagging those terms. src/advance.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/Make.package src/diffusion/diffusion.cpp src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/eb_wallflux_mod.f90 src/diffusion/incflo_compute_divtau.cpp src/diffusion/incflo_redist_diff.cpp src/diffusion/incflo_redist_diff.hpp src/diffusion/set_diff_bcs.f90 src/incflo.H src/utilities/Make.package commit 574a41385cd9a98f85a76e082dbed879a7597812 Author: Ann Almgren Date: Sat Sep 21 16:17:36 2019 -0700 Fix bug in set-up of channel_cylinder_y src/boundary_conditions/incflo_set_velocity_bcs.cpp commit 586e0489c868274dc90f799d04eac6608ad92101 Author: Ann Almgren Date: Sat Sep 21 16:07:28 2019 -0700 Change from f90 to C++ boundary conditions. src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/bc_mod_F.H src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/incflo_set_velocity_bcs.cpp src/boundary_conditions/set_velocity_bcs.f90 src/derive/derive.cpp src/incflo.H src/incflo.cpp src/setup/init.cpp commit 489684e5d4674670d7f89584378720a602c58512 Author: Ann Almgren Date: Sat Sep 21 15:34:02 2019 -0700 Update how we use c0,c1,c2 in set_velocity_bcs.f90 -- now we first multiply and add, then we divide by 3 src/boundary_conditions/set_density_bcs.f90 src/boundary_conditions/set_tracer_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 commit 75e3dc63b4e6d4b54ecafdb382f03601f91e52d9 Author: Ann Almgren Date: Sat Sep 21 15:09:57 2019 -0700 Add precision to init and boundary values src/boundary_conditions/incflo_fillpatch.cpp src/setup/init_fluid.f90 commit 3a79cd5cc01a4819080e7998014d8ccab0640a3c Author: Weiqun Zhang Date: Fri Sep 20 09:09:03 2019 -0700 move compute_dhidn_3d from amrex to incflo src/diffusion/eb_wallflux_mod.f90 commit 44560731d821ac4e30c3a96f6476b688db5c7f57 Author: Ann Almgren Date: Mon Sep 16 09:36:30 2019 -0700 update advection of density/tracer src/convection/convection.cpp commit 9abc6a17598982c6489b0a600bf70623df674d70 Author: Ann Almgren Date: Sun Sep 15 17:23:44 2019 -0700 Get probtype = 1 1 working. src/advance.cpp src/boundary_conditions/incflo_fillpatch.cpp src/embedded_boundaries/eb_tuscan.cpp src/setup/init.cpp src/setup/init_fluid.f90 test/benchmark.tuscan commit fcffce9d0ab27198af07c7c204dceb282b66688b Author: Ann Almgren Date: Sun Sep 15 12:01:47 2019 -0700 We want the flow on the inside of the Tuscan geometry src/embedded_boundaries/eb_tuscan.cpp commit b934c09468afa9b173616afe6d71d57b8e1f1a5e Author: Ann Almgren Date: Sun Sep 15 11:22:43 2019 -0700 Default tracer to 0 so we don't break regression tests right now src/setup/incflo_arrays.cpp src/setup/init_fluid.f90 commit 84d192fab229bd40570b6da6d039724302f27222 Author: Ann Almgren Date: Sun Sep 15 10:58:18 2019 -0700 updated to actually advance density and tracer in time src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/incflo_fillpatch.cpp src/boundary_conditions/set_density_bcs.f90 src/boundary_conditions/set_tracer_bcs.f90 src/convection/MacProjection.cpp src/convection/convection.cpp src/convection/incflo_compute_velocity_at_faces.cpp src/convection/incflo_slopes.cpp src/derive/derive.cpp src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc_type.f90 src/setup/setup_F.H src/utilities/diagnostics.cpp src/utilities/io.cpp commit be8fcead855084c2fed433c36bdabd260d30b2fd Author: Ann Almgren Date: Sat Sep 14 17:21:27 2019 -0700 Make sure we use the right velocity array in computing the face velocities going into the MAC projection. src/convection/incflo_compute_velocity_at_faces.cpp commit 68c2a989bab5010d008331cc13af4dbdd6a26f49 Author: Ann Almgren Date: Sat Sep 14 16:58:24 2019 -0700 just clean-up src/projection/PoissonEquation.cpp src/projection/projection.cpp commit 4d14117eb13401c66274f0d5791d322b676e8b41 Author: Ann Almgren Date: Sat Sep 14 14:32:13 2019 -0700 fix some component errors src/convection/convection.cpp commit 2ec4973b1f838f64f704e130f5d0bde31416e555 Author: Ann Almgren Date: Sat Sep 14 13:30:14 2019 -0700 Clean up incflo_slopes so it and mfix_slopes.cpp match. src/convection/incflo_slopes.cpp commit bb0184ffaaf497e4b4bc7bbbe744a1f5ec11a978 Author: Ann Almgren Date: Sat Sep 14 12:34:39 2019 -0700 Write "density" not "ro" src/utilities/io.cpp commit 8199b8516735e43128867a07b882540dec5f7d3a Author: Ann Almgren Date: Sat Sep 14 12:15:48 2019 -0700 Fix a few component numbering bugs and clean up the code a little. src/convection/convection.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/convection/incflo_slopes.cpp src/diffusion/diffusion_mod.f90 src/incflo.H src/rheology/rheology_mod.f90 src/setup/incflo_to_fortran.F90 src/setup/init.cpp src/utilities/constant_mod.f90 commit f6e1504128d43a5d0abdba286b3b4eaeb95aebda Author: Ann Almgren Date: Sat Sep 14 11:30:06 2019 -0700 Add the full functionality for updating density and tracer. src/advance.cpp src/convection/Make.package src/convection/convection.cpp src/convection/incflo_compute_velocity_at_faces.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_slopes.cpp src/incflo.H src/setup/incflo_arrays.cpp src/utilities/io.cpp commit 3ac8fcdc4dd3105fa78f18a71761c149a7d6991e Author: Ann Almgren Date: Fri Sep 13 20:18:05 2019 -0700 Getting closer to updating density and tracer; also fixed the problem of not updating the bc's of eta after updating eta itself. src/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/derive/derive.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_mod.f90 src/incflo.H src/incflo.cpp src/incflo_compute_dt.cpp src/projection/projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit 5b5aaf58bb5f73256fbc098f8d973f9fc2bc20a0 Author: Ann Almgren Date: Fri Sep 13 17:02:46 2019 -0700 Replace Fortran convection routines by C++ GPU-ready versions taken from mfix. src/Make.package src/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/Make.package src/convection/convection.cpp src/convection/incflo_divop_conv.cpp src/convection/incflo_divop_conv.hpp src/convection/ugradu_eb_mod.f90 src/convection/ugradu_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/embedded_boundaries/eb_tuscan.cpp src/incflo.H src/incflo_bclist.H src/param_mod.f90 src/param_mod_F.H src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/divop_mod.f90 test/benchmark.tuscan commit ee1dadad40e23297731a24fa1845e17731201881 Author: Ann Almgren Date: Fri Sep 13 09:17:13 2019 -0700 1) Add new geometry to be used for comparison with experimental setup 2) Add ability to write vtp file of geometry for displaying in paraview (controlled from inputs file by incflo.write_eb_surface = true/false) src/advance.cpp src/embedded_boundaries/Make.package src/embedded_boundaries/eb_tuscan.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/main.cpp src/setup/init.cpp commit 9c846ac8826feeab513f4c3013b874389503c5f9 Author: Ann Almgren Date: Thu Sep 12 04:57:23 2019 -0700 Have channel_cylinder tests in all three directions as separate inputs files. test/benchmark.channel_cylinder test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit 5e43641c5f1577ead92680e585ff1eec825da6bb Merge: 4d8cd51b 1a056fd4 Author: Ann Almgren Date: Thu Sep 12 04:53:42 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 4d8cd51bce522cc53e7d759eda397a841aa12007 Author: Ann Almgren Date: Thu Sep 12 04:45:59 2019 -0700 Fix the way we were setting minf in one direction and nsw in another direction ... make sure nsw always over-rides minf ... src/advance.cpp src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/setup/init.cpp src/setup/init_fluid.f90 test/benchmark.channel_cylinder-x test/benchmark.channel_cylinder-y test/benchmark.channel_cylinder-z commit 1a056fd41b88a5d48f59030fad6487deaed3e300 Author: knutsvk Date: Tue Sep 10 00:20:28 2019 +0100 rotate the channel_cylinder test case back again exec/inputs.channel_cylinder src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/setup/init_fluid.f90 test/benchmark.channel_cylinder commit c427f30ecec91ab35e0a93132d12a5d5add19fb2 Author: knutsvk Date: Mon Sep 9 16:09:42 2019 +0100 fix inconsistent BCs test/benchmark.channel_cylinder commit 02856f997783de8be13f84b02eae7d60bd61eb24 Author: knutsvk Date: Mon Sep 9 15:10:43 2019 +0100 update input to be rotated correctly test/benchmark.channel_cylinder commit 09bf29b3db40847d7c78e4c022daef18b9a83306 Author: knutsvk Date: Mon Sep 9 13:34:16 2019 +0100 bugfix: factor half src/derive/derive.cpp commit d69257531439a68cff7d859fc39665a42b125d99 Author: knutsvk Date: Mon Sep 9 10:51:40 2019 +0100 fix bug in computation of strainrate and vorticity: revert to CC velocity as input src/derive/derive.cpp commit bd673ca57e056e92e58424423a0175b2af75b9bf Author: Ann Almgren Date: Sun Sep 8 06:13:34 2019 -0700 Part-way towards making a 2d version. src/Make.package src/advance.cpp src/convection/MacProjection.cpp src/convection/convection.cpp src/derive/derive.cpp src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/incflo.cpp src/incflo_compute_dt.cpp src/projection/PoissonEquation.cpp src/projection/projection.cpp src/rheology/rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit d5e5e1e53c381b797cf889efc7f51bc77d3ccea2 Author: Ann Almgren Date: Sun Sep 8 04:07:04 2019 -0700 Add option to use "./incflo*ex --describe" to show build information. src/main.cpp src/utilities/Make.package src/utilities/incflo_build_info.cpp commit d89a3c192a7f293085c227dd27fc628322e0e5b1 Author: Weiqun Zhang Date: Mon Sep 2 16:30:39 2019 -0700 copy deleted amrex function into inclfo src/utilities/divop_mod.f90 commit efc42b13f34c33d6273fc2957445b2c257ed841c Merge: c64944e1 8af7cfff Author: knutsvk Date: Mon Aug 26 09:22:13 2019 +0200 Merge branch 'drag' into development commit 8af7cfff43e10f569ae2ebe1d0ec9d2fae07967f Author: knutsvk Date: Fri Aug 9 16:16:37 2019 +0200 fix input exec/inputs.channel_cylinder_bingham commit 2c8b3ce9bab8005a02ab8650d4bcc04c44cdec0b Author: knutsvk Date: Fri Aug 9 12:32:31 2019 +0200 move all derived quantity computation to c++ exec/inputs.channel_cylinder_bingham src/derive/Make.package src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_eb_mod.f90 src/derive/derive_mod.f90 commit 9594d527028be0209ff74e09b4d7678ce4d8a990 Author: knutsvk Date: Tue Aug 6 14:50:12 2019 +0200 comment out unused stencil src/derive/derive.cpp commit 703b0c71a430e35cd871e0da40a8bf8c81327218 Author: knutsvk Date: Tue Aug 6 14:49:02 2019 +0200 try computing (non-EB) strainrate with MAC velocities src/derive/derive.cpp commit c34faacc9bb025240d18c891f8b4c05a0a13478d Author: knutsvk Date: Mon Aug 5 18:08:08 2019 +0100 taylor expansion actually more accurate for very small strain rates src/rheology/rheology_mod.f90 commit 49cfe2572eb1339d8bced0c1647c842d8d261e90 Author: knutsvk Date: Mon Aug 5 18:07:13 2019 +0100 base settings for convergence analysis exec/inputs.poiseuille_plane_bingham exec/inputs.poiseuille_plane_newtonian commit c64944e14782e289284d03fcfc77fd04c3c5e2b4 Author: Ann Almgren Date: Sun Jul 28 10:44:37 2019 -0700 Add option to set max_coarsening_level. src/convection/MacProjection.cpp commit 730933fd62719090d8d273ddfb2a1cd59f08324f Author: knutsvk Date: Tue Jul 2 17:01:52 2019 +0100 biggest mesh for convergence study exec/inputs.poiseuille_plane_bingham commit 62cf9938cea09976b5f9ae5bf337804e3cb13344 Author: knutsvk Date: Sun Jun 23 17:33:56 2019 +0100 last drag coef simulation input exec/inputs.channel_cylinder_bingham commit 13a70e4d4c6dc44a0fcce1529cb4c573940093aa Author: knutsvk Date: Thu Jun 20 19:02:21 2019 +0100 this was the last inputs run in convergence test for drag coef exec/inputs.channel_sphere commit 1bd6b336d80c312c625513d6dd70a340e8a0b664 Author: knutsvk Date: Thu Jun 20 14:08:57 2019 +0100 try to check if we get the right drag force for newtonian sphere exec/inputs.channel_sphere src/advance.cpp commit 40832815f9c70140a43ae8851e0b2f44ad70d7a7 Author: knutsvk Date: Thu Jun 20 12:57:53 2019 +0100 compute drag along z-direction to fit with our EB paper resluts exec/inputs.channel_cylinder src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/derive/derive.cpp src/setup/init_fluid.f90 commit 899cb79891654cb08f5fe0112d11875af5ba9219 Author: knutsvk Date: Wed Jun 19 18:00:00 2019 +0100 computation of drag now works in parallel exec/inputs.channel_cylinder src/advance.cpp src/derive/derive.cpp src/incflo.H src/setup/incflo_arrays.cpp commit aad7e95ba903c39a6c33d81ef30e4630e1e24fd4 Author: knutsvk Date: Wed Jun 19 16:46:18 2019 +0100 change inputs file exec/inputs.channel_cylinder commit 7cac4027183971ce1bda029ade0572de188f3255 Author: knutsvk Date: Wed Jun 19 16:40:02 2019 +0100 this works when running on a single core exec/inputs.channel_cylinder src/derive/derive.cpp commit a500611651aa177af1a54467e8d22c0919565618 Author: knutsvk Date: Wed Jun 19 00:22:53 2019 +0100 bug is inside ComputeDragForce exec/inputs.channel_cylinder src/derive/derive.cpp commit 272093d72c35144675a28c840d9fde8937379bf3 Author: knutsvk Date: Tue Jun 18 18:02:34 2019 +0100 still something off..: exec/inputs.channel_cylinder commit 59c5dcea1a961174fff900f831c770ea74d22cf3 Author: knutsvk Date: Tue Jun 18 16:34:51 2019 +0100 try to recreate esults from matlab tutorial video exec/inputs.channel_cylinder src/derive/derive.cpp src/setup/init_fluid.f90 commit 5c9d7cd2b0cf18c77b2fdd3eb6a23acd938973ea Author: knutsvk Date: Mon Jun 17 15:35:28 2019 +0100 start working on drag force computation src/advance.cpp src/derive/derive.cpp src/incflo.H commit 0bce152e15a5286b24e84c4e2e327b2fe2d008e1 Author: Ann Almgren Date: Mon Jun 10 19:19:43 2019 -0700 Update to fit with amrex changes src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp commit a896493aa6199400951add3b0985227d3a44dc82 Author: knutsvk Date: Mon Jun 3 09:29:47 2019 +0200 remove dependencies on blitz and algoim README.md exec/GNUmakefile src/extern/algoim/LICENSE src/extern/algoim/README.md src/extern/algoim/examples/examples_quad.cpp src/extern/algoim/src/algoim_blitzinc.hpp src/extern/algoim/src/algoim_boundingbox.hpp src/extern/algoim/src/algoim_gaussquad.hpp src/extern/algoim/src/algoim_interval.hpp src/extern/algoim/src/algoim_multiloop.hpp src/extern/algoim/src/algoim_quad.hpp src/extern/algoim/src/algoim_real.hpp src/extern/algoim/src/algoim_utility.hpp test/GNUmakefile commit 8f62de62391e5f9008b35c2fdf89c80c9622d922 Merge: 828c7cc7 499c560a Author: Knut Sverdrup Date: Tue May 21 19:03:07 2019 +0100 Merge pull request #32 from AMReX-Codes/geometry Looks good, thanks! commit 499c560a2f0ee097021d1211a9c798f96d2db5a5 Author: Weiqun Zhang Date: Tue May 21 10:50:41 2019 -0700 prepare for upcoming changes in amrex::Geometry src/utilities/io.cpp commit 828c7cc77cbe3ecef27365f9f4636c4fe3afe83c Merge: 226d6c70 3cd6394f Author: Knut Sverdrup Date: Fri May 10 13:01:56 2019 +0100 Merge pull request #31 from AMReX-Codes/rot-cyl Rot cyl commit 3cd6394f0b6db1031b54e2d16da4053a97f9fb5f Author: knutsvk Date: Fri May 10 12:56:09 2019 +0100 rotating cylinder in couette flow exec/inputs.couette_cylinder commit a12f162ff41a2e6a95d6dd66fe8d11e6685663f4 Author: knutsvk Date: Thu May 9 19:52:52 2019 +0100 clean up unused variables src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_eb_mod.f90 src/diffusion/eb_wallflux_mod.f90 src/incflo.H src/setup/init.cpp src/utilities/divop_mod.f90 commit 8cf9e3aa079dca182295a54058c86c013b1138bf Author: knutsvk Date: Thu May 9 19:24:49 2019 +0100 taylor couette test case works, and moves to analytical steady-state solution with exponential decay in time as expected exec/inputs.taylor_couette commit 7d8905453b82fe5f378c6bfd1febd023a19cbc14 Author: knutsvk Date: Thu May 9 18:25:23 2019 +0100 rotating cylinder works exec/inputs.rotating_cylinder src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/eb_wallflux_mod.f90 src/setup/init.cpp commit 0627cd6deb44adc57f071187bb3a512ad1c9ceb6 Author: knutsvk Date: Thu May 9 13:17:27 2019 +0100 a few comments on how to prescribe Dirichlet BC for diffusion solve src/diffusion/DiffusionEquation.cpp commit 019212eede4f0ffd4e6378b42933543cafaf8eac Author: knutsvk Date: Tue May 7 15:28:49 2019 +0100 try to prescribe velocity on cylinder -- looks like just prescribing in eb_wallflux_mod is not enough. should try prescribing the Dirichlet condition in DiffusionEquation, and also possibly fixing convective fluxes which are non-zero at EB bonudaries now... exec/inputs.rotating_cylinder src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_eb_mod.f90 src/diffusion/eb_wallflux_mod.f90 src/incflo.H src/setup/init.cpp src/utilities/divop_mod.f90 commit 226d6c70eb831900fa3e73bacda6040fe7d6cb53 Author: knutsvk Date: Tue May 7 10:40:08 2019 +0100 move the cylinders further apart exec/inputs.couette_twocylinders commit b5a722f7a5c1e66e6b5d214311bc748edc0bfa58 Author: knutsvk Date: Sun May 5 14:04:28 2019 +0100 mfix tracker mfix_tracker commit 660ad921d099df0be5fa84a2efc35e2a7f799761 Author: knutsvk Date: Sun May 5 14:01:20 2019 +0100 gp copy nComp mfix_tracker src/setup/incflo_arrays.cpp commit c8467dc780145ec3a6fbe0d890d3bb5aa85a64e0 Merge: 5a373040 2c6c2899 Author: knutsvk Date: Thu May 2 16:59:38 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 2c6c2899ad2bc5f9e40e1a4e578af7bd173b6371 Author: knutsvk Date: Thu May 2 09:41:04 2019 +0100 mfix_tracker mfix_tracker commit 5a37304035c767083ae14259243047bb47115841 Author: knutsvk Date: Tue Apr 30 18:32:03 2019 +0100 take eta as half of old and new values in corrector src/advance.cpp src/incflo.H src/setup/incflo_arrays.cpp commit b2bd01b6b7873813502731d5c9f4b3dc502498f0 Author: knutsvk Date: Tue Apr 30 17:31:34 2019 +0100 catch up mfix tracker exec/inputs.poiseuille_cylinder mfix_tracker src/advance.cpp src/convection/MacProjection.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp commit 327e779c49ad8b49c5b303281c8358481997fd84 Author: knutsvk Date: Tue Apr 30 15:33:21 2019 +0100 remove commented out setEBHOdirichlet call mfix_tracker src/diffusion/DiffusionEquation.cpp commit df83a1afc10841096044f777eeafb5afa7aabedc Author: knutsvk Date: Tue Apr 30 14:59:03 2019 +0100 simplify MAC coefficient update mfix_tracker src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp commit 230ba10497157bbe41f5728501413ccfb7ea8449 Author: Ann Almgren Date: Sat Apr 27 10:47:13 2019 -0700 Update bottom_solver_default for nodal projection src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp commit f0cea3e30faff3cb4c4c5f3bbeaf76e1d2ea80f2 Merge: 30274218 e89b926d Author: knutsvk Date: Sat Apr 27 12:02:36 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 302742185c5bbf5f1e18a0853e200adf40a06742 Author: knutsvk Date: Sat Apr 27 12:02:17 2019 +0100 try this higher res on csd3 exec/inputs.channel_spherecube commit e89b926d0cadd272f36458cc89551261e197566f Author: knutsvk Date: Wed Apr 24 12:18:51 2019 +0100 remove unused var index src/diffusion/eb_wallflux_mod.f90 commit 812e99817109ad10d902b8835be9d236518f4481 Author: knutsvk Date: Wed Apr 24 12:18:08 2019 +0100 dont write stress to plotfile by default src/incflo.H commit 5719f1a205cd0bafeee0498756bb5c522e1e8d1b Author: Ann Almgren Date: Tue Apr 23 16:02:03 2019 -0700 Fix bug that got introduced in computation of wall fluxes. src/diffusion/eb_wallflux_mod.f90 commit adabe7eb7766106ca5087b6b898553326fcb47f3 Author: Ann Almgren Date: Tue Apr 23 15:21:39 2019 -0700 Oops -- we need to zero out covered cells before we write the plotfile src/utilities/io.cpp commit db97bf536f11dfc09d83576e8779b557701c069a Author: Ann Almgren Date: Tue Apr 23 14:43:18 2019 -0700 Fix the plotting when more than one level (don't write the variable names twice) src/utilities/io.cpp commit 8aacfa18992bb46c471cc5e1fad3d6e8fa6ed149 Author: Ann Almgren Date: Tue Apr 23 14:07:46 2019 -0700 Make the variables in the plotfile match the CCSE regression test. src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit 21503a06b14550e10678101f1f03166ef4f75741 Author: Ann Almgren Date: Tue Apr 23 13:02:24 2019 -0700 USE_ALGOIM --> AMREX_USE_ALGOIM exec/GNUmakefile test/GNUmakefile commit 47a85dda1e7edfbf5445762b337425a16128d31e Author: Ann Almgren Date: Tue Apr 23 12:45:20 2019 -0700 areafrac's are only allocated on FABs that have cut cells, so we can't try to access them on regular FABs src/convection/convection.cpp commit 72b44c0f6eee45a4e6d9e2a811674c5d86fa6279 Author: knutsvk Date: Wed Apr 17 20:07:44 2019 +0100 bugfix: regtest plot switch src/setup/init.cpp commit ef1e7736b79b60504de793e3274a4ef0eb4725f9 Author: knutsvk Date: Tue Apr 16 19:02:30 2019 +0100 update mfix tracker mfix_tracker commit c02ac8b09735dfe0c70560a0b1041c1558b3f988 Author: knutsvk Date: Tue Apr 16 18:59:42 2019 +0100 simplify computation of coefficients in macprojector mfix_tracker src/convection/MacProjection.H src/convection/MacProjection.cpp commit 28fdfbea6598be9903ef0ed6234953ce6f834015 Author: knutsvk Date: Tue Apr 16 17:34:35 2019 +0100 need to set the regtest fflag so that all variables are written to plotfile in benchmark test/benchmark.channel_cylinder test/benchmark.channel_spherecube test/benchmark.couette test/benchmark.couette_poiseuille test/benchmark.double_shear_layer test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian test/benchmark.taylor_green_vortices test/benchmark.uniform_velocity_sphere commit 6af707f2bd0b1eb8439caa8bbf102935cb84fedd Author: knutsvk Date: Tue Apr 16 17:31:10 2019 +0100 control which variables to plot exec/inputs.channel_cylinder mfix_tracker src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit 13512443d4ebef8a8eafc28a1b73b90dce289461 Author: knutsvk Date: Mon Apr 15 12:10:49 2019 +0100 update mfix_tracker mfix_tracker commit c0d598f652ea5907a80df6334fe313c81f765ff4 Author: knutsvk Date: Mon Apr 15 12:09:08 2019 +0100 move correct_slopes to C++ mfix_tracker src/convection/Make.package src/convection/convection.cpp src/convection/convection_F.H src/convection/slopes_mod.f90 commit 99bf7ef43e3d8254517e3af2705059103040509e Author: knutsvk Date: Mon Apr 15 11:54:40 2019 +0100 move computation of MAC vel at faces to c++, rename convection module to ugradu module since that is the only stuff still in those files src/convection/Make.package src/convection/convection.cpp src/convection/convection_F.H src/convection/ugradu_eb_mod.f90 src/convection/ugradu_mod.f90 