commit 2418c86665f0bc0cbc157dfbe8033c600428b020 Author: Hannah Klion Date: Thu Oct 15 12:44:10 2026 -0700 Set W to zero at the bed inside compute_W (#721) compute_W read W(i,j,0) as the start of its integration up the column but never set it, so every caller had to zero it first. Set it in compute_W. The callers still zero the whole MultiFab, since other code reads W's ghost cells, so nothing changes. Source/TimeIntegration/REMORA_compute_W.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp commit fd71b79b0104e2eda0dcdc21c10f2e41674e713f Author: Hannah Klion Date: Thu Oct 15 11:10:26 2026 -0700 Diagnose the true vertical velocity into z_velocity, and add an omega plot variable (#714) * Pull the vertical integration for W into compute_W advance_3d and prestep_t_advection each carried the same three kernels that integrate the horizontal mass flux divergence up the column to get W. Move them into one static REMORA::compute_W, unchanged. * Diagnose the true vertical velocity into zvel_new, and add an omega plot variable zvel_new was never written, so the plotted, checkpointed and taggable z_velocity was identically zero. compute_wvel now fills it at the end of each advance_3d_ml with a port of ROMS wvelocity: omega, plus the stretching of the levels by the moving free surface, plus the motion along the sloping levels moved to w-points with ROMS's cubic stencil. Like ROMS, nothing in the dynamics reads it. compute_omega gives the velocity across the levels from W, and the new 3D plot variable omega writes it at cell centers. Huon and Hvom are now set from the velocities when a level is made or restored, as ROMS set_massflux does at initialization, so omega is meaningful before the first step; setup_step overwrites them before anything else reads them. The z_velocity tagging mask is widened to the 3x3 block, the same as vorticity, since w now reads u and v on both faces of its cell. * Regenerate gold files for the diagnosed z_velocity Every test that plots z_velocity changes only in that field: it was identically zero before. The golds are rewritten with the rank count each was made with, so their file layout is unchanged. * Diagnose w and omega from the current velocities' fluxes, and at t=0, as ROMS does ROMS writes w and omega from fluxes that set_massflux rebuilds from the current velocities at the start of each step (main3d: set_massflux, omega, wvelocity, then output). compute_wvel and the omega plot variable read the time-averaged fluxes update_massflux_3d leaves instead, which shifted z_velocity by 0.1-6% of its maximum in the regression tests. compute_diagnostic_omega now builds the ROMS fluxes in temporaries (set_massflux_3d), and compute_omega takes the fluxes as arguments. ROMS also diagnoses w before its first history record, so InitData now calls compute_wvel too. DU_avg1 is zero there in both codes. Without the need for fluxes at t=0, init_massflux_3d and its call sites go away. Only z_velocity changes; the golds that plot it are regenerated. CMake/BuildREMORAExe.cmake Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_compute_W.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_H Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Channel_Test/job_info Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Cell_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Cell_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/job_info 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Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/job_info Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/job_info Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_logdrag/job_info Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_qdrag/job_info commit 4206e88bf9c35c94c7dfb3555a9d55d9288257f0 Author: remora-inputs-bot[bot] <342223535+remora-inputs-bot[bot]@users.noreply.github.com> Date: Wed Oct 14 15:56:41 2026 -0700 Update generated inputs_generic (#712) Co-authored-by: hklion <5033030+hklion@users.noreply.github.com> Exec/Generic/inputs_generic commit 21147594d0c514b6a109c2155a7e7ae05fa54790 Author: Hannah Klion Date: Wed Oct 14 15:56:30 2026 -0700 Keep the coarse wall in a refined level's ghost mask beyond the domain (#718) * Keep the coarse wall in a refined level's ghost mask beyond the domain FillCoarsePatchPC fills the fine rho-mask's out-of-domain ghost cells by foextrap, which copies the interior outward. At a river mouth on the domain edge that made the land behind the river wet on the fine level, and the boundary's salt mixed into the river cell: on the refined IdealRivGrid case the fine level held 3% too little river freshwater after 10 steps and 11% after 50. Inject the coarser level's mask there instead. * Test that a refined patch against the walls keeps the mask ring DogboneAnalytic_MLmaskring runs a two-level mask_ring case with the fine mask injected from level 0 and again with it evaluated on level 1 by hires_grid_level; the two must agree. Without the out-of-domain injection they differ by 34% in x_velocity and 100% in y_velocity on level 1. * Inject the coarse mask across periodic seams too, and test it foextrap extrapolates the fine mask across periodic edges as well, so inject every out-of-domain ghost from the coarser level, and give the hires full-domain mask the periodic FillBoundary level 0 has. Synchronize before the temporary goes out of scope, default uncovered cells to water, use amrex::coarsen, and skip fabs inside the domain. Add DogboneAnalytic_MLmaskring_periodic, which the old periodic skip and a zero-everything fill both fail; include the base input from the hires ones instead of copying it; list both tests in RegressionTests.rst. * Simplify regtest explanation Docs/sphinx_doc/RegressionTests.rst Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp Tests/CTestList.cmake Tests/test_files/DogboneAnalytic_MLmaskring/DogboneAnalytic_MLmaskring.i Tests/test_files/DogboneAnalytic_MLmaskring/DogboneAnalytic_MLmaskring_hires.i Tests/test_files/DogboneAnalytic_MLmaskring_periodic/DogboneAnalytic_MLmaskring_periodic.i Tests/test_files/DogboneAnalytic_MLmaskring_periodic/DogboneAnalytic_MLmaskring_periodic_hires.i commit 47a9cd76ca611119312813611b1a2bb18e249526 Author: Hannah Klion Date: Wed Oct 14 15:11:56 2026 -0700 Follow myROMS's bulk flux, with COARE 3.0 or 3.5 roughness lengths (#715) * Follow myROMS's bulk flux, with COARE 3.0 or 3.5 roughness lengths REMORA's bulk flux came from COAWST's older ROMS. Bring it in line with myROMS's bulk_flux.F (31cabd31): - remora.bulk_flux_scheme = coare30 | coare35 (default coare30) selects the Charnock parameter and the moisture and thermal roughness lengths: the two blocks myROMS switches on COARE_30 - whichever COARE version, as in myROMS: - the gustiness buoyancy flux has Qstar in its denominator - the vector stress is normalized by the wind speed without gustiness (Wilkin and Pareja-Roman 2024). The old form added the rain stress as Taur*sign(u), so a zero wind component still got a stress: that is BoundaryLayer's 43% change in x_velocity - the rain heat flux and stress take the magnitude of the rain, negative rain being snow - net longwave is masked on land - the eps guards in the wind speed, Qsea and evaporation sit where myROMS has them The BoundaryLayer and Upwelling_Fennel gold files are regenerated. * Keep the bulk-flux stress finite where the air density is zero ROMS writes the stress coefficient rhoAir*(Wstar^2+Taur/rhoAir), which divides by the air density, so a cell with zero air pressure (a land fill value) gives NaN that masking does not remove and the u-face average spreads to wet cells. (rhoAir*Wstar^2+Taur) is the same and finite. Also drop the transfer coefficient Cd, which nothing reads since the stress no longer uses it, and a comment the matched Qsea guard made stale. * Remove superscript * Clarify bulk flux description * whitespace Docs/sphinx_doc/Inputs.rst Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp Tests/REMORA_Gold_Files/BoundaryLayer/Header Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_H Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/BoundaryLayer/job_info Tests/REMORA_Gold_Files/Upwelling_Fennel/Header Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_H commit a5a500e16e41c413f904e7cf190efa33b24485bd Author: Hannah Klion Date: Wed Oct 14 14:33:52 2026 -0700 Add opt-in volume-weighted tracer average-down (#713) * Add opt-in volume-weighted tracer average-down remora.cf_avgdown_volume_weighted = 1 averages the fine tracers onto the coarse level weighted by cell volume, Hz/(pm*pn), as well as by the mask. The default stays ROMS's area mean of concentration, which on the refined IdealRivGrid case leaves level 0 with 17% more river freshwater than the fine level holds; weighted by volume it agrees to 0.04%. * Address review of the volume-weighted average-down Share one weighted kernel between the mask and volume weights, form the volume weight once per call with layout asserts, and say what the flag does and does not conserve, including that the initial high-resolution cascade keeps the area mean. Add DogboneAnalytic_MLvel_volavg, which must match its own gold and differ from MLvel's. Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA.cpp Source/Utils/REMORA_MaskedAverageDown.H Tests/CTestList.cmake Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel_volavg/job_info Tests/test_files/DogboneAnalytic_MLvel_volavg/DogboneAnalytic_MLvel_volavg.i commit b17b3138a60d8b2d098d57895d153ee19dfe7713 Author: Hannah Klion Date: Wed Oct 14 14:31:50 2026 -0700 Continue NetCDF output numbering after a checkpoint restart (#710) * Continue NetCDF output numbering after a checkpoint restart The output written at restart passed step 0 to the NetCDF writer, so per-step files restarted at plt00000 and the history file was moved aside and rewritten from its first record. Pass the restart step instead, and store the history record in the checkpoint so a restart appends to the history file it continues; with no file to append to, it begins a new one. Closes #524. * Take the restart record from the history file's own times Continue an existing history file from its first record at or after the restart time rather than trusting the checkpoint's count, so a short file gets no gap and a file from another grid is moved aside. Record the final-step plot in last_plot_file_step so a checkpoint written then does not count it twice, give levels made by a regrid after restart the same treatment, and pass the record into WriteNCPlotFile_which instead of recomputing it there. * Tighten restart history-file comments, docs, and log message Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.H Source/REMORA.cpp commit 5f6613c559367b07c5dc35e9e994e69f81d74765 Author: Hannah Klion Date: Wed Oct 14 11:17:05 2026 -0700 Document NetCDF grid and initial-condition files for refined levels (#709) * Document NetCDF grid and initial-condition files for refined levels * Correct refined-level input docs against the code Both high-resolution files are re-read on restart; regridded levels take their state from the coarser level; mask_rho is required by default with NetCDF ICs; analytic ICs with a NetCDF mask still read a grid file; name only the variables the size check covers; match the example to inputs_synth_hires; and bring the parameter table in line. Docs/sphinx_doc/Inputs.rst commit dbac74b4e4610e6e522934b1b7c7196bb1f1e9b8 Author: Hannah Klion Date: Wed Oct 14 11:09:10 2026 -0700 Tagging test docs extras (#711) * Update regression test descriptions in documentation * tagging test docs: the points #708 leaves out - MLcoastskip/MLcoasttag: correct the pair claim. MLcoasttag runs the unguarded path (null mask), so a guard that tags nothing passes both; MLvel and MLhires catch it, Advection_ML does not (unmasked runs skip the guard). - why MLcoastskip and MLdryface need regrid_int = 2 (temp is 10 on land at init; masking during stepping creates the contrast). - MLdryface threshold 0.025 sits mid-band: 6480 cells for roughly [0.019, 0.032], 8640+ below, 5760 above. - the vorticity stencil is untested, and why. - testing.rst: pin n_error_buf, blocking_factor and grid_eff in grid-structure inputs; main.cpp sets the first two. sphinx-build clean. Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/testing.rst commit 73f816ec80f5db8729fecfe8dada931eb7e9350e Author: Hannah Klion Date: Wed Oct 14 09:48:48 2026 -0700 Update regression test descriptions in documentation (#708) Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/testing.rst commit e32b5dfbae556d7bca209200bbe7aa6db07ffa42 Author: remora-inputs-bot[bot] <342223535+remora-inputs-bot[bot]@users.noreply.github.com> Date: Tue Oct 13 15:57:08 2026 -0700 Update generated inputs_generic (#707) Co-authored-by: hklion <5033030+hklion@users.noreply.github.com> Exec/Generic/inputs_generic commit 6a030d59441301d6f110c0d040d7ff823c80b0ee Author: Hannah Klion Date: Tue Oct 13 15:55:48 2026 -0700 Regenerate inputs_generic with a bot PR after merges (#704) * Make inputs_generic stable under unrelated source edits The generated Exec/Generic/inputs_generic changed whenever unrelated code moved, which caused most of its diff churn and merge conflicts: - Drop line numbers from the "# source:" fallback comment; name the file only. - Take a description only from a comment directly attached to the query (trailing, or a block directly above with no blank or code line between) or to the variable's declaration. Previously the extractor skipped code lines to borrow comments that belonged to neighboring parameters, and matched comments that merely mentioned the variable name. - Read the full text of multi-line description cells in Inputs.rst grid tables instead of only the first line. - Remove the line-number stripping from check_generic_inputs.sh, which no longer has anything to strip, and update GenericInputs.rst. * Regenerate inputs_generic with a bot PR after merges Feature branches no longer commit Exec/Generic/inputs_generic, so it stops conflicting when merging development. - generic-inputs-update.yml: on push to development, regenerate the file and open or update one PR from bot/inputs-generic. It uses GITHUB_TOKEN and pushes only to that branch, so branch protection on development applies. - generic-inputs-validate.yml: fail a PR that edits inputs_generic, unless it is the bot PR or carries the inputs-generic-hand-edit label. Otherwise run check_generic_inputs.sh --preview, which warns with the diff the merge will cause and does not fail. - check_generic_inputs.sh: add --preview, which restores the committed file afterward so running it locally leaves the tree clean. - Document the workflow in GenericInputs.rst. * Tighten inputs_generic description extraction Address review of the attached-comment rules: - Use only the nearest declaration of the variable; an earlier one with the same name belongs to another scope and could lend its comment. - Track /* ... */ blocks when scanning upward, so a code line ending in a trailing block comment is not taken as a comment line, code included. - Read the whole attached comment block instead of at most 5 lines. - Let preprocessor lines sit between a comment and its query. - Recognize Long, unsigned, size_t, auto