commit d078768ef71880287d797560cc3f7c624c0fb15d Author: knutsvk Date: Mon Apr 15 11:45:24 2019 +0100 need to pass vfrac to the new dphidn call src/diffusion/eb_wallflux_mod.f90 src/utilities/divop_mod.f90 commit 6357cf12ebe8817aa03850fdadf2c207fa99143e Author: knutsvk Date: Mon Apr 15 10:50:56 2019 +0100 try the new LO stencil src/diffusion/eb_wallflux_mod.f90 commit 87295cc8a781ac010f05fc8a2a334b02fd9c2392 Merge: 90889259 37c612dd Author: knutsvk Date: Mon Apr 8 23:03:26 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 90889259bac8af3bbc8670731ffde0bca2b4f45f Author: knutsvk Date: Mon Apr 8 23:00:49 2019 +0100 default to not using hypre exec/GNUmakefile exec/inputs.poiseuille_cylinder commit b0910e6211c8765ee4a67a6b91c698de30709d9c Author: knutsvk Date: Mon Apr 8 22:57:56 2019 +0100 managed to run with hypre, but it was twice as slow for our problem exec/GNUmakefile exec/inputs.poiseuille_cylinder commit 37c612dd110569771d2628de416e921d74137b1d Author: knutsvk Date: Mon Apr 8 21:15:58 2019 +0100 no hypre support on battra (regtest machine) src/projection/PoissonEquation.H test/GNUmakefile commit ec68dc951e95c98ab59b88b7da692908475df9ff Author: knutsvk Date: Mon Apr 8 20:00:49 2019 +0100 try to run the regtests with HYPRE src/projection/PoissonEquation.H test/GNUmakefile commit 676a6cfd6d10519117b60dd6bbc4b4f60095d84f Author: knutsvk Date: Mon Apr 8 19:45:48 2019 +0100 want to try HYPRE on this case which breaks for MLMG, but so far unable to build with HYPRE... exec/GNUmakefile exec/inputs.poiseuille_cylinder commit 4967cce83ddcba487f71a7b698617e0c777c27b0 Author: knutsvk Date: Mon Apr 8 18:46:25 2019 +0100 update mfix tracker mfix_tracker commit 1aabdaab4959ec71bd0cf0e7c16caf8ebab9d7c8 Author: knutsvk Date: Mon Apr 8 18:44:40 2019 +0100 Track updates: 1. Allow the use of HYPRE solver for PoissonEquation (TODO: test runtime) 2. Fix hack to set coefficients in DiffusionEquation 3. Get rid of more Fortran exec/GNUmakefile src/convection/convection.cpp src/convection/convection_F.H src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/incflo.H src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp commit 3e4c06b1bbb444c04e2e1f44eafb1852d9daf8ae Author: knutsvk Date: Mon Apr 8 16:50:21 2019 +0100 fix: need nghost = 5 for some cut cell cases exec/inputs.poiseuille_cylinder src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/incflo.H src/utilities/divop_mod.f90 commit a8e73981d1275c561f9c908937c7c5cb745c4524 Merge: 9f8c44a2 83204e79 Author: knutsvk Date: Mon Apr 8 14:49:37 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 9f8c44a2bb17dcb229a4adad140867c553dfbd99 Author: knutsvk Date: Mon Apr 8 14:48:32 2019 +0100 try to get this to work exec/inputs.poiseuille_cylinder commit 83204e79e61786fcdb5d5994ba33c060adb4df23 Merge: 644aed3e 28210974 Author: knutsvk Date: Mon Apr 8 09:17:12 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 644aed3e91ee582d1fd53c3ac57655ab4b404376 Author: knutsvk Date: Mon Apr 8 09:17:04 2019 +0100 update ryos case 1 inputs exec/inputs.couette_cylinder commit 28210974c7e175c5d42d2a5341f194c674546de5 Author: knutsvk Date: Sat Apr 6 18:49:13 2019 +0100 avoid domains with fewer than 8 cells in each direction exec/inputs.channel_cylinder exec/inputs.couette exec/inputs.lid_driven_cavity exec/inputs.poiseuille_cylinder exec/inputs.uniform_velocity_sphere test/benchmark.channel_cylinder test/benchmark.couette test/benchmark.double_shear_layer test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham commit e03ad11e4a739e803ee54be6c744f807421f52fe Author: knutsvk Date: Sat Apr 6 16:42:28 2019 +0100 add test files to gitignore .gitignore commit d30ab2ca1bd92ff0eb84bc63269e3b64747f3185 Author: knutsvk Date: Fri Apr 5 18:59:27 2019 +0100 add two-cylinder couette flow case (Ryo) exec/inputs.couette_twocylinders src/embedded_boundaries/Make.package src/embedded_boundaries/eb_twocylinders.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit 683c779ba35b8d42bc660fb056811edd2d8ba29a Author: knutsvk Date: Fri Apr 5 15:43:39 2019 +0100 simulate smaller domain exec/inputs.couette_cylinder commit 58a9c7e98dce8a0f3b7a266dd90ac057c50237aa Author: knutsvk Date: Fri Apr 5 15:22:01 2019 +0100 smaller dt exec/inputs.couette_cylinder commit 234cf473fa0620811331f796f2a7c725267557a9 Author: knutsvk Date: Fri Apr 5 14:53:30 2019 +0100 couette cylinder run with bingham fluid, Ryos paramter values2 exec/inputs.couette_cylinder src/setup/init_fluid.f90 commit 666918e0ed5f0d0d252463d962ad1c6af50477ca Author: knutsvk Date: Fri Apr 5 12:26:14 2019 +0100 ryos case 1 exec/inputs.couette_cylinder commit 384e9b7cbe40527468f8e22d07f2b0ae958951e6 Author: knutsvk Date: Fri Apr 5 12:25:52 2019 +0100 add some whitespace exec/inputs.channel_cylinder commit f85fa717331963577cc2c0b7276e79e443529c34 Author: knutsvk Date: Fri Apr 5 11:11:49 2019 +0100 track mfix: update settings for the different solvers mfix_tracker src/advance.cpp src/convection/MacProjection.H src/convection/MacProjection.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit a7ceeb2b321208050f5572e3ab79ac5bc53904d3 Author: knutsvk Date: Fri Apr 5 10:33:38 2019 +0100 track mfix mfix_tracker src/utilities/io.cpp commit ae3470f29befe338f6df914052b8d92f6d8e9ad7 Author: knutsvk Date: Thu Apr 4 18:36:17 2019 +0100 bugfix: + -> * src/diffusion/diffusion_mod.f90 commit 22b37ee3a1298dc59a545b74815a10429a0cef0b Author: knutsvk Date: Thu Apr 4 10:43:34 2019 +0100 (1) remove explicit_diffusion option: always use semi-implicit diffusion (2) add and improve comments in code src/advance.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/eb_wallflux_mod.f90 src/incflo.H src/projection/projection.cpp src/setup/init.cpp src/utilities/divop_mod.f90 commit ae980a06fdec5ef435d86705bbf7eca1f169b855 Author: knutsvk Date: Wed Apr 3 17:51:48 2019 +0100 revert the previous commit. it was correct the way it was. not just from looking at the results, but after thoroughly examining the code again B-) src/diffusion/eb_wallflux_mod.f90 commit 4708c50fa2dd4dd019e1235b79cce731866a0a0f Author: knutsvk Date: Tue Apr 2 20:15:29 2019 +0100 confused about the explicit/implicit terms again -- want to see how this change alters the benchmark tests src/diffusion/eb_wallflux_mod.f90 commit e9aa4d2378348bac72c27518c0c277d1a4a8d8db Author: knutsvk Date: Tue Apr 2 07:34:17 2019 +0100 catch up to mfix mfix_tracker src/convection/MacProjection.H commit 139aee469d0d457dfb1e0f1bc0bda3adc4ea8a76 Author: knutsvk Date: Thu Mar 28 18:28:44 2019 +0000 move cylinder (geometry) before BCs in inputs file exec/inputs.channel_cylinder commit b9fbb983e800f33f9907de5b8b4bcdaed4f630a3 Author: knutsvk Date: Thu Mar 28 17:58:48 2019 +0000 update mfix tracker mfix_tracker commit 5ce6dd8874352cdb30888ebb25841d789a330ce0 Author: knutsvk Date: Thu Mar 28 17:54:11 2019 +0000 add spherecube benchmark test test/benchmark.channel_spherecube test/incflo-tests.ini commit 60ff6fd5ecf6417391528c2cf684b49eecae562a Author: knutsvk Date: Thu Mar 28 17:49:23 2019 +0000 this spherecube works as a first example exec/inputs.channel_spherecube src/embedded_boundaries/eb_spherecube.cpp commit 51e2cc73e6a1a30d2af0cadde8091a04deba644f Author: knutsvk Date: Wed Mar 27 19:03:43 2019 +0000 making spherecube problem exec/inputs.channel_spherecube src/embedded_boundaries/Make.package src/embedded_boundaries/eb_spherecube.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit 66ec5819eab802a3f1dd4f9ebf72265981ae164d Author: knutsvk Date: Wed Mar 27 20:42:50 2019 +0000 use high-order version of compute_dphidn_3d (amrex changed the function handle) src/diffusion/eb_wallflux_mod.f90 commit c22996e4a0c51b8192019656cbf2396bc184f372 Author: knutsvk Date: Wed Mar 27 19:45:49 2019 +0000 bugfix: removed one FillVelocityBC call to many src/advance.cpp commit f246fd384e0cc69a518635b46bf428260f61585d Author: knutsvk Date: Tue Mar 26 20:06:48 2019 +0000 cyclicicty in vector src/setup/incflo_to_fortran.F90 src/setup/init.cpp src/setup/setup_F.H commit c4367222f03c22e1b200b213e90174e900923b28 Author: knutsvk Date: Tue Mar 26 19:51:09 2019 +0000 set periodicity (Fortran variables) in incflo_to_fortran module, previously amrex_to_incflo src/boundary_conditions/bc_mod.f90 src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_velocity_bcs.f90 src/setup/Make.package src/setup/incflo_to_fortran.F90 src/setup/init.cpp src/setup/setup_F.H commit 711242b0d4fbc71bddb668fdc3d409c533c74b6b Author: knutsvk Date: Mon Mar 25 23:29:48 2019 +0000 remove what I think are unnecessary calls to FillVelocityBC. remember to check benchmarks src/advance.cpp commit d9a901bc2c66b8f2b0df09e3d48690dcf29ac319 Merge: ced1e9ab 22b16440 Author: knutsvk Date: Sun Mar 24 10:47:39 2019 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit ced1e9ab657d9d73aadb0b969dbf89cd8ca69f80 Author: knutsvk Date: Sun Mar 24 10:47:12 2019 +0000 use EB interpolation routine from amrex mfix_tracker src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/convection_eb_mod.f90 src/embedded_boundaries/Make.package src/embedded_boundaries/eb_interpolation_mod.f90 src/utilities/divop_mod.f90 commit 22b16440ee34fc6ceb76ff12dd60708845b7c23b Merge: 204ad344 8b3557c5 Author: knutsvk Date: Fri Mar 22 13:24:34 2019 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 204ad344bbaf5a91a7a5776bb4f235edb428b303 Author: knutsvk Date: Fri Mar 22 13:24:11 2019 +0000 max_lev > 1 not yet suppoted, changing ng from 5 to 4 caused benchmark to crash test/benchmark.uniform_velocity_sphere commit 8b3557c580f7b0d6e4699116d3fb73077a2c4150 Author: knutsvk Date: Thu Mar 21 19:57:52 2019 +0000 reduce number of ghost cells from 5 to 4 src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/incflo.H src/utilities/divop_mod.f90 commit 8a6b9e4ac6db53496fd0fc756a28d127d4de9c5d Author: knutsvk Date: Wed Mar 20 17:37:07 2019 +0000 max_step = 1 test/benchmark.uniform_velocity_sphere commit 2e724e753cb4ad9e6ed709f56c2bf0ab6a99a8cd Author: knutsvk Date: Wed Mar 20 16:52:23 2019 +0000 make benchmark test runtimes shorter test/benchmark.channel_cylinder test/benchmark.couette_poiseuille test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian commit 9f8ba0b22ac40cdf99d2211c312b92194e09e10e Author: knutsvk Date: Wed Mar 20 13:24:44 2019 +0000 added the incflo-tests.ini file used for regtesting test/incflo-tests.ini commit ae8648bb6600476992b7e4f8abc142b5f4683bd3 Merge: f56ee381 3f8b8a00 Author: knutsvk Date: Wed Mar 20 13:19:17 2019 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit f56ee3814c486032d4316a9f07c2a7fcb4cbad29 Author: knutsvk Date: Wed Mar 20 13:19:07 2019 +0000 add benchmark test cases test/benchmark.channel_cylinder test/benchmark.couette test/benchmark.couette_poiseuille test/benchmark.lid_driven_cavity test/benchmark.poiseuille_cylinder_bingham test/benchmark.poiseuille_cylinder_newtonian test/benchmark.poiseuille_plane_bingham test/benchmark.poiseuille_plane_newtonian test/benchmark.taylor_green_vortices test/benchmark.uniform_velocity_sphere commit 3f8b8a005707c6806a0460020116ba1b354ad107 Author: Ann Almgren Date: Tue Mar 19 14:07:00 2019 -0700 Add BLITZ_HOME to include list. test/GNUmakefile commit 1cbfde1613ae91a2fa0b684e7f6fc724eda2bc0b Author: knutsvk Date: Tue Mar 19 16:29:45 2019 +0000 put for loop over levels inside FillScalarBC(), apply to both ro and eta every time src/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/incflo.H src/setup/incflo_arrays.cpp src/setup/init.cpp commit 941c9e2e784c667aac74c2aba55d6f741461cbbc Merge: 43e9f4ec 82325506 Author: Knut Sverdrup Date: Tue Mar 19 15:10:54 2019 +0000 Merge pull request #27 from AMReX-Codes/benchmark Benchmark commit 823255066d093ab86577cc3de26b1fba4f895a0e Author: knutsvk Date: Tue Mar 19 15:09:39 2019 +0000 a few comments test/README.md commit 521932a2010926833491b438de342c4652a78f24 Author: knutsvk Date: Tue Mar 19 15:05:23 2019 +0000 see if this works with incflo-tests.ini file sent to Ann test/GNUmakefile test/benchmark.double_shear_layer test/incflo-tests.ini commit 26ccfe066a56f0a618bcf2b59b6e74a34a96854d Author: knutsvk Date: Tue Mar 19 14:13:45 2019 +0000 try to do a test run of benchmarking on tycho test/benchmark.double_shear_layer test/incflo-tests.ini commit e792003ce0d32d0a5027adba47d68b510ac86cf7 Author: knutsvk Date: Mon Mar 18 19:12:29 2019 +0000 add test directory with README explaining the benchmarking suite and an initial incflo.tests.ini file README.md test/README.md test/incflo-tests.ini commit 43e9f4ec6510634089b9bbb52b380e0b1a075716 Merge: c0a52b9d 4d24e838 Author: Knut Sverdrup Date: Tue Mar 19 13:59:33 2019 +0000 Merge pull request #26 from AMReX-Codes/debug_ann Debug ann commit 4d24e838c920208f871a7916982d44ed40cec2ff Author: knutsvk Date: Tue Mar 19 13:58:13 2019 +0000 debug complete - channel_cylinder working properly with restart and everything exec/GNUmakefile exec/inputs.channel_cylinder commit 6ff1a5ea0d31c2aab79a87f8e091e3bbf5c478d0 Author: knutsvk Date: Tue Mar 19 13:45:33 2019 +0000 bugfix: set covered cells to zero in I/O src/utilities/io.cpp commit 148eb6c3e3c3341a692a6bad88390815afd2fc38 Author: knutsvk Date: Tue Mar 19 13:36:17 2019 +0000 introduce member variable boundary_val which ghost cells are set to (and reshuffle incflo.H) src/boundary_conditions/boundary_conditions.cpp src/incflo.H commit 546e48578429ee1f1d0bea44f242897c3096f954 Author: knutsvk Date: Tue Mar 19 13:14:14 2019 +0000 bugfix: covered cells must be set to zero when computing norms src/convection/MacProjection.H src/convection/MacProjection.cpp src/setup/init.cpp src/utilities/diagnostics.cpp commit 377e47c42a58bb01cc82d3ca97833687ec479d57 Author: knutsvk Date: Tue Mar 19 12:17:29 2019 +0000 add variable covered_val to incflo.H instead of using random numbers everywhere src/boundary_conditions/boundary_conditions.cpp src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/convection.cpp src/diffusion/diffusion.cpp src/incflo.H src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit f2018b1cc7013ccb28c8894dcb94e17740434011 Author: knutsvk Date: Tue Mar 19 11:55:09 2019 +0000 remove print statements src/boundary_conditions/boundary_conditions.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_eb_mod.f90 commit ce6ab9b1dce864fd2b38cefe760997a84bee579b Author: knutsvk Date: Tue Mar 19 11:50:11 2019 +0000 bugfix: fill ghost cells for all valid BC types (copy value in domain) src/boundary_conditions/fill_bc0.f90 commit b42dcaa5a948fb133e9df8dd91954d9487e9f732 Author: knutsvk Date: Tue Mar 19 11:49:31 2019 +0000 remove print statement, add TODO comments to remove superfluous FillVelocityBC calls src/advance.cpp commit 1fa980bb423bc4c1b54d8df7f6f0ce5e29d41b4a Author: Ann Almgren Date: Mon Mar 18 14:20:36 2019 -0700 Commit code with debugging print statements -- inflow bc's need to be set for eta exec/inputs.channel_cylinder src/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_eb_mod.f90 commit c0a52b9d9fb6772af812651b98c29f6b95771cde Author: knutsvk Date: Mon Mar 18 19:05:25 2019 +0000 inputs file to show NaN appearance after restart exec/GNUmakefile exec/inputs.channel_cylinder commit 03fabfa9b3d6ee508f50e063a3d5c262d0ee066c Author: knutsvk Date: Mon Mar 18 19:01:06 2019 +0000 there is a loop over levels inside the FillVelocityBCs function src/setup/init.cpp commit 5c60e02b761c34ea2315e4f5bae82d3b24d010ea Merge: 34bc1755 47bce1a3 Author: knutsvk Date: Mon Mar 18 18:35:29 2019 +0000 merge with Anns hack commit 34bc175562c885fe45512a95e603768b4dbefed6 Author: knutsvk Date: Mon Mar 18 18:33:43 2019 +0000 remove unused BCRecs src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/derive/derive.cpp src/incflo.H src/setup/incflo_arrays.cpp commit 47bce1a34a4083fad6a8d7d89ee3d5dbf23907d0 Author: Ann Almgren Date: Mon Mar 18 11:27:04 2019 -0700 This seems to fix the problem with dying in the boundary fill routine due to undefined values. src/boundary_conditions/boundary_conditions.cpp commit 2fe65f27b5c9b589018e3bb5ecb8d9ad8f706dd3 Author: knutsvk Date: Mon Mar 18 15:21:53 2019 +0000 whitespce src/diffusion/diffusion.cpp commit 7a56ffa717352ec8c5d61d695c4458a40e4808d1 Author: knutsvk Date: Mon Mar 18 13:44:13 2019 +0000 FillBoundary -> FillVelocityBC src/setup/init.cpp commit 27c00d9be05ad4127d986cc44aa112a73623f787 Author: knutsvk Date: Mon Mar 18 13:43:55 2019 +0000 also check ro for nans src/utilities/diagnostics.cpp commit 6073686d1281b5a13fe227365cb42a6860e77938 Author: knutsvk Date: Mon Mar 18 12:19:58 2019 +0000 poiseuille_cylinder problem got left out earlier exec/inputs.poiseuille_cylinder commit 92e260a9719fd0e90ad243574ecd7f4eb31d87e0 Author: knutsvk Date: Mon Mar 18 11:00:33 2019 +0000 update gitignore after one less depth of directories in exec/ .gitignore commit 94ce08753505053eab2e6e66f37d2e0f91326231 Merge: 89f34ed9 1fec3cb2 Author: Knut Sverdrup Date: Sun Mar 17 19:17:03 2019 +0000 Merge pull request #25 from AMReX-Codes/poisson_dirichlet Poisson dirichlet commit 1fec3cb22e3edbb4ab2bd94f63fa732353be598f Author: knutsvk Date: Sun Mar 17 19:03:02 2019 +0000 since problems are now uniquely defined by their inputs file, we dont need separate directories for each problem README.md exec/GNUmakefile exec/channel_cylinder/GNUmakefile exec/channel_cylinder_bingham/GNUmakefile exec/channel_sphere/GNUmakefile exec/couette_plane/GNUmakefile exec/couette_poiseuille/GNUmakefile exec/double_shear_layer/GNUmakefile exec/inputs.channel_cylinder exec/inputs.channel_cylinder_bingham exec/inputs.channel_sphere exec/inputs.couette exec/inputs.couette_poiseuille exec/inputs.double_shear_layer exec/inputs.lid_driven_cavity exec/inputs.poiseuille_annulus exec/inputs.poiseuille_plane_bingham exec/inputs.poiseuille_plane_newtonian exec/inputs.taylor_green_vortices exec/inputs.uniform_velocity_sphere exec/lid_driven_cavity/GNUmakefile exec/poiseuille_annulus/GNUmakefile exec/poiseuille_annulus/plot_velocity_profile.py exec/poiseuille_annulus/visit.curve exec/poiseuille_cylinder/GNUmakefile exec/poiseuille_cylinder/inputs exec/poiseuille_plane_bingham/GNUmakefile exec/poiseuille_plane_newtonian/GNUmakefile exec/taylor_green_vortices/GNUmakefile exec/uniform_velocity_sphere/GNUmakefile commit 77561ba5867e9743ab93b6d1d656a80fb03edf31 Author: knutsvk Date: Sun Mar 17 18:08:34 2019 +0000 use probtype from inputs file to set problem-specific BCs src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/mac_F.H src/incflo.H src/setup/init.cpp commit bfbe53227edd341ab92ce934a64dc52a8bfd393b Author: knutsvk Date: Sun Mar 17 18:07:53 2019 +0000 typo: prob_type -> probtype exec/channel_cylinder/GNUmakefile exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 commit 0034edac68294135c511044c01d4ffe522ae5886 Author: knutsvk Date: Sat Mar 16 23:42:11 2019 +0000 introduce probtype flag to inputs file rather than keeping separate init_fluid.f90 files for each test case exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/double_shear_layer/init_fluid.f90 exec/double_shear_layer/inputs exec/taylor_green_vortices/init_fluid.f90 exec/taylor_green_vortices/inputs src/incflo.H src/setup/init.cpp src/setup/init_fluid.f90 src/setup/setup_F.H commit 9f936ec08b751172230500d5a1f68da232d027a4 Author: knutsvk Date: Sat Mar 16 22:37:00 2019 +0000 remove unused module bc_fill_nd src/boundary_conditions/Make.package src/boundary_conditions/bc_fill_nd.F90 commit ed828efef53f02aa379a98896e8eb5ffbbca33f9 Author: knutsvk Date: Sat Mar 16 19:53:48 2019 +0000 major cleanup. after also moving ICs to inputs file, incflo.dat is obsolete along with lots of outdated fortran code exec/Make.incflo exec/channel_cylinder/incflo.dat exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 exec/channel_cylinder_bingham/incflo.dat exec/channel_cylinder_bingham/inputs exec/channel_sphere/incflo.dat exec/channel_sphere/inputs exec/couette_plane/incflo.dat exec/couette_poiseuille/incflo.dat exec/double_shear_layer/incflo.dat exec/double_shear_layer/init_fluid.f90 exec/lid_driven_cavity/incflo.dat exec/poiseuille_annulus/incflo.dat exec/poiseuille_cylinder/incflo.dat exec/poiseuille_plane_bingham/incflo.dat exec/poiseuille_plane_newtonian/incflo.dat exec/taylor_green_vortices/incflo.dat exec/taylor_green_vortices/init_fluid.f90 exec/uniform_velocity_sphere/incflo.dat exec/uniform_velocity_sphere/inputs src/boundary_conditions/bc_mod.f90 src/boundary_conditions/set_velocity_bcs.f90 src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 src/convection/slopes_mod.f90 src/derive/derive_eb_mod.f90 src/derive/derive_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/eb_wallflux_mod.f90 src/embedded_boundaries/eb_interpolation_mod.f90 src/embedded_boundaries/get_eb_walls.f90 src/incflo.H src/include/initial_conditions.inc src/projection/projection_mod.f90 src/rheology/rheology_mod.f90 src/setup/Make.package src/setup/amrex_to_incflo.F90 src/setup/ic_mod.f90 src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc_type.f90 src/setup/set_delp_dir.f90 src/setup/set_p0.f90 src/setup/setup_F.H src/utilities/Make.package src/utilities/constant_mod.f90 src/utilities/divop_mod.f90 src/utilities/param_mod.f90 src/utilities/read_namelist.f90 src/utilities/utilities_mod.f90 commit ae223a07da3a57c6291e2874b2039013d967d982 Author: knutsvk Date: Sat Mar 16 18:22:53 2019 +0000 initial conditions are now applied to entire domain, which allows us to retire more old code exec/channel_cylinder/incflo.dat exec/channel_cylinder_bingham/incflo.dat exec/channel_sphere/incflo.dat exec/uniform_velocity_sphere/incflo.dat exec/uniform_velocity_sphere/inputs src/include/initial_conditions.inc src/setup/Make.package src/setup/calc_cell.f90 src/setup/ic_mod.f90 src/setup/init_fluid.f90 src/setup/set_p0.f90 src/utilities/read_namelist.f90 commit 449a08f89473066d164bc5086aa819bd8171bd26 Author: knutsvk Date: Sat Mar 16 16:45:22 2019 +0000 get rid of dim_ic - only allow constant initial conditions throughout domain unless using a custom init_fluid() function for the problem exec/channel_cylinder/incflo.dat exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder_bingham/incflo.dat exec/channel_sphere/incflo.dat exec/double_shear_layer/init_fluid.f90 exec/uniform_velocity_sphere/incflo.dat src/setup/ic_mod.f90 src/setup/init_fluid.f90 src/setup/set_p0.f90 src/utilities/param_mod.f90 commit b2e1bd7bf0310b2281d358e294acb4d43537db40 Author: knutsvk Date: Sat Mar 16 16:16:06 2019 +0000 dont need separate init_fluid.f90 file for this case anymore exec/uniform_velocity_sphere/init_fluid.f90 commit e78ebac86d75e6dc9293859347e8b84e03aee69d Author: knutsvk Date: Sat Mar 16 16:14:00 2019 +0000 simplify ICs: can set uniform velocity direcly through incflo.dat file exec/uniform_velocity_sphere/incflo.dat exec/uniform_velocity_sphere/init_fluid.f90 commit 0403edb1e770c3521a8e339823db7ae5d36c6576 Author: knutsvk Date: Sat Mar 16 15:21:11 2019 +0000 pass delp through inputs file in all problems exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs exec/couette_poiseuille/incflo.dat exec/couette_poiseuille/inputs exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane_bingham/incflo.dat exec/poiseuille_plane_bingham/inputs exec/poiseuille_plane_newtonian/inputs commit 6110e80c5ca1828339baae2e223b397706e2e623 Author: knutsvk Date: Fri Mar 15 20:57:18 2019 +0000 compile in debug mode to trap NaN in VelFillBox exec/channel_cylinder/GNUmakefile commit 0652013f4c19162e2e58ca88a8898b2fbe09a4e8 Author: knutsvk Date: Fri Mar 15 20:38:16 2019 +0000 poiseuille_plane_newtonian works with the new delp exec/poiseuille_plane_newtonian/incflo.dat exec/poiseuille_plane_newtonian/inputs commit 27224bc45820ffad80361daa2ef220fee8513177 Author: knutsvk Date: Fri Mar 15 20:30:56 2019 +0000 this works when the x and y walls are periodic, but not othewise exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs commit 24d12e9958bd0b89b1f5c5f5bc0bf12e6a2dfa34 Author: knutsvk Date: Fri Mar 15 19:57:58 2019 +0000 try to set initial conditions to zero again exec/poiseuille_cylinder/incflo.dat commit c6d0bff53df6db168165ac4ed734b5d8393f4637 Author: knutsvk Date: Fri Mar 15 19:57:38 2019 +0000 lowercase set_bc_mod src/setup/set_bc_type.f90 commit dec600eb2bada643399661c15e7eb6e2f426d48e Author: knutsvk Date: Fri Mar 15 18:44:56 2019 +0000 try to move delp setting to inputs file rather than incflo.dat exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs src/boundary_conditions/bc_mod.f90 src/incflo.H src/include/geometry.inc src/setup/amrex_to_incflo.F90 src/setup/init.cpp src/setup/set_delp_dir.f90 src/setup/set_p0.f90 src/setup/setup_F.H src/utilities/constant_mod.f90 src/utilities/read_namelist.f90 commit 5323b667e33264529c1f5d4f5ad955c197100f72 Author: knutsvk Date: Fri Mar 15 18:21:48 2019 +0000 combine remove_comment module into utilities module src/utilities/Make.package src/utilities/read_namelist.f90 src/utilities/remove_comment.f90 src/utilities/utilities_mod.f90 commit af405371ff92d14cf8db1c4ffad3b271338f2e42 Author: knutsvk Date: Fri Mar 15 17:57:46 2019 +0000 more fortran cleanup src/boundary_conditions/bc_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/calc_cell.f90 src/setup/set_bc_type.f90 src/setup/set_p0.f90 src/utilities/param_mod.f90 src/utilities/read_namelist.f90 commit bce89595f7fcccee67c72830e2319bf1d0ced00c Author: knutsvk Date: Fri Mar 15 17:29:14 2019 +0000 cleanup param and constant modules src/utilities/constant_mod.f90 src/utilities/param_mod.f90 commit e58577eaa503e20e2cee1aed1cba6b227dc2b2c1 Author: knutsvk Date: Fri Mar 15 17:28:45 2019 +0000 bracketize if statement src/setup/init.cpp commit 7afb2ee06286bcbb1ff86919557ab3c2b1ff22ea Author: knutsvk Date: Fri Mar 15 17:05:20 2019 +0000 try to get rid of get_data and init_namelist, and initialize directly in fortran modules src/boundary_conditions/bc_mod.f90 src/setup/Make.package src/setup/amrex_to_incflo.F90 src/setup/get_data.f90 src/setup/ic_mod.f90 src/setup/init_namelist.f90 commit 3a4727b5914ac4c83996e7495d8c8b8c9479d96a Author: knutsvk Date: Fri Mar 15 17:04:46 2019 +0000 get rid of unused variables src/utilities/param_mod.f90 commit a15a29e75f9d1e0210caa2a26af4bf2d6bdee327 Author: knutsvk Date: Fri Mar 15 17:03:16 2019 +0000 lowercase module name src/setup/calc_cell.f90 commit d77d340753b24259d7ca6ea2e2ec5cb89f0e06be Author: knutsvk Date: Fri Mar 15 16:55:20 2019 +0000 remove unused member multifab flag, this is always found on the fly when needed src/incflo.H commit 7812023bde74726013711edea664d37a37975a8a Author: knutsvk Date: Fri Mar 15 16:54:48 2019 +0000 remove unused variable in order to get rid of compiler warnings src/convection/convection.cpp src/diffusion/diffusion.cpp src/embedded_boundaries/get_eb_walls.f90 src/incflo.cpp src/include/initial_conditions.inc src/setup/set_bc_type.f90 src/utilities/read_namelist.f90 commit 3583c6090d5b10ee3588b942b7ab47468bb91c77 Author: knutsvk Date: Fri Mar 15 16:49:52 2019 +0000 remove unused variable direction from sphere geometry src/embedded_boundaries/eb_sphere.cpp commit a7f4b61267acd777c0332af504153e234e1374d5 Author: knutsvk Date: Fri Mar 15 16:49:25 2019 +0000 remove unused variable e_i src/diffusion/diffusion_mod.f90 commit 124666338cc323a8d8a75bc02aee365e80974996 Author: knutsvk Date: Fri Mar 15 16:46:53 2019 +0000 less verbose compilation exec/Make.incflo commit d4d12ce8f3f7c9037bfb7d0c9d6398da4c53e293 Author: knutsvk Date: Fri Mar 15 16:46:19 2019 +0000 alter inputs exec/channel_cylinder/inputs commit 3c5e4bad632a8ccc34e21be3e36391e24fe1e6ad Author: knutsvk Date: Fri Mar 15 16:44:54 2019 +0000 remove unused variables exec/channel_cylinder/init_fluid.f90 commit ea013135f4ac454ec0cb049a9263178457543c46 Author: knutsvk Date: Fri Mar 15 13:58:43 2019 +0000 remove unused calc_cell_bc functionality src/setup/calc_cell.f90 src/setup/set_bc_type.f90 commit 1af6aa9dd5aea63ea5f402d060f7be46ec5ba32b Author: knutsvk Date: Fri Mar 15 13:58:07 2019 +0000 update mfix tracker mfix_tracker commit df83ce734d9e91540fec6006987bde82f6b76e39 Author: knutsvk Date: Fri Mar 15 12:42:46 2019 +0000 check that poiseuille_cylinder works with n_cell 64 64 8 after fixing pressure initialisation exec/poiseuille_cylinder/inputs commit 6a81ed28084df6a259fd85f85b7f1e2198ebcdd5 Author: knutsvk Date: Fri Mar 15 12:22:50 2019 +0000 initialize pj to zero in case no ICs are set in incflo.dat src/setup/set_p0.f90 commit a2999c312c2f9d0cb5c65def20461947761aea4f Author: knutsvk Date: Fri Mar 15 12:05:48 2019 +0000 Make sure the timestep is not set to zero after a plot_per stop src/advance.cpp commit 9646ffadb5f1174047fdff6311ebe49968b9ce26 Author: knutsvk Date: Thu Mar 14 14:45:31 2019 +0000 verify poiseuille annulus test case, remove all initial condition bits from incflo.dat files where everything is set to zero exec/couette_plane/incflo.dat exec/couette_poiseuille/incflo.dat exec/lid_driven_cavity/incflo.dat exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane_bingham/incflo.dat exec/poiseuille_plane_newtonian/incflo.dat commit a58cf4a9ba40a2e639df35dc346b7e82997e2021 Author: knutsvk Date: Thu Mar 14 13:19:01 2019 +0000 these input files work with the new viscous treatments. careful with max_grid_size and n_cell exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs commit fb26069e03fd274f8ce9dcb8be8da9be5644ab24 Author: knutsvk Date: Thu Mar 14 13:18:19 2019 +0000 fix computation of derived quantities, get rid of eb_gradu module src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_eb_mod.f90 src/embedded_boundaries/Make.package src/embedded_boundaries/eb_gradu.f90 commit 19d007e000f3e5d22852a976bdf96463ccfe9657 Author: knutsvk Date: Wed Mar 13 17:23:24 2019 +0000 bugfix: ux -> uz src/diffusion/eb_wallflux_mod.f90 commit e28048cb80d173353ba82df138950f64c60fa852 Author: knutsvk Date: Wed Mar 13 17:23:01 2019 +0000 move computation of coefficients to C++ src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_mod.f90 commit e227d0e31e23df2a9ff708dc3ba2dd8acbab1119 Author: knutsvk Date: Wed Mar 13 17:21:10 2019 +0000 remove unused variables src/convection/MacProjection.cpp commit d7c137b0da66a51c4474d8229a166a27857d3ad0 Author: knutsvk Date: Wed Mar 13 12:36:41 2019 +0000 tidy src/diffusion/eb_wallflux_mod.f90 commit c8c048334bc12e7c195313dd1b2e2de7f41a2d83 Author: knutsvk Date: Wed Mar 13 12:14:30 2019 +0000 no need to have an array of only one BC type src/boundary_conditions/fill_bc0.f90 commit 05272a44d8492972697844d8c82e45559e991e12 Author: knutsvk Date: Wed Mar 13 12:02:44 2019 +0000 bugfix: need to call fill_bc0 (via FillScalarBC) in order to get correct values of eta (and ro, if it was variable) in ghost cells src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/fill_bc0.f90 src/incflo.H src/setup/incflo_arrays.cpp src/setup/init.cpp commit a0ab3aec10894b62ef59cf1f46e0378b4d7cb19d Author: knutsvk Date: Tue Mar 12 17:24:25 2019 +0000 bugfix: same int for each direction src/diffusion/DiffusionEquation.cpp commit 1f40712751ed8c33b56ce565ed01c00dc720f19d Author: knutsvk Date: Tue Mar 12 16:12:33 2019 +0000 increase accuracy exec/double_shear_layer/inputs commit ac720154a24bef54cc3413ba96c4a28b2936d063 Author: knutsvk Date: Tue Mar 12 16:00:12 2019 +0000 try to fix diffusion by activating dirichlet BCs at EBs in diffusion equation solver src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion_mod.f90 commit 93717fc0e378e78d1dbe43fe07b63f075ee378ed Author: knutsvk Date: Tue Mar 12 15:46:14 2019 +0000 some formatting src/diffusion/diffusion_eb_mod.f90 commit 308445422fef43736c89c4ae32b563feb22dad5f Author: knutsvk Date: Tue Mar 12 15:44:06 2019 +0000 use amrex built-in algorithm for computing velocity gradients on EBs used to compute viscous wall fluxes src/diffusion/eb_wallflux_mod.f90 commit 8abef894f6be875f8f486303bfbec5993899c3d9 Author: knutsvk Date: Tue Mar 12 15:41:31 2019 +0000 (1) is_viscous -> is_dirichlet (2) pass flags to compute_diff_wallflux src/utilities/divop_mod.f90 commit 18a74c3bd6a39e969c813f5749b0ab26e1cc8576 Author: knutsvk Date: Tue Mar 12 15:38:23 2019 +0000 fill velocity BCs after implciit diffusion src/advance.cpp commit a26a6f1054e34209ada657bb1cbecbea6bfba714 Author: knutsvk Date: Mon Mar 11 19:37:43 2019 +0000 major catch-up with mfix changes. after getting diffusion to work properly with Dirichlet BCs in call to DiffusionEquation, we need to go back and check every test csae exec/channel_cylinder/incflo.dat exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 exec/channel_cylinder_bingham/incflo.dat exec/channel_cylinder_bingham/inputs exec/channel_sphere/incflo.dat exec/channel_sphere/inputs exec/couette_plane/incflo.dat exec/couette_plane/inputs exec/couette_poiseuille/incflo.dat exec/couette_poiseuille/inputs exec/double_shear_layer/inputs exec/lid_driven_cavity/incflo.dat exec/lid_driven_cavity/inputs exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane_bingham/incflo.dat exec/poiseuille_plane_bingham/inputs exec/poiseuille_plane_newtonian/incflo.dat exec/poiseuille_plane_newtonian/inputs exec/taylor_green_vortices/inputs exec/uniform_velocity_sphere/inputs mfix_tracker src/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/fill_bc0.f90 src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/Make.package src/convection/convection.cpp src/convection/convection_F.H src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 src/convection/mac_F.H src/convection/macproj_mod.f90 src/convection/slopes_mod.f90 src/derive/derive.cpp src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_mod.f90 src/embedded_boundaries/eb_gradu.f90 src/embedded_boundaries/get_eb_walls.f90 src/embedded_boundaries/get_walls.cpp src/incflo.H src/include/boundary_conditions.inc src/main.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_namelist.f90 src/setup/set_bc_type.f90 src/setup/setup_F.H src/utilities/param_mod.f90 src/utilities/read_namelist.f90 commit 4b850fd7511dea46eea3e9f6d1da2563bdb6e3f6 Author: knutsvk Date: Fri Mar 8 13:31:09 2019 +0000 use proper Dirichlet BCs in implicit veloctiy diffusion src/diffusion/DiffusionEquation.cpp commit 89f34ed959081d3a54cfa5d36df7c076150be134 Author: knutsvk Date: Fri Mar 1 13:11:05 2019 +0000 fix wallflux mod again -- need to keep the is_viscous logics since divop module is called both for diffusive and convective terms src/diffusion/eb_wallflux_mod.f90 src/utilities/divop_mod.f90 commit e85571f670ab81115972e35f5ce4139d2c021967 Author: knutsvk Date: Fri Mar 1 13:10:21 2019 +0000 fix state_error src/derive/derive_F.H src/derive/derive_mod.f90 src/incflo.cpp commit dffc64d763667fddc0c71fe45d85c24b9e724580 Author: knutsvk Date: Fri Mar 1 13:09:49 2019 +0000 remove print statements src/setup/amrex_to_incflo.F90 commit fd1e55eaf848a676d1e5389a17d1b9b2394cb459 Author: knutsvk Date: Fri Mar 1 13:09:12 2019 +0000 use correct function name in amrex_abort src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 commit dec11607c792cb6fd532fe77d1fb9fee2f5752ad Author: knutsvk Date: Fri Mar 1 13:08:28 2019 +0000 get large sphere simulation ready exec/channel_sphere/incflo.dat exec/channel_sphere/inputs commit 6a392979e8dc1da9b073631bad76b52b1ce380bd Author: knutsvk Date: Thu Feb 28 16:44:48 2019 +0000 simplify rheology module + some other cleanup src/diffusion/eb_wallflux_mod.f90 src/rheology/rheology.cpp src/rheology/rheology_F.H src/rheology/rheology_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/init.cpp src/setup/setup_F.H src/utilities/constant_mod.f90 src/utilities/divop_mod.f90 commit ff0199b05b2a481a530f9318a0cb603464e491d8 Author: knutsvk Date: Wed Feb 27 18:25:26 2019 +0000 move vorticity computation in non-eb cells to c++ src/derive/derive.cpp src/derive/derive_mod.f90 commit ab338071b824c5954083e8d3e1bb40bef7a6c154 Author: knutsvk Date: Wed Feb 27 17:02:55 2019 +0000 add test case for cylinder at rest in channel filled with Bingham fluid moving at constant velocity exec/channel_cylinder_bingham/GNUmakefile exec/channel_cylinder_bingham/incflo.dat exec/channel_cylinder_bingham/inputs commit 2dc4e8a8a66bbec2d9f85912a9c230a3f0dc6d6a Author: knutsvk Date: Wed Feb 27 16:21:01 2019 +0000 hotfix: compute viscosity AT boundary for diffusive wallflux at cut cells. needs to be done properly (update rheology module) src/diffusion/eb_wallflux_mod.f90 commit b164bed1850b95e3e10ead1d64969517f6734d85 Author: knutsvk Date: Wed Feb 27 16:20:12 2019 +0000 bugfix: make sure to fill all edge ghost cells src/setup/set_bc_type.f90 commit 9a3859adc8482708f2c2630f39835123828a6287 Merge: 25f05b8a d868a435 Author: knutsvk Date: Wed Feb 27 16:18:12 2019 +0000 merge from origin Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 25f05b8acb91750b7384f302e80dac2cc360b197 Author: knutsvk Date: Wed Feb 27 16:17:56 2019 +0000 poiseuille cylinder: make surrounding domain twice as large, use Bingham fluid exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs commit d868a4352d9b9cb5416ce570b21be0b3fa03591e Author: knutsvk Date: Wed Feb 27 15:29:01 2019 +0000 fix lid driven cavity inputs exec/lid_driven_cavity/inputs commit 398036e1a3232d61d7be456d79a2d315d6731e29 Author: knutsvk Date: Wed Feb 27 15:17:29 2019 +0000 lid-driven cavity: use bingham rheology and high resolution exec/lid_driven_cavity/incflo.dat exec/lid_driven_cavity/inputs commit 4e03e6d87a64273bf857eddcaa8b0b1a6b336e9d Author: knutsvk Date: Fri Feb 15 15:37:53 2019 +0000 revisit bingham poiseuille plane ... exec/poiseuille_plane_bingham/inputs commit cf4e97d3118a92910d9b157f56d08786ddd4934d Author: knutsvk Date: Fri Feb 15 14:22:45 2019 +0000 (1) always apply corrector (2) bugfix: dont get stuck on plot_per times src/advance.cpp commit a2616f659ed41e12d40cbf32e0d20b47aecdde5f Author: knutsvk Date: Wed Feb 13 13:53:42 2019 +0000 try longer domain for the periodic BCs exec/channel_sphere/incflo.dat exec/channel_sphere/inputs commit c44501247262e8b6c6e66c48963fd9f2572b2fe9 Author: knutsvk Date: Tue Feb 12 20:49:53 2019 +0000 add couette poiseuille test case: combination of constant background pressure gradient (poiseuille) and moving wall (couette) exec/couette_poiseuille/GNUmakefile exec/couette_poiseuille/incflo.dat exec/couette_poiseuille/inputs commit 7704f962afc9f3b62462130a01d9190aaa8c2906 Author: knutsvk Date: Tue Feb 12 20:48:24 2019 +0000 new try for channel sphere problem exec/channel_sphere/inputs commit 65e6b254dba168a23b07a703da183fd30b8b397e Author: knutsvk Date: Tue Feb 12 20:48:07 2019 +0000 use tighter plot_per condition for writing output src/incflo.cpp commit 3b5e1e26e22a41ab05f7252589dee91843fbe086 Author: knutsvk Date: Tue Feb 12 20:32:38 2019 +0000 use periodic BCs exec/channel_sphere/incflo.dat commit ed0ff97753072037d3752211d78be473a852a4a9 Author: knutsvk Date: Tue Feb 12 20:32:05 2019 +0000 bugfix: forgot minus sign src/derive/derive_eb_mod.f90 commit 51147a3e1a53f44842245fe7c32578a8097bfb3c Author: knutsvk Date: Tue Feb 12 13:39:23 2019 +0000 do longer run of channel_sphere exec/channel_sphere/inputs commit 7fd9eddfe76076b3218b8b14fe8a5320302f8fc1 Author: knutsvk Date: Tue Feb 12 13:10:32 2019 +0000 cleanup and simplify EB code src/embedded_boundaries/Make.package src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/embedded_boundaries_F.H src/embedded_boundaries/get_eb_walls.f90 src/embedded_boundaries/get_walls.cpp src/incflo.H src/utilities/Make.package src/utilities/eb_to_pvd.f90 commit 60cdf1c8f68ab1150d3d4423c04bde19a1a188f2 Author: knutsvk Date: Mon Feb 11 18:54:41 2019 +0000 inputs to run channel_sphere a little longer.. exec/channel_sphere/inputs commit 7857b5e5abe82ed578a33c0cc71167c5714a890e Author: knutsvk Date: Mon Feb 11 18:20:42 2019 +0000 updates from mfix and BC fixes exec/channel_sphere/inputs exec/couette_plane/GNUmakefile exec/couette_plane/incflo.dat exec/couette_plane/inputs exec/lid_driven_cavity/inputs exec/poiseuille_annulus/inputs exec/poiseuille_annulus/plot_velocity_profile.py exec/taylor_green_vortices/init_fluid.f90 mfix_tracker src/advance.cpp src/convection/MacProjection.cpp src/embedded_boundaries/eb_interpolation_mod.f90 src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_p0.f90 src/setup/setup_F.H commit 554f7de0e8ff3ebfea2ca40ddb7e76ce9668c46f Author: knutsvk Date: Fri Feb 8 19:09:59 2019 +0000 fix computation of strainrate and vorticity near cut cells (specifically, neighbours need to alter their difference stencils to one-sided quadratic extrapolators) exec/poiseuille_cylinder/inputs src/derive/derive_eb_mod.f90 src/utilities/io.cpp commit 9dca5b4152fd35f5583e6aa0bb4f20ef07faf1be Author: knutsvk Date: Fri Feb 8 16:23:15 2019 +0000 consistent computation of vort in eb and non-eb code src/derive/derive_eb_mod.f90 src/derive/derive_mod.f90 commit 2e9c24eddfca1e291cb04a7dda67824be8c4cfc1 Author: knutsvk Date: Fri Feb 8 15:50:32 2019 +0000 separate directory for newtonian and bingham poiseuille plane flows exec/poiseuille_plane_bingham/GNUmakefile exec/poiseuille_plane_bingham/incflo.dat exec/poiseuille_plane_bingham/inputs exec/poiseuille_plane_newtonian/GNUmakefile exec/poiseuille_plane_newtonian/incflo.dat exec/poiseuille_plane_newtonian/inputs commit ca747a273222b19e56e6a87688eeb1c1816b818e Author: knutsvk Date: Fri Feb 8 15:50:03 2019 +0000 use implicit diffusion exec/channel_sphere/inputs commit cdeecac8ad4f837bec05efc98d48584729d647d4 Author: knutsvk Date: Fri Feb 8 15:46:03 2019 +0000 use quadratic rather than linear extrapolation to ghost cell CCs src/boundary_conditions/set_velocity_bcs.f90 commit 467b33e33c0bda3766c476532ac8fb5a7a6db0a8 Author: knutsvk Date: Fri Feb 8 15:44:50 2019 +0000 make poiseuille plane flow bingham exec/poiseuille_plane/inputs commit 020a948c498b6b60a3bf8b1ab61676bb66389ff3 Author: knutsvk Date: Fri Feb 8 15:32:27 2019 +0000 dont need to plot quite so much exec/couette/inputs commit ffe84d899509c53302bae665ddaea15339ae5f16 Author: knutsvk Date: Fri Feb 8 13:47:41 2019 +0000 although stable with high cfl, not as accurate (although we can still be an order of magnitude higher than this..) exec/couette/inputs commit 81c9136c45de9bb0d8eb1f6a15b4c6b7a4b1823e Author: knutsvk Date: Fri Feb 8 13:15:03 2019 +0000 add couette test case. with implicit diffusion, this is stable for cfl=300, so we need to find a better way to compute dt exec/couette/GNUmakefile exec/couette/incflo.dat exec/couette/inputs commit 059802e4dd0715f35e183cbc8653dc75c4d8f9a7 Author: knutsvk Date: Fri Feb 8 13:14:18 2019 +0000 stabilize computation of dt src/advance.cpp commit e729b67e7fd5fd652ac011672c725fde48815b83 Author: knutsvk Date: Fri Feb 8 13:14:08 2019 +0000 change extrap_dir_bcs in boundary conditions to give correct results for derived variables src/boundary_conditions/boundary_conditions.cpp commit 70a03de764d24027f1d775cd2f51b22e921b2782 Author: knutsvk Date: Fri Feb 8 12:42:02 2019 +0000 oops: commited this by mistake src/derive/derive_eb_mod.f90 commit 9a8c3d8658c48d1a74a253d3b1afe0ebde7b8b39 Author: knutsvk Date: Fri Feb 8 12:27:34 2019 +0000 remove unused generic_fill comments exec/channel_sphere/inputs src/boundary_conditions/boundary_conditions.cpp src/derive/derive_eb_mod.f90 commit eefa6fa4a6a1071ba52efd08a373b5bf09220bbb Author: knutsvk Date: Fri Feb 8 10:56:20 2019 +0000 rename periodic test cases exec/double_shear_layer/GNUmakefile exec/double_shear_layer/incflo.dat exec/double_shear_layer/init_fluid.f90 exec/double_shear_layer/inputs exec/taylor_green_vortices/GNUmakefile exec/taylor_green_vortices/incflo.dat exec/taylor_green_vortices/init_fluid.f90 exec/taylor_green_vortices/inputs exec/uniform_velocity_sphere/GNUmakefile exec/uniform_velocity_sphere/incflo.dat exec/uniform_velocity_sphere/init_fluid.f90 exec/uniform_velocity_sphere/inputs commit f1552d6a5e971a662faa5812c68f864052aeeeeb Author: knutsvk Date: Thu Feb 7 17:44:56 2019 +0000 rinse out unused EB stuff src/embedded_boundaries/Make.package src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit 7ba708ea192ff0f5ec6fac360fc89edc937d94ff Author: knutsvk Date: Thu Feb 7 17:35:23 2019 +0000 flow past sphere in channel working, but discovered that we need to take consideration in computing strainrate (and vorticity) near domain boundaries exec/channel_sphere/incflo.dat exec/channel_sphere/init_fluid.f90 exec/channel_sphere/inputs exec/channel_sphere/set_mac_velocity_bcs.f90 exec/channel_sphere/set_velocity_bcs.f90 commit eaf1d7429a1af3520b27463bc62232c44669e182 Author: knutsvk Date: Thu Feb 7 17:34:10 2019 +0000 add sphere EB src/embedded_boundaries/Make.package src/embedded_boundaries/eb_sphere.