and std::array declarations when looking up a variable's declaration comment. - Test the Inputs.rst grid-table parser and each of the cases above. - Correct the docs on what changes the generated file. * Address review of the inputs_generic bot workflow - Preview a PR by regenerating the file at its base and its head, each with its own generator, and diffing those. Comparing against the committed file blamed a PR for changes other merged PRs had made while a bot PR was still open (development is currently stale this way since #705). The preview no longer writes to the working tree, so it cannot discard local edits. - Drop the strict check on the bot PR: GITHUB_TOKEN-opened PRs do not trigger workflows, so it never ran. A manual workflow run checks strictly. - Move the hand-edit gate into its own light job with a depth-2 checkout, run it alone on label events, and keep label events from cancelling a preview. - Trigger on the Submodules/AMReX gitlink, so AMReX bumps get a preview. - Skip only opening #if/#ifdef/#ifndef lines between a comment and its query; #endif/#else/#elif end the scan. - Recognize declarations of any type when finding a variable's nearest declaration, so an unrecognized one cannot let an unrelated comment through. - Docs: describe the preview and qualify the code-motion guarantee. * Open the inputs_generic bot PR with a GitHub App token The organization policy does not allow GITHUB_TOKEN to create pull requests. Open the bot PR with a short-lived token from a dedicated GitHub App instead, as Dependabot does: - The token is minted after the generator runs, limited to this repository and to contents and pull-requests write, and revoked when the job ends. The App's client ID and private key live in the inputs-bot environment. The job's GITHUB_TOKEN drops to read-only. - App-token PRs trigger workflows, so the validate workflow now checks the bot PR strictly against a regeneration of the merge result. * Address second review of the inputs_generic bot workflow - Declaration lookup: treat "a * name" and "a & name" (spaces on both sides) as expressions, not declarations, so continuation lines no longer stop the scan; recognize direct initialization "Type name(args);", "Type const& name", and extern/struct/class/enum declarations. - Hand-edit gate: read the PR's labels from the API rather than the event payload, so overlapping label and code runs cannot act on a stale label list; give a restore command that fetches upstream development, which also works from forks. - check_generic_inputs.sh: require the base for --preview and reject unknown arguments, instead of silently comparing against HEAD or running strict; if the base AMReX commit cannot be fetched, warn and skip the preview rather than fail. - Docs: new restore command; declaration-derived description, default and type can all change when a query moves far from its declaration. .github/workflows/generic-inputs-update.yml .github/workflows/generic-inputs-validate.yml .github/workflows/style/check_generic_inputs.sh Docs/sphinx_doc/GenericInputs.rst Exec/Generic/build_schema_remora.py Exec/Generic/tests/test_build_schema_remora.py commit 3d58ef1ccd5ef49f94a425de266597b29080e3fa Author: Hannah Klion Date: Tue Oct 13 14:32:49 2026 -0700 turn off GLS length capping in BioToy and BoundaryLayer tests to match ported version of COAWST-ROMS (#706) Exec/BioToy/inputs Exec/BoundaryLayer/inputs commit 016ef448b1eee51821a0cbbb1d19776bd5b4a68f Author: Hannah Klion Date: Tue Oct 13 13:59:34 2026 -0700 Make inputs_generic stable under unrelated source edits (#703) * Make inputs_generic stable under unrelated source edits The generated Exec/Generic/inputs_generic changed whenever unrelated code moved, which caused most of its diff churn and merge conflicts: - Drop line numbers from the "# source:" fallback comment; name the file only. - Take a description only from a comment directly attached to the query (trailing, or a block directly above with no blank or code line between) or to the variable's declaration. Previously the extractor skipped code lines to borrow comments that belonged to neighboring parameters, and matched comments that merely mentioned the variable name. - Read the full text of multi-line description cells in Inputs.rst grid tables instead of only the first line. - Remove the line-number stripping from check_generic_inputs.sh, which no longer has anything to strip, and update GenericInputs.rst. * Tighten inputs_generic description extraction Address review of the attached-comment rules: - Use only the nearest declaration of the variable; an earlier one with the same name belongs to another scope and could lend its comment. - Track /* ... */ blocks when scanning upward, so a code line ending in a trailing block comment is not taken as a comment line, code included. - Read the whole attached comment block instead of at most 5 lines. - Let preprocessor lines sit between a comment and its query. - Recognize Long, unsigned, size_t, auto and std::array declarations when looking up a variable's declaration comment. - Test the Inputs.rst grid-table parser and each of the cases above. - Correct the docs on what changes the generated file. .github/workflows/style/check_generic_inputs.sh Docs/sphinx_doc/GenericInputs.rst Exec/Generic/build_schema_remora.py Exec/Generic/inputs_generic Exec/Generic/render_inputs_generic.py Exec/Generic/tests/test_build_schema_remora.py commit 2ffe868c30eba05d41e0577ae23bf02827ff0d73 Author: Hannah Klion Date: Tue Oct 13 13:43:28 2026 -0700 Document remora.gls_length_cap input (#705) * Document remora.gls_length_cap input * Clarify descriptions in Inputs.rst documentation * Revert "Clarify descriptions in Inputs.rst documentation" This reverts commit a517cc2d0369eb1391ed3a36ac168682bba1c8c9. Docs/sphinx_doc/Inputs.rst commit b34b70ebf68512ea0b7da5c3b4a6260c87d99d75 Author: Dimitrios K. Fytanidis Date: Mon Oct 12 23:32:22 2026 -0500 Cap the GLS turbulent length scale at kappa*Depth (#702) The Galperin bound is applied only where buoy2 > 0, which is correct -- under unstable stratification there is no overturning bound to apply -- but it leaves the length scale unbounded wherever N^2 <= 0. With n = -1, L = (cmu0^3) k^(3/2) / eps, so when eps collapses onto gls_Pmin while k stays finite, L diverges. In a Lake Michigan season this reached Akv = 4e6 m2/s in a 23 m cell at dt = 300. Adds remora.gls_length_cap (default true), bounding L by vonKar*Depth after the Galperin limiter, as ROMS does in gls_corstep.F. gls is recomputed from the limited scale below, so the cap feeds back into the closure state. BoundaryLayer's reference output predates the cap, so that test now sets the flag false; with it false the test matches the reference to 1.9e-08. Exec/Generic/inputs_generic Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_gls.cpp Tests/test_files/BoundaryLayer/BoundaryLayer.i commit 292b8e2a872c62dd7383656cf7000d0a999a1685 Author: Jean M. Sexton Date: Fri Oct 9 16:23:48 2026 -0700 Check wet surface temperature in one pass (#700) * Check wet surface temperature in one pass - Count, min/max, NaN and example in one reduction - Still once per exchange, at pack time * Exclude NaN from wet min/max and share one masked reduction - CheckWetRange skips NaN in min/max (NaN in a min/max reduction depends on reduction order); NaN is still counted, and the example value is carried by a sum from the owning rank so a NaN example survives the reduction - Replace WetMinMax with CheckWetRange (comp argument, lowest-k slab) so the SST check and the flux validation share one definition; flux rows now report NaN counts - Reduce min and -max in one allreduce - Drop the comment about ERF's own SST check frequency - Wrap new lines to 80 columns --------- Co-authored-by: Hannah Klion Source/REMORA_Coupling.cpp commit 7a06cc254c6bbd9e570fec1c372bc7a2d0c08b7e Author: Hannah Klion Date: Fri Oct 9 09:02:22 2026 -0700 Fill a hires level's metric ghosts from its own grid, not the coarse level's (#701) * Fill a hires level's metric ghosts from its own grid, not the coarse level's With remora.hires_grid_level set, set_grid_vars_averaged_down copied the level's pm/pn from the full-domain array and then FillPatched them, which on a refined level overwrote the whole ghost ring with the coarse level's pm/pn, unscaled by the refinement ratio. Every coarse-fine interface face was then 50% too long: on Channel_Seamount the refined patch's perimeter cells took a 30-50% mass-flux imbalance, the free surface jumped 0.28 m across the interface after one step, and y-velocity at the four patch corners -- where the resulting pressure ridge along each x-interface ends -- grew to 3e-2 by step 2 against a 1e-2 background, in both drivers and under one-way coupling. A flat-bathymetry hires grid reproduced it exactly, so the bathymetry had nothing to do with it. Ghost metrics now come from the level's own full-domain array, with FillBoundary, EnforcePeriodicity and the physical-boundary extrapolation, and never from another level; the bathymetry ghosts follow the same route, so a refined level's ghost ring carries the file's h rather than an interpolant of the coarse. The full-domain rescale of pm/pn by the ratio now covers every grow cell: it left the outermost ring at the fine value, which the old FillPatch on level 0 happened to hide. With the fix the hires run reproduces the no-hires one to three digits at the interface and the corners, and a flat-h hires run matches the flat no-hires run to 1e-14. All fifteen hires lanes are unchanged. ctest 64/64 (PnetCDF build). * Compile extrapolate_metric_to_physical_boundaries in every build The previous commit calls it from set_bathymetry_averaged_down and set_grid_vars_averaged_down, which the analytic hires path runs too, but it was defined in REMORA_init_from_netcdf.cpp inside the file's REMORA_USE_NETCDF guard, so builds without NetCDF failed to link. It has no NetCDF dependency; it now lives in REMORA.cpp. Non-NetCDF Debug build links; hires lanes pass in both builds. Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.cpp commit 0990e70fdda5f476a44d704e7e00faf329311b5e Author: Hannah Klion Date: Thu Oct 8 15:54:54 2026 -0700 Measure refinement time windows from remora.start_time (#698) * Measure refinement time windows from remora.start_time A refinement indicator's start_time and end_time are now seconds since remora.start_time, as in ERF, rather than times on the model clock. The new start_total_time and end_total_time give the same bounds on the model clock. Each bound may be given in only one form; giving both aborts. With the default remora.start_time = 0 the two coincide, so existing tests are unchanged. * Regenerate inputs_generic, wrap new lines, and document restart behavior of elapsed refinement windows Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst Exec/Generic/inputs_generic Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp commit afc2dcae83eb61b7c6d4e6670526d003c833b560 Author: Hannah Klion Date: Thu Oct 8 15:11:11 2026 -0700 move ubar/vbar fillpatch into river block (#699) Source/TimeIntegration/REMORA_advance_2d.cpp commit e7ebd27b50966687076dced428391b460ee8e6ba Author: Hannah Klion Date: Thu Oct 8 12:53:50 2026 -0700 remove spatial_order option since it is always set to 2 (#697) Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA_DataStruct.H commit 2eff6f6dd85ab11961fb02df782d0eb7b0fd8b9b Author: Hannah Klion Date: Thu Oct 8 10:23:23 2026 -0700 Mask tracer and free-surface wall values, and leave the state unchanged when writing output (#696) * Mask tracer and free-surface wall values as ROMS does ROMS multiplies the closed and gradient boundary values of the tracers and the free surface by the land mask (t3dbc, zetabc). REMORA's foextrap and reflect branches copied the interior value onto land at the boundary, so the land ring held the neighbouring water value. That value reached Zt_avg1 and from it the vertical grid on the ring. Fields filled with the foextrap types stay unmasked, as ROMS's bc_r2d/bc_r3d leave them. * Leave the state unchanged when writing output WritePlotFile filled ghost cells of the state and wrote fill values onto land in place. The pass meant to undo that set Zt_avg1, temp, salt, visc2 and diff2 to zero on land rather than restoring them, so writing output changed the next step and a checkpoint held different values from the run that wrote it. Keep a copy of what the output touches and put it back afterwards; ROMS masks only its output buffers. * Add regression tests for land on the boundary ring A remora.prob.mask_ring option for the DogboneAnalytic mask makes the ring of grow cells outside the non-periodic domain edges land, beside interior water, as in a ROMS closed basin. Three tests use it: a gold test of the wall values, a check that writing output every step leaves the solution unchanged, and a check that a run restarted from its step-5 checkpoint finishes where the continuous run does. The last needs a new add_test_restart helper. * update generic inputs * Revert "Leave the state unchanged when writing output" This reverts commit e7b8f4e7c7cdb62b8d1eeae0737bb28fdfd1b230. * Mask tke and gls wall values as ROMS does ROMS multiplies the boundary values of tke and gls by the land mask (tkebc) but leaves those of w alone (bc_w3d). REMORA filled tke and gls like w, copying the interior value onto land at the boundary. They now fill under tke_bc, which takes w's boundary types, and impose_zvel_bcs puts zero on land for that type only. Exec/Generic/inputs_generic Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/TimeIntegration/REMORA_gls.