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H commit c44a5d92f3e43bfea6f9d373a8cd915abb89ee61 Author: knutsvk Date: Thu Feb 7 17:32:22 2019 +0000 bugfix: division by dx is already done when computing gradu src/derive/derive_eb_mod.f90 commit cdb3586e15caeded8d288c64f8972f5c285ed2e0 Merge: 67f85287 851ffac5 Author: knutsvk Date: Thu Feb 7 14:03:40 2019 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 67f85287c745d70f56e7ff72c0c4f61bb83575e7 Author: knutsvk Date: Thu Feb 7 14:03:22 2019 +0000 allow NSW boundaries to have prescribed tangential velocity, add lid-driven cavity test case to verify that this works exec/lid_driven_cavity/GNUmakefile exec/lid_driven_cavity/incflo.dat exec/lid_driven_cavity/inputs src/boundary_conditions/set_velocity_bcs.f90 commit 851ffac58ddec46aac14af68151b06a102dbe3c9 Author: knutsvk Date: Thu Feb 7 11:20:53 2019 +0000 update channel_cylinder inputs exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs commit e951ee567e47750488ba9c63da164345cf5fe941 Author: knutsvk Date: Thu Feb 7 08:45:15 2019 +0000 plot: rename volfrac->vfrac so that it can be drawn as Boundary in VisIt src/incflo.H commit adca1c70ca42759644a74f663f89850ed7b0d5e2 Merge: 809516f3 cccfdcc6 Author: knutsvk Date: Wed Feb 6 17:51:27 2019 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 809516f3b5ad6984a6cc9836f2a551d92eacb0cf Author: knutsvk Date: Wed Feb 6 17:50:33 2019 +0000 plan to make bingham flow past sphere in channel test exec/channel_sphere/GNUmakefile exec/channel_sphere/incflo.dat exec/channel_sphere/init_fluid.f90 exec/channel_sphere/inputs exec/channel_sphere/set_mac_velocity_bcs.f90 exec/channel_sphere/set_velocity_bcs.f90 commit f8334d1b98e559b3efa294e95bc57acc0cf01716 Author: knutsvk Date: Wed Feb 6 17:47:58 2019 +0000 new annulus results exec/poiseuille_annulus/plot_velocity_profile.py exec/poiseuille_annulus/visit.curve commit cccfdcc6cbe1d6f0a4855ada6c2060a2c062c583 Author: knutsvk Date: Wed Feb 6 16:24:59 2019 +0000 update settings for annulus test exec/poiseuille_annulus/inputs commit d12d6c467bb7c141f596b20fb93416c0abc8decf Author: knutsvk Date: Wed Feb 6 14:31:54 2019 +0000 steady-state without stop_time exec/poiseuille_cylinder/inputs commit d77f59b292ebc7198fe8f2cd4a18ca434c82562b Author: knutsvk Date: Wed Feb 6 13:17:20 2019 +0000 set default verbosity for PoissonEquation off src/projection/PoissonEquation.H commit 7b2a976021e354272ac08d31766d362d68914e92 Author: knutsvk Date: Wed Feb 6 12:28:27 2019 +0000 add comment src/utilities/io.cpp commit 3a7b63c6a0f2e7a738025db734b6c5e03146fc3f Author: knutsvk Date: Wed Feb 6 12:13:15 2019 +0000 use GetArrOfConstPtrs rather than making a separate const mf src/utilities/io.cpp commit b99e71fe2fcbcb4cef805d6a00eed96da200a0da Author: knutsvk Date: Wed Feb 6 11:56:52 2019 +0000 dont write pre-init plotfile, remote writeEBsurface src/embedded_boundaries/Make.package src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp commit d095883294a9d9dd5df87b3a6fa528a04497dca4 Author: knutsvk Date: Tue Feb 5 22:20:53 2019 +0000 multilevel working nicely for uniform flow past cylinder exec/periodic_uniform_velocity/GNUmakefile exec/periodic_uniform_velocity/inputs commit 14cd1a5d5dbd07b35a82b4c59fcb3d1fc5b18e7f Author: knutsvk Date: Tue Feb 5 08:35:55 2019 +0000 remove unused LSCore stuff src/incflo.cpp commit 6eb55e22f1c476673344787cb08e398cf60498ef Author: knutsvk Date: Tue Feb 5 08:32:57 2019 +0000 trying to debug failing initial projection exec/periodic_uniform_velocity/inputs src/projection/PoissonEquation.H commit 10ba57837811e0d3cf859408fc9b4bcfc1f6c23b Author: knutsvk Date: Tue Feb 5 08:32:31 2019 +0000 gp has 3 comps src/setup/incflo_arrays.cpp commit aaf423240bcc1ed813c4398eb49beff1a0905ee7 Author: knutsvk Date: Tue Feb 5 08:32:08 2019 +0000 lev <= finest_level, not < src/advance.cpp commit d660518a66d324ae634d1672129100bc51f28ad5 Author: knutsvk Date: Mon Feb 4 18:10:22 2019 +0000 this inputs file works, but changing amr.max_level from 1 to 2 causes the initial projection to fail and everything to become zero... exec/periodic_uniform_velocity/inputs commit d3b0d869dc922fa30b7f1fa41b7b661b3e8013eb Author: knutsvk Date: Mon Feb 4 18:04:00 2019 +0000 update comment src/utilities/diagnostics.cpp commit 71770b7b3ef0d821a1e1e493361a15404082fb01 Author: knutsvk Date: Mon Feb 4 18:01:55 2019 +0000 use the same settings as mfix (although these should be deafult in amrex) src/projection/PoissonEquation.cpp commit 6ab488422d18271d136478ecce885f589ecf6292 Author: knutsvk Date: Mon Feb 4 18:00:53 2019 +0000 only need one initial iteration to see if it works exec/periodic_uniform_velocity/inputs commit 5257b14d4857695d394cb4e495fb26a57235af9c Author: knutsvk Date: Mon Feb 4 17:01:24 2019 +0000 update mfix tracker mfix_tracker commit 81bcc9f5ed6e7d2a5ea61ac07af633ea22642904 Author: knutsvk Date: Mon Feb 4 16:53:05 2019 +0000 make sure MFs are EB-aware also in PoissonEquation and DiffusionEquation classes src/diffusion/DiffusionEquation.cpp src/projection/PoissonEquation.cpp commit c691e55b0209ccd3c829b0f98c047f654a737f9a Author: knutsvk Date: Mon Feb 4 14:48:11 2019 +0000 needed nghost>=5 after all, to avoid out of bounds error when computing gradu at EBs src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/incflo.H src/utilities/divop_mod.f90 commit 045c9d704e4fe681979d292d57c0432abcf3fa91 Author: knutsvk Date: Mon Feb 4 13:27:53 2019 +0000 bugfix: use correct version of setVal for MFs with only 1 comp exec/periodic_uniform_velocity/inputs src/derive/derive.cpp src/incflo.H commit 508e8df5d22f0d5452efe2dd1d48b4506250c773 Author: knutsvk Date: Fri Feb 1 17:43:54 2019 +0000 grid generation looks OK (as seen from plot000-1) but something goes wrong in incflo::InitialIterations - bugseek exec/periodic_uniform_velocity/GNUmakefile exec/periodic_uniform_velocity/inputs src/incflo.cpp commit af674a0de52ec585cb46fb7b5b8018ebb7d5a53d Author: knutsvk Date: Fri Feb 1 16:38:33 2019 +0000 try to get amr to work on finer levels by mimicing grid generation as in mfix (doesnt work..) exec/periodic_uniform_velocity/inputs src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp commit 9c55cf033fe41204386c077463bd917bb0383571 Author: knutsvk Date: Fri Feb 1 13:06:38 2019 +0000 fortran prettify src/diffusion/eb_wallflux_mod.f90 commit 065fcfadceeee16bc3239fe5771ed89e05c9af94 Author: knutsvk Date: Fri Feb 1 13:06:15 2019 +0000 dont average down nodal arrays src/incflo.cpp commit f304d51ea5281bbc338863ff853aef0bea29bf0e Author: knutsvk Date: Thu Jan 31 19:19:23 2019 +0000 try tagging for refinement using LSCoreBase::FillVolfracTags (unsuccesfully) exec/periodic_uniform_velocity/inputs src/incflo.cpp commit 3d151ea7652bf297068e02f6969eac384a89e116 Author: knutsvk Date: Thu Jan 31 16:24:30 2019 +0000 update cylinder in channel test case exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs src/utilities/io.cpp commit e449a127f54d1cafc21e3de0c7edfb90baacd105 Author: knutsvk Date: Thu Jan 31 16:23:26 2019 +0000 call average down after projection rather than in derive src/derive/derive.cpp src/projection/projection.cpp commit 25e8d297b06b80851e762451f39ce02f14a6a908 Author: knutsvk Date: Wed Jan 30 16:21:38 2019 +0000 multilevel flow past cylinder with 2 layers of refinement near EB working and producing correct plots of vorticity, strainrate etc exec/channel_cylinder/inputs src/derive/derive.cpp commit 5887f1f1b951a5bf9afd7de62d67701513818654 Author: knutsvk Date: Wed Jan 30 15:53:01 2019 +0000 fix computation of derived quantities vort, strainrate, stress in the case of multilevel simulations src/derive/derive.cpp commit baa5d460ffaf1bc727bb057edad21da28e4679c6 Author: knutsvk Date: Tue Jan 29 18:22:20 2019 +0000 trying to debug vorticity calculation at fine/coarse boundary exec/periodic_uniform_velocity/inputs src/incflo.cpp commit 57768d799850051162f0e93f9098a6f42f2432f1 Author: knutsvk Date: Tue Jan 29 17:55:45 2019 +0000 TagCutCells working, remove TODO comment src/incflo.cpp commit 8bfff8e285d32a7b27b80502620886ffb27984e4 Author: knutsvk Date: Tue Jan 29 17:48:29 2019 +0000 catch up with mfix development mfix_tracker commit 404429e65fe579b2e10b4b41a6ba23bedf36cf82 Author: knutsvk Date: Tue Jan 29 17:47:26 2019 +0000 use previous phi as initial guess in MAC projector exec/poiseuille_annulus/inputs src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/convection.cpp commit c1f80d40b83f00b096c76bd79838dd857bda5f65 Author: knutsvk Date: Tue Jan 29 17:31:11 2019 +0000 protect function upwind_normal against tiny velocities src/convection/convection_mod.f90 commit ecd01c2600d836964ca0346d4092e137a0b4629e Author: knutsvk Date: Tue Jan 29 17:04:15 2019 +0000 fix bug in interpolation routine src/embedded_boundaries/eb_interpolation_mod.f90 src/main.cpp commit 93bdc78953bee4521c59a5814242b8f20c189e1d Author: knutsvk Date: Tue Jan 29 16:38:57 2019 +0000 try flow past cylinder with AMR - working to some extent exec/channel_cylinder/inputs src/setup/set_p0.f90 commit 15279732870170488d386f7127dfd3be8bf4256b Author: knutsvk Date: Tue Jan 29 16:21:33 2019 +0000 require min 4 ghost cells rather than 5 exec/poiseuille_annulus/inputs src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/incflo.H src/utilities/divop_mod.f90 commit c1e70a424807a607ca0a67073adc402a2cbea16b Author: knutsvk Date: Tue Jan 29 16:06:22 2019 +0000 remove print statement src/advance.cpp commit bf99ac97acd215651a8626f2f3703ddce5d99895 Author: knutsvk Date: Tue Jan 29 16:03:53 2019 +0000 need to apply BCs before computing divu src/derive/derive.cpp commit 87ffa4a85912199739229a300e0e31ba7e92612b Author: knutsvk Date: Tue Jan 29 15:51:40 2019 +0000 dont use corrector if solving for steady-state exec/poiseuille_plane/inputs mfix_tracker src/advance.cpp src/derive/derive.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_regular.cpp commit 4cbe2e788444dbf26737632882da3008182cc40d Author: knutsvk Date: Tue Jan 29 14:26:30 2019 +0000 initial projection / iterations controlled by input file exec/periodic_uniform_velocity/inputs mfix_tracker src/embedded_boundaries/eb_cylinder.cpp src/incflo.H src/setup/init.cpp src/utilities/io.cpp commit efe34664af6a920e8116a60146ff37c09b1543d4 Author: knutsvk Date: Tue Jan 29 11:53:10 2019 +0000 make all MFs EB-aware, let UpdateEBFactory return bool src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/setup/incflo_arrays.cpp commit aa0dc0516fd6106ef296eb8ea13496762d6cfefd Author: knutsvk Date: Mon Jan 28 18:56:05 2019 +0000 make ro EB aware: allows us to use TagCutCells to refine exec/periodic_uniform_velocity/inputs src/derive/derive_mod.f90 src/incflo.cpp src/setup/incflo_arrays.cpp commit d3309cff55352a0b68daef26f3d1297cf6e34308 Merge: b4525ee3 99caa343 Author: knutsvk Date: Mon Jan 28 18:19:29 2019 +0000 merge due to work without pulling first Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit b4525ee3b0a25ef17ba13ccff3e5892a60181f17 Author: knutsvk Date: Mon Jan 28 18:17:23 2019 +0000 tag on volfrac src/derive/derive_mod.f90 commit 72c8566a430fc0ee3d2e07639b23693a4f24651a Author: knutsvk Date: Mon Jan 28 17:10:43 2019 +0000 manage flow past a cylinder with refinement near cylinder up to 2 levels of AMR (but not 3). also cant get amrex::TagCutCells to work and unable to not tag inner part of cylinder for refinement exec/periodic_uniform_velocity/inputs src/derive/derive_mod.f90 src/incflo.cpp commit cc9bd1b18f0922228f1ea70ea54b5fffdbcb64ce Author: knutsvk Date: Mon Jan 28 15:41:59 2019 +0000 debugging simplest possible refinement case exec/periodic_uniform_velocity/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane/inputs src/incflo.cpp commit befe3249790e52fc2eb90f46a814e31efddeff2c Author: knutsvk Date: Mon Jan 28 15:41:33 2019 +0000 shouldnt override coarsening strategy RAF when compiling with EB src/projection/PoissonEquation.cpp commit 99caa3438a7d3ec5a835dbf680933930ca8b2ec7 Author: knutsvk Date: Tue Dec 11 16:06:46 2018 +0000 remove coarsening strategy option which should only be used for non-EB src/projection/PoissonEquation.cpp commit 08de95e7f928999f4212f6e57b274317575eee43 Author: knutsvk Date: Tue Dec 11 12:16:02 2018 +0000 move convection EB functionality to convection_eb_mod.f90 src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 commit 219e2d82f6bed4f665fa8f0f2302733864c99b49 Author: knutsvk Date: Thu Dec 6 19:21:12 2018 +0000 update mfix tracker mfix_tracker commit 6376b108b82e9f3fc30de03904f7c32a9073ba14 Author: knutsvk Date: Thu Dec 6 19:09:48 2018 +0000 improve verbosity exec/poiseuille_cylinder/inputs src/advance.cpp src/projection/projection.cpp commit ad6165169079a71f19063d9142dec6bf74ee2791 Author: knutsvk Date: Thu Dec 6 19:01:14 2018 +0000 lower resolution as deafult exec/periodic_taylor_green/inputs commit cc86ad0f3fe24737130d3fbe0e69980ac77034c4 Author: knutsvk Date: Thu Dec 6 13:43:49 2018 +0000 add taylor green test case for grid convergence study, rename vortex test case to double shear layer exec/periodic_double_shear_layer/GNUmakefile exec/periodic_double_shear_layer/incflo.dat exec/periodic_double_shear_layer/init_fluid.f90 exec/periodic_double_shear_layer/inputs exec/periodic_taylor_green/GNUmakefile exec/periodic_taylor_green/incflo.dat exec/periodic_taylor_green/init_fluid.f90 exec/periodic_taylor_green/inputs commit 1732ef842f60aad8fca5554ed9ba7de2a08898dc Merge: c32330e0 c4461cc4 Author: Knut Sverdrup Date: Wed Dec 5 17:19:52 2018 +0000 Merge pull request #22 from AMReX-Codes/level-set merge level-set branch (we are not using the level-set after all, don't need to when we don't have particles) commit c4461cc4eadbf35381abd655dfe53d4f1463627e Author: knutsvk Date: Wed Dec 5 17:09:31 2018 +0000 add periodic test case with uniform velocity illustrating multilevel problem at coarse/fine boundary exec/periodic_uniform_velocity/GNUmakefile exec/periodic_uniform_velocity/incflo.dat exec/periodic_uniform_velocity/init_fluid.f90 exec/periodic_uniform_velocity/inputs commit 326eed001b1828b1b39eb6f6bc5f3002c681da0b Author: knutsvk Date: Wed Dec 5 17:08:47 2018 +0000 reset verbosity exec/poiseuille_cylinder/inputs commit 5a88a29d6f654c7e66a1404f26c5e40943fe2b4c Author: knutsvk Date: Wed Dec 5 16:14:48 2018 +0000 update diagnostics src/advance.cpp src/utilities/diagnostics.cpp commit 6589be0e36db7a3a2d262940c94bf43f88e11a43 Author: knutsvk Date: Wed Dec 5 15:16:25 2018 +0000 bugfix: TagCutCells not yet working + abs -> std::abs in ComputeDt() exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs src/incflo.cpp commit bae178a748b4c9b40cd695e32f2763349681b898 Author: knutsvk Date: Wed Dec 5 15:01:36 2018 +0000 bugfix: resize new bcs and t_ vectors needed for fillpatch stuff exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs exec/poiseuille_cylinder/inputs src/incflo.H src/setup/incflo_arrays.cpp commit 547a3695405c27dd035851490f24db4ef976800a Author: knutsvk Date: Wed Dec 5 14:25:16 2018 +0000 bugfix: must resize arrays before making geometry src/incflo.cpp commit a689311af5c901193b1646aee159f2dd23eaa7cb Author: knutsvk Date: Wed Dec 5 13:42:44 2018 +0000 trying to debug segfault after succesfully compiling with new fillpatch stuff exec/periodic_vortices/inputs src/boundary_conditions/boundary_conditions.cpp src/embedded_boundaries/eb_cylinder.cpp src/incflo.H commit c33e0fd73ee6e6d04af2b6cef242f8cbeefeb48c Author: knutsvk Date: Tue Dec 4 18:29:10 2018 +0000 fixed some compiler errors, but incflo class has no member named GetParGDB exec/periodic_vortices/inputs src/boundary_conditions/boundary_conditions.cpp src/incflo.H src/incflo.cpp commit 1fa323e63f4ddded8df53017fea2f83b00413b8b Author: knutsvk Date: Tue Dec 4 18:19:44 2018 +0000 update mfix changes in the previous weeks, except level-set stuff since we won't need it mfix_tracker src/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/main.cpp src/projection/projection.cpp commit 4ff7010df6290d016195472039e337220ae3008a Author: knutsvk Date: Tue Dec 4 13:48:56 2018 +0000 add level-set member variables to incflo class src/incflo.H commit 77b498cacc415c9edf6e8e3e7bb4805dfb18fcb4 Author: knutsvk Date: Mon Dec 3 22:10:54 2018 +0000 unnecessary to set these settings since they are default values src/projection/PoissonEquation.cpp commit 4b16211594da3f99d196ba5bcd5e9494fb3b8008 Author: knutsvk Date: Sun Dec 2 13:39:29 2018 +0000 fix description of nodal projection decomposition src/projection/projection.cpp commit b2c9c6b4ce4c73efe302462688c47285702226e2 Author: knutsvk Date: Sat Dec 1 18:57:55 2018 +0000 minor cleanups / documentation src/advance.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp commit 4f40bcc595af3c2415698f9b97b2bbf7621d3e83 Author: knutsvk Date: Thu Nov 29 15:54:21 2018 +0000 doc change src/advance.cpp commit 6a5daf823d11177a345ddd8ebeed6e4698cff9fd Author: knutsvk Date: Wed Nov 28 19:43:31 2018 +0000 dont regularise term w/o singularity src/rheology/rheology_mod.f90 commit 57380c36e5d757b571beacd56b478b8f80dc58fe Author: knutsvk Date: Wed Nov 28 19:42:25 2018 +0000 remove unnecessary include src/incflo.H commit 0444f5e0cad1afbdb91749afae42e5e4791802cc Author: knutsvk Date: Mon Nov 26 17:29:58 2018 +0000 working towards including aMR level set for geometry src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.cpp commit c32330e071c6c7d72ea08bf6acd1de23d5c875b2 Author: knutsvk Date: Wed Dec 5 13:54:00 2018 +0000 fix bug (invalid spaces from IDE or something) src/incflo.cpp commit dffdeaca9224041e79f92525ff4e62a11cccebd1 Author: knutsvk Date: Mon Dec 3 23:53:57 2018 +0000 enable writing plotfiles when cur_time is divisable by plot_per exec/periodic_vortices/inputs src/advance.cpp src/incflo.H src/incflo.cpp src/setup/init.cpp commit aa293e824e48e83ca7d16ab84ad7b5733f97f470 Author: knutsvk Date: Mon Nov 26 14:10:34 2018 +0000 make conv and divtau class members src/advance.cpp src/incflo.H src/setup/incflo_arrays.cpp src/setup/init.cpp commit e8b0b8e0483a9b5c4851e25017645757537be418 Author: knutsvk Date: Fri Nov 23 15:56:33 2018 +0100 DiffusionEquation: proper documentation + some more simplification src/advance.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_mod.f90 src/incflo.H src/projection/projection.cpp commit 45c03314000581ca35e3bda14ed1c04de05fb44b Author: knutsvk Date: Thu Nov 22 21:52:06 2018 +0000 more cleanup + get rid of lots of unnecessary #includes in headers src/convection/MacProjection.H src/diffusion/DiffusionEquation.H src/incflo.H src/projection/PoissonEquation.H src/utilities/constants.H commit 3e86338864e7a40203ef20a59595a75d0a90787f Author: knutsvk Date: Thu Nov 22 21:33:21 2018 +0000 make sure it is necessary to make tmp and b_tmp... src/diffusion/DiffusionEquation.cpp commit 161a14e6a449a1db99525d596932597d2a3899b9 Merge: 3d1d35fb 32ef67ae Author: Knut Sverdrup Date: Thu Nov 22 19:26:51 2018 +0000 Merge pull request #20 from AMReX-Codes/multilev Safe multilev changes commit 32ef67aebfd94eafe519d1782f93d6901d8b9ed9 Author: knutsvk Date: Thu Nov 22 19:21:29 2018 +0000 moved poisson equation to separate class PoissonEquation src/advance.cpp src/derive/derive.cpp src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/incflo.H src/projection/Make.package src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp src/projection/projection.cpp src/projection/projection_F.H src/projection/projection_mod.f90 src/setup/incflo_arrays.cpp src/setup/init.cpp commit 125058db792162cc19df09697d877a0c8a193c61 Author: knutsvk Date: Thu Nov 22 14:18:48 2018 +0000 update headers src/projection/PoissonEquation.H src/projection/PoissonEquation.cpp src/projection/projection.cpp commit 25cdc54e4164846e1c2221bc69f18fcca01eea72 Author: knutsvk Date: Thu Nov 22 14:11:12 2018 +0000 big cleanup after deciding to remove nodal_pressure option. we now always use nodal pressure since it is inherently better than CC exec/Make.incflo exec/periodic_vortices/inputs exec/poiseuille_plane/inputs src/Make.package src/advance.cpp src/advance/Make.package src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_pressure_bcs.f90 src/derive/derive.cpp src/diffusion/Make.package src/diffusion/eb_wallflux_mod.f90 src/divergence/Make.package src/divergence/average_cc_to_fc.f90 src/divergence/divergence.cpp src/divergence/divergence_F.H src/incflo.H src/projection/projection.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_p0.f90 src/setup/setup_F.H src/utilities/Make.package src/utilities/divop_mod.f90 src/utilities/io.cpp commit 8c9b8a9527fdb739c15ecf456f4bdae4cc34ee3a Author: knutsvk Date: Thu Nov 22 12:56:16 2018 +0000 get rid of bool proj_2, determine decomposition based on step counter instead src/advance/advance.cpp src/incflo.H src/incflo.cpp src/projection/projection.cpp src/setup/init.cpp commit e6ecef154d7e7f7f51c407d1502fb4fa9c0cb680 Author: knutsvk Date: Thu Nov 22 12:03:34 2018 +0000 use same notation in predicor and corrrector src/advance/advance.cpp commit 2554fc37311682deb22009cc2a9648004f55f84b Author: knutsvk Date: Wed Nov 21 16:54:49 2018 +0000 some notes in comments src/diffusion/DiffusionEquation.H src/utilities/diagnostics.cpp commit f074ff4f98fc7db619ab87aaa6ccfccaf2ea4060 Author: knutsvk Date: Wed Nov 21 16:44:26 2018 +0000 bugfix: need to reset rhs to ro after every direction src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/diffusion.cpp src/utilities/diagnostics.cpp commit 277b6f424969831cb399027d31b473b6bf182c93 Author: knutsvk Date: Wed Nov 21 15:53:16 2018 +0000 move diffusion equation solver to separate class exec/poiseuille_plane/inputs src/convection/MacProjection.H src/diffusion/DiffusionEquation.H src/diffusion/DiffusionEquation.cpp src/diffusion/Make.package src/diffusion/diffusion.cpp src/incflo.H src/setup/init.cpp src/utilities/constants.H commit 5b2ac1e7b3e61c8d1f3112d6f18de24ab223a725 Author: knutsvk Date: Wed Nov 21 11:45:23 2018 +0000 diffusion solve now works with local Vectors exec/periodic_vortices/inputs src/diffusion/diffusion.cpp src/setup/incflo_arrays.cpp commit a3870f547ab6ab5b0c200b886cba9dec291d042f Author: knutsvk Date: Tue Nov 20 17:09:02 2018 +0000 tried to make diffusion solve variables local, but get segfault at matrix.setLevelBC(lev, sol) src/diffusion/diffusion.cpp src/incflo.H src/setup/incflo_arrays.cpp commit 6c3c6e902c966be1c1053e868e8323036effbadb Author: knutsvk Date: Tue Nov 20 15:20:02 2018 +0000 update function explanation for ApplyProjection() src/projection/projection.cpp commit 6bf8a54dc7c177437c7041881db2e69b53fb9bcd Author: knutsvk Date: Tue Nov 20 14:46:14 2018 +0000 rename t->cur_time .gitignore src/advance/advance.cpp src/convection/convection.cpp src/derive/derive.cpp src/incflo.H src/incflo.cpp src/setup/init.cpp src/utilities/diagnostics.cpp src/utilities/io.cpp commit 8d68b3bd1c507ee25740203bbd70111af2951fa8 Author: knutsvk Date: Tue Nov 20 14:34:49 2018 +0000 bugfix: diff_vel must have 3 comps src/advance/advance.cpp src/utilities/diagnostics.cpp commit 69a50f94b332b4ea19f259e0014aa75da69afef3 Author: knutsvk Date: Tue Nov 20 14:17:50 2018 +0000 Major cleanup/restructure: (1) Continue renaming member functions to CapitalisedCamelCase (2) Decided to avoid if/for one-liners without curly brackets (3) Combine the 4 norm functions into one (4) Combine the 2 ugradu functions into one (5) Move ComputeDivU() to derive exec/periodic_vortices/inputs src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/derive/derive.cpp src/diffusion/diffusion.cpp src/divergence/divergence.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/projection/projection.cpp src/rheology/rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/Make.package src/utilities/diagnostics.cpp commit f0ebdf1bf7e11fb6bcbfa70a1e611fb31180d5d2 Author: knutsvk Date: Mon Nov 19 20:35:42 2018 +0000 fix segfault using Weiquns clever curly brackets src/main.cpp commit 8478e0c987944ee8de04e5727301026542d983f8 Author: knutsvk Date: Mon Nov 19 18:25:37 2018 +0000 clean up and update recent MFiX commits. bug introduced from recent AMReX changes causes segfault in amrex::Finalize() exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs mfix_tracker src/advance/advance.cpp src/boundary_conditions/fill_bc0.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/diffusion/diffusion.cpp src/divergence/divergence.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/projection/projection.cpp src/setup/init.cpp src/utilities/io.cpp commit afdb5f4c6858c08b4cda1abb77adf0f14162fc68 Author: knutsvk Date: Thu Nov 15 17:05:54 2018 +0000 remove unused tools directory README.md tools/C++/fextract.cpp tools/DEBUG/amrex-max-vel tools/DEBUG/ascii-reader.f08 tools/DEBUG/ascii-tools.f08 tools/F90/fcompare_par.f90 tools/F90/fextract.f90 tools/F90/fjoin_par.f90 tools/F90/plt_compare_diff_grids.f90 commit f8e15977cf065f128bca21fbfc9e2c1abbcbd923 Author: knutsvk Date: Thu Nov 15 16:59:57 2018 +0000 rm unused DOxyfile .gitignore doc/Doxyfile.in commit a9ff369806f204eb80ac66b936c8d318e48677b0 Author: knutsvk Date: Wed Nov 14 21:33:26 2018 +0000 periodic_vortices inputs file with max_level=1 exec/periodic_vortices/inputs commit 86b8e6bdf2060e0e59baef1c6799bf0e4201ae0d Author: knutsvk Date: Wed Nov 14 21:11:05 2018 +0000 initial projection and iterations: fix function names and verbosity src/incflo.H src/setup/init.cpp commit 5890f3fd5567e592b5ed36d3b97999d36255b6d5 Author: knutsvk Date: Wed Nov 14 21:07:09 2018 +0000 Clean up SetBCTypes() in PostInit() src/incflo.H src/setup/init.cpp commit 22c2df04cbd618581427532b1b18dc05ea429ee5 Author: knutsvk Date: Wed Nov 14 20:57:41 2018 +0000 cleanup initfluid and setting of background pressure. dont fill unnecessary BCs all the time exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs exec/poiseuille_cylinder/inputs src/incflo.H src/setup/init.cpp commit 3752e0ed26594d40021bc671177d584c940a7f7f Author: knutsvk Date: Wed Nov 14 20:42:00 2018 +0000 start moving towards CamelCase function names, to be consistent with existing code src/advance/advance.cpp src/incflo.H src/incflo.cpp src/setup/init.cpp commit d13f519f4fee2715ef84e9d7f3bf6970b6670714 Author: knutsvk Date: Wed Nov 14 20:30:41 2018 +0000 remove unnecessary extra velocity BC function set_vec_bcs() src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_velocity_bcs.f90 src/divergence/divergence.cpp commit 3dd8e4a28e5f8dc404d8b4f171bed78c7c3a2007 Author: knutsvk Date: Wed Nov 14 19:43:42 2018 +0000 Remove duplicate function set_scalar_bcs, since fill_mf_bc does the same src/advance/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_scalar_bcs.f90 src/divergence/divergence.cpp src/incflo.H src/setup/init.cpp commit 8d86928b75ea512af5a9491eb1436f9aab6faa29 Author: knutsvk Date: Wed Nov 14 17:35:57 2018 +0000 remove deprecated function set_bc0 src/setup/set_bc0.f90 commit 70265a1043b4254c87e28363d8e586b0ce058047 Author: knutsvk Date: Wed Nov 14 17:35:41 2018 +0000 remove deprecated functions set_bc0 and init_fluid_restart exec/periodic_vortices/init_fluid.f90 src/incflo.H src/setup/Make.package src/setup/init.cpp src/setup/init_fluid.f90 src/setup/setup_F.H commit 2e25f7310945889c63adb32a558b637ba86eb4e1 Author: knutsvk Date: Wed Nov 14 16:51:22 2018 +0000 restructure - documentation - cleanup src/incflo.H src/incflo.cpp src/setup/init.cpp src/utilities/io.cpp commit 7897e8c333f6b7fa06b8fbc615931bec1447b541 Author: knutsvk Date: Wed Nov 14 16:49:43 2018 +0000 comment out until we understand how this is supposed to work and implement it... src/boundary_conditions/boundary_conditions.cpp commit 93c624530dae652caf9f2077762f6cd7328766eb Author: knutsvk Date: Tue Nov 13 17:38:31 2018 +0000 remove #if 0 statement in FillPatch() -- this function probably needs to be implemented and used properly src/boundary_conditions/boundary_conditions.cpp commit ef51d0ea738040fea46ba2004e89e64b90b93e00 Author: knutsvk Date: Tue Nov 13 16:35:08 2018 +0000 try to debug error in comp_divu for multilevel solve. write plotfile immediately before initial projection exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs src/setup/init.cpp commit 840e6f7b5785783c60502122f0d39b4634638c26 Author: knutsvk Date: Tue Nov 13 16:34:15 2018 +0000 (1) add function update_derived_quantities() (2) use EB_average_down() instead of average_down src/advance/advance.cpp src/derive/derive.cpp src/incflo.H src/incflo.cpp commit d2dc6c7adf7c2bdb8df55291d1f24696d1291b5d Author: knutsvk Date: Tue Nov 13 16:32:42 2018 +0000 remove print statement src/embedded_boundaries/embedded_boundaries.cpp commit 4849fe6c65d38a0e6741da25243c1328a920559f Author: knutsvk Date: Tue Nov 13 16:32:27 2018 +0000 for max_level > 0, need to have istep.size() equal to finest_level + 1 src/utilities/io.cpp commit f3ac4350acfa1b99fa850e6892664198bb696465 Author: knutsvk Date: Tue Nov 13 16:31:36 2018 +0000 bugfix: pass lev to setSigma() instead of 0 src/projection/projection.cpp commit 738918301efff1e01970d920be063c5b4daf92fc Author: knutsvk Date: Mon Nov 12 21:33:32 2018 +0000 more work to try and get max_level = 1 to work... exec/periodic_vortices/inputs src/derive/derive_F.H src/derive/derive_mod.f90 src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit 1130be182b93694f25d8847847b8dd1a19e76de7 Author: knutsvk Date: Mon Nov 12 17:32:27 2018 +0000 add commented out skeleton code for what we for dynamic regridding src/incflo.cpp commit 8e29fdb4de6a38709eda8cebb6bf9b5c3d716bb2 Author: knutsvk Date: Mon Nov 12 17:19:37 2018 +0000 move timing of single timestep into Advance() src/advance/advance.cpp src/incflo.cpp commit 1bd24af584f13a7f0ae55700a7b020b69e87a8ff Author: knutsvk Date: Mon Nov 12 17:14:00 2018 +0000 update makefiles: move problem-independent bits to Make.incflo, only retain parallelisation/debug/profiling exec/Make.incflo exec/channel_cylinder/GNUmakefile exec/periodic_vortices/GNUmakefile exec/poiseuille_annulus/GNUmakefile exec/poiseuille_cylinder/GNUmakefile exec/poiseuille_plane/GNUmakefile src/incflo.cpp commit 1fb2a03422aec0adad81ae6e329f4239ea97b876 Author: knutsvk Date: Mon Nov 12 16:40:52 2018 +0000 simplify advance loop and exit criteria exec/periodic_vortices/inputs exec/periodic_vortices/inputs_init exec/periodic_vortices/inputs_restart exec/poiseuille_plane/GNUmakefile exec/poiseuille_plane/inputs src/advance/advance.cpp src/incflo.H src/incflo.cpp commit f8bc0358c15be8b30c1f971446682a3ddf37aeb3 Author: knutsvk Date: Mon Nov 12 15:57:16 2018 +0000 move initial plot and check writing, implement AverageDownTo src/incflo.H src/incflo.cpp commit d0613b63f373e9add08e27b90bec713db1b2726f Author: knutsvk Date: Mon Nov 12 15:30:46 2018 +0000 first (untested) implementation of AverageDown() src/incflo.H src/incflo.cpp commit 8299a7540ca7cc1bc2a8d5fc7e66caf164a99232 Author: knutsvk Date: Mon Nov 12 14:03:06 2018 +0000 move post-inintalisation stuff to PostInit() src/incflo.cpp src/setup/init.cpp src/utilities/io.cpp commit e604400a1d8ed147c5c0ca03bac61ca993c1844b Author: knutsvk Date: Mon Nov 12 13:38:17 2018 +0000 more cleanup and restructure, this now works with restart exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs_init exec/periodic_vortices/inputs_restart src/boundary_conditions/boundary_conditions.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit a51fab4624f5f731d8e87d0694a321bbf09e4aa0 Author: knutsvk Date: Sun Nov 11 14:22:03 2018 +0000 input files for checking restart capability exec/periodic_vortices/inputs_init exec/periodic_vortices/inputs_restart commit 4de315223daf2f6a18df30530192996a0ee641c1 Author: knutsvk Date: Sun Nov 11 14:21:35 2018 +0000 working on checkpoint/restart bugfix exec/periodic_vortices/GNUmakefile src/incflo.cpp src/utilities/io.cpp commit 18d7209bbde78e43b7631cf881b1ba7a4e0e6145 Author: knutsvk Date: Sun Nov 11 12:53:10 2018 +0000 cleanup compilation procedure, ensure it works on macOS README.md exec/Make.incflo exec/periodic_vortices/GNUmakefile extern/blitz/.cvsignore extern/blitz/Makefile.am extern/blitz/Makefile.in extern/blitz/README extern/blitz/array-impl.h extern/blitz/array.cc extern/blitz/array.h extern/blitz/array/.cvsignore extern/blitz/array/Makefile.am extern/blitz/array/Makefile.in extern/blitz/array/asexpr.cc extern/blitz/array/asexpr.h extern/blitz/array/cartesian.h extern/blitz/array/cgsolve.h extern/blitz/array/complex.cc extern/blitz/array/convolve.cc extern/blitz/array/convolve.h extern/blitz/array/cycle.cc extern/blitz/array/domain.h extern/blitz/array/et.h extern/blitz/array/expr.cc extern/blitz/array/expr.h extern/blitz/array/fastiter.h extern/blitz/array/funcs.h extern/blitz/array/functorExpr.h extern/blitz/array/geometry.h extern/blitz/array/indirect.h extern/blitz/array/interlace.cc extern/blitz/array/io.cc extern/blitz/array/iter.h extern/blitz/array/map.h extern/blitz/array/methods.cc extern/blitz/array/misc.cc extern/blitz/array/multi.h extern/blitz/array/newet-macros.h extern/blitz/array/newet.h extern/blitz/array/ops.cc extern/blitz/array/ops.h extern/blitz/array/reduce.cc extern/blitz/array/reduce.h extern/blitz/array/resize.cc extern/blitz/array/shape.h extern/blitz/array/slice.h extern/blitz/array/slicing.cc extern/blitz/array/stencil-classes.cc extern/blitz/array/stencil-et-macros.h extern/blitz/array/stencil-et.h extern/blitz/array/stencilops.h extern/blitz/array/stencils.cc extern/blitz/array/stencils.h extern/blitz/array/storage.h extern/blitz/array/where.h extern/blitz/array/zip.h extern/blitz/bench.cc extern/blitz/bench.h extern/blitz/benchext.cc extern/blitz/benchext.h extern/blitz/blitz.h extern/blitz/bounds.h extern/blitz/bzconfig.h extern/blitz/bzdebug.h extern/blitz/compiler.h extern/blitz/config.h extern/blitz/config.h.in extern/blitz/constpointerstack.h extern/blitz/et-forward.h extern/blitz/etbase.h extern/blitz/funcs.h extern/blitz/generate/.cvsignore extern/blitz/generate/Makefile.am extern/blitz/generate/Makefile.in extern/blitz/generate/arroperands.h extern/blitz/generate/arroptuple.h extern/blitz/generate/bzfstream.h extern/blitz/generate/genarrbops.cpp extern/blitz/generate/genarruops.cpp extern/blitz/generate/genmatbops.cpp extern/blitz/generate/genmathfunc.cpp extern/blitz/generate/genmatuops.cpp extern/blitz/generate/genpromote.cpp extern/blitz/generate/genstencils.py extern/blitz/generate/genvecbfn.cpp extern/blitz/generate/genvecbops.cpp extern/blitz/generate/genvecuops.cpp extern/blitz/generate/genvecwhere.cpp extern/blitz/generate/makeloops.py extern/blitz/generate/operands.h extern/blitz/generate/operands2.h extern/blitz/generate/optuple.h extern/blitz/generate/optuple2.h extern/blitz/globeval.cc extern/blitz/gnu/bzconfig.h extern/blitz/indexexpr.h extern/blitz/indexmap-forward.h extern/blitz/levicivita.h extern/blitz/limits-hack.h extern/blitz/listinit.h extern/blitz/memblock.cc extern/blitz/memblock.h extern/blitz/meta/.cvsignore extern/blitz/meta/Makefile.am extern/blitz/meta/Makefile.in extern/blitz/meta/dot.h extern/blitz/meta/matassign.h extern/blitz/meta/matmat.h extern/blitz/meta/matvec.h extern/blitz/meta/metaprog.h extern/blitz/meta/product.h extern/blitz/meta/sum.h extern/blitz/meta/vecassign.h extern/blitz/minmax.h extern/blitz/numinquire.h extern/blitz/numtrait.h extern/blitz/ops.h extern/blitz/prettyprint.h extern/blitz/promote.h extern/blitz/range.cc extern/blitz/range.h extern/blitz/ranks.h extern/blitz/reduce.h extern/blitz/shapecheck.h extern/blitz/simdtypes.h extern/blitz/stamp-h1 extern/blitz/tau.h extern/blitz/timer.h extern/blitz/tinymat2.cc extern/blitz/tinymat2.h extern/blitz/tinymat2io.cc extern/blitz/tinyvec-et.h extern/blitz/tinyvec.cc extern/blitz/tinyvec2.cc extern/blitz/tinyvec2.h extern/blitz/tinyvec2io.cc extern/blitz/tm2fastiter.h extern/blitz/tmevaluate.h extern/blitz/traversal.cc extern/blitz/traversal.h extern/blitz/tuning.h extern/blitz/tv2assign.h extern/blitz/tv2fastiter.h extern/blitz/tvcross.h extern/blitz/tvecglobs.h extern/blitz/tvevaluate.h extern/blitz/types.h extern/blitz/update.h extern/blitz/vector2.h extern/blitz/wrap-climits.h src/extern/algoim/LICENSE src/extern/algoim/README.md src/extern/algoim/examples/examples_quad.cpp src/extern/algoim/src/algoim_blitzinc.hpp src/extern/algoim/src/algoim_boundingbox.hpp src/extern/algoim/src/algoim_gaussquad.hpp src/extern/algoim/src/algoim_interval.hpp src/extern/algoim/src/algoim_multiloop.hpp src/extern/algoim/src/algoim_quad.hpp src/extern/algoim/src/algoim_real.hpp src/extern/algoim/src/algoim_utility.hpp commit b80aaa78aa8e15a510f9b59d79b9954186f5996e Author: knutsvk Date: Fri Nov 9 17:55:10 2018 +0000 need to properly understand when we can set_bc_type and reset MAC projection class. currently works when starting from scratch, but NOT when restarting... src/incflo.cpp commit 607969c5593b885de7e81b7b7582bda92c3a5690 Author: knutsvk Date: Fri Nov 9 17:31:28 2018 +0000 AverageDown has not yet been implemented src/incflo.cpp commit 4b9b02f097965b627ce5baa27ba352deeddb378e Author: knutsvk Date: Fri Nov 9 17:17:28 2018 +0000 some more work towards initializing using AmrCore class properly. this does not run exec/periodic_vortices/GNUmakefile exec/periodic_vortices/inputs src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit ebdc455a29ad226b40b9b6551e7712734c8f05a1 Author: knutsvk Date: Fri Nov 9 16:06:42 2018 +0000 remove member variables from function calls src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/incflo.H src/incflo.cpp src/setup/init.cpp src/utilities/io.cpp commit 513df1c127ee20acc7b3aa26438f9faa5b8c01c3 Author: knutsvk Date: Fri Nov 9 14:28:42 2018 +0000 allow the time step to grow by 10% per time step src/advance/advance.cpp commit ba5fafe957f2eafa78039ff348ed5dc72968acd3 Author: knutsvk Date: Fri Nov 9 13:59:44 2018 +0000 get rid of dt in function calls since it is now a member var src/advance/advance.cpp src/diffusion/diffusion.cpp src/incflo.H src/incflo.cpp src/projection/projection.cpp src/setup/init.cpp src/utilities/io.cpp commit 60993fddfe9b67990279a6cb240a050ab0dc2339 Author: knutsvk Date: Fri Nov 9 13:39:57 2018 +0000 (1) get rid of member variable nlev, use instead inherited members max_level and finest_level from AmrMesh (2) remove unused old-time variables for density and pressure (3) add some TODO items exec/periodic_vortices/inputs src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/derive/derive.cpp src/diffusion/diffusion.cpp src/divergence/divergence.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/projection/projection.cpp src/rheology/rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit 0221565616610913339f5035eb00c5d5a6ffec06 Author: knutsvk Date: Wed Nov 7 19:34:16 2018 +0000 remove parmparse include src/incflo.cpp commit 6de5446abc199fbd759cbc6d78860299c2f2af2a Author: knutsvk Date: Wed Nov 7 19:28:19 2018 +0000 mfix updates mfix_tracker src/advance/advance.cpp src/incflo.H commit c05528387d2125a105640616c879fcdfde0f64b8 Author: knutsvk Date: Wed Nov 7 19:21:33 2018 +0000 implement InitData() before Evolve() src/incflo.cpp commit 18ebcbc06ab65bc9ca2f222489efc317325d8dc7 Merge: f267eb56 bc390bde Author: knutsvk Date: Wed Nov 7 19:19:00 2018 +0000 Merge branch 'multilev' of https://github.com/AMReX-Codes/incflo into multilev commit f267eb5652bc289de03f16c08390bdc26a6b1e93 Author: knutsvk Date: Wed Nov 7 19:18:38 2018 +0000 lots of cleanup and restructure exec/channel_cylinder/inputs exec/periodic_vortices/inputs exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane/inputs src/convection/MacProjection.H src/convection/MacProjection.cpp src/embedded_boundaries/embedded_boundaries.cpp src/incflo.H src/incflo.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit e5364f0cc0ad47829536ec546c9a49a866e6e688 Author: knutsvk Date: Wed Nov 7 16:14:16 2018 +0000 remove unneecssary #includes src/incflo.H src/incflo.cpp commit aa5f2546423b9150288b25fd6c3a01fb8c400414 Author: knutsvk Date: Wed Nov 7 15:59:34 2018 +0000 starting to restructure code, inspired by AmrCore advection tutorial exec/periodic_vortices/inputs extern/algoim/src/algoim_blitzinc.hpp src/incflo.H src/incflo.cpp src/main.cpp src/projection/projection.cpp src/setup/init.cpp src/utilities/io_F.H src/utilities/read_namelist.f90 commit bc390bdecf7e644a8a2d2d729b478dc318233324 Author: Knut Sverdrup Date: Wed Nov 7 12:55:40 2018 +0000 Update README.md README.md commit 8df60e6e68c8c3ea3cc92dfb941d6c51a9c322d5 Author: knutsvk Date: Wed Nov 7 12:54:09 2018 +0000 Blitz and Algoim acknowledgements README.md commit 1ca3c6b9e4262b02877e54eeb367dd9eac60695a Author: knutsvk Date: Wed Nov 7 12:50:37 2018 +0000 add external libraries Algoim and Blitz++ directly to incflo repo (and give them creds) README.md dependencies exec/Make.incflo extern/algoim/LICENSE extern/algoim/README.md extern/algoim/examples/examples_quad.cpp extern/algoim/src/algoim_blitzinc.hpp extern/algoim/src/algoim_boundingbox.hpp extern/algoim/src/algoim_gaussquad.hpp extern/algoim/src/algoim_interval.hpp extern/algoim/src/algoim_multiloop.hpp extern/algoim/src/algoim_quad.hpp extern/algoim/src/algoim_real.hpp extern/algoim/src/algoim_utility.hpp extern/blitz/.cvsignore extern/blitz/Makefile.am extern/blitz/Makefile.in extern/blitz/README extern/blitz/array-impl.h extern/blitz/array.cc extern/blitz/array.h extern/blitz/array/.cvsignore extern/blitz/array/Makefile.am extern/blitz/array/Makefile.in extern/blitz/array/asexpr.cc extern/blitz/array/asexpr.h extern/blitz/array/cartesian.h extern/blitz/array/cgsolve.h extern/blitz/array/complex.cc extern/blitz/array/convolve.cc extern/blitz/array/convolve.h extern/blitz/array/cycle.cc extern/blitz/array/domain.h extern/blitz/array/et.h extern/blitz/array/expr.cc extern/blitz/array/expr.h extern/blitz/array/fastiter.h extern/blitz/array/funcs.h extern/blitz/array/functorExpr.h extern/blitz/array/geometry.h extern/blitz/array/indirect.h extern/blitz/array/interlace.cc extern/blitz/array/io.cc extern/blitz/array/iter.h extern/blitz/array/map.h extern/blitz/array/methods.cc extern/blitz/array/misc.cc extern/blitz/array/multi.h extern/blitz/array/newet-macros.h extern/blitz/array/newet.h extern/blitz/array/ops.cc extern/blitz/array/ops.h extern/blitz/array/reduce.cc extern/blitz/array/reduce.h extern/blitz/array/resize.cc extern/blitz/array/shape.h extern/blitz/array/slice.h extern/blitz/array/slicing.cc extern/blitz/array/stencil-classes.cc extern/blitz/array/stencil-et-macros.h extern/blitz/array/stencil-et.h extern/blitz/array/stencilops.h extern/blitz/array/stencils.cc extern/blitz/array/stencils.h extern/blitz/array/storage.h extern/blitz/array/where.h extern/blitz/array/zip.h extern/blitz/bench.cc extern/blitz/bench.h extern/blitz/benchext.cc extern/blitz/benchext.h extern/blitz/blitz.h extern/blitz/bounds.h extern/blitz/bzconfig.h extern/blitz/bzdebug.h extern/blitz/compiler.h extern/blitz/config.h extern/blitz/config.h.in extern/blitz/constpointerstack.h extern/blitz/et-forward.h extern/blitz/etbase.h extern/blitz/funcs.h extern/blitz/generate/.cvsignore extern/blitz/generate/Makefile.am extern/blitz/generate/Makefile.in extern/blitz/generate/arroperands.h extern/blitz/generate/arroptuple.h extern/blitz/generate/bzfstream.h extern/blitz/generate/genarrbops.cpp extern/blitz/generate/genarruops.cpp extern/blitz/generate/genmatbops.cpp extern/blitz/generate/genmathfunc.cpp extern/blitz/generate/genmatuops.cpp extern/blitz/generate/genpromote.cpp extern/blitz/generate/genstencils.py extern/blitz/generate/genvecbfn.cpp extern/blitz/generate/genvecbops.cpp extern/blitz/generate/genvecuops.cpp extern/blitz/generate/genvecwhere.cpp extern/blitz/generate/makeloops.py extern/blitz/generate/operands.h extern/blitz/generate/operands2.h extern/blitz/generate/optuple.h extern/blitz/generate/optuple2.h extern/blitz/globeval.cc extern/blitz/gnu/bzconfig.h extern/blitz/indexexpr.h extern/blitz/indexmap-forward.h extern/blitz/levicivita.h extern/blitz/limits-hack.h extern/blitz/listinit.h extern/blitz/memblock.cc extern/blitz/memblock.h extern/blitz/meta/.cvsignore extern/blitz/meta/Makefile.am extern/blitz/meta/Makefile.in extern/blitz/meta/dot.h extern/blitz/meta/matassign.h extern/blitz/meta/matmat.h extern/blitz/meta/matvec.h extern/blitz/meta/metaprog.h extern/blitz/meta/product.h extern/blitz/meta/sum.h extern/blitz/meta/vecassign.h extern/blitz/minmax.h extern/blitz/numinquire.h extern/blitz/numtrait.h extern/blitz/ops.h extern/blitz/prettyprint.h extern/blitz/promote.h extern/blitz/range.cc extern/blitz/range.h extern/blitz/ranks.h extern/blitz/reduce.h extern/blitz/shapecheck.h extern/blitz/simdtypes.h extern/blitz/stamp-h1 extern/blitz/tau.h extern/blitz/timer.h extern/blitz/tinymat2.cc extern/blitz/tinymat2.h extern/blitz/tinymat2io.cc extern/blitz/tinyvec-et.h extern/blitz/tinyvec.cc extern/blitz/tinyvec2.cc extern/blitz/tinyvec2.h extern/blitz/tinyvec2io.cc extern/blitz/tm2fastiter.h extern/blitz/tmevaluate.h extern/blitz/traversal.cc extern/blitz/traversal.h extern/blitz/tuning.h extern/blitz/tv2assign.h extern/blitz/tv2fastiter.h extern/blitz/tvcross.h extern/blitz/tvecglobs.h extern/blitz/tvevaluate.h extern/blitz/types.h extern/blitz/update.h extern/blitz/vector2.h extern/blitz/wrap-climits.h commit 8a1aca5b06f76351231f9b76aea9c98cf33dca2a Author: knutsvk Date: Tue Nov 6 16:14:39 2018 +0000 need to write this functionality in order for multileve to work src/incflo.H src/incflo.cpp src/setup/init.cpp commit 78514f470b9698061b5bc3753d1a1eddea35fe3f Author: knutsvk Date: Tue Nov 6 16:14:06 2018 +0000 bugfix after changing variable names src/advance/advance.cpp commit 69465d78ae5b24ba1cc6b1f8b1837c16fc32003e Author: knutsvk Date: Tue Nov 6 15:29:42 2018 +0000 cleanup (gets rid of all incflo compiler warnings) exec/poiseuille_plane/GNUmakefile src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/derive/derive_eb_mod.f90 src/diffusion/diffusion.cpp src/embedded_boundaries/get_walls.cpp src/projection/projection.cpp src/setup/init.cpp src/setup/init_namelist.f90 src/setup/set_bc0.f90 src/utilities/io.cpp commit 4c56958c4dd23dfdb9a25760464942efaebf6ee9 Author: knutsvk Date: Sat Nov 3 10:26:05 2018 +0000 illustrate the problem which occurs after Saxpy(gp) at level 1 in projection exec/poiseuille_plane/inputs commit b9dac3d7e0a462fd860dbf44e7e5a26cd20b9742 Author: knutsvk Date: Sat Nov 3 10:25:21 2018 +0000 try to get multilevel projection working src/diffusion/diffusion.cpp src/projection/projection.cpp commit 4a5626524de8478af5bac498f20eb88d055a84d0 Author: knutsvk Date: Sat Nov 3 10:24:29 2018 +0000 cleanup, remove unused pressure correction variable pp src/incflo.H src/setup/incflo_arrays.cpp commit b0ca9add4be8ea48cf52fa6a6fe61dc56c28f02c Author: knutsvk Date: Sat Nov 3 10:23:17 2018 +0000 bugfix in refinement of centre part of domain src/setup/init.cpp commit 3d1d35fbf155c7a335c7245f865dcff2228af91b Author: knutsvk Date: Tue Nov 6 14:04:21 2018 +0000 update mfix tracker mfix_tracker commit db7f852348e67e2bcdd3b58e790ef578df7d3c04 Author: knutsvk Date: Tue Nov 6 12:48:43 2018 +0000 update problem-specific BC file to work with nodal projection also exec/channel_cylinder/set_velocity_bcs.f90 commit 85fb822efdb135ccdc5570c763bc33dd0f460100 Merge: f0f793ba 96362eeb Author: Knut Sverdrup Date: Tue Nov 6 12:15:49 2018 +0000 Merge pull request #19 from AMReX-Codes/nodal-projection Nodal projection commit 96362eeb6cd5d3724013d5f9d371a473f5070a52 Author: knutsvk Date: Tue Nov 6 12:13:02 2018 +0000 check that nodal pressure also works for periodic vortices test exec/periodic_vortices/inputs commit 23eb7876028fef5e26ee4d6e8806e65e69e28162 Author: knutsvk Date: Tue Nov 6 11:46:32 2018 +0000 confirm poiseuille_plane case works with nodal projection exec/poiseuille_plane/GNUmakefile exec/poiseuille_plane/inputs mfix_tracker commit 170567440e8915c6b109b688775625c6a78bc5d6 Author: knutsvk Date: Tue Nov 6 11:45:59 2018 +0000 bugfix: when pressure is nodal its array is 1 element longer in each direction. need to make sure we dont go out of bounds on bctypes src/setup/incflo_arrays.cpp src/setup/set_p0.f90 commit c0ba0cde8073e5e8a0a0345035cba35845efbeb6 Author: knutsvk Date: Tue Nov 6 10:06:14 2018 +0000 with nodal pressure: dependencies on Algoim and blitz dependencies commit 606c9079cdb3bbba6b1048656d61cffbfe485631 Author: knutsvk Date: Tue Nov 6 10:04:25 2018 +0000 update usage of ALGOIM_HOME exec/Make.incflo mfix_tracker commit 0ab0b1733bbe3b311afb2c0e7b6ce2564dfca9ab Author: knutsvk Date: Mon Nov 5 17:53:40 2018 +0000 need to initialise perssure with ghost cells src/setup/incflo_arrays.cpp commit c1b37993f6afcc859bf8403d113b7e7d7b06a83c Author: Ann Almgren Date: Mon Nov 5 09:01:51 2018 -0800 Need to define MLNodeLaplacian with the ebfactory src/divergence/divergence.cpp src/projection/projection.cpp commit 32090580a927ca41c0445303307cd5f47b062b30 Author: knutsvk Date: Mon Nov 5 16:03:32 2018 +0000 trying to debug runtime error (std::bad_cast) exec/Make.incflo exec/poiseuille_plane/GNUmakefile exec/poiseuille_plane/inputs commit 5aff5ab0548ee2f16722f7319a5f60a4b1d8882d Author: knutsvk Date: Mon Nov 5 14:59:32 2018 +0000 nodal projection compiles but throws std::bad_cast when running, need to debug exec/Make.incflo exec/poiseuille_plane/inputs src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_velocity_bcs.f90 src/divergence/divergence.cpp src/incflo.H src/projection/projection.cpp src/projection/projection_F.H src/projection/projection_mod.f90 src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_p0.f90 src/setup/setup_F.H src/utilities/io.cpp commit f0f793bab596ff7455e0920b7e9d2aad5f86bfa9 Author: knutsvk Date: Tue Oct 30 18:03:59 2018 +0000 apply mfix updates mfix_tracker src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/setup/set_p0.f90 commit dc88a45a1f7af6a192ea87feeddfe44ad3fbcba4 Author: knutsvk Date: Tue Oct 30 17:37:50 2018 +0000 bugfix: abs -> std::abs in compute_dt exec/poiseuille_annulus/inputs src/advance/advance.cpp commit 6684dbe8fc2c1763c2a4dba4b27f77fcd0f46f99 Author: knutsvk Date: Tue Oct 30 17:37:33 2018 +0000 remove figure files exec/poiseuille_annulus/Screenshot from 2018-10-30 14-12-07.png exec/poiseuille_annulus/Screenshot from 2018-10-30 14-12-22.png exec/poiseuille_annulus/annulus.jpeg commit f3bdb5ee933168ef0e9062906805dce748063806 Merge: 73aacde4 b6e0eae4 Author: knutsvk Date: Tue Oct 30 16:57:22 2018 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 73aacde49f04f881ea230297c0ca622fb8c61db4 Author: knutsvk Date: Tue Oct 30 14:17:38 2018 +0000 inputs for the nalytical solution in python script exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs commit b6e0eae44682aa09d8dfdd29edc98a896eb92212 Author: knutsvk Date: Tue Oct 30 14:14:10 2018 +0000 some figures for BP-ICAM conference (Paulo) exec/poiseuille_annulus/Screenshot from 2018-10-30 14-12-07.png exec/poiseuille_annulus/Screenshot from 2018-10-30 14-12-22.png exec/poiseuille_annulus/annulus.jpeg exec/poiseuille_annulus/plot_velocity_profile.py exec/poiseuille_annulus/visit.curve commit a3a878f6cec3a8134079208a7b1191da98c64f59 Merge: 614135aa 7a22a609 Author: knutsvk Date: Tue Oct 30 11:54:20 2018 +0000 Merge upstrem development branch Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 7a22a6096fbf29c6cfc7271916840dfcd89b1b64 Author: knutsvk Date: Thu Oct 18 14:34:12 2018 +0100 clean up exec files exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs exec/poiseuille_annulus/inputs exec/poiseuille_annulus/plot_velocity_profile.py exec/poiseuille_cylinder/inputs exec/poiseuille_plane/N16/movie.visit exec/poiseuille_plane/N16/y0_0/Header exec/poiseuille_plane/N16/y0_0/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_0/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_0/Level_0/Cell_H exec/poiseuille_plane/N16/y0_0/incflo_job_info exec/poiseuille_plane/N16/y0_1/Header exec/poiseuille_plane/N16/y0_1/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_1/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_1/Level_0/Cell_H exec/poiseuille_plane/N16/y0_1/incflo_job_info exec/poiseuille_plane/N16/y0_2/Header exec/poiseuille_plane/N16/y0_2/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_2/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_2/Level_0/Cell_H exec/poiseuille_plane/N16/y0_2/incflo_job_info exec/poiseuille_plane/N16/y0_3/Header exec/poiseuille_plane/N16/y0_3/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_3/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_3/Level_0/Cell_H exec/poiseuille_plane/N16/y0_3/incflo_job_info exec/poiseuille_plane/N16/y0_4/Header exec/poiseuille_plane/N16/y0_4/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_4/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_4/Level_0/Cell_H exec/poiseuille_plane/N16/y0_4/incflo_job_info exec/poiseuille_plane/N16/y0_5/Header exec/poiseuille_plane/N16/y0_5/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_5/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_5/Level_0/Cell_H exec/poiseuille_plane/N16/y0_5/incflo_job_info exec/poiseuille_plane/N16/y0_6/Header exec/poiseuille_plane/N16/y0_6/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_6/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_6/Level_0/Cell_H exec/poiseuille_plane/N16/y0_6/incflo_job_info exec/poiseuille_plane/N16/y0_7/Header exec/poiseuille_plane/N16/y0_7/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_7/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_7/Level_0/Cell_H exec/poiseuille_plane/N16/y0_7/incflo_job_info exec/poiseuille_plane/N32/y0_0/Header exec/poiseuille_plane/N32/y0_0/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_0/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_0/Level_0/Cell_H exec/poiseuille_plane/N32/y0_0/incflo_job_info exec/poiseuille_plane/N32/y0_1/Header exec/poiseuille_plane/N32/y0_1/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_1/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_1/Level_0/Cell_H exec/poiseuille_plane/N32/y0_1/incflo_job_info exec/poiseuille_plane/N32/y0_2/Header exec/poiseuille_plane/N32/y0_2/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_2/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_2/Level_0/Cell_H exec/poiseuille_plane/N32/y0_2/incflo_job_info exec/poiseuille_plane/N32/y0_3/Header exec/poiseuille_plane/N32/y0_3/Level_0/Cell_D_00000 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fb25f7407be9e8367141a9f588afa33d94ebb169 Author: knutsvk Date: Wed Oct 17 15:51:34 2018 +0100 update channel cylinder test csae exec/channel_cylinder/incflo.dat exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/utilities/io.cpp commit 614135aafc3f82a9363fc86728861fbc2ff40d2d Author: knutsvk Date: Tue Oct 16 14:58:42 2018 +0100 some more timestep experimenting exec/poiseuille_plane/bingham_poiseuille.dat exec/poiseuille_plane/timestep.py commit a70b51b1e20814ac010b13a760a468e6ebb4ecf9 Author: knutsvk Date: Tue Oct 16 12:42:28 2018 +0100 trying to make sense of timestep restrictions exec/poiseuille_plane/N16/movie.visit exec/poiseuille_plane/N16/y0_0/Header exec/poiseuille_plane/N16/y0_0/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_0/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_0/Level_0/Cell_H exec/poiseuille_plane/N16/y0_0/incflo_job_info exec/poiseuille_plane/N16/y0_1/Header exec/poiseuille_plane/N16/y0_1/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_1/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_1/Level_0/Cell_H exec/poiseuille_plane/N16/y0_1/incflo_job_info exec/poiseuille_plane/N16/y0_2/Header exec/poiseuille_plane/N16/y0_2/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_2/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_2/Level_0/Cell_H exec/poiseuille_plane/N16/y0_2/incflo_job_info exec/poiseuille_plane/N16/y0_3/Header exec/poiseuille_plane/N16/y0_3/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_3/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_3/Level_0/Cell_H exec/poiseuille_plane/N16/y0_3/incflo_job_info exec/poiseuille_plane/N16/y0_4/Header exec/poiseuille_plane/N16/y0_4/Level_0/Cell_D_00000 exec/poiseuille_plane/N16/y0_4/Level_0/Cell_D_00001 exec/poiseuille_plane/N16/y0_4/Level_0/Cell_H exec/poiseuille_plane/N16/y0_4/incflo_job_info 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exec/poiseuille_plane/N32/y0_5/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_5/Level_0/Cell_H exec/poiseuille_plane/N32/y0_5/incflo_job_info exec/poiseuille_plane/N32/y0_6/Header exec/poiseuille_plane/N32/y0_6/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_6/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_6/Level_0/Cell_H exec/poiseuille_plane/N32/y0_6/incflo_job_info exec/poiseuille_plane/N32/y0_7/Header exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00002 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00003 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00004 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00005 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00006 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00007 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00008 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00009 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00010 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00011 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00012 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00013 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00014 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_D_00015 exec/poiseuille_plane/N32/y0_7/Level_0/Cell_H exec/poiseuille_plane/N32/y0_7/incflo_job_info exec/poiseuille_plane/N32/y0_8/Header exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00000 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00001 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00002 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00003 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00004 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00005 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00006 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00007 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00008 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00009 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00010 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00011 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00012 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00013 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00014 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_D_00015 exec/poiseuille_plane/N32/y0_8/Level_0/Cell_H exec/poiseuille_plane/N32/y0_8/incflo_job_info exec/poiseuille_plane/N64/y0_0/Header exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00000 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00001 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00002 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00003 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00004 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00005 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00006 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00007 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00008 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00009 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00010 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00011 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00012 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00013 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00014 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_D_00015 exec/poiseuille_plane/N64/y0_0/Level_0/Cell_H exec/poiseuille_plane/N64/y0_0/incflo_job_info exec/poiseuille_plane/N64/y0_5/Header exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00000 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00001 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00002 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00003 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00004 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00005 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00006 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00007 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00008 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00009 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00010 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00011 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00012 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00013 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00014 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_D_00015 exec/poiseuille_plane/N64/y0_5/Level_0/Cell_H exec/poiseuille_plane/N64/y0_5/incflo_job_info exec/poiseuille_plane/bingham_poiseuille.dat exec/poiseuille_plane/timestep.py commit d4c98f0eb2a1dc736d5c4b77a14c9705b84ef63b Author: knutsvk Date: Mon Oct 15 10:26:13 2018 +0200 inputs for testing y0 vs CFL and dt on apollo exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit bb0ab50ace71450fd42abe5c8357ba4a36bc02ff Author: knutsvk Date: Fri Oct 12 17:41:53 2018 +0100 fix cfl so that it works for viscoplastics (?) need to check thoroughly exec/poiseuille_plane/inputs src/advance/advance.cpp src/incflo.H src/setup/init.cpp commit 1ebf5ca5e376e30c630936b30ff1fa0551d67f58 Author: knutsvk Date: Fri Oct 12 13:32:35 2018 +0100 rewrite steady-state checker src/advance/advance.cpp commit e51d5f714c8c8c45845df0bc3b7360e78818a988 Author: knutsvk Date: Fri Oct 12 11:20:54 2018 +0100 cleanup and simplify: use built-in multifab functionality to add gravity src/advance/Make.package src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/incflo.H commit 889e5e2fc4bad19dfebc4329474d9bc0c3e01d27 Author: knutsvk Date: Thu Oct 11 18:01:54 2018 +0100 add idea about how to simplify add_forcing (no Fortran routine) src/advance/advance.cpp commit ca46e8d554204d807337807b34a9aee89a4c3716 Author: knutsvk Date: Thu Oct 11 17:54:45 2018 +0100 move computation of dt out of Fortran routine src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 commit be156ef78d2bd51e6c42d2d51f7a3f396d2b9f15 Author: knutsvk Date: Wed Oct 10 19:23:20 2018 +0100 playing around with CFL criterion when using implicit solve: we may get away with worrying about convective and forcing terms... exec/poiseuille_plane/inputs src/advance/advance.cpp src/advance/advance_mod.f90 commit 4d0714770ed12144799983d9dc768b80ef5c9a2c Author: knutsvk Date: Wed Oct 10 18:47:11 2018 +0100 (1) dont recompute viscosity for Newtonian fluids (2) update periodic_vortices test case exec/periodic_vortices/init_fluid.f90 src/rheology/rheology.cpp src/rheology/rheology_F.H src/rheology/rheology_mod.f90 commit 5577006c40848eaebec62f5cf68e458c157590ae Author: knutsvk Date: Wed Oct 10 18:15:40 2018 +0100 major viscosity update: 5 types of rheology model supported (Newtonian, power-law, Bingham, Herschel-Bulkley, de Souza Mendes-Dutra) exec/channel_cylinder/inputs exec/periodic_vortices/inputs exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/inputs exec/poiseuille_plane/inputs src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_scalar_bcs.f90 src/diffusion/diffusion.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/divergence/divop_mod.f90 src/divergence/eb_wallflux_mod.f90 src/incflo.H src/rheology/rheology.cpp src/rheology/rheology_F.H src/rheology/rheology_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc0.f90 src/setup/setup_F.H src/utilities/constant_mod.f90 src/utilities/io.cpp commit 4110e22640fccd6bedd205aa8858216052103586 Author: knutsvk Date: Wed Oct 10 14:57:53 2018 +0100 update with mfix: periodic BC bug fixed mfix_tracker src/advance/advance.cpp src/diffusion/diffusion_eb_mod.f90 commit 8fb753dc039fc30480e5bb69d0e174484658d50d Author: knutsvk Date: Wed Oct 10 14:41:10 2018 +0100 Fix EB divop for period case mfix_tracker src/divergence/divop_mod.f90 commit 8f0d57c372e7a558c9333ac25ca8f0607b6de008 Author: knutsvk Date: Wed Oct 10 14:28:49 2018 +0100 some cleanup + update mfix commits exec/poiseuille_cylinder/inputs mfix_tracker src/advance/advance.cpp src/diffusion/diffusion_mod.f90 src/projection/projection.cpp src/setup/init.cpp commit 49368d3aef7677865ddc2d5bf8375fa4d8e0f0d1 Author: knutsvk Date: Wed Oct 10 13:23:52 2018 +0100 allow time-dependent BCs mfix_tracker src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/convection.cpp src/convection/mac_F.H src/diffusion/diffusion.cpp src/divergence/divergence.cpp src/incflo.H src/projection/projection.cpp src/setup/init.cpp src/utilities/io.cpp commit a555f84bea8818578bd8f5119fc172b3550fe2f1 Author: knutsvk Date: Tue Oct 9 18:40:50 2018 +0100 these values give u_max = 1 at steady-state (revisited dimensional analysis exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit 84bd802b83dceffbb6ea7fbc21cb34ac9eac288b Author: knutsvk Date: Tue Oct 9 17:32:37 2018 +0100 Bingham flow also works for poiseuille cylinder exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs exec/poiseuille_plane/inputs commit 5f23edbd1c611b5f5803d5d5a658ad0fb132b368 Author: knutsvk Date: Tue Oct 9 17:09:46 2018 +0100 Bingham fluid working in plane Poiseuille flow, although (1) CFL criterion is all wrong and (2) steady-state doesnt work exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs src/advance/advance.cpp src/convection/convection.cpp src/incflo.H src/rheology/Make.package src/rheology/calc_mu.f90 src/rheology/rheology_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/init.cpp src/setup/init_fluid.f90 src/setup/setup_F.H commit a75bce6db7043be93a21100908d9215175c14e9f Author: knutsvk Date: Mon Oct 8 17:19:59 2018 +0100 add derived variables and plot them correctly for EB cells src/derive/Make.package src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_eb_mod.f90 src/derive/derive_mod.f90 src/divergence/eb_wallflux_mod.f90 src/embedded_boundaries/Make.package src/embedded_boundaries/eb_gradu.f90 src/utilities/io.cpp commit 34c373c584cf6138846fa8c22968d75e7b23ec53 Author: knutsvk Date: Fri Oct 5 16:44:51 2018 +0100 workign towards computing strainrate, need to add wall effects for EB cells src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_eb_mod.f90 src/derive/derive_mod.f90 src/diffusion/diffusion.cpp src/diffusion/diffusion_mod.f90 src/divergence/eb_wallflux_mod.f90 commit 0b87011bf728aa0d4378c6c46629ca62d6f7148a Author: knutsvk Date: Fri Oct 5 14:27:48 2018 +0100 cleanup: get rid of lambda exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/boundary_conditions/set_scalar_bcs.f90 src/diffusion/diffusion.cpp src/diffusion/diffusion_F.H src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/divergence/divop_mod.f90 src/divergence/eb_wallflux_mod.f90 src/incflo.H src/rheology/calc_mu.f90 src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/init_fluid.f90 src/setup/set_bc0.f90 src/setup/setup_F.H src/utilities/io.cpp commit 064ee43b9c8dfcc5939b223e7b34839595ec9863 Author: knutsvk Date: Fri Oct 5 12:59:52 2018 +0100 poiseuille_plane: this illustrates the BC problem we get when using NSW on two walls meeting at an edge: non-zero velocity transverse velocity components in corners exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit 4fdf0b2e32d407887970ad3ae0b302588421cac9 Author: knutsvk Date: Fri Oct 5 11:51:11 2018 +0100 update amrex/mfix mfix_tracker src/convection/MacProjection.cpp src/convection/convection.cpp src/derive/derive.cpp src/diffusion/diffusion.cpp src/embedded_boundaries/writeEBsurface.cpp commit cc9ec6fff403e0c05544837fcb0cce30d51d90fc Author: knutsvk Date: Thu Oct 4 17:27:29 2018 +0100 fix poiseuille plane inputs exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit e4d176840febe865cdda0e9aa01d202e4d1b2b91 Author: knutsvk Date: Thu Oct 4 11:33:06 2018 +0100 playing around with annulus test case exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs exec/poiseuille_annulus/plot_velocity_profile.py commit 2d3ccfd715a6aa55332cb9927030e628c3afab34 Author: knutsvk Date: Wed Oct 3 17:17:14 2018 +0100 make MPI by default, remove deprecated amr.verbose exec/poiseuille_cylinder/GNUmakefile exec/poiseuille_cylinder/inputs commit 6731bb26deede0a44b911e9ce1ff4705dec6827c Author: knutsvk Date: Wed Oct 3 17:04:25 2018 +0100 poiseuille plane: cleanup inputs, make sure still works and gives u_max = 1m/s exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs src/diffusion/diffusion.cpp commit a2f1e0d12b5fa0a207255c4542a5b552d694c9ee Author: knutsvk Date: Wed Oct 3 15:58:26 2018 +0100 improve verbosity src/advance/advance.cpp src/main.cpp src/projection/projection.cpp commit f46d330e2f528fb25b3cdc00f15f206586045140 Author: knutsvk Date: Wed Oct 3 15:58:17 2018 +0100 periodic vortices: clean up, make sure still works exec/periodic_vortices/inputs commit 9a7a62e270981a26ed185b8259974936c79d8f9c Author: knutsvk Date: Wed Oct 3 14:07:48 2018 +0100 bugfix: <= -> < src/utilities/io.cpp commit 45d9f4e51ec99b6d0932cc686e5b6e40bb5878c5 Author: knutsvk Date: Wed Oct 3 13:17:33 2018 +0100 updated latest mfix develop changes. code still compiles but segfaults when writing plotfile, could easily be other bugs introduced as well. mfix_tracker src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/boundary_conditions/Make.package src/boundary_conditions/bc_fill_nd.F90 src/boundary_conditions/boundary_conditions.cpp src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/convection.cpp src/convection/convection_F.H src/convection/convection_mod.f90 src/convection/mac_F.H src/convection/macproj_mod.f90 src/derive/derive.cpp src/diffusion/diffusion.cpp src/divergence/divergence.