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Header Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_maskring/job_info Tests/test_files/DogboneAnalytic_maskring/DogboneAnalytic_maskring.i Tests/test_files/DogboneAnalytic_maskring_plotint/DogboneAnalytic_maskring_plotint.i Tests/test_files/DogboneAnalytic_maskring_restart/DogboneAnalytic_maskring_restart.i commit 8f1f606ece6d6d9fb3fe0954cc500e4c63fb79cc Merge: 8a18262d 49b88618 Author: Hannah Klion Date: Tue Oct 6 15:39:25 2026 -0700 Merge pull request #694 from hklion/worktree-subcycle-phase0 Fix `nu_z` in mesh refinement plotfiles commit 8a18262d275697ee7ebdb4426bbd2f838545711e Merge: 1c840b63 00cc7527 Author: Hannah Klion Date: Fri Oct 2 23:08:14 2026 -0700 Merge pull request #693 from hklion/split_model_time Split time into model time and elapsed time commit 1c840b631e7b3fa87458ea3b933aef5d861838eb Merge: fe853d1f 51bb96f6 Author: Hannah Klion Date: Fri Oct 2 23:07:30 2026 -0700 Merge pull request #692 from hklion/time_ref_double_calendar Do calendar arithmetic in double so time_ref dates work in single precision commit 49b88618c38f80f9f2e45b94d35b6e166d710490 Author: Hannah Klion Date: Fri Oct 2 23:04:54 2026 -0700 codespell .codespell-ignore-words commit 8f9c92d02b3da8f46f5fc0f778ccc651d8477e98 Merge: 8aa386fb fe853d1f Author: Hannah Klion Date: Fri Oct 2 23:01:18 2026 -0700 Merge branch 'development' into worktree-subcycle-phase0 commit 8aa386fba4f80056730046d2ff4bf6f7da4caf34 Author: Hannah Klion Date: Fri Oct 2 22:58:51 2026 -0700 generic inputs Exec/Generic/inputs_generic commit 8759a46c3d8d466bec8a05e583778d493ade008a Author: Hannah Klion Date: Thu Oct 1 17:44:09 2026 -0700 Check the plotfile's nodal z in CI and with a viewer-style script Tests/tools/check_mapped_grid.py rebuilds every level's node positions from a plotfile the way amrexplorer does -- the Header's per-level dx plus Nu_nd, ratio line ignored -- and checks the nodal boxes against the Cell boxes, bottom and top against h and zeta where the plotfile carries them, monotonicity in k, and the coarse-fine mismatch at coincident nodes. It fails the committed Advection_ML gold, whose level-1 Nu_nd has 17 node layers against a Header domain of 32, and passes every plotfile written after the fix. BoundaryLayer_ML_plot_z runs the refined BoundaryLayer with expand_plotvars_to_unif_rr and check_plot_z, so reaching the printed line asserts the nodal set matches the Header geometry on both levels; the coarse-fine figure it prints, 2e-2 m from each level's own analytic bathymetry, is reported rather than asserted. Plotfiles.rst now states the displacement convention and what the expand path refines. ctest 55/55. Docs/sphinx_doc/Plotfiles.rst Tests/CTestList.cmake Tests/test_files/BoundaryLayer_ML_plot_z/BoundaryLayer_ML_plot_z.i Tests/tools/check_mapped_grid.py commit 81c6b79650f3ec5b6f016ec39363df07338c0244 Author: Hannah Klion Date: Thu Oct 1 17:44:09 2026 -0700 Refine the plotfile nodal set in z with the cell data under expand_plotvars_to_unif_rr A viewer places node (i,j,k) of a level at prob_lo + (i,j,k)*dx from the Header plus the Nu_nd displacement. With expand_plotvars_to_unif_rr the refined level's Header dz is the native one over the ratio, but Nu_nd was still written at native resolution against the native dz: reconstructed, the patch bottom was right and its surface N*dz*(1 - 1/r) too deep -- 32 m on BoundaryLayer at ratio 3, 25 m on Channel_Test, the whole 400 m column on the IdealMiniGrid synthetic hires case -- with the node layers above k = N falling back to the coarse level. That is the squashed, jagged patch amrexplorer showed. The nodal set is now refined in z with the cell data, z interpolated linearly between native node layers so node r*k coincides with native node k, and the displacement is computed against the geometry the Header describes, as z_phys - (prob_lo_z + k*dz), which also drops the old formula's assumption that prob_hi_z = 0. The face-velocity sets are refined the same way (piecewise constant for u, v; linear for w), and x_cc/y_cc include prob_lo. remora.check_plot_z rebuilds z the viewer's way at write time and aborts unless every level's bottom and top node layers reproduce z_phys_nd; it also prints the coarse-fine mismatch at coincident nodes, interior and perimeter, held to check_plot_z_tol only when that is set. The writer always asserts that each extra set's z extent matches the Header geometry. Native plotfiles are unchanged to rounding (1e-14 on Nu_nd; fcompare reads only Cell). ctest 55/55. Exec/Generic/inputs_generic Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 51bb96f655c9dba3dae31059b3c77412e61b1637 Author: Hannah Klion Date: Fri Oct 2 22:09:34 2026 -0700 generic inputs Exec/Generic/inputs_generic commit 00cc75276b0ee74d993fc8ef6bb0c06555784479 Author: Hannah Klion Date: Fri Oct 2 17:39:37 2026 -0700 Keep refinement time windows on the model clock Converting a refinement indicator's start_time/end_time to elapsed time when the inputs are read fixed them against that start_time, so a later SetStartTime moved the clock but not the windows. Hold each window in double on the REMORAErrorTag instead and test it in ErrorEst against model_time(time). That also keeps a calendar-scale window out of AMRErrorTagInfo, whose times are Real. Source/REMORA.H Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp commit f5334b3cca807fc246a8e1ddac173af494dea572 Author: Hannah Klion Date: Fri Oct 2 17:22:39 2026 -0700 Fix comment typo in DateClock unit test Tests/Unit/REMORA_DateClock_test.cpp commit 6ebe4e4bf77254743fed54d03d78797f53cb4f6e Author: Hannah Klion Date: Fri Oct 2 17:22:39 2026 -0700 Fix comment typo in DateClock unit test Tests/Unit/REMORA_DateClock_test.cpp commit fe853d1fb5ed05d218067c449830180683dc9506 Merge: ee47c536 6780aa69 Author: Hannah Klion Date: Fri Oct 2 11:48:30 2026 -0700 Merge pull request #691 from hklion/remove-grid-init-count-check Allow hires grid file without level 0 grid file commit eab4a1fc9c753f76f9486951b7f713d480564e2f Author: Hannah Klion Date: Thu Oct 1 17:59:00 2026 -0700 Split model time into a double start_time and a Real elapsed time t_new and t_old now count seconds since remora.start_time, which is kept in double, as ROMS splits DSTART from the time it advances. The solver, FillPatch time interpolation and kernels see only elapsed time, which a single-precision build can resolve; seconds since a calendar epoch cannot (near 7.6e8 s a float rounds a 40 s step to 64 s, so the clock ran 60% fast). Everything that needs a time on the model clock goes through model_time() in double: the NetCDF forcing, boundary, river and climatology readers (whose file times are now read and stored in double), the Fennel pCO2 calendar, ocean_time (now NC_DOUBLE) and the plotfile time. User-given times stay on the model clock: stop_time, and refinement start_time/end_time, which are converted to elapsed time where they are read. Checkpoints store elapsed t_new plus a trailing start_time line; a checkpoint without that line holds model-clock time and is rebased on restart. Double-precision output is bit-for-bit unchanged, including runs with a nonzero start_time. Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst Source/Biology/REMORA_Biology.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 6780aa695e4f567b4da24c5d899d45b883a0d2b7 Author: Hannah Klion Date: Thu Oct 1 17:11:01 2026 -0700 generic inputs Exec/Generic/inputs_generic commit 1fdfa909e1860ff8e31572c0b57683579bec27c7 Author: Hannah Klion Date: Thu Oct 1 17:04:48 2026 -0700 bump generic inputs Exec/Generic/inputs_generic commit 01961adcb14566dfa496640cf18330e4cac22c04 Merge: 77db1d69 ee47c536 Author: Hannah Klion Date: Thu Oct 1 17:03:42 2026 -0700 Merge remote-tracking branch 'upstream/development' into remove-grid-init-count-check commit ee47c536d6fc0caabe034d4fd30a2fb89a2a293c Author: Hannah Klion Date: Thu Oct 1 17:02:08 2026 -0700 codespell ignore .codespell-ignore-words commit b6fe4c812d11a8f8d2fe00385955ee15ac6118d7 Merge: cd431fcd 79b48002 Author: Hannah Klion Date: Thu Oct 1 17:00:18 2026 -0700 Merge pull request #690 from seahorce-scidac/dependabot/submodules/Submodules/AMReX-19d64c6 Bump Submodules/AMReX from `f2cbba4` to `19d64c6` commit 0e59dc04ddfe0f46f1b105f9e5658761ed203a6d Author: Hannah Klion Date: Thu Oct 1 16:59:34 2026 -0700 Do calendar arithmetic in double so time_ref dates work in single precision Docs/sphinx_doc/Inputs.rst Source/Biology/REMORA_Biology.cpp Source/REMORA_DataStruct.H Source/Utils/REMORA_DateClock.H Tests/Unit/CMakeLists.txt Tests/Unit/REMORA_DateClock_test.cpp commit cd431fcdc14022daf278d882fdf5735b58a1b9ae Author: Rob Hetland Date: Thu Oct 1 16:00:02 2026 -0700 Added documentation describing vscode syntax highlighting extension for remora input files Docs/sphinx_doc/Inputs.rst commit ed4130cde362d4d2b128d9b702fbe85c8660ca9f Author: Rob Hetland Date: Thu Oct 1 15:51:28 2026 -0700 Added vscode syntax highlighting extension for remora input files Tools/vscode/remora-input/README.md Tools/vscode/remora-input/language-configuration.json Tools/vscode/remora-input/sample.inputs Tools/vscode/remora-input/syntaxes/remora-input.tmLanguage.json commit 79b480020201df7183b5cb77e7a91b991655ea62 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Oct 1 21:09:25 2026 +0000 Bump Submodules/AMReX from `f2cbba4` to `19d64c6` Bumps [Submodules/AMReX](https://github.com/amrex-codes/AMReX) from `f2cbba4` to `19d64c6`. - [Release notes](https://github.com/amrex-codes/AMReX/releases) - [Commits](https://github.com/amrex-codes/AMReX/compare/f2cbba4afc9eb3cc0a68b311112def524ada8cd3...19d64c697f1a68fd3d2d3566ff97bc89363d2366) --- updated-dependencies: - dependency-name: Submodules/AMReX dependency-version: 19d64c697f1a68fd3d2d3566ff97bc89363d2366 dependency-type: direct:production ... Signed-off-by: dependabot[bot] Submodules/AMReX commit 77db1d696c7a270584cfb9b98ca24b18066a058a Author: Hannah Klion Date: Wed Sep 30 21:47:42 2026 -0700 Allow hires grid file without level 0 grid file Source/REMORA.cpp commit 22d75345616fc41b25f565edf2d840de9ea00add Merge: 3c3b081c a99f4226 Author: Hannah Klion Date: Wed Sep 30 21:38:33 2026 -0700 Merge pull request #689 from hklion/time_ref_double explicitly make time_ref a double rather than amrex::Real so it works even in single-precision commit a99f4226be41d904f2462d64dc53d8352033af94 Author: Hannah Klion Date: Wed Sep 30 21:37:52 2026 -0700 explicitly make time_ref a double rather than amrex::Real so it works even in single-precision Source/REMORA_DataStruct.H commit 3c3b081c0d636d4c0de4984d22a900374fce23f8 Merge: 5a7a6ea4 ff9c226c Author: Hannah Klion Date: Wed Sep 30 21:15:04 2026 -0700 Merge pull request #688 from hklion/worktree-float-particles-fix Patches to single precision commit ff9c226c31ec859b2b7017cf37ac6f80a2d82cde Author: Hannah Klion Date: Wed Sep 30 16:18:15 2026 -0700 Snap a subcycled level's time to its parent's on the last substep Summing an inexact dt (dt/3 in single precision) left the fine level's clock one ulp behind its parent, so the next step's t_old fell before the parent's bracket and REMORAFillPatcher::Fill aborted (DogboneAnalytic inputs_ml_mask, PRECISION=FLOAT). Source/TimeIntegration/REMORA_TimeStep.cpp commit f94bbf6577885529657c7bee51cbe11021c52e96 Author: Hannah Klion Date: Wed Sep 30 11:44:24 2026 -0700 Fix particle mass deposition build in single precision ParticleReal stays double under PRECISION=FLOAT, so the deposition lambda returned double while the mesh is float, and AddNoRet(float*, double) failed to deduce. Source/Particles/REMORA_PC_Utils.cpp commit 5a7a6ea49e77756c114226d9beb5985a8b4b01c6 Merge: c98b6e27 c3405390 Author: Hannah Klion Date: Mon Sep 28 16:20:44 2026 -0700 Merge pull request #687 from hklion/tag_on_bathymetry Tag on bathymetry commit c3405390f3e3403f9d8e451f86ec3189a91a20fa Author: Hannah Klion Date: Mon Sep 28 15:04:40 2026 -0700 formatting Source/REMORA_Tagging.cpp commit 62725aed94fe9ddb3fc62b35ccaca407c53768bf Author: Hannah Klion Date: Mon Sep 28 14:52:45 2026 -0700 support refinement tagging on bathymetry Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_Tagging.cpp commit c98b6e279e312b5986ae608fd4dedb2168fac9c9 Merge: c27def5d d81a0e0d Author: Hannah Klion Date: Mon Sep 28 11:49:01 2026 -0700 Merge pull request #684 from hklion/worktree-hires-init-analytic Enable hires_init_level for analytic initial conditions commit c27def5dcf5a93e3757b832fafe266910a2e9cb1 Merge: f0e94a91 230447de Author: Hannah Klion Date: Mon Sep 28 08:48:26 2026 -0700 Merge pull request #686 from hklion/worktree-subcycle-phase0 Drop timeStepML's post-step velocity fill commit d81a0e0d16638d71074e0ad22da067178cdfb72b Author: Hannah Klion Date: Fri Sep 25 15:04:59 2026 -0700 Restore the zeta average-down in analytic hires init Resolving the cherry-pick onto development kept development's average-down loop in init_full_domain_from_analytic. That loop shadows the local lev (-Wshadow) and skips vec_zeta_full_domain, so level-0 zeta stayed 0. No test caught it: every hires_init case had zero zeta. DogboneAnalytic_hires_init_zeta reads the averaged-down zeta back through VOLUME at t = 0, whose closed form is 63566666.667. With the zeta line dropped it reports 63000000 and fails. ctest 60/60. Docs/sphinx_doc/RegressionTests.rst Source/Initialization/REMORA_init.cpp Tests/CTestList.cmake Tests/test_files/DogboneAnalytic_hires_init_zeta/DogboneAnalytic_hires_init_zeta.i commit 39dcdce39bfb3545bc366922b85b0c1b594d3e86 Author: Hannah Klion Date: Fri Sep 25 14:36:48 2026 -0700 spelling Docs/sphinx_doc/MeshRefinement.rst commit 80698be667d6690c70577deb0535395b6b9dc6fe Author: Hannah Klion Date: Thu Sep 24 14:22:32 2026 -0700 gpu build Source/REMORA.H commit d6e6aac0a13896acf4e980d35fdca5fd95a6d210 Author: Hannah Klion Date: Fri Sep 11 16:05:14 2026 -0700 create and reference a single distribution mapping for full-domain boxes (cherry picked from commit a241f201c0f95e623b5e28a19faf1d61306aa75e) commit 57c9a9069126605a67936b17a1186df46c377df8 Author: Hannah Klion Date: Wed Sep 23 14:11:58 2026 -0700 Enable hires_init_level for analytic initial conditions init_full_domain_from_analytic builds coordinates for hires_init_level on the full-domain layout and passes them through ProbCoords: - x_r, y_r from the cell size; a non-constant grid_scale_type now aborts, replacing the blanket abort - zeta from init_analytic_zeta, then z_r, z_w from the new stretch_transform_full_domain, which shares a stretched_depth helper with stretch_transform - h from vec_h_full_domain if hires_grid_level >= hires_init_level, else init_analytic_bathymetry at hires_init_level State, zeta, and biology are averaged down with the masked average_down_with_grow_cells. init_full_domain_zeta_from_analytic is folded in. Tests/reference/hires_init_analytic_reference.py rebuilds Seamount's level-0 temp in NumPy. It matches to 7e-15 (ratio 3), 1.1e-14 (init above grid, ratio 6) and 7e-15 (init below grid), vs 7-8e-2 for the plain level-0 evaluation. The below-grid lane is 6.9e-3 off a reference using analytic h, so it does use the grid data. Bitwise identical on 1, 2 and 4 ranks. Filling the full-domain arrays with 1e10 instead of 0 changes no plotfile, so unwritten grow cells never reach the output. New tests: Seamount_hires_init{,_above_grid,_below_grid} (reference extrema; each fails by 1.4e-4 at tol 1e-8 if the flag is ignored), DogboneAnalytic_MLmask_hires_init (rest stays rest through partial masks), Upwelling_Fennel_hires_init_ic, and Seamount_hires_init_gridscale_abort, which replaces Seamount_hires_init_abort. ctest 53/53. Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/ProblemSetup.rst Docs/sphinx_doc/RegressionTests.rst Source/Initialization/REMORA_ProbCoords.H Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp Source/Utils/REMORA_DepthStretchTransform.H Tests/CTestList.cmake Tests/reference/hires_init_analytic_reference.py Tests/test_files/DogboneAnalytic_MLmask_hires_init/DogboneAnalytic_MLmask_hires_init.i Tests/test_files/Seamount_hires_init/Seamount_hires_init.i Tests/test_files/Seamount_hires_init_above_grid/Seamount_hires_init_above_grid.i Tests/test_files/Seamount_hires_init_below_grid/Seamount_hires_init_below_grid.i Tests/test_files/Seamount_hires_init_gridscale_abort/Seamount_hires_init_gridscale_abort.i Tests/test_files/Upwelling_Fennel_hires_init_ic/Upwelling_Fennel_hires_init_ic.i commit c58a1e883c9618d3e67b01ded87cea6cb79dd27b Author: Hannah Klion Date: Wed Sep 23 13:44:06 2026 -0700 Pass coordinates to the prob functions explicitly init_analytic_prob and init_analytic_zeta read z_r and x_r from remora.vec_z_r[lev] / vec_xr[lev] through the MFIter of the MultiFab they fill, so they only work on an existing level's BoxArray. That blocked analytic hires_init_level. They now take a ProbCoords (x_r, y_r, z_r, z_w) on the target's layout; REMORA::prob_coords(lev) returns a level's own. ProbCoords has its own header because REMORA.H and REMORA_prob_common.H include each other. The Dogbone zeta hook now writes mf_zeta.nComp() components instead of 3, since the full-domain zeta has one. No behavior change: ctest 48/48, no gold files touched. Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Source/Initialization/Make.package Source/Initialization/REMORA_ProbCoords.H Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_prob_common.H Source/Prob/REMORA_InitAnalyticProb_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_ParticleAdvectionFlat.H Source/Prob/REMORA_InitAnalyticProb_Seamount.H Source/Prob/REMORA_InitAnalyticProb_Upwelling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticZeta_DogboneAnalytic.H Source/REMORA.H Source/REMORA.cpp commit 230447de9d4811d7a74ceacaee03217ba6655f99 Author: Hannah Klion Date: Fri Sep 25 12:57:23 2026 -0700 Drop timeStepML's post-step velocity fill After each step timeStepML re-filled every level's velocity with FillPatch at t_new -- the physical boundary conditions on level 0, the parent's profile on a child -- where Advance does nothing on level 0 and re-fills a child only under cf_fill_vel_after. A deck that declares amr.max_level = 1 without refining anything ran through timeStepML before the subcycling default and through Advance after, and its answer moved by 1e-3 at open boundaries. Measured against a single-grid ROMS on the ROMS-matched dogbone with every side open: the step without the fill matches ROMS to 9e-15, 1.4e-14 and 1.3e-13 at steps 100, 300 and 600; with it, 2e-8, 3.6e-8 and 5e-8, almost all from the u fill. Closed walls are insensitive either way. So timeStepML now does what Advance does, and the two drivers agree bit for bit on a single level. ctest 54/54. Source/REMORA.H Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit f0e94a91a8b196d3e45d69dda18ce0351603a8c8 Author: Rob Hetland Date: Thu Sep 24 13:58:03 2026 -0700 Improved Mesh Refinement documentation. Reorganized, and made sure the examples were correct (e.g., with amr.ref_ratio_vect). Docs/sphinx_doc/MeshRefinement.rst commit 7540d0d4e0f390dcaeabcaa5dfd3200355bd6dce Merge: 2b968d49 b33ae367 Author: Hannah Klion Date: Thu Sep 24 13:34:14 2026 -0700 Merge pull request #676 from hklion/worktree-subcycle-phase0 Subcycle refined levels in time commit b33ae367fa72ee96cc1dbd1f751bed5d3d2225d9 Merge: aac83677 2b968d49 Author: Hannah Klion Date: Thu Sep 24 11:38:51 2026 -0700 Merge remote-tracking branch 'upstream/development' into worktree-subcycle-phase0 commit aac83677cb10415aa326d5e0f18550dd9093cdeb Author: Hannah Klion Date: Thu Sep 24 11:36:37 2026 -0700 update generic inputs Exec/Generic/inputs_generic commit 6202adfcb7d455d3f41bc2aaac3b1c1e307ee458 Merge: 7ddc0859 3e93b383 Author: Hannah Klion Date: Thu Sep 24 11:35:26 2026 -0700 Merge branch 'development' into worktree-subcycle-phase0 commit 2b968d49d814321e60de360751a5b3383857a34a Merge: 6faef6da 1613812d Author: Hannah Klion Date: Thu Sep 24 11:32:31 2026 -0700 Merge pull request #685 from jmsexton03/masked-coupling-diagnostics Masked coupling diagnostics commit 7ddc085985d8259c4b0e12931e061727316a906a Author: Hannah Klion Date: Thu Sep 24 09:46:20 2026 -0700 Record the size of the cf_fill_vel_after offset On the ratio-3 Dogbone, two-way, 20 steps, re-filling the child's velocity from the parent after the step moves level-1 x-velocity by 4.1e-3 relative and level 0 by 1.9e-4; temperature 4e-5 and 1.4e-5. The default path keeps the offset; the doc comment now gives its size. Source/REMORA.H commit 944dd2e9ed3214061044249dbff01ab68b91fbd8 Author: Hannah Klion Date: Thu Sep 24 09:46:20 2026 -0700 Tighten the edge-tiling tolerance and mark the measured-only figures The three cf_metrics lanes asserted only the 1e-12 default, four orders above what any grid measures (0, 1.4e-16, 2.5e-16). They now set remora.check_cf_tol = 1e-14, within a factor of 40 of the largest. The conservation lane comments quoted figures no lane isolates -- 1.4e-08 for cf_time_interp_zeta alone, 3e-10 for the stencil, the neutral cf_flux_pc, single-level exactness on Dogbone -- as though asserted. They now say measured. The three tiling lanes pass at 1e-14. Tests/CTestList.cmake Tests/test_files/Advection_ML_cf_metrics/Advection_ML_cf_metrics.i Tests/test_files/BoundaryLayer_ML_cf_metrics/BoundaryLayer_ML_cf_metrics.i Tests/test_files/DogboneAnalytic_ML_cf_metrics/DogboneAnalytic_ML_cf_metrics.i commit 090b6df072cf7d7a0c8f1c7e28ca606a2de47eaa Author: Hannah Klion Date: Wed Sep 23 16:30:30 2026 -0700 Assert the lockstep volume drift and the ratio-3 edge tiling Two figures in the evidence table were measured but asserted nowhere. DogboneAnalytic_ML_conservation_lockstep reruns the volume case with remora.do_substep=0 and requires the drift to exceed 1e-7; it measures 2.011483e-06. It is also the must-drift control the two subcycled lanes lacked: if lockstep ever conserves, neither bound is still measuring the coarse-fine treatment. DogboneAnalytic_ML_cf_metrics runs check_cf_metrics on the ratio-3 grid the DogboneAnalytic_ML golds and both volume lanes are measured on, not only Advection's ratio 2. Max relative residual 1.421085472e-16 on on_u and om_v. ctest 50/50. Tests/CTestList.cmake Tests/test_files/DogboneAnalytic_ML_cf_metrics/DogboneAnalytic_ML_cf_metrics.i commit 2cbc40cce715444bffbb25805200209797808c5a Author: Hannah Klion Date: Wed Sep 23 16:25:43 2026 -0700 Compile out the cf_print_iface diagnostic on GPU builds Its loops run on the host over Array4s that are device memory under CUDA and HIP, so enabling the knob there would fault. Guarded with AMREX_USE_GPU and a one-shot warning; staging every fab through the pinned arena is not worth it for a diagnostic. Host branch byte-identical; GPU branch compiles clean under -Wall -Wextra. ctest 48/48. Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit fd058964910920b6e97a09bd552bfb47cfbb85b0 Author: Hannah Klion Date: Wed Sep 23 16:25:36 2026 -0700 Remove the remora.cf_d_knew diagnostic Building D from knew instead of know matches ROMS but moves the step-1 Channel_Test interface velocity by at most 1.2e-07 against a 2.4e-03 artifact, and changes neither the Dogbone volume drift nor the Channel_Test blow-up. Only the default was ever taken, so set_2d_cf_bcs reads know directly; the measurement stays in its doc comment. Exec/Generic/inputs_generic regenerated for the generic-inputs CI job. ctest 48/48. Exec/Generic/inputs_generic Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 8175308587d9f835a0a1334f9f305fde9b900381 Author: Hannah Klion Date: Wed Sep 23 16:15:08 2026 -0700 Refresh interface ghosts after set_2d_cf_bcs, and add a periodic-seam regression lane set_2d_cf_bcs writes the interface faces inside each box's valid region and left the neighbouring box's ghost copies at the FillPatch value, so where a box boundary met the interface the shared face was advanced from different neighbours and the answer depended on the box layout: on refined Channel_Test, one rank against two differed by 1.7e-4 relative in level-1 y_velocity after one step, almost all through Coriolis. Both DogboneAnalytic_ML inputs run Coriolis off, which is why no lane saw it. A FillBoundary on the component just written makes one and two ranks bit-identical. Channel_Test_ML_seam puts a patch on the periodic seam with Coriolis on, gold from one rank: the only lane whose fine level touches a periodic boundary, so the only one holding the four periodic-seam fixes, and the level-1 box split under MPI holds this one. Exec/Channel_Test/inputs_ml_seam is the same deck at 400 steps. Every existing gold passes. ctest 49/49. Exec/Channel_Test/inputs_ml_seam Source/TimeIntegration/REMORA_advance_2d.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Header Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Cell_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Cell_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Channel_Test_ML_seam/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/Channel_Test_ML_seam/job_info Tests/test_files/Channel_Test_ML_seam/Channel_Test_ML_seam.i commit 3366ec171405b307cba0a45aeec65d37a04a8ad2 Author: Hannah Klion Date: Wed Sep 23 15:27:27 2026 -0700 Document remora.g and the coarse-fine operator options Neither remora.g nor the eight remora.cf_* options had a docs entry, and five of the cf_* defaults change every multi-level answer. Add them to the Mesh Refinement notes in Inputs.rst with defaults and measured costs, add a section on the barotropic coarse-fine operators to MeshRefinement.rst, and replace the physics table's remora.ggrav row, a parameter nothing reads, with remora.g. docutils: no new warnings. Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst commit 3cdbedc54453c4f69ee5cb7a0535a65d1dc24efd Author: Hannah Klion Date: Wed Sep 23 15:27:27 2026 -0700 Thread remora.g through the radiation boundary conditions and bulk fluxes The Flather and Chapman conditions, the COARE bulk-flux formulas and the DoubleGyre initial state still read the compile-time constant, so a NetCDF-forced run at remora.g = 9.81 had two gravities. Remove the constant; nothing else used it, and the compiler now enforces the rule. Bit-identical at the default. ctest 48/48. Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/REMORA_Constants.H Source/TimeIntegration/REMORA_bulk_flux.cpp commit 298214c2caf5d856caead3b08e8aeabb2b4466f5 Author: Hannah Klion Date: Wed Sep 23 14:31:01 2026 -0700 remove force PNetCDF ON Exec/GNUmakefile commit 6faef6da036ccf4857d4fccbeb6b4619d71c9e2e Merge: 78520333 8bde5997 Author: Hannah Klion Date: Wed Sep 23 13:42:33 2026 -0700 Merge pull request #683 from hklion/worktree-mask-aware-gradient-tag Mask-aware gradient tag commit 8bde599768de0b6e98dee6b26cf2137bbdad34f7 Author: Hannah Klion Date: Wed Sep 23 13:27:23 2026 -0700 clarify docs Docs/sphinx_doc/MeshRefinement.rst commit 666e2db5021fc8b903dad4711b164614e919539d Author: Hannah Klion Date: Wed Sep 23 12:13:35 2026 -0700 add warning about subcycling being experimental Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst Source/REMORA.cpp commit 1613812d4a274eaf1df4fa67746068cb124d50f0 Author: Jean M. Sexton Date: Wed Sep 23 10:50:51 2026 -0700 Catch NaN in the surface temperature check and re-warn if worse - Check every exchange; count NaN wet cells - Repeat the warning only on a new extreme - Document coupled output under remora.v 1 Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA_Coupling.cpp commit 5d286ec36d17beae6ccf755122181f23e722bcc3 Author: Hannah Klion Date: Wed Sep 23 09:51:10 2026 -0700 fix unused variable Source/TimeIntegration/REMORA_rho_eos.cpp commit 39720153caaf8fa0568946b40363f2b8024f5beb Author: Hannah Klion Date: Wed Sep 23 09:41:44 2026 -0700 update generic inputs Exec/Generic/inputs_generic commit a7b0f6903b5d0dc8331e26e699d1869ddafddd1b Author: Hannah Klion Date: Wed Sep 23 09:37:02 2026 -0700 Tighten the comments added by the coarse-fine work A concision and clarity pass over the comments the preceding six commits introduced: the knob documentation in REMORA.H, the coarse-fine operator and periodic-seam blocks in REMORA.cpp, FillPatch.cpp, FillPatcher.cpp, advance_2d.cpp, Advance.cpp and set_2d_cf_bcs.cpp, the two conservation-lane comments in CTestList.cmake, and the knob block in inputs_roms_refined. Cut: mechanisms re-explained after their first statement, framing wrapped around numbers that already speak for themselves, and narrative connectives. Kept: every measurement, every ROMS routine name, and every statement of what a knob's non-default setting does. 160 comment lines become 136; no quantitative claim was dropped. Comments only -- filtering the diff for non-comment lines leaves nothing, and the build is clean. Exec/DogboneAnalytic/inputs_roms_refined Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp Tests/CTestList.cmake commit 058592457713fcccfc9fa471c898905903e1d059 Author: Hannah Klion Date: Tue Sep 22 22:17:44 2026 -0700 Refresh periodic ghosts that coarse-fine transfers leave stale Channel_Test blows up around step 270 whenever a refinement patch reaches the periodic x boundary. It reproduces with level 1 covering the whole domain, which has no coarse-fine interface anywhere, and it is insensitive to every coarse-fine knob. Two mechanisms, one root assumption: a transfer between levels rewrote valid data and left the ghost cells imaging it across the periodic seam holding the old value. In a staggered grid the u-face at node 0 and at node Nx of a periodic direction are the same physical face, each computed independently from its own stencil. They stay bit-identical as long as those stencils read identical data -- on a single level, measured 0.0 over 300 steps. Either mechanism below hands the two copies different values for the same physical cell, and the mismatch then grows by about 2.8x every 20 steps until the run fails. 1. A level created mid-run by MakeNewLevelFromCoarse (a refinement box with start_time > 0, as in Exec/Channel_Test/inputs_ml) is filled by FillCoarsePatchMap, which enforced periodicity on cell-centred fields only. Face-centred vbar and yvel kept the coarse interpolation's x ghosts, which do not match their periodic images: 1.9e-4 to 5.9e-4 at creation while zeta's were exact. That seeds a 5.1e-6 mismatch at the first barotropic substep. A level present from t=0 escapes only because vbar is identically zero then. Fix: FillBoundary after coarse interpolation of a face-centred field, the face analogue of the EnforcePeriodicity already applied to cell-centred ones. 2. For a patch that touches the seam without spanning it, two-way average-down rewrites the coarse ubar and vbar under the patch but not the coarse ghosts imaging those cells across the seam, and nothing refreshes them before the next barotropic step. Bisected to exactly that operator: cf_avgdown_bar=0 or one-way coupling gives a coarse-copy mismatch of exactly zero, every other knob leaves it at 3.4e-4 by step 20. Fix: FillBoundary the coarse ubar and vbar after the average-down. Measured on Channel_Test with both fixes, level created by regrid: level 1 covering the whole domain NaN at 271 -> 400 steps, peak vel 0.63 half-width patch on the seam, 8 levels NaN at 321 -> 0.67, matching an interior patch same at full resolution, dt = 400 NaN at 281 -> 400 steps, peak vel 0.73 The two-copy mismatch is exactly 0 on both levels throughout, and an interior patch is bit-identical. ctest 48/48, gold files unchanged. Neither fix touches the amplifier: two independently computed copies of one physical face are still reconciled nowhere, since AMReX's nodaltilebox keeps both, so any future operator that hands them different data will fail the same way. Reconciling them explicitly -- ROMS's IstrU convention, or OverrideSync -- is a structural change left for a separate decision. Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.cpp commit 33d2151bd734be05fe58f52b067c0ae162ff669e Author: Hannah Klion Date: Tue Sep 22 15:23:33 2026 -0700 Treat a periodic seam as a real coarse-fine boundary Two places assumed a fine patch either spans a periodic direction entirely or never reaches it. Both are wrong for a patch covering only part of the width, where the far side of the seam is coarse and the seam is a genuine coarse-fine interface. BuildMask derives the interface from a purely geometric complement and then, per b518794, cleared every face sitting on a domain edge. That is right for a patch wrapping onto itself (those faces really are interior) and at a physical wall (the boundary condition owns them), but it discards a real interface otherwise. On Channel_Test's bottom_quart box, covering x 0-50000 of a periodic 0-100000, 60 of 120 marked x-faces lay on the seam and were cleared -- half the x-normal interface never imposed. Add the periodic images of the fine boxes before taking the complement, as ERF does, and restrict the clear to non-periodic directions; the three cases then fall out geometrically. BuildMask is shared by every REMORAFillPatcher, so this covers 3D momentum as well as the barotropic system. fill_ghost_kcomps skipped its leapfrog synchronisation for any ghost outside the domain bounds, unconditionally. In a periodic direction those are not physical-boundary cells: either the level wraps onto itself and FillBoundary has already marked them valid, or the patch is partial and they are ordinary coarse-fine ghosts that FillPatch just filled from the parent across the seam. Left unsynchronised, the records the 2D solver reads there were a full parent step stale. Refined minus unrefined surface v at step 20 near the patch corners: the seam corner goes from 1.81e-02 to 5.04e-03, and an equivalent interior patch is bit-identical, so the change reaches only the seam case. ctest 48/48 with gold files unchanged, consistent with b518794's observation that nothing in the suite refines up to a domain boundary. This does not fix the blow-up Channel_Test hits with a patch at the periodic boundary. That is a separate defect: insensitive to every coarse-fine operator, and reproducing with a level 1 covering the whole domain, which has no coarse-fine interface anywhere. Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit a05cb71489b387768355a6430d7e6ece4f47e800 Author: Hannah Klion Date: Mon Sep 21 11:33:47 2026 -0700 Enable the ROMS-matching coarse-fine knobs by default cf_avgdown_stencil, cf_flux_pc, cf_fill_all_kcomp and cf_time_interp_zeta were added defaulting to the previous behaviour. They reproduce ROMS's nesting.F operators and are now on by default; passing them explicitly reproduces the new defaults bit for bit. On the ROMS-matched dogbone the refinement perturbation in the parent's ubar at the interface goes from 1.28-1.36x ROMS's to 1.011-1.014x. The residual 1% closes only with cf_impose_flux, which stays off: worth 100x to 4000x while the flow is linear, about 10-20% worse once it is not. Volume conservation on the subcycled dogbone goes from 2.0e-09 to 2.9e-08, so that lane's bound is relaxed to 1e-7 and a control lane pins the conservative path at 1e-8. The cost is not in the restriction stencil, which was the first assumption: measured one knob at a time, cf_fill_all_kcomp gives 2.9e-08 and cf_time_interp_zeta 1.4e-08, while cf_avgdown_stencil costs about 3e-10 and cf_flux_pc is exactly neutral. Those two write the free surface in the fine ghost band and volume is its integral, so the control lane switches them off rather than the stencil. Comments in REMORA.H and inputs_roms_refined are corrected to match. The MLvel and MLquad golds are remade, since the flip moves x_velocity there by 1.8% and 6.1%. They come from 1-rank runs so they keep the one-box-per-level decomposition the committed golds and development already use. MLhires, which compares against MLvel's gold, still reproduces it exactly. ctest 48/48. Exec/DogboneAnalytic/inputs_roms_refined Source/REMORA.H Tests/CTestList.cmake Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit fa668ddafdd45e33677b5897ab66ad486255ce89 Author: Hannah Klion Date: Sat Sep 19 13:18:46 2026 -0700 Match ROMS's coarse-fine operators, and write refined levels to NetCDF Measured against the ROMS nested dogbone (COAWST, h=50, DT == 3.0 1.0, NDTFAST == 20 20) with the time refinement matched. The single-level pair already agreed to ~1e-14, so refinement was the entire source of the gap. Four places where REMORA used an AMReX-native operator and ROMS uses a different one. Each is a runtime knob defaulting to the previous behaviour, so no answer changes unless it is set. cf_avgdown_stencil -- fine2coarse2d averages the donor over a (Rscale-1)/2 half-width stencil in both horizontal directions, so at ratio 3 a coarse face is the mean of nine fine faces; average_down_faces takes only the three that tile it. ROMS's coarse ubar equals the nine-point mean of its child to 1.0000 at every face and step, REMORA's equalled the three-point mean. The dominant term, and deliberately not conservative: the nine-point mean does not preserve transport across the interface, a trade ROMS accepts. cf_flux_pc -- get_persisted2d copies DU_avg2 at the donor face chosen by integer division of the fine index, so every fine face under one parent face carries the same transport, scaled by edge length; AMReX's face interpolator varies it linearly instead. Both conserve the total. ROMS's interface ubar is piecewise constant in groups of three, REMORA's varied across them. cf_time_interp_zeta -- FillPatch has a subcycling branch that interpolates the parent between two stored states, but no call site passed them, so a subcycled child always saw the parent frozen at the end of its step. Wired up for zeta via roll_2d_snapshot. cf_fill_all_kcomp -- put_refine2d writes all three leapfrog records and Zt_avg1; REMORA wrote only the one FillPatch fills, leaving the others in the ghost band a full parent step stale. The last two are faithful but inert here: the fine zeta halo is never read, so a 21x change in it moves the answer by 9e-17. At the interface face the refinement perturbation relative to ROMS's goes from 1.29x through the linear regime, 2.13x once nonlinear, to 1.000x at every step. Whole-field agreement against the ROMS nested run improves one to one and a half orders of magnitude on the parent, and the child's free surface by ten to fifty times. The NetCDF writer was pinned to level 0. It now runs per level, each to its own file -- _d01, _d02 and up, as ROMS names a nested grid -- with dimensions from boxes_at_level, which gives a refined level exactly ROMS's child shape. Four blocks of write offsets assumed level-0 index space and are now subdomain-relative, and the guard for the vertical coordinate arrays keyed on the global origin, which no refined-level box contains. Only the first subdomain of a multi-box level is written. This is what made a direct level-1 against ROMS-child comparison possible. Also here: remora.prob.depth for the dogbone bathymetry, remora.prob.quiescent for Channel_Test, and the [IFACE]/[HALO] interface diagnostics behind cf_print_iface (default -1). ctest 47/47. Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/inputs_roms_baseline Exec/DogboneAnalytic/inputs_roms_refined Exec/GNUmakefile Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/Prob/REMORA_InitAnalyticBathymetry_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticSMFlux_ChannelTest.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 64e06124df74444a0729b514ceaa60f2a91b9c3c Author: Hannah Klion Date: Thu Sep 17 22:13:07 2026 -0700 Exclude the coarse-fine perimeter from the fine-to-coarse velocity average ROMS's fine2coarse returns every covered cell to the parent except the child's perimeter normal-velocity faces. For the refined dogbone, a child covering coarse cells 14..29 has a contact list holding u-faces 15..29 and v-faces 7..10, so the two faces at each end are left alone -- exactly the faces u2dbc_im writes the donor's DU_avg2 onto. The transport ROMS imposes at the interface is never returned to the grid it came from. REMORA closed that loop: set_2d_cf_bcs imposed the parent's flux, then AverageDownTo averaged those faces back down, overwriting the parent's barotropic solution with a stale copy of its own transport. Apply ROMS's rule -- update a coarse normal-velocity face from the fine grid only when both cells it separates are covered. build_covered_mask carries one grow cell so an edge face can see the uncovered cell outside it, and restore_perimeter_faces puts the perimeter back after the existing averages, leaving the interior feedback untouched. remora.cf_avgdown_perimeter = 0 restores the old behaviour. Measured on the dogbone, matched to ROMS to 6e-14 unrefined, comparing each code's nested run against its own unrefined one over the pre-saturation window: barotropic mode 44x ROMS -> 5.2x baroclinic shear 32x ROMS -> 1.26x Dropping the 2D momentum feedback altogether reaches 1.5x on the mode but leaves the shear 164x worse, so the exclusion is the better trade as well as the one ROMS makes. Regenerates the DogboneAnalytic_MLvel and _MLquad golds; _MLhires compares against _MLvel's. Single-level answers are bit-identical, and Advection_ML is unaffected because only momentum faces change. Source/REMORA.H Source/REMORA.cpp Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit d4b081d16653c2e4d93cc443f76db4b6fd6de4bd Author: Hannah Klion Date: Thu Sep 17 22:08:53 2026 -0700 Make gravity a runtime parameter, remora.g ROMS uses g = 9.81 exactly; REMORA hard-coded 9.80665. On the dogbone that alone separates the two models by 3.4e-4 in velocity, swamping any coarse-fine effect. SolverChoice::g defaults to 9.80665, so existing answers are unchanged. The five sites that affect the solution -- barotropic pressure gradient, prsgrd, both EOS Brunt-Vaisala blocks, the timestep limit -- read solverChoice.g; the constant in REMORA_Constants.H stays as the fallback elsewhere. With remora.g = 9.81 the single-level dogbone matches ROMS to 6e-14 relative over 600 steps in u, v, zeta, ubar and vbar. Exec/DogboneAnalytic/inputs_roms_baseline Exec/DogboneAnalytic/inputs_roms_refined Source/REMORA_Constants.H Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp commit 4a58d64333c226f0bfe1b240a0e8374db292bd3a Author: Jean M. Sexton Date: Wed Sep 23 09:08:38 2026 -0700 Validate coupled fluxes and surface temperature on wet cells - Mask flux validation min/max with mskr, msku, mskv - Print it once per run unless remora.v >= 1 - Warn once on wet surface temperature out of range Source/REMORA.H Source/REMORA_Coupling.cpp commit 78520333c43a0b8692c76edbb9ad69277b78ef9f Author: Rob Hetland Date: Mon Sep 21 16:47:26 2026 -0700 Added Spack instructions in the getting started. Docs/sphinx_doc/GettingStarted.rst commit 627e746cc679bd7a91f7bb207390f2f6afa1d52a Author: Hannah Klion Date: Mon Sep 21 16:10:02 2026 -0700 spelling Tests/check_max_level.sh commit ab5302c173156075411e53f071a4f33beb4151fc Author: Hannah Klion Date: Mon Sep 21 16:09:14 2026 -0700 update generic inputs Exec/Generic/inputs_generic commit c75eac8624f22e03036e91f7d4e3991f649ddb22 Author: Hannah Klion Date: Mon Sep 21 15:54:34 2026 -0700 tighten the comments that five review rounds accreted Comment-only in the sources: no non-comment line changed, and the suite is unaffected. Five passes of review left the same explanations written out in several places and at more length than they earn. The main cut is duplication. The mask_lo/mask_hi contract was stated fully in REMORA_ErrorTag.H and again on the definition in REMORA_Tagging.cpp, which is two places to drift -- and drift is exactly what the last round found. The definition now carries only what a reader of the body needs and points at the declaration. The per-field reasoning likewise lived both in the header's parameter docs and beside the code that sets the values; it stays where the values are set, and the header describes the parameter. Everything else is wordiness: the class doc loses a third of its length without losing an argument, the three new input headers say the same things in about 20% fewer lines, and the pinned-grid block repeated across five inputs drops from seven lines to five. The draft PR message got the same treatment. Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i Tests/test_files/DogboneAnalytic_MLdryface/DogboneAnalytic_MLdryface.i Tests/test_files/DogboneAnalytic_MLmask/DogboneAnalytic_MLmask.i Tests/test_files/DogboneAnalytic_MLmask_rr2/DogboneAnalytic_MLmask_rr2.i commit 58a8e20cb42b0c893ff8d9f729414c9c1e02572a Author: Hannah Klion Date: Mon Sep 21 11:35:47 2026 -0700 add xamrex pointer to docs Docs/sphinx_doc/Visualization.rst commit a333791594ad5c12dc6af467da2f8c82c840c6f7 Author: Hannah Klion Date: Fri Sep 18 22:58:56 2026 -0700 fix a docs example that still aborts, and prose that drifted behind the code A fifth review, again with no knowledge of the earlier ones, found no correctness defect and said merge. What it did find was the docs example wrong a second time, and several comments describing revisions of this branch rather than its current state. The field-name example still aborted. The previous commit replaced field_name = scalar, which is not a state variable name, with tracer -- but cons_names carries "tracer" only when remora.nscalar > 0, and that defaults to 0, so the corrected example aborts in the default configuration exactly as the original did. The example now uses temp, which is always present, and the surrounding text says which tracers exist under which input rather than listing a fixed set. The durable fix is the abort itself: it said "Use a tracer name", which is actively unhelpful when the name given *is* a tracer name in some other configuration. It now prints the names this run actually has, which would have made both mistakes self-evident. Comments that had drifted: - Both new inputs named Advection_ML as the case that would catch a guard which had stopped tagging anything. That stopped being true one commit ago: Advection_ML sets no mask_type, and the short-circuit added there sends an unmasked run down AMReX's own path, so it never enters the guarded code. DogboneAnalytic_MLvel, _MLhires and _MLdryface are the cases that catch it. - The pinned-grid block in five inputs said REMORA sets "the first two" of the three parameters imperatively; it sets the first and the last, and grid_eff is pinned to the value AMReX already defaults to. - The MLdryface threshold band skipped a step: the count goes 6480 -> 8640 -> 10800 as the threshold falls, not 6480 -> 10800. Measured and written down. - zvel_new was described as never written. It is written, by a copy from W_old; what is true is that nothing ever puts a computed value in it. - The mskr3d contract gave one reason a caller passes nullptr; there are now two. - The vorticity note carried cell counts from a one-off experiment, which will rot. Trimmed to the part that stays true. The docs paragraph this branch rewrote was also internally inconsistent from before it: "two user-named criteria" over three bullets, "the second" pointing at the third, an example block omitting the criterion the new prose discusses, and the available tests still named greater_than/less_than while every input key says value_greater/value_less. All reconciled, and the mask exemption is now stated next to the two unconditional claims it contradicts rather than forty lines later. One latent gap closed: the guard covers GRAD, LESS and GREATER because those are the only tests refinement_criteria_setup can build, but RELGRAD and VORT read a field cell by cell too and would have taken the unguarded path in silence if that ever changed. They now trip an assert instead -- the same silent-bypass mistake the private inheritance makes ill-formed at the call site, given the same treatment one level in. Not taken: the review suggested a gold-file comparison alongside MLdryface's cell count, so that a physics change surfaces as a value diff rather than as "tagging failed". The concern is right, but blessing a gold file from this branch's own output adds a baseline that is only as good as the run that made it, on a case whose purpose is grid structure. The threshold band and a note saying what to check first carry the same diagnostic weight without that. Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i Tests/test_files/DogboneAnalytic_MLdryface/DogboneAnalytic_MLdryface.i Tests/test_files/DogboneAnalytic_MLmask/DogboneAnalytic_MLmask.i Tests/test_files/DogboneAnalytic_MLmask_rr2/DogboneAnalytic_MLmask_rr2.i commit 0c8a718d06ca4b4108b1f24f4b51feab75ec4815 Author: Hannah Klion Date: Fri Sep 18 22:19:55 2026 -0700 harden the grid assertions and make the base class unreachable A fourth review, again with no knowledge of the earlier ones, found no correctness bug and nothing unsafe in the newly reachable configurations. It checked the things a diff reading cannot: it refined a fine grid wholly over land, restarted from a checkpoint with level 1 straddling a coast, ran three levels, and swept ranks and grid parameters. All clean. What it did find was brittleness and structure. The MLdryface cell count sat about 5% from the edge of its stable band. Only the ratio of the field's adjacent differences to the threshold matters, so a physics change moving near-coast velocities by that much would have turned the case red with a tagging failure message while tagging was fine -- on a case with no gold file, where the count is the only signal. Swept it here: 6480 cells holds for thresholds in roughly [0.019, 0.032], so the threshold moves to 0.025, near the middle, with about 30% margin either way. The band is recorded in the input so the next person does not have to rediscover it. The five cases that assert grid structure now pin n_error_buf, blocking_factor and grid_eff rather than inheriting them. Each moves the assertions on its own -- n_error_buf = 1 takes MLdryface from 6480 to 19440 -- and REMORA sets two of them imperatively in main.cpp while Inputs.rst documents a different value, so a commit reconciling those would have turned these cases red for a reason unrelated to what they test. The per-field mask stencil was a second if/else chain on the field name, parallel to the one that fills the data, and a field added to one but not the other would silently get the plain cell test -- which is exactly the bug fixed two commits ago for the face velocities. The stencil now sits in the same branch as the fill it belongs to, so the two cannot drift apart. REMORAErrorTag now inherits privately. The guard lives on an overload of a non-virtual base operator(), so binding an AMRErrorTag const& or copying into one would have compiled and quietly run AMReX's unguarded test on masked data; the previous commit could only warn about that in a comment. Private inheritance makes it ill-formed while keeping the protected members the class is built on. Only the constructors and Field() are re-exported, which is all any caller uses. Also: an unmasked run now takes AMReX's own path rather than paying for a guard that cannot fire, the guarded path gets a BL_PROFILE like its neighbors, and the lo_vort example no longer claims that giving a field criterion a box restricts it to that box -- AMReX consults the realbox only for the BOX test, so the field test applies domain-wide. One gap is left open deliberately. The vorticity stencil, the largest and the only one needing two rings of mask ghosts, has no regression test. It is not dead code -- collapsing it moves MLdryface keyed on vorticity from 12528 cells to 19440 -- but the only masked problem available is near-irrotational, so its vorticity is down at 1e-7 and the cell count varies continuously with the threshold instead of sitting on a plateau. An exact assertion there would be pinned to roundoff and would drift with the compiler, which is the failure mode this commit is otherwise removing. Covering it wants a masked case with real shear along a coast; the situation is written down where the stencil is set. Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i Tests/test_files/DogboneAnalytic_MLdryface/DogboneAnalytic_MLdryface.i Tests/test_files/DogboneAnalytic_MLmask/DogboneAnalytic_MLmask.i Tests/test_files/DogboneAnalytic_MLmask_rr2/DogboneAnalytic_MLmask_rr2.i commit 635500e50226392769f1c5b4434ea9884e8a626b Author: Hannah Klion Date: Thu Sep 17 23:02:19 2026 -0700 cover the per-field mask stencil, and fix a docs field name that aborts A third review, again run without knowledge of the earlier ones, found that the per-field mask stencil had no test at all: replacing the whole x_velocity / y_velocity / vorticity block with mask_lo = mask_hi = 0, the plain cell test, left the suite green. It also caught that the field list this branch rewrote names "scalar", which is not in cons_names {"temp","salt","tracer"} and aborts the run -- so a list presented as a correction was itself wrong, as was the pre-existing example three paragraphs above it that a user would copy. DogboneAnalytic_MLdryface closes the coverage gap. The free-surface bump drives x < 1100, so the dogbone's land band is moved into it to put real flow beside a coast; at the shipped 2800/5600 the water there is nearly stagnant and the artifact zero cannot be told from its neighbors. It asserts the number of cells level 1 covers, because that is what changes -- guarded by mskr(i,j) alone the refined region reaches the coastal columns and covers 12960 cells, with the face stencil 6480 -- and the two regions share a bounding box, so check_level_extent.sh cannot separate them. A cell count is summed over boxes and so survives load-balance chopping; confirmed identical at 1, 2 and 3 ranks. MLmask_rr2 gets MLmask's extent assertion too, so the ref-ratio-2 path of the box fix is covered rather than only the ratio-3 one. Script hardening, both from the same review. check_max_level.sh treated an unparseable log as level 0, which is exactly what MLcoastskip asserts, so a reworded print or interleaved MPI output would have made it pass vacuously; it now requires the level 0 line that every run emits. check_level_extent.sh had no terminator for an absent level and parsed the rest of the header as coordinates, reporting a nonsense span; it now stops at the first non-coordinate line and checks that it saw three lines per declared box. Comments that asserted the wrong mechanism, all found by that review: check_max_level.sh claimed the GRIDS AT LEVEL line is printed on every regrid when it is printed only when a level's grids are built or rebuilt; z_velocity's radius-0 entry was justified as being masked in place and as sitting on a k-face, when in truth nothing masks or even writes zvel_new and the taggable field is identically zero; the mask exemption's rationale was stated for all three tests when it is specific to the gradient one; and the mask_rho sidecar note in the two new inputs was changed last round to say fcompare passes it, when the original wording -- fcompare ignores it -- was right, since mask_rho is written to a rho2d section the comparison never reads. Also: mask_lo/mask_hi vertical components are now rejected rather than silently ignored, the non-virtual base operator() is documented where the class is declared, and the doc line newly advertising _count warns that adjacent_difference_greater on it is decomposition-dependent, since nothing fills its ghost cells. Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/CTestList.cmake Tests/check_level_cells.sh Tests/check_level_extent.sh Tests/check_max_level.sh Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i Tests/test_files/DogboneAnalytic_MLdryface/DogboneAnalytic_MLdryface.i commit 5961671e4d733e167d657c9283bb8daf510e9655 Author: Hannah Klion Date: Thu Sep 17 22:02:18 2026 -0700 guard a field by the cells its value depends on, and test the box fix A second review, run without knowledge of the first, found two substantive things. The face velocities were guarded with the wrong mask. x_velocity and y_velocity are stored at a cell index but live on a face, and vert_mean_3d multiplies them by msku = mskr(i-1,j)*mskr(i,j) and mskv = mskr(i,j-1)*mskr(i,j). So u at a water cell whose i-1 neighbor is land is an exact zero that is purely a mask artifact, and the previous cell test -- is this cell wet -- passed it. Since the old GRAD-on-mask derefine criterion had cleared exactly those cells, this was a regression: value_less = 0.05 on x_velocity over any masked grid now tagged every dry face. The shipped cases escape it only because their +-0.05 thresholds straddle the zero. The scalar field_radius from the previous commit could not express that, being symmetric, so the guard now takes the actual range of rho-cells a value depends on: zero for a tracer or w, (-1,0)..(0,0) and (0,-1)..(0,0) for u and v, and (-1,-1)..(1,1) for vorticity. At zero it is bit-identical to the plain cell test, so tracers are unaffected. The change's whole purpose -- a static box across a coast is refined in full -- also had no test. MLmask and MLmask_rr2 are stationary self-comparisons and pass either way; restoring the old derefine criteria changes MLmask's level-1 grids from the full box to its water part and no test noticed. add_test_extent and check_level_extent.sh assert where a level reaches, and MLmask now requires level 1 to span y in [0,750] rather than the [250,500] the old code produced. Confirmed by reinjecting the derefine criteria and watching it fail. Also corrected: MLcoasttag's header claimed to be a control for the guard, but the mask exemption is implemented by passing a null mask, so that case runs AMReX's unguarded test and never enters REMORA's guarded path. The docs claimed field criteria are evaluated "on water cells only", which is not the right predicate for a face-staggered value, and listed a closed set of field names that omitted tracers, biology tracers and particle counts. Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/CTestList.cmake Tests/check_level_extent.sh Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i commit 59074e7ce636377b1d3cdb1602e74a46699fcdcb Author: Hannah Klion Date: Wed Sep 16 21:40:38 2026 -0700 guard derived fields by their stencil, and make the skip test real Review of the branch turned up two things. DogboneAnalytic_MLcoastskip was vacuous. Its premise is that advance_3d_ml zeroes the tracers on land, leaving temp jumping the full 10 at the coast for the guard to suppress. But it set regrid_int = -1, so ErrorEst ran only inside InitFromScratch, where init_analytic_prob has written temp over land and water alike and the field is uniformly 10. The GRAD test saw no difference anywhere, with or without the guard. Tagging now happens every second step, once land has been zeroed; verified by disabling the guard and watching the test fail, which it did not do before. The guard also did not cover vorticity, and removing the derefine criteria made that field newly able to tag the coastline. remora_dervort centers a difference on i+-1 and j+-1 without masking it -- there is a standing TODO to fix that -- so a water cell touching land already carries the land-side zero velocity as a large spurious shear. Being water, it passed the old cell test. So the guard now asks whether a value was computed from water alone, rather than whether it is stored in a water cell: field_radius says how far the field reaches for its own value, and GRAD applies the same question to the neighbor it differences against. At radius 0 this is exactly the previous behavior, so state fields are unaffected. Vorticity passes radius 1 until its derive is masked, at which point this drops back to 0. Docs: the mask-keyed example claimed adjacent_difference_greater tags "exactly the cells that have a land neighbor". It tags both sides of the coast, since GRAD tags any cell whose neighbor differs. Corrected, and the vorticity caveat written down. Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i commit cba8a309dfd49827572ac093444fe63a55627d4c Author: Hannah Klion Date: Wed Sep 16 16:22:04 2026 -0700 cover the mask guard with a pair of tagging tests Nothing in the suite ran a gradient criterion on a masked domain, so the guard added in the previous commit had no test at all. The two multilevel masked cases that exist, DogboneAnalytic_MLmask and _rr2, tag with a static box. Grid structure is the only place a tagging bug shows. A run that wrongly refines the coast, or one that has quietly stopped tagging anything, still writes a self-consistent plotfile, so fcompare cannot tell either from a correct run. add_test_nlevels asserts the deepest level a run actually built, via Tests/check_max_level.sh, and then applies the usual stationary check. The two cases have to be read as a pair. MLcoastskip keys an adjacent_difference_greater on temp, which jumps the full 10 at the coast because advance_3d_ml zeroes the tracers on land, and requires that nothing is tagged. MLcoasttag keys the same criterion on the mask, which is exempt from the guard, and requires that level 1 is built along the coast. Alone, either one passes for the wrong reason: a REMORAErrorTag that tagged nothing at all would still satisfy MLcoastskip. MLcoasttag fails on the previous commit's parent, where the appended GRAD-on- mask derefine criterion cleared exactly the cells the user's own GRAD-on-mask criterion had tagged. MLcoastskip passes there too, since the old code tagged the coast and then cleared it again; it guards against a future removal of the guard rather than against the old behavior. Tests/CTestList.cmake Tests/check_max_level.sh Tests/test_files/DogboneAnalytic_MLcoastskip/DogboneAnalytic_MLcoastskip.i Tests/test_files/DogboneAnalytic_MLcoasttag/DogboneAnalytic_MLcoasttag.i commit f3df71682d0da59b4bde6ba45e1cf592162da1c6 Author: Hannah Klion Date: Wed Sep 16 16:10:24 2026 -0700 guard refinement criteria with the mask instead of untagging the coast REMORA appended two derefine criteria to every tagging setup: one clearing every land cell, one clearing every cell beside one. They existed so that a gradient criterion would not tag the whole coastline, where a field's jump from its value in the water down to the zero it is held at on land looks like structure. Because they ran over the whole TagBoxArray after the user's own criteria, they also cleared tags that a static in_box_lo/in_box_hi region had deliberately set. A box drawn across a coast came back refined only on its water part, which is not what specifying a box means. Guard each criterion as it is evaluated instead. AMRErrorTag already has the shape for this: alongside each