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/get_walls.cpp src/incflo.H src/incflo.cpp src/main.cpp src/projection/projection.cpp src/projection/projection_F.H src/projection/projection_mod.f90 src/rheology/rheology.cpp src/setup/init.cpp src/utilities/io.cpp commit 7633652161917b9c3c82f461bffb16ec0a9d497d Author: knutsvk Date: Tue Oct 2 16:08:26 2018 +0100 update mfix commit: Remove lev as argument to writeEBsurface mfix_tracker src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/main.cpp commit 28627e0d6ea8385142c473417a6fd5452552af50 Author: knutsvk Date: Tue Oct 2 15:59:04 2018 +0100 incflo_level -> incflo in preparation of multi-level exec/poiseuille_cylinder/inputs src/Make.package src/advance/advance.cpp src/advance/advance_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/convection/convection.cpp src/convection/macproj_mod.f90 src/derive/derive.cpp src/diffusion/diffusion.cpp src/diffusion/diffusion_mod.f90 src/divergence/divergence.cpp src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/get_walls.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo.H src/incflo.cpp src/main.cpp src/projection/projection.cpp src/projection/projection_mod.f90 src/rheology/rheology.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp src/utilities/io.cpp commit 482f06f603f8590665e0c21c1ce3580090c5d690 Author: knutsvk Date: Tue Oct 2 15:49:20 2018 +0100 cleanup: combined dirs io and modules into utilities exec/Make.incflo src/modules/Make.package src/utilities/Make.package src/utilities/constant_mod.f90 src/utilities/eb_to_pvd.f90 src/utilities/io.cpp src/utilities/io_F.H src/utilities/param_mod.f90 src/utilities/read_namelist.f90 src/utilities/remove_comment.f90 src/utilities/utilities_mod.f90 commit 4c472b0bdc0e08e3e4d6366106d3a5b32729caed Author: knutsvk Date: Mon Oct 1 06:51:06 2018 -0700 first steps towards non-Newtonian flow exec/periodic_vortices/inputs src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_mod.f90 src/incflo_level.H src/io/io.cpp src/main.cpp src/modules/constant_mod.f90 src/rheology/Make.package src/rheology/rheology.cpp src/rheology/rheology_F.H src/rheology/rheology_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/incflo_arrays.cpp src/setup/init_fluid.f90 commit cd6d1f3276bf44b454207bc97a6d77e270d021ff Author: knutsvk Date: Sun Sep 30 23:42:31 2018 -0700 more restructure: move functions out of advance and incflo_level src/advance/advance.cpp src/boundary_conditions/boundary_conditions.cpp src/derive/Make.package src/derive/derive.cpp src/derive/derive_F.H src/derive/derive_mod.f90 src/embedded_boundaries/embedded_boundaries.cpp src/incflo_level.cpp src/setup/incflo_arrays.cpp src/setup/init.cpp commit c9d688b4cf280d28d115f70d4cb3b86985580a73 Author: knutsvk Date: Sun Sep 30 23:03:00 2018 -0700 more cleanup restructure exec/Make.incflo src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/boundary_conditions/Make.package src/boundary_conditions/bc_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/boundary_conditions_F.H src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/mac_F.H src/convection/macproj_mod.f90 src/divergence/Make.package src/divergence/average_cc_to_fc.f90 src/divergence/divergence.cpp src/divergence/divergence_F.H src/divergence/divop_mod.f90 src/divergence/eb_wallflux_mod.f90 src/divop/Make.package src/incflo_level.H src/incflo_level.cpp src/io/io.cpp src/modules/Make.package src/projection/projection.cpp src/setup/Make.package src/setup/ic_mod.f90 src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_bc0.f90 src/setup/setup_F.H src/setup/zero_wall_norm_vel.f90 commit 1eb1af2c05fa4a62892c874c6ff38cd3c539e072 Author: knutsvk Date: Sun Sep 30 21:42:23 2018 -0700 remove nodal pressure exec/poiseuille_cylinder/GNUmakefile src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/set_velocity_bcs.f90 src/incflo_level.H src/io/io.cpp src/projection/projection.cpp src/projection/projection_F.H src/projection/projection_mod.f90 src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_bc0.f90 src/setup/set_p0.f90 src/setup/setup_F.H commit 15609f1c4380f93efe3417cf36808b81344ae8a5 Author: knutsvk Date: Sun Sep 30 20:00:12 2018 -0700 more cleanup and restructure exec/Make.incflo src/Make.package src/advance/advance.cpp src/boundary_conditions/Make.package src/boundary_conditions/boundary_conditions.cpp src/boundary_conditions/fill_bc0.f90 src/boundary_conditions/set_mac_velocity_bcs.f90 src/boundary_conditions/set_pressure_bcs.f90 src/boundary_conditions/set_scalar_bcs.f90 src/boundary_conditions/set_velocity_bcs.f90 src/convection/Make.package src/embedded_boundaries/Make.package src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/embedded_boundaries.cpp src/embedded_boundaries/embedded_boundaries_F.H src/embedded_boundaries/get_walls.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo_level.cpp src/rheology/Make.package src/rheology/calc_mu.f90 src/setup/Make.package src/setup/incflo_arrays.cpp src/setup/init.cpp src/setup/set_bc_flow.f90 src/setup/setup_F.H commit 380e798f798b480c7a266c86c238203d14c251d2 Author: knutsvk Date: Sat Sep 29 12:21:06 2018 -0700 fix indentation in all f90 files exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 exec/periodic_vortices/init_fluid.f90 src/advance/advance_mod.f90 src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 src/convection/macproj_mod.f90 src/convection/set_mac_velocity_bcs.f90 src/convection/slopes_mod.f90 src/derive/derive.f90 src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/divop/divop_mod.f90 src/divop/eb_wallflux_mod.f90 src/embedded_boundaries/eb_interpolation_mod.f90 src/embedded_boundaries/get_eb_walls.f90 src/io/eb_to_pvd.f90 src/io/read_namelist.f90 src/io/remove_comment.f90 src/modules/bc_mod.f90 src/modules/constant_mod.f90 src/modules/ic_mod.f90 src/modules/param_mod.f90 src/modules/utilities_mod.f90 src/projection/projection_mod.f90 src/setup/amrex_to_incflo.F90 src/setup/calc_cell.f90 src/setup/calc_mu.f90 src/setup/fill_bc0.f90 src/setup/get_data.f90 src/setup/init_fluid.f90 src/setup/init_namelist.f90 src/setup/set_bc0.f90 src/setup/set_bc_flow.f90 src/setup/set_bc_type.f90 src/setup/set_delp_dir.f90 src/setup/set_p0.f90 src/setup/set_pressure_bcs.f90 src/setup/set_scalar_bcs.f90 src/setup/set_velocity_bcs.f90 src/setup/zero_wall_norm_vel.f90 tools/F90/fcompare_par.f90 tools/F90/fextract.f90 tools/F90/fjoin_par.f90 tools/F90/plt_compare_diff_grids.f90 commit 8a9fca6da670de42e47d35f60f350b0bd718bc9d Author: knutsvk Date: Fri Sep 28 18:18:35 2018 -0700 get rid of static int naccess src/advance/advance.cpp src/incflo_level.H src/main.cpp commit ce10519c52ff8be91bcca5e562634591c8df6d9d Author: knutsvk Date: Fri Sep 28 17:59:53 2018 -0700 more cleanup, reorg and mfix update exec/Make.incflo exec/poiseuille_cylinder/inputs mfix_tracker src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/convection/MacProjection.H src/convection/MacProjection.cpp src/convection/Make.package src/convection/convection_F.H src/convection/mac_F.H src/convection/macproj_mod.f90 src/convection/set_mac_velocity_bcs.f90 src/derive/derive_F.H src/diffusion/diffusion_F.H src/incflo_level.H src/incflo_level.cpp src/io/io_F.H src/main.cpp src/projection/Make.package src/projection/projection_F.H src/setup/Make.package src/setup/amrex_to_incflo.F90 src/setup/bc.cpp src/setup/calc_cell.f90 src/setup/calc_mu.f90 src/setup/fill_bc0.f90 src/setup/get_data.f90 src/setup/init.cpp src/setup/init_fluid.f90 src/setup/init_namelist.f90 src/setup/set_bc0.f90 src/setup/set_bc_flow.f90 src/setup/set_bc_type.f90 src/setup/set_delp_dir.f90 src/setup/set_p0.f90 src/setup/set_pressure_bcs.f90 src/setup/set_scalar_bcs.f90 src/setup/set_velocity_bcs.f90 src/setup/setup_F.H src/setup/zero_wall_norm_vel.f90 commit 57c0a865a4cf6ddf7d481abbd1a6fdbf9f94e0b8 Author: knutsvk Date: Fri Sep 28 17:28:39 2018 -0700 mfix update mfix_tracker src/diffusion/diffusion_eb_mod.f90 commit 4e330a8687a885bc0dadf49d8b72b85a7c4b64b6 Author: knutsvk Date: Fri Sep 28 16:25:34 2018 -0700 cleanup and restructure exec/Make.incflo src/Make.package src/advance/Make.package src/advance/advance.cpp src/advance/advance_F.H src/advance/advance_mod.f90 src/incflo_level.H src/incflo_level.cpp src/incflo_regrid.cpp src/init_and_boundary_conds/Make.package src/init_and_boundary_conds/bc.cpp src/init_and_boundary_conds/icbc_F.H src/init_and_boundary_conds/init.cpp src/init_and_boundary_conds/set_pressure_bcs.f90 src/init_and_boundary_conds/set_scalar_bcs.f90 src/projection/Make.package src/projection/projection_F.H src/projection/projection_mod.f90 commit c8d6a832de6771411f4d129e990215d53bf3f565 Author: knutsvk Date: Fri Sep 28 14:33:43 2018 -0700 cleanup and restructure src/Make.package src/advance.cpp src/convection/convection.cpp src/derive/Make.package src/derive/derive.f90 src/derive/derive_F.H src/embedded_boundaries/Make.package src/embedded_boundaries/eb.cpp src/embedded_boundaries/eb_F.H src/embedded_boundaries/eb_annulus.cpp src/embedded_boundaries/eb_box.cpp src/embedded_boundaries/eb_cylinder.cpp src/embedded_boundaries/eb_general.cpp src/embedded_boundaries/eb_hopper.cpp src/embedded_boundaries/eb_if.H src/embedded_boundaries/eb_regular.cpp src/embedded_boundaries/get_walls.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo_level.H src/incflo_level.cpp src/incflo_regrid.cpp src/init_and_boundary_conds/Make.package src/init_and_boundary_conds/icbc_F.H src/init_and_boundary_conds/init.cpp src/io/Make.package src/io/io.cpp src/io/io_F.H src/main.cpp src/projection/MacProjection.cpp src/projection/Make.package src/projection/mac_F.H src/projection/projection.cpp src/projection/projection_F.H commit 1f0048fca656b860d6f2975d3038d0239a9f9270 Author: knutsvk Date: Fri Sep 28 12:13:44 2018 -0700 forgot to add in last commit src/diffusion/diffusion_F.H commit f4d78e879787962a546ef2b70da541b2746bee53 Author: knutsvk Date: Fri Sep 28 12:13:23 2018 -0700 more cleanup: dont need header files in Make.package files, restructuring convection / diffusion / projection... src/Make.package src/convection/Make.package src/convection/convection.cpp src/convection/convection_F.H src/derive/Make.package src/diffusion/Make.package src/diffusion/diffusion.cpp src/diffusion/incflo_diff_F.H src/embedded_boundaries/Make.package src/init_and_boundary_conds/Make.package src/io/Make.package src/projection/Make.package src/projection/incflo_mac_F.H src/projection/incflo_proj_F.H commit f27618368f3973cbd9ddcdb89014c4cf04d5d947 Author: knutsvk Date: Fri Sep 28 12:05:43 2018 -0700 remove deprecated CMake stuff CMakeLists.txt src/CMakeLists.txt src/convection/CMakeLists.txt src/derive/CMakeLists.txt src/diffusion/CMakeLists.txt src/divop/CMakeLists.txt src/embedded_boundaries/CMakeLists.txt src/init_and_boundary_conds/CMakeLists.txt src/io/CMakeLists.txt src/modules/CMakeLists.txt src/projection/CMakeLists.txt tools/CMake/INCFLO_Options.cmake tools/CMake/INCFLO_Tags.cmake tools/CMake/INCFLO_Typecheck.cmake tools/CMake/INCFLO_Utils.cmake tools/CMakeLists.txt commit 15f466a590ab6d3b17678b287d7d4f86cceb22d6 Author: knutsvk Date: Fri Sep 28 11:06:40 2018 -0700 cleanup inputs exec/poiseuille_cylinder/inputs src/incflo_advance.cpp src/main.cpp commit 6f7cf0a405f808fbc4d42e1b6624e525eb9b3c6b Author: knutsvk Date: Thu Sep 27 19:29:03 2018 -0700 update latest mfix develop commits mfix_tracker src/divop/divop_mod.f90 src/projection/MacProjection.cpp commit 109f45b2a2f354dff4c4e0a6cfa8acf207dbe037 Author: knutsvk Date: Thu Sep 27 19:19:08 2018 -0700 new dir for computation of derived vars src/derive/CMakeLists.txt src/derive/Make.package src/derive/compute_vort.f90 src/derive/incflo_derive_F.H commit cfedb52e8a15ceff47907de77f0ec8bd6ae8179e Author: knutsvk Date: Thu Sep 27 19:18:42 2018 -0700 more cleanup exec/Make.incflo src/CMakeLists.txt src/Make.package src/convection/incflo_convection.cpp src/incflo_F.H src/incflo_advance.cpp src/incflo_level.cpp src/incflo_regrid.cpp src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/init_namelist.f90 src/io/incfloIO.cpp src/io/read_namelist.f90 src/main.cpp src/modules/CMakeLists.txt src/modules/Make.package src/modules/bc_mod.f90 src/modules/compute_vort.f90 src/modules/ic_mod.f90 src/modules/utilities_mod.f90 src/projection/MacProjection.cpp src/projection/incflo_projection.cpp commit d34aebdea8cf96b6da8fecd47718895feac3edb1 Author: knutsvk Date: Thu Sep 27 18:54:46 2018 -0700 remove deprecated comment src/io/incfloIO.cpp commit 68711d3a096bb6b2cb4a5e72e92c1fea233ade00 Author: knutsvk Date: Thu Sep 27 18:54:36 2018 -0700 remove numerical_params.inc src/include/numerical_params.inc commit 0ad9833827f4b99176a29f236b455a80397413b4 Author: knutsvk Date: Thu Sep 27 18:40:06 2018 -0700 remove write_error module src/io/CMakeLists.txt src/io/write_error.f90 commit 44e620b9b722a8a96bd6fb6b5644958977df352d Author: knutsvk Date: Thu Sep 27 18:37:35 2018 -0700 remove error_manager module src/io/CMakeLists.txt src/io/Make.package src/io/error_manager_mod.f90 commit d8bd14e21a772bf2098e76729ad0ab25021f9928 Author: knutsvk Date: Thu Sep 27 18:34:59 2018 -0700 remove check_data exec/Make.incflo exec/poiseuille_plane/inputs src/CMakeLists.txt src/check_data/CMakeLists.txt src/check_data/Make.package src/check_data/check_bc_flow.f90 src/check_data/check_bc_geometry.f90 src/check_data/check_bc_inflow.f90 src/check_data/check_bc_outflow.f90 src/check_data/check_bc_walls.f90 src/check_data/check_boundary_conditions.f90 src/check_data/check_gas_properties.f90 src/check_data/check_initial_conditions.f90 src/check_data/incflo_checkdat_F.H src/incflo_level.H src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/set_bc0.f90 src/init_and_boundary_conds/zero_wall_norm_vel.f90 commit 194253c4751450454d88ab9d28b6f49dd1d8b3f0 Author: knutsvk Date: Thu Sep 27 18:11:41 2018 -0700 major cleanup exec/poiseuille_plane/inputs src/check_data/CMakeLists.txt src/check_data/Make.package src/check_data/check_boundary_conditions.f90 src/check_data/check_gas_properties.f90 src/check_data/check_inputs.f90 src/check_data/incflo_checkdat_F.H src/incflo_level.H src/incflo_level.cpp src/include/boundary_conditions.inc src/include/gas_phase.inc src/include/physical_params.inc src/include/species.inc src/include/species_indices.inc src/init_and_boundary_conds/amrex_to_incflo.F90 src/init_and_boundary_conds/calc_mu.f90 src/init_and_boundary_conds/incflo_icbc_F.H src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/init_fluid.f90 src/init_and_boundary_conds/init_namelist.f90 src/init_and_boundary_conds/set_bc0.f90 src/init_and_boundary_conds/set_p0.f90 src/io/CMakeLists.txt src/io/Make.package src/io/parse_line.f90 src/io/read_namelist.f90 src/main.cpp src/modules/CMakeLists.txt src/modules/Make.package src/modules/bc_mod.f90 src/modules/constant_mod.f90 src/modules/fld_constants_mod.f90 src/modules/ic_mod.f90 src/modules/param_mod.f90 src/modules/run_mod.f90 src/modules/scales_mod.f90 src/projection/set_scalar_bcs.f90 commit bd03af82ab6cf48f1db05c1edcc43dc8e06db697 Author: knutsvk Date: Thu Sep 27 14:51:48 2018 -0700 feat: regrid functionality mfix_tracker src/convection/incflo_convection.cpp src/incflo_arrays.cpp src/incflo_level.H src/incflo_level.cpp src/incflo_regrid.cpp src/init_and_boundary_conds/incflo_init.cpp src/main.cpp commit 4289c964c81b3a4410f2d0a0b170ae42cdfb7329 Author: knutsvk Date: Thu Sep 27 10:41:56 2018 -0700 use steady-state solver, implicit diffusion, and rescale so that u_max = 1 m/s at steadystate exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit e727fec218c86312e0032df8b90577c417649624 Author: knutsvk Date: Wed Sep 26 17:56:02 2018 -0700 update mfix tracker mfix_tracker commit 2615afd6e421dcc20aa9332d4c7ff6a180e539f3 Author: knutsvk Date: Wed Sep 26 17:41:24 2018 -0700 cleanup src/diffusion/diffusion_eb_mod.f90 src/diffusion/incflo_diffusion.cpp src/divop/divop_mod.f90 src/embedded_boundaries/incflo_eb_annulus.cpp src/embedded_boundaries/incflo_eb_cylinder.cpp src/embedded_boundaries/incflo_eb_general.cpp src/embedded_boundaries/incflo_eb_hopper.cpp src/incflo_advance.cpp src/init_and_boundary_conds/incflo_init.cpp src/projection/MacProjection.cpp src/projection/incflo_projection.cpp commit 7b5b78b3c76becc031b9de04a8ae1cc8dbb66eac Author: knutsvk Date: Wed Sep 26 16:47:48 2018 -0700 feat: implicit diffusion for diagonal elements of viscous stress src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/incflo_diffusion.cpp src/divop/divop_mod.f90 src/divop/eb_wallflux_mod.f90 src/projection/incflo_projection.cpp src/projection/projection_mod.f90 commit 6f5b744336f2576a8897f07ff85b5481103d1ef6 Author: knutsvk Date: Wed Sep 26 16:43:25 2018 -0700 normalise maxvel at steady-state to 1m/s, use implicit diffusion exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs commit fdc4cc05d5d85392cbea169b30695532e3e2288f Author: knutsvk Date: Tue Sep 25 18:27:24 2018 -0700 cleanup src/incflo_advance.cpp commit 102686add353f01e8508591dd33792a1d589e615 Author: knutsvk Date: Tue Sep 25 18:27:13 2018 -0700 if verbose amrex::Print src/diffusion/incflo_diffusion.cpp commit ecb50dafa035b7b7e5f443d9d78197fc49ad9835 Author: knutsvk Date: Tue Sep 25 18:26:22 2018 -0700 this takes around 30 sec to steady state exec/poiseuille_cylinder/inputs commit 50d1a19555a7e503a2171c1ce0dee19978274cc3 Author: knutsvk Date: Tue Sep 25 18:09:27 2018 -0700 fix some verbosity issues exec/poiseuille_cylinder/inputs src/incflo_advance.cpp src/incflo_level.H src/init_and_boundary_conds/incflo_init.cpp src/projection/MacProjection.H src/projection/incflo_projection.cpp commit 154b06b36a2aa7c9aaf8c6563c0eff470f0511d8 Author: knutsvk Date: Tue Sep 25 16:59:39 2018 -0700 uneven grid spacing seems to work by itself as long as divop module is changed, dont need this test exec/channel_empty/GNUmakefile exec/channel_empty/incflo.dat exec/channel_empty/init_fluid.f90 exec/channel_empty/inputs exec/channel_empty/set_mac_velocity_bcs.f90 exec/channel_empty/set_velocity_bcs.f90 commit 0a8614535e8752cae371b95d1823352ba56a9a5b Author: knutsvk Date: Tue Sep 25 16:58:57 2018 -0700 nonzero IC vel exec/channel_cylinder/incflo.dat commit 3152e70e918245a633c131112355e3d60480f00d Author: knutsvk Date: Tue Sep 25 16:19:06 2018 -0700 remove obsolete comments exec/poiseuille_annulus/incflo.dat exec/poiseuille_cylinder/incflo.dat exec/poiseuille_plane/incflo.dat commit fa6e4884b76a8a5375693f71fbdb8254476a5407 Merge: 7f3807d7 daa71a15 Author: knutsvk Date: Tue Sep 25 16:15:42 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/incflo into development commit 7f3807d7e22a64fa5c0f6858a2fb534de4fa3c9f Author: knutsvk Date: Tue Sep 25 16:15:36 2018 -0700 parabolic inflow in empty channel, to try dx != dy computations in exec/channel_empty/GNUmakefile exec/channel_empty/incflo.dat exec/channel_empty/init_fluid.f90 exec/channel_empty/inputs exec/channel_empty/set_mac_velocity_bcs.f90 exec/channel_empty/set_velocity_bcs.f90 commit f238698f3d016ad6893b8ffb8cdbc46ef93394e8 Author: knutsvk Date: Tue Sep 25 16:14:29 2018 -0700 enable setting mean velocity of parabolic profile in initial conditions exec/channel_cylinder/init_fluid.f90 commit 4bc064d993e3a6f061c98bc3039c36e135e0d304 Author: knutsvk Date: Tue Sep 25 15:52:20 2018 -0700 