data-dependent test it carries an embedded-boundary form that skips a covered cell and differences only across a face EBCellFlag reports as open. REMORAErrorTag is that form with the land/sea mask in place of the flags, so value_greater, value_less and adjacent_difference_greater are evaluated on water only, and the coastline is suppressed without touching any other criterion's tags. m_test, m_value and m_info are protected in AMRErrorTag, so this is a derivation rather than a reimplementation: the base class keeps the input parsing, the per-level thresholds, and the level/time gating, and still handles BOX, PARSER and USER unchanged. field_name = mask is exempt and now documented -- a criterion keyed on the mask is asking where the coast is, and guarding it would leave it nothing to find. Docs/sphinx_doc/MeshRefinement.rst Source/Make.package Source/REMORA.H Source/REMORA.cpp Source/REMORA_ErrorTag.H Source/REMORA_Tagging.cpp commit 1b0e25b1f5cf98a3025c84badc15e6226640808b Author: Hannah Klion Date: Mon Sep 14 16:03:26 2026 -0700 Add remora.cf_impose_flux: write the parent's flux onto DUon/DVom directly set_2d_cf_bcs imposes the interface condition as a velocity, ubar = Dubar/D(know). The solver then rebuilds the flux that actually moves mass as DUon = ubar(krhs) * on_u * 0.5*(Drhs(i)+Drhs(i-1)) with Drhs = zeta(krhs)+h, so what it carries is Dubar * D(krhs)/D(know), not Dubar. Neither zeta slot fixes that: the correct denominator is whichever D the solver will use when it reads the velocity back as krhs, which is not known when it is written. set_2d_cf_flux sidesteps the round trip by writing the flux itself onto the interface faces, which is exact whatever the depth does. Measured on a refined Channel_Test, volume drift at step 300 goes from -1.0e-03 to +3.1e-06. Off by default, so no answers move -- 47/47 with gold files unchanged. It is off because it does not fix the problem it was written for. The two-level barotropic instability in that case is present with the ordinary interpolated-velocity coarse-fine condition too, with no flux imposition anywhere, so it is not caused by how the interface condition is expressed. Imposing the flux improves the conservation error by roughly sixty times early on and slows the growth, but the run still reaches a 25% volume error by step 1000 where single level holds exactly zero. Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit b518794aa8f7d6ba2d962b89ca14db5a3ed387d9 Author: Hannah Klion Date: Mon Sep 14 15:35:18 2026 -0700 Never treat a domain-boundary face as a coarse-fine interface BuildMask derives the interface from fba.complementIn(grow(fba.minimalBox(),1)), a purely geometric construction. Where the fine patch reaches the edge of the domain, that complement includes the slab just outside it, and growing the complement one cell inward leaves the boundary faces marked as "set". They are then overwritten from the parent every time the interface is filled -- by set_2d_cf_bcs from the parent's mass flux under subcycling, and by FillSet from the parent's velocity on both drivers. Neither is right. Across a periodic edge the fine level wraps, so those faces have fine neighbours on both sides and are interior. At a physical edge the boundary condition owns them. Measured on Exec/Channel_Test/inputs_ml, whose patch spans the periodic x and sits on the ylo wall: of the faces marked on level 1, all 120 u-faces lay on the periodic seam -- that configuration has no x-normal interface at all, so every one was spurious -- and 40 of 80 v-faces lay on the wall. 40 of 160 marked faces were a real coarse-fine interface. The artefacts the user sees on the seam are the parent's coarse flux being imposed there every barotropic substep. ERF hit this too and fixes it in its own BuildMask by inserting periodic images of the fine boxes before the complement, noting that complementIn otherwise reports the corner cells as uncovered coarse-fine boundary. Clearing the mask on domain-boundary faces covers the periodic case and the physical-wall case together, and needs no image construction. 47/47 tests pass with gold files unchanged, so nothing in the suite refines up to a domain boundary today. Channel_Test with a refined lower half still fails later, from a separate instability in the interface imposition itself. Source/BoundaryConditions/REMORA_FillPatcher.cpp commit 3e93b383d45172ecd2b418d0e3fe36a769983096 Merge: 93faf293 7a62e1b1 Author: Hannah Klion Date: Fri Sep 11 17:45:26 2026 -0700 Merge pull request #679 from hklion/worktree-mask-refinement add informative error message when high resolution file misses variable commit 7a62e1b1b43f6ecb3999b80258461bce38a1bfc1 Author: Hannah Klion Date: Fri Sep 11 17:44:56 2026 -0700 add informative error message when high resolution file misses variable Source/IO/REMORA_ReadFromInitNetcdf.cpp commit 93faf2930d0e6e9250d3314776c832fa034b45ad Merge: 660efe5e 47ba06b6 Author: Hannah Klion Date: Fri Sep 11 16:20:07 2026 -0700 Merge pull request #678 from hklion/worktree-mask-refinement Single DM for full-domain data multifabs commit 47ba06b65db4682fb579a4bfaf9ae64c0539f3a7 Author: Hannah Klion Date: Fri Sep 11 16:18:18 2026 -0700 add assert for distribution map matching Source/REMORA.cpp commit a241f201c0f95e623b5e28a19faf1d61306aa75e Author: Hannah Klion Date: Fri Sep 11 16:05:14 2026 -0700 create and reference a single distribution mapping for full-domain boxes Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp commit 660efe5eaa9eaaf2d979ede4c2bc0df9005062b0 Merge: f094b638 b0d03390 Author: Hannah Klion Date: Fri Sep 11 15:03:04 2026 -0700 Merge pull request #677 from hklion/worktree-mask-refinement add input files for partially masked cells in dogbone analytic commit b0d03390b9332e154b9aeb157625bcb1c06abe2c Author: Hannah Klion Date: Fri Sep 11 15:02:00 2026 -0700 add input files for partially masked cells in dogbone analytic Exec/DogboneAnalytic/inputs_ml_mask Exec/DogboneAnalytic/inputs_ml_mask_rr2 commit 2ca6ffef24785e284b20e421907cc22c605e0e74 Author: Hannah Klion Date: Fri Sep 11 13:31:52 2026 -0700 comment clarity Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.cpp commit f094b6384d865de9529bf104c5eae19ee0258191 Author: Hannah Klion Date: Fri Sep 11 11:06:26 2026 -0700 update viz docs with paraview version info Docs/sphinx_doc/Visualization.rst commit 11fdf9724767c9e0456034df5f56c15ec4f0d2fe Author: Hannah Klion Date: Thu Sep 10 21:40:40 2026 -0700 Ask for the coarse level at one time when there is only one coarse state FillPatch's coarse fallback passes mfs[lev-1] twice but labelled it with two different times, t_old[lev-1] and t_new[lev-1]. In lockstep the fine level always asks at exactly t_old[lev-1], so FillPatchSingleLevel took its time == t0 branch and copied. Subcycling makes the fine level ask at times strictly inside the parent's step, which selects the interpolation branch instead: it reads a second source fab that, on this path, was never filled -- only mfs[lev-1] gets a FillBoundary. Under MPI the unfilled region is reachable, and a Debug build initialises it to signalling NaN, so it traps. That is why it survived here and failed on the GCC runner: the local build was Release and serial, where the same read returns unremarkable garbage that the 1e-11 tolerance absorbs. Reproduced exactly with -DCMAKE_BUILD_TYPE=Debug -DREMORA_ENABLE_MPI=ON and two ranks: the same six DogboneAnalytic lanes, including the two mask lanes that assert stationarity against no gold at all. The fallback means "this state, whatever time you asked for", so it now says so with matching times and lets AMReX copy. The genuine old/new pair keeps the real bracket, and both of its MultiFabs are filled rather than relying on the new one happening to alias mfs[lev-1]. Bit-identical in lockstep, which took the copy branch already. 47/47 in both configurations. Source/BoundaryConditions/REMORA_FillPatch.cpp commit 171a006955ee56f31c98ec467567dab8e695a2db Author: Hannah Klion Date: Thu Sep 10 16:10:46 2026 -0700 methods public to build on CUDA Source/REMORA.H commit f5917c380b070c285f5b3bf385c2697abca88ea7 Author: Hannah Klion Date: Thu Sep 10 16:08:39 2026 -0700 update generic inputs Exec/Generic/inputs_generic commit daa6efbfeef7eb978ebe4f0167bab202e0bcef5f Author: Hannah Klion Date: Thu Sep 10 16:07:52 2026 -0700 handle time series data at multiple levels Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp commit e1593fcb676174dbe6bf942383a066939f996936 Author: Hannah Klion Date: Wed Sep 9 21:30:30 2026 -0700 clarify comment about time_interp_flux Source/REMORA.H commit 9568a84b4cf45b203d2e2a279a5d06c946ccf567 Author: Hannah Klion Date: Tue Sep 8 21:50:46 2026 -0700 Rebuild the fill patchers and flux register on every remake, as ERF does RemakeLevel guarded both behind "this level's ba or dm changed". Each of them holds this level's layout and the one below it, so each has to be rebuilt when either moves -- and the guard skips exactly the case where only the coarse side did. AmrCore::regrid propagates coarse_ba_changed and calls RemakeLevel on the finer level with its own ba and dm unchanged, which is the one call the guard throws away. ERF has no such guard: init_stuff reconstructs advflux_reg[lev] from grids[lev-1]/dmap[lev-1] unconditionally, and RemakeLevel and MakeNewLevelFromCoarse always call it. AmrCore only invokes RemakeLevel when something the level depends on changed, so the guard bought nothing. This subsumes 09950cd's rebuild of the next level's register, which was working around the guard rather than removing it, so that goes away again. The path is not rare: Advection_3L_conservation reaches it 21 times in 20 steps. It is, however, harmless in that case -- the run is bit-identical with the guard and without it, because REMORAFillPatcher resolves the coarse layout by intersection when it copies rather than trusting the BoxArray it was defined with. So this is correctness by construction, not a fix for observed damage. Define_REMORAFillPatchers printed on every call, which unconditional rebuilding makes noisy; it now prints only under remora.v > 0. Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 65442be9d215e632a5333df208e183acfbcc1d8a Author: Hannah Klion Date: Tue Sep 8 13:49:33 2026 -0700 Reflux at the end of the step of the level being corrected Advance(lev) resets the register for the lev/lev+1 interface, but post_timestep applied it once per step of level 0. Those coincide only when lev is 0. With three levels the register for the 1/2 interface was cleared on every step of level 1 and applied once per step of level 0, so every correction but the last was discarded. Refluxing at the end of lev's own step, inside timeStep after the recursion, puts the whole accumulate-and-apply window inside one step of lev, which is where ERF does it. Tying the reset to the reflux instead is not sufficient, and Advection_3L_ conservation is what showed it: with regrid_int = 1, level 1's own timeStep regrids level 2 partway through the level-0 step, and define_flux_register rebuilds the register mid-accumulation. Only the relocation avoids that window entirely. Three-level tracer drift goes from 1.441676e-05 to exactly 0. Added with a control that must drift, so the lane cannot pass by having nothing to correct -- the same pairing as the two-level pair above it. Two-level and single-level drifts are unchanged. The cost is that the correction now lands before the average-down rather than between two of them, so it divides by the coarse level's own end-of-step Hz rather than one recomputed by stretch_transform from the averaged-down state. That is the Hz the correction was accumulated against. Flat-bottom cases are bit-identical, which is why Advection does not move; DogboneAnalytic_MLvel and MLquad shift by 1.6e-5 relative in level-0 temperature and their gold files are regenerated here. MLhires reuses MLvel's gold and still matches it, so the high-resolution-bathymetry average-down stays exact under the new ordering. A gold file asserts "unchanged", not "correct". What argues for these answers over the ones they replace is the three-level conservation measurement above. Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info Tests/test_files/Advection_3L_conservation/Advection_3L_conservation.i commit c061cbd6ac04dda78b3c97ed5d8dea85f8e38dcc Author: Hannah Klion Date: Tue Sep 8 13:48:02 2026 -0700 Apply the flux correction only to the cells it reaches The correction arrives in Hz*t units, so post_timestep scaled the whole coarse level into those units, refluxed, and scaled back. That round trip is not exact: for realistic layer thicknesses and temperatures about a tenth of cells come back one ulp different. Two consequences. do_reflux perturbed every coarse level under a finer one, not just the interface. And the clamp, which was confined to cells where the tracer differed from a pre-reflux copy, could not distinguish the correction from the round trip, so a legitimately negative tracer -- temperature in Celsius, or a signed passive scalar -- was liable to be zeroed anywhere on the level, on every step, with reflux_clamp at its default of 1. Reflux into a scratch fab instead and add the quotient. YAFluxRegister::Reflux only adds into the state it is handed, so a zeroed fab comes back holding the correction alone; cells it never reached are then bit-identical and the clamp applies exactly where intended. This also drops the pre-reflux copy of the whole level and folds clamp_reflux into reflux_to, extracted here as a method. Answers and conservation are unchanged -- 42/42 against the existing gold files, tracer drift still 0 with refluxing and 7.8e-5 without, Dogbone volume still 3.07e-10 -- because no case in the suite carries a negative tracer. Source/REMORA.H Source/REMORA.cpp commit eaaa7774ebdbe6438f4fdf94629a722b8a242a26 Author: Hannah Klion Date: Tue Sep 8 13:45:58 2026 -0700 Record why the interface depth comes from know, not knew Review suggested this was an index slip: set_2d_cf_bcs writes ubar(knew) but divides by a depth built from zeta(know), and the river transport thirty lines below builds the identical velocity-from-transport using zeta(knew). Changing it makes Dogbone's volume drift 93x worse, 3.07e-10 to 2.86e-08. The reason is that ROMS builds D from indx1 in put_refine2d -- the current, valid state -- and REMORA's analogue of indx1 is know. knew is only the component the FillPatch writes into. Noting it where the choice is made, since it is a plausible-looking change to retry. Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 1f2e9f812e1a0d034ab61a8cdc298b101bcb6548 Author: Hannah Klion Date: Tue Sep 8 13:45:41 2026 -0700 Seed Dubar_old from the first step's own flux store_2d_flux copies new into old before computing the new value, so on the first call old keeps the zero it was constructed with. With remora.time_interp_flux = 1 the first parent step then hands its child a bracket of {0, flux} and the child's early substeps see a fraction of the real one. Constant extrapolation is the right value for a step with no predecessor. Harmless at the default, where old is aliased to new and never read, which is why no test moves. Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit c3af107a49c805fbde397e9b08614e719f9616bc Author: Hannah Klion Date: Tue Sep 8 13:45:26 2026 -0700 Rebuild a flux register when the level on its coarse side is remade advflux_reg[lev] holds both lev's and lev-1's BoxArray and DistributionMapping, but was rebuilt only when lev's own grids changed. If lev-1 is remade with a different mapping while lev's grids happen to come back identical, the register keeps the old coarse layout and the ParallelCopy inside Reflux targets it. Also zero the register where it is built. The constructor sizes m_crse_data and m_cfpatch without initialising them, and Reflux adds the whole of m_crse_data to the state, so anything not written by CrseAdd has to be zero. The reset in Advance does precede every use today; making it unconditional at construction means the new rebuild path above cannot introduce one that does not. Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 98bce361f3d636d94bb23cae84cda4396babb10f Author: Hannah Klion Date: Tue Sep 8 13:44:41 2026 -0700 Average ubar and vbar down with the coarse geometry Passing an int selected the average_down_faces overload that takes ngcrse rather than a Geometry. The fine and coarse BoxArrays are not MFIterSafe, so that overload falls through to crse.ParallelCopy(ctmp,...) with a default, non-periodic Periodicity, and a fine patch abutting a periodic domain edge does not reach the matching coarse face. The Geometry overload passes crse_geom.periodicity(), which is why the velocity average-down fifteen lines above already takes geom[crse_lev]. No answers move in the suite -- no case here refines up to a periodic edge -- so this is latent rather than observed. Source/REMORA.cpp commit 6cc2ec0fc13444dba28edb559ff8f57529b6ffcb Author: Hannah Klion Date: Tue Sep 8 13:44:21 2026 -0700 Pick the same driver in EvolveOneStep as in Evolve Evolve chooses timeStep when max_level == 0 or do_substep; EvolveOneStep, the driver-coupled entry point, still chose on max_level alone. Since do_substep became the default, a multi-level coupled run therefore took the lockstep path with all the subcycle-only code still enabled -- set_2d_cf_bcs reading a fill patcher whose coarse data timeStepML never registers, an advective flux register that accumulates with nothing to reset it, and ubar/vbar averaged down on a path whose answers were recorded without it. No test covers the coupled driver, so this was found by reading rather than by failing. Source/REMORA_Coupling.cpp commit 92cf33432b77997bb72460bc2b6dad813b7a7f70 Author: Hannah Klion Date: Tue Sep 8 13:44:05 2026 -0700 Drop an unused pm binding in store_2d_flux The u-loop builds on_u from pn only; pm is used in the v-loop below, which binds it for itself. Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 84b2c994a4ed24ada4cfd083c9e451f0ae6bba02 Author: Hannah Klion Date: Tue Sep 8 11:58:26 2026 -0700 Trim the newest subcycling comments Source/Prob/REMORA_InitAnalyticGridScale_BoundaryLayer.H Tests/CTestList.cmake Tests/test_files/BoundaryLayer_ML_cf_metrics/BoundaryLayer_ML_cf_metrics.i commit a82fecaa136a5d7b51e7a46edf123fbbae35994a Author: Hannah Klion Date: Fri Sep 4 16:19:24 2026 -0700 Make BoundaryLayer's analytic grid scale refinement-aware, and test it refined The stretch set dx from the cell index and the domain's cell count, so a refined level got cells the same physical size as its parent's and the two levels covered different ground. Written instead as a face-position mapping differenced across each cell, the widths telescope: a level's cells subdivide its parent's exactly, whatever the ratio. The constants are chosen to reproduce the original spacing at the 39-cell base resolution, and they do so exactly -- BoundaryLayer is bit-identical against its existing gold file, so this is a pure refactor there and needs no regeneration. BoundaryLayer_ML_cf_metrics then runs it at two levels with a refinement ratio of 3. That matters because check_cf_metrics was until now only ever measured on uniform grids, where the identity it asserts holds for a reason that says nothing about the general case. Here dx varies by nearly a factor of four across the domain and the om_v residual is 2.5e-16 -- the direction in which pm actually varies, so the zero means something. This is the CI-runnable half of the curvilinear coverage. The NetCDF path, where a finer level interpolates its metrics from the parent's and rescales them rather than evaluating them itself, is the case that could still fail and needs a nightly test. Source/Prob/REMORA_InitAnalyticGridScale_BoundaryLayer.H Tests/CTestList.cmake Tests/test_files/BoundaryLayer_ML_cf_metrics/BoundaryLayer_ML_cf_metrics.i commit 548205e0a4ae7254d2ae6f99f603c5b9b9d539a5 Author: Hannah Klion Date: Fri Sep 4 15:22:47 2026 -0700 Cut the comments added for subcycling down toward the house rate Measured against the pre-existing Source tree at 18.8% comment lines, the code added here was 29.0%, and the whole excess sat in doxygen headers: 18.2% against 8.7%, with inline comments already at the house rate. The headers had grown into two and three paragraphs of design rationale where the repo's are a brief and a parameter list. Each is now a brief plus @param. Rationale that earns its place moved down to the line it explains -- why ubar components 0 and 1 are the safe pair, why clamping costs conservation, why zeta is absent from the average-down -- and the rest went. Roughly 60 lines out, 29.0% to 25.1%, block comments 18.2% to 12.6%. Still above 18.8%, and the remainder looks structural rather than trimmable: this adds nine functions in 840 lines, a far higher function count per line than editing existing code, and each carries a header the repo's conventions ask for. The ROMS cross-references stayed throughout, being the hardest thing here to reconstruct from the code. Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_scale_rhs_vars.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 92b646ae71a784b0b80505c786675f899fb3b5d5 Author: Hannah Klion Date: Fri Sep 4 15:13:10 2026 -0700 Tighten the comments and docs added for subcycling Three had gone stale when the multi-level baselines were regenerated. Two claimed the gold files were generated against timeStepML and that subcycled answers carry none; both are now the other way round. A third called Advection_ML "the lockstep lane", which it stopped being. Dropped "blessed" from a solver comment -- it is the test suite's vocabulary for a gold file and means nothing next to AverageDownTo -- and "latch" for keeping a value. Cut the do_substep startup note from five lines to three: it said "shared barotropic loop" twice and the consequence is the part worth printing. The Inputs.rst entry had the same repetition plus line breaks left mid-sentence by an earlier edit, and now splits the deprecated amr spelling into its own bullet rather than burying it in the first sentence. Also removed a "later phase" that survived the earlier sweep because it carried no number. Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle/Advection_ML_subcycle.i commit 4c83ba018195a672e366fad587975e637bac49aa Author: Hannah Klion Date: Fri Sep 4 14:50:55 2026 -0700 Move do_substep to the remora namespace, keeping amr.do_substep working amrex owns the amr namespace, so the option belongs under remora with the rest of the subcycling controls. amr.do_substep is the spelling existing inputs use, so it stays as a deprecated alias, following the same shape as remora.fixed_ndtfast_ratio: read the alias first, warn, and abort if both spellings are set rather than picking one by an invisible precedence rule. Two lanes cover it. Advection_ML_do_substep_alias asserts the deprecation warning, which is the observable proof the fallback was read rather than quietly ignored -- an alias that silently does nothing looks identical to one that works. Advection_ML_do_substep_both_abort asserts the conflict is caught. Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_cf_metrics/Advection_ML_cf_metrics.i Tests/test_files/Advection_ML_do_substep_alias/Advection_ML_do_substep_alias.i Tests/test_files/Advection_ML_do_substep_both_abort/Advection_ML_do_substep_both_abort.i Tests/test_files/Advection_ML_subcycle/Advection_ML_subcycle.i Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i Tests/test_files/DogboneAnalytic_ML_subcycle/DogboneAnalytic_ML_subcycle.i commit 970d245c0b59564ab4edaf5515a7415e3ab1df85 Author: Hannah Klion Date: Fri Sep 4 13:20:57 2026 -0700 Re-make the multi-level baselines against the subcycled default Advection_ML, DogboneAnalytic_MLvel and DogboneAnalytic_MLquad no longer pin themselves to amr.do_substep = 0; they run the default and their gold files are regenerated for it. DogboneAnalytic_MLhires reuses MLvel's gold and still matches it, so the high-resolution bathymetry average-down is exact under subcycling too -- that lane would have caught it otherwise. The default now has baselines and the suite covers what users actually get. A gold file asserts "unchanged", not "correct", and nothing here validates the subcycled answers against an external reference; what argues for them over the ones they replace is conservation, measured in the lanes beside them. timeStepML is still exercised. Advection_ML_subcycle_identity runs it as one half of its comparison, so lockstep answers stay pinned relative to the subcycled driver at a timestep ratio of 1 and neither can drift alone. What no longer exists is a gold file holding lockstep to its own historical answers. Tests/REMORA_Gold_Files/Advection_ML/Header Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/Advection_ML/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i commit 6c8b22369ccffe885e7d3710c7025e6a3e48c234 Author: Hannah Klion Date: Fri Sep 4 12:56:58 2026 -0700 Make subcycling the default, keep lockstep as a comparison path amr.do_substep now defaults to 1. The evidence for the flip is conservation: on DogboneAnalytic the subcycled driver holds volume to 3.1e-10 where lockstep drifts 2.0e-6, and on Advection refluxing holds tracer mass exactly where the lockstep path has no correction to apply at all. timeStepML stays, unchanged, and every one of its answers stays blessed. The four gold lanes that would otherwise have moved -- Advection_ML, DogboneAnalytic_MLvel, DogboneAnalytic_MLquad and DogboneAnalytic_MLhires -- now set amr.do_substep = 0 explicitly. That is not a workaround: those baselines predate subcycling, and pinning them is what keeps a comparison path worth comparing against. The startup message is inverted to match. It used to warn that do_substep = 1 was unvalidated; it now notes, when someone selects 0, that the lockstep driver conserves less well and why -- its shared barotropic loop cannot hand a finer level the parent's completed mass flux, so the interface treatment that conserves is structurally unavailable to it. Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA.cpp Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i commit ed68cb1f96228b318413147bc787e7b8dff1716f Author: Hannah Klion Date: Fri Sep 4 12:50:25 2026 -0700 Revert "Apply the coarse-fine corrections to the lockstep driver too" This reverts commit 6797da1f0f6176b0584a57483d30979290f42e4d. Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit 65c6cc378259907aa4053b03a8e1d44652889109 Author: Hannah Klion Date: Fri Sep 4 12:31:29 2026 -0700 Apply the coarse-fine corrections to the lockstep driver too Two of the three corrections were gated behind do_substep purely so the multi-level gold files would keep matching. Neither is subcycling-specific: - FillPatch handed FillPatchTwoLevels the same coarse MultiFab twice, so the coarse contribution was the parent's NEW state whatever time was asked for, including where the fill is meant to be at the start of the step. It now interpolates between the parent's old and new states on both drivers. - AverageDownTo returned cons, Zt_avg1 and the three 3D velocities to the parent but not ubar or vbar, so two-way coupling replaced the baroclinic state under a fine patch and left the barotropic state alone. Regenerated DogboneAnalytic_MLvel and DogboneAnalytic_MLquad; MLhires reuses MLvel's. The answer moves ~1e-3 relative in x_velocity and ~1e-6 in temperature; salt and y_velocity are unchanged to roundoff. Advection_ML does not move at all, and the ratio-1 identity lane still holds, so the two drivers still agree where they should. Be clear about what this does not buy: lockstep volume drift is unchanged at 2.0e-6, because that leak comes from the interface treatment, which is the one correction that could NOT be un-gated. set_2d_cf_bcs needs the parent's completed fast-time-averaged flux, and timeStepML marches every level through one shared barotropic loop, so at the point a child needs it the parent's DU_avg2 is still accumulating. That gate is structural, not bookkeeping, and the comment now says so. Closing it would mean either a step-lagged flux -- a different and probably worse scheme, since lockstep's co-marching ubar is more current in time -- or restructuring timeStepML so a parent finishes before its child starts, which is what the recursive driver already does. So these two changes rest on being correct rather than on a metric that improves: no test measures either of them getting better, because the metric that would is controlled by the gate that stayed. Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit 4896f92f6bd032d1f3a73e343bafcfee2df12380 Author: Hannah Klion Date: Fri Sep 4 12:14:40 2026 -0700 Drop the development-process framing from comments and test inputs The phase and tier numbering was scaffolding for the order the work happened in and means nothing to someone reading the code. check_cf_metrics no longer justifies itself by which phase depends on it, but by what breaks without it. Same for the tense. A comment saying the barotropic coupling "is unfinished" or that a lane should be promoted "once the 2D contact treatment lands" was describing a moment, and both moments have passed. What a reader needs is why these lanes carry no gold file at all -- amr.do_substep is not validated for science runs, so blessing its output would fix numbers nobody is prepared to defend -- which is true now and stays true until that changes. The Phase 0/1/2 comments in build_schema_remora.py and the Tier 1 rows in tag_map.md are untouched: those number stages of a parser and levels of a tagging scheme, not stages of this work. Source/REMORA.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_cf_metrics/Advection_ML_cf_metrics.i Tests/test_files/Advection_ML_subcycle/Advection_ML_subcycle.i Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i Tests/test_files/DogboneAnalytic_ML_subcycle/DogboneAnalytic_ML_subcycle.i commit 00129260dc69cfabc1b6c6c10dbaf7e43c968951 Author: Hannah Klion Date: Fri Sep 4 10:53:42 2026 -0700 Add the Tier 2 coarse-fine metric check, and drop the per-face residual check_cf_metrics measures whether the fine cell edges sum to the coarse edge across an interface -- sum of on_u_f over the r covering faces against on_u_c. Everything set_2d_cf_bcs does rests on that identity: it hands the child the parent's mass flux per unit edge length and lets each fine face multiply its own length