channel_cylinder replaces this as test case for flow past cylinder exec/open_cylinder/GNUmakefile exec/open_cylinder/incflo.dat exec/open_cylinder/inputs commit daa71a15dec80a33cb20083b6c0f37f0ab11718a Author: knutsvk Date: Tue Sep 25 23:34:51 2018 +0100 this inputs file gives nice results for viscous flow past cylinder in channel exec/channel_cylinder/inputs commit ac8e0c1a4cbb82b5549d74d15a432bdb2ba8eab9 Author: knutsvk Date: Tue Sep 25 12:25:53 2018 -0700 bugfix: can now restart from checkpoint files again exec/channel_cylinder/inputs src/io/incfloIO.cpp commit e2200bc1619c1b1a104cb0a6a6c60f8880f013aa Author: knutsvk Date: Tue Sep 25 12:17:39 2018 -0700 write velocity to file as vector, multiply variables by volfrac before writing to plotfile (if ebfactory[lev]) src/io/incfloIO.cpp commit 439764e00eb8dd3b4d68ec81ecb672397c255755 Author: knutsvk Date: Tue Sep 25 11:19:59 2018 -0700 remove _g suffices from all exec files exec/open_cylinder/incflo.dat exec/open_cylinder/inputs exec/periodic_vortices/init_fluid.f90 exec/periodic_vortices/inputs exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit 1c1abc3322ec56b5d0bb5ecda7b95f365a6d45a3 Author: knutsvk Date: Tue Sep 25 11:17:20 2018 -0700 also remove _g suffices from inputs exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs commit 54759e19d8ed91454e37d6df54aa4f136cc13132 Author: knutsvk Date: Tue Sep 25 11:01:08 2018 -0700 mwe inputs file for Weiqun to see EB bug exec/channel_cylinder/inputs commit 9e95186dcfa5f25cb15e15ea268bffd3175fdf60 Author: knutsvk Date: Tue Sep 25 10:50:47 2018 -0700 get rid of obsolete _g suffixes throughout code exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 src/check_data/check_bc_flow.f90 src/check_data/check_bc_inflow.f90 src/check_data/check_bc_outflow.f90 src/check_data/check_bc_walls.f90 src/check_data/check_boundary_conditions.f90 src/check_data/check_gas_properties.f90 src/check_data/check_initial_conditions.f90 src/convection/incflo_convection.cpp src/diffusion/diffusion_mod.f90 src/diffusion/incflo_diff_F.H src/diffusion/incflo_diffusion.cpp src/incflo_F.H src/incflo_advance.cpp src/incflo_arrays.cpp src/incflo_level.H src/incflo_level.cpp src/include/boundary_conditions.inc src/include/gas_phase.inc src/include/initial_conditions.inc src/init_and_boundary_conds/CMakeLists.txt src/init_and_boundary_conds/Make.package src/init_and_boundary_conds/amrex_to_incflo.F90 src/init_and_boundary_conds/calc_mu.f90 src/init_and_boundary_conds/incflo_icbc_F.H src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/init_fluid.f90 src/init_and_boundary_conds/init_namelist.f90 src/init_and_boundary_conds/set_bc0.f90 src/init_and_boundary_conds/set_bc_flow.f90 src/init_and_boundary_conds/set_p0.f90 src/init_and_boundary_conds/set_velocity_bcs.f90 src/init_and_boundary_conds/zero_wall_norm_vel.f90 src/io/incfloIO.cpp src/io/read_namelist.f90 src/main.cpp src/modules/bc_mod.f90 src/modules/compute_vort.f90 src/modules/constant_mod.f90 src/modules/fld_constants_mod.f90 src/modules/ic_mod.f90 src/modules/param_mod.f90 src/projection/incflo_mac_F.H src/projection/incflo_proj_F.H src/projection/incflo_projection.cpp src/projection/macproj_mod.f90 src/projection/projection_mod.f90 src/projection/set_mac_velocity_bcs.f90 src/projection/set_scalar_bcs.f90 commit 58d17f409054e18d5cb4eca00a148209f419c7c2 Author: knutsvk Date: Tue Sep 25 03:12:32 2018 +0100 after bugfix in amrex, all resolutions now work for cylinder channel exec/channel_cylinder/inputs commit 226d5f06c52638ade4b9f9084174450fbf0ad713 Author: knutsvk Date: Mon Sep 24 14:34:41 2018 -0700 flow past cylinder in channel, same settings as COMSOL example found online exec/channel_cylinder/incflo.dat exec/channel_cylinder/init_fluid.f90 exec/channel_cylinder/inputs exec/channel_cylinder/set_mac_velocity_bcs.f90 exec/channel_cylinder/set_velocity_bcs.f90 commit 24c11d3c53f450bfbc93b353fd5af5a60e73939c Author: knutsvk Date: Fri Sep 21 14:50:16 2018 -0700 up to date with mfix 916baf849e4b9a6418610ffc084f04baa94344f4 TODO mfix_tracker src/embedded_boundaries/incflo_eb_cylinder.cpp commit dfd91bd225717a9a0a1f5f93878e52f221f3fa72 Author: knutsvk Date: Fri Sep 21 14:32:57 2018 -0700 up to date with mfix commit 5f0a6254 exec/Make.incflo src/embedded_boundaries/incflo_eb_annulus.cpp src/embedded_boundaries/incflo_eb_box.cpp src/embedded_boundaries/incflo_eb_cylinder.cpp src/embedded_boundaries/incflo_eb_hopper.cpp src/embedded_boundaries/incflo_eb_regular.cpp src/incflo_level.H src/incflo_level.cpp src/init_and_boundary_conds/incflo_init.cpp src/projection/MacProjection.H src/projection/MacProjection.cpp src/projection/incflo_projection.cpp commit 1bcf6566a19c757704812ed1068e485f94396fe0 Author: knutsvk Date: Thu Sep 20 15:32:45 2018 -0700 trying to understand why flow past cylinder sometimes becomes ustable (but not always) exec/open_cylinder/incflo.dat exec/open_cylinder/inputs commit 973db98a75e76a90211d5e2054043007c97ed7c7 Author: knutsvk Date: Thu Sep 20 14:23:39 2018 -0700 concentric cylinders exec/poiseuille_annulus/inputs commit e6a86a569e1319f4ed65f91a68fa2546853abeaf Author: knutsvk Date: Thu Sep 20 14:22:22 2018 -0700 curve python script for comparing with analytical solution exec/poiseuille_annulus/plot_velocity_profile.py exec/poiseuille_annulus/visit.curve commit 0e5e26240915e1605bb7f4f146bb7b559e64c0f6 Merge: c078d21a b8234348 Author: Knut Sverdrup Date: Wed Sep 19 14:41:54 2018 -0700 Merge pull request #8 from AMReX-Codes/knut-dev merge knut-dev (branch will now be deleted) commit b8234348826b832ba832def2b0ecd6a0f67f36c1 Author: knutsvk Date: Wed Sep 19 14:20:55 2018 -0700 bugfix: need nghost >= 5 now that the diffusive wall fluxes have been implemented src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/divop/divop_mod.f90 src/incflo_level.H commit 804ea9d6eacc00cabb78d8f52ef53a7e866d35fb Author: knutsvk Date: Wed Sep 19 13:32:04 2018 -0700 trying to fix tiling issue in compute_divtau function exec/poiseuille_annulus/inputs src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 commit cfab6dcdc35199e60fd357afca23a7cf384db851 Author: knutsvk Date: Wed Sep 19 10:17:20 2018 -0700 up to date with mfix commit edc557fc src/convection/convection_mod.f90 src/incflo_advance.cpp src/projection/MacProjection.cpp src/projection/incflo_projection.cpp commit 7a776b3337a3d12220dda7a3e969f3fdc91ed203 Author: knutsvk Date: Tue Sep 18 16:01:05 2018 -0700 added concentric annular cylinders test case, which seems to work exec/poiseuille_annulus/GNUmakefile exec/poiseuille_annulus/incflo.dat exec/poiseuille_annulus/inputs src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/Make.package src/embedded_boundaries/incflo_eb.cpp src/embedded_boundaries/incflo_eb_annulus.cpp src/incflo_level.H commit 60866b20f6a47a28bc5fdc17f6c55668d863fb52 Author: knutsvk Date: Tue Sep 18 12:26:29 2018 -0700 check mass redistribution signs for michele, everything looks right src/divop/divop_mod.f90 commit 23bac1725efdaf0c2f7e7aaa4258c0897de1832b Author: knutsvk Date: Tue Sep 18 11:06:19 2018 -0700 added poiseuille flow through cylinder, renamed poiseuille through infinite planes exec/poiseuille_cylinder/GNUmakefile exec/poiseuille_cylinder/incflo.dat exec/poiseuille_cylinder/inputs exec/poiseuille_plane/GNUmakefile exec/poiseuille_plane/incflo.dat exec/poiseuille_plane/inputs commit 415ab7d7aca5a65d4caa26eb3f6fd14d992e77f3 Author: knutsvk Date: Tue Sep 18 10:09:05 2018 -0700 vortex shedding occurs for flow around cylinder in pipe! in order to validate properly we would need to use proper velocity inlet condition exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs commit c078d21a2e2cbe3ef795e0be8dddb8ff3e514fda Merge: 839e58bd 6272a298 Author: Knut Sverdrup Date: Mon Sep 17 18:17:31 2018 -0700 Merge pull request #7 from AMReX-Codes/knut-dev no slip boundary conditions working (for explicit diffusion and dx=dy=dz) commit 6272a29816f6af3ba81bf01cfe16fd7b12d34981 Author: knutsvk Date: Mon Sep 17 18:16:05 2018 -0700 up to date with mfix commit fdcbc8ab src/incflo_advance.cpp src/init_and_boundary_conds/incflo_init.cpp src/projection/incflo_projection.cpp commit 885f8ffc52425d760116aa801ded6f27a8197dd0 Author: knutsvk Date: Mon Sep 17 18:06:51 2018 -0700 open cylinder working (with explicit diffusion) exec/open_cylinder/inputs commit fad73e64e7b654ddbee2849e8c0887097c3013b3 Author: knutsvk Date: Mon Sep 17 17:53:53 2018 -0700 empty channel with no-slip boundaries working exec/empty_channel/incflo.dat exec/empty_channel/inputs src/divop/divop_mod.f90 commit 3829f6ef1a7e7d9cf8ca5caab654f1ca2f834f6d Author: knutsvk Date: Mon Sep 17 12:53:02 2018 -0700 up to date with mfix commit c8978e4f src/convection/convection_eb_mod.f90 src/init_and_boundary_conds/set_p0.f90 commit 566bc9f9238549c4b28d425f64bd3f5fa46a370c Author: knutsvk Date: Mon Sep 17 10:46:05 2018 -0700 these runtime parameters don't blow up too badly, but there are definitely still problems for small cut cells... exec/open_cylinder/incflo.dat exec/open_cylinder/inputs commit 523be66b5efba2dd341d534f000cbedc3d34f6fa Author: knutsvk Date: Mon Sep 17 10:17:03 2018 -0700 incorporate relevant changes up to mfix commit ae0f4119 src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/divop/divop_mod.f90 src/init_and_boundary_conds/incflo_icbc_F.H src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/set_p0.f90 commit c1d783ed6c0d698da6d0182e451667a2d09a1cd3 Author: knutsvk Date: Fri Sep 14 18:49:10 2018 -0700 add empty channel test case to try and get poiseuille flow to work exec/empty_channel/GNUmakefile exec/empty_channel/incflo.dat exec/empty_channel/inputs commit 32a9d246540df38d686ebc2450ef7e4bbe5bb5db Author: knutsvk Date: Fri Sep 14 18:40:13 2018 -0700 remove print statements src/diffusion/diffusion_eb_mod.f90 commit f293dfba63bb0ce3640aeb9281aef8d21ece937d Author: knutsvk Date: Fri Sep 14 17:36:13 2018 -0700 make more readable src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 commit 21d054516d34d34362f8c64444493eb90e4c98c3 Author: knutsvk Date: Fri Sep 14 17:36:01 2018 -0700 cleanup + bugfix: vlo->vllo src/divop/divop_mod.f90 commit 040086d7f91072e2680814b3b2011775d4eae618 Author: knutsvk Date: Fri Sep 14 15:32:13 2018 -0700 reduce amount of cells in (periodic) z-direction exec/periodic_vortices/inputs commit 07852b833e019ad1b2d764982c59ac11ac14cbbf Author: knutsvk Date: Fri Sep 14 12:24:18 2018 -0700 a few bugfixes src/diffusion/diffusion_mod.f90 src/incflo_advance.cpp src/io/eb_to_pvd.f90 src/modules/param_mod.f90 commit 03eaf4bc3d382922529b0788a3494c219ca945e5 Author: knutsvk Date: Fri Sep 14 11:22:10 2018 -0700 viscous wall fluxes src/convection/convection_eb_mod.f90 src/convection/incflo_convection.cpp src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/incflo_diff_F.H src/diffusion/incflo_diffusion.cpp src/divop/CMakeLists.txt src/divop/Make.package src/divop/divop_mod.f90 src/divop/eb_wallflux_mod.f90 src/embedded_boundaries/eb_interpolation_mod.f90 src/incflo_advance.cpp src/projection/incflo_mac_F.H src/projection/incflo_projection.cpp commit 839e58bdbe8e724560647d8881c62b63a4d6359f Merge: 7b9ab80f 4ff3746f Author: Knut Sverdrup Date: Thu Sep 13 17:38:56 2018 -0700 Merge pull request #6 from AMReX-Codes/knut-dev initial test of cylinder in channel working commit 4ff3746f5053eb7f03e34c0030537c19173b9715 Author: knutsvk Date: Thu Sep 13 17:37:41 2018 -0700 first test of cylinder in channel flow working exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs commit f013fa8a9a643f20be9227170e8705f6bf36aa67 Merge: a03e0a5f 3b0f8015 Author: knutsvk Date: Thu Sep 13 15:44:33 2018 -0700 merge Merge branch 'knut-dev' of https://github.com/AMReX-Codes/incflo into knut-dev commit a03e0a5f07c963506be111ae8763887e0b82d9d3 Author: knutsvk Date: Thu Sep 13 15:44:28 2018 -0700 decent flow past open cylinder results exec/cylinder/incflo.dat exec/cylinder/inputs commit 3b0f8015a6884d305377935bf61e57eb404b5dd0 Author: knutsvk Date: Thu Sep 13 15:43:01 2018 -0700 trying to get duct flow without cylinder to work with dirichlet velocity inlet exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs commit f96427ea0d1a55d5f6c3f168585fcb538fef6f0d Author: knutsvk Date: Thu Sep 13 15:22:02 2018 -0700 start work on proper benchmarking test: flow past cylinder in channel exec/channel_cylinder/GNUmakefile exec/channel_cylinder/incflo.dat exec/channel_cylinder/inputs exec/open_cylinder/GNUmakefile exec/open_cylinder/incflo.dat exec/open_cylinder/inputs commit 8abcce36b9c39a70a62721a611fa320806e45cfc Author: knutsvk Date: Thu Sep 13 10:20:27 2018 -0700 ignore files called movie.visit .gitignore commit a1d4e04c9b189355746997e4c230fc8790802c22 Author: knutsvk Date: Thu Sep 13 10:19:54 2018 -0700 update readme README.md commit 1f3bc60e5d3c56d44e668d834b02c6d994bcf59b Author: knutsvk Date: Thu Sep 13 10:19:31 2018 -0700 use new infinite cylidner EB geometry exec/cylinder/incflo.dat exec/cylinder/inputs src/embedded_boundaries/incflo_eb_cylinder.cpp commit 779dbd600132dd5962723e34e9378e4e50b5b724 Author: knutsvk Date: Thu Sep 13 08:56:01 2018 -0700 bugfix: cannot call amrex::Abort before amrex::Initialize src/main.cpp commit 7b9ab80f3df484685df74d8a8375fd60ea4a553b Merge: 869f2253 903a6bd2 Author: Knut Sverdrup Date: Wed Sep 12 21:12:47 2018 -0700 Merge pull request #5 from AMReX-Codes/knut-dev cylinder working commit 903a6bd2f996c68cff3c344dad26d4af9133b4f4 Author: knutsvk Date: Wed Sep 12 21:10:53 2018 -0700 look at some results with higher resolution exec/cylinder/GNUmakefile exec/cylinder/incflo.dat exec/cylinder/inputs commit 7ee7e3c61068c245b7e18124f4abbbdbf89ee66d Author: knutsvk Date: Wed Sep 12 18:11:56 2018 -0700 bugfix - no more nans for viscous flow src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 commit 2c2c6b2daca8d5e83999bad7352de97a828dee7f Author: knutsvk Date: Wed Sep 12 17:46:16 2018 -0700 start adding EB diffusion stuff. need to compute normal velocities at EB walls in order to apply BCs exec/Make.incflo exec/cylinder/inputs src/CMakeLists.txt src/convection/CMakeLists.txt src/convection/Make.package src/convection/convection_eb_mod.f90 src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/incflo_diff_F.H src/diffusion/incflo_diffusion.cpp src/divop/CMakeLists.txt src/divop/Make.package src/divop/divop_mod.f90 commit b7679bcc45a05fd0a47850eb1263ee3946e19e6d Author: knutsvk Date: Wed Sep 12 15:46:43 2018 -0700 update divop src/convection/divop_mod.f90 commit 869f22530425893fd63e5a231a89f7c53c549415 Merge: 1186e1e9 709c019a Author: Knut Sverdrup Date: Wed Sep 12 15:22:53 2018 -0700 Merge pull request #4 from AMReX-Codes/knut-dev cylinder problem working (for a few time steps) commit 709c019aaf405bb40ddbda2415fd185d05a0335b Author: knutsvk Date: Wed Sep 12 15:19:20 2018 -0700 flow past cylinder OK for a few steps, then fails in the diffusion EB module, which has not yet been implemetned in incflo, so great exec/cylinder/inputs src/incflo_advance.cpp commit 38aa91a4288b0b1b13a8b1b82669beffd631d7b8 Author: knutsvk Date: Wed Sep 12 14:18:22 2018 -0700 open the bottom of the cylinder exec/cylinder/inputs src/embedded_boundaries/incflo_eb_cylinder.cpp commit 1186e1e9f98e76ce1dcf3f046904f46edbc28053 Merge: f8def4b4 266df0c6 Author: Knut Sverdrup Date: Wed Sep 12 13:56:32 2018 -0700 Merge pull request #3 from AMReX-Codes/knut-dev debugging cylinder cont commit 266df0c6fb13a97c5b663898554a7370b3681a1a Author: knutsvk Date: Wed Sep 12 13:55:24 2018 -0700 divu is nonsymmetric in z even when we set the fc vel to constant (1,0,0) just before calling EB_computeDivergence() src/incflo_advance.cpp commit ed3fbe8a3170d94e95738602ceb9fcf004e695b9 Author: knutsvk Date: Wed Sep 12 13:33:25 2018 -0700 bugfix: missing arguments src/incflo_advance.cpp commit f8def4b479a0f6e2c5bdb278e7cddf496b12dd47 Merge: e6fc8f25 18b5c064 Author: Knut Sverdrup Date: Wed Sep 12 11:55:13 2018 -0700 Merge pull request #2 from AMReX-Codes/knut-dev work on cylinder test case (EB) commit 18b5c064a4a1b5ffe1ce928e82cba5de45879b23 Author: knutsvk Date: Wed Sep 12 10:30:28 2018 -0700 use micheles version of computing div(u), but with filled boundaries src/incflo_advance.cpp src/incflo_level.H commit 1ca6ae984cc2ec78dfaa89a346ad8b16f4a603ec Author: knutsvk Date: Tue Sep 11 18:50:22 2018 -0700 working on debugging the cylinder test case. problem seems to be in the computation of div(u) before the initial projection, since divu is non-constant in z near the domain boundaries src/incflo_advance.cpp commit c0e0119ae8045c608b5f8357d9ed7d6e2d0cb87e Author: knutsvk Date: Tue Sep 11 18:49:19 2018 -0700 update cylinder inputs exec/cylinder/inputs commit 6bb2af967e2174cac9d4d4ccdda64e1319dc9b0f Author: knutsvk Date: Tue Sep 11 16:55:31 2018 -0700 use amrex::Print() src/io/incfloIO.cpp src/main.cpp commit e6fc8f257c137ce5b9d6778a916b08b5fd67375e Merge: e7351212 99781ad0 Author: Knut Sverdrup Date: Tue Sep 11 11:53:19 2018 -0700 Merge pull request #1 from AMReX-Codes/knut-dev new divop module + bugfixes commit 99781ad0f467ff1d401aedc72d37cdb2d86d98a2 Author: knutsvk Date: Tue Sep 11 11:44:38 2018 -0700 fix typo in inputs files. now double shear layer gives same results if we multiply rho and mu by the same factor exec/cylinder/inputs exec/periodic_vortices/inputs commit a13ee2ffeeac6fceb74ed63e30324ddbad87dceb Author: knutsvk Date: Tue Sep 11 11:17:26 2018 -0700 remember to compute vorticity before writing final plotfile if time=stop_time src/main.cpp commit 30752730f3a4a47af9937e31a46c1ee5fb5c8695 Author: knutsvk Date: Tue Sep 11 10:51:07 2018 -0700 get separate divergence operator module for EB from mfix .gitignore src/convection/CMakeLists.txt src/convection/Make.package src/convection/convection_eb_mod.f90 src/convection/divop_mod.f90 commit e7351212bd63f67023259e44716ac936a1af674b Author: knutsvk Date: Mon Sep 10 19:00:05 2018 -0700 migrate incflo to AMReX-Codes .clang-format .gitignore CMakeLists.txt README.md TODO doc/Doxyfile.in exec/Make.incflo exec/cylinder/GNUmakefile exec/cylinder/incflo.dat exec/cylinder/inputs exec/periodic_vortices/GNUmakefile exec/periodic_vortices/incflo.dat exec/periodic_vortices/init_fluid.f90 exec/periodic_vortices/inputs src/CMakeLists.txt src/Make.package src/check_data/CMakeLists.txt src/check_data/Make.package src/check_data/check_bc_flow.f90 src/check_data/check_bc_geometry.f90 src/check_data/check_bc_inflow.f90 src/check_data/check_bc_outflow.f90 src/check_data/check_bc_walls.f90 src/check_data/check_boundary_conditions.f90 src/check_data/check_gas_properties.f90 src/check_data/check_initial_conditions.f90 src/check_data/check_inputs.f90 src/check_data/incflo_checkdat_F.H src/convection/CMakeLists.txt src/convection/Make.package src/convection/convection_eb_mod.f90 src/convection/convection_mod.f90 src/convection/incflo_convection.cpp src/convection/slopes_mod.f90 src/diffusion/CMakeLists.txt src/diffusion/Make.package src/diffusion/diffusion_eb_mod.f90 src/diffusion/diffusion_mod.f90 src/diffusion/incflo_diff_F.H src/diffusion/incflo_diffusion.cpp src/embedded_boundaries/CMakeLists.txt src/embedded_boundaries/Make.package src/embedded_boundaries/eb_interpolation_mod.f90 src/embedded_boundaries/get_eb_walls.f90 src/embedded_boundaries/get_walls.cpp src/embedded_boundaries/incflo_eb.cpp src/embedded_boundaries/incflo_eb_F.H src/embedded_boundaries/incflo_eb_box.cpp src/embedded_boundaries/incflo_eb_cylinder.cpp src/embedded_boundaries/incflo_eb_general.cpp src/embedded_boundaries/incflo_eb_hopper.cpp src/embedded_boundaries/incflo_eb_if.H src/embedded_boundaries/incflo_eb_regular.cpp src/embedded_boundaries/writeEBsurface.cpp src/incflo_F.H src/incflo_advance.cpp src/incflo_arrays.cpp src/incflo_level.H src/incflo_level.cpp src/incflo_regrid.cpp src/include/boundary_conditions.inc src/include/gas_phase.inc src/include/geometry.inc src/include/initial_conditions.inc src/include/numerical_params.inc src/include/physical_params.inc src/include/species.inc src/include/species_indices.inc src/init_and_boundary_conds/CMakeLists.txt src/init_and_boundary_conds/Make.package src/init_and_boundary_conds/amrex_to_incflo.F90 src/init_and_boundary_conds/calc_cell.f90 src/init_and_boundary_conds/calc_mu_g.f90 src/init_and_boundary_conds/fill_bc0.f90 src/init_and_boundary_conds/get_data.f90 src/init_and_boundary_conds/incflo_icbc_F.H src/init_and_boundary_conds/incflo_init.cpp src/init_and_boundary_conds/init_fluid.f90 src/init_and_boundary_conds/init_namelist.f90 src/init_and_boundary_conds/set_bc0.f90 src/init_and_boundary_conds/set_bc_flow.f90 src/init_and_boundary_conds/set_bc_type.f90 src/init_and_boundary_conds/set_delp_dir.f90 src/init_and_boundary_conds/set_p0.f90 src/init_and_boundary_conds/set_velocity_bcs.f90 src/init_and_boundary_conds/zero_wall_norm_vel.f90 src/io/CMakeLists.txt src/io/Make.package src/io/eb_to_pvd.f90 src/io/error_manager_mod.f90 src/io/incfloIO.cpp src/io/incflo_io_F.H src/io/parse_line.f90 src/io/read_namelist.f90 src/io/remove_comment.f90 src/io/write_error.f90 src/main.cpp src/modules/CMakeLists.txt src/modules/Make.package src/modules/bc_mod.f90 src/modules/compute_vort.f90 src/modules/constant_mod.f90 src/modules/fld_constants_mod.f90 src/modules/ic_mod.f90 src/modules/param_mod.f90 src/modules/run_mod.f90 src/modules/scales_mod.f90 src/modules/utilities_mod.f90 src/projection/CMakeLists.txt src/projection/MacProjection.H src/projection/MacProjection.cpp src/projection/Make.package src/projection/incflo_mac_F.H src/projection/incflo_proj_F.H src/projection/incflo_projection.cpp src/projection/macproj_mod.f90 src/projection/projection_mod.f90 src/projection/set_mac_velocity_bcs.f90 src/projection/set_pressure_bcs.f90 src/projection/set_scalar_bcs.f90 tools/C++/fextract.cpp tools/CMake/INCFLO_Options.cmake tools/CMake/INCFLO_Tags.cmake tools/CMake/INCFLO_Typecheck.cmake tools/CMake/INCFLO_Utils.cmake tools/CMakeLists.txt tools/DEBUG/amrex-max-vel tools/DEBUG/ascii-reader.f08 tools/DEBUG/ascii-tools.f08 tools/F90/fcompare_par.f90 tools/F90/fextract.f90 tools/F90/fjoin_par.f90 tools/F90/plt_compare_diff_grids.f90 commit 75c30613a4067b10cca3b26000f937095bc8b33c Author: WeiqunZhang Date: Fri Sep 7 16:22:15 2018 -0700 Initial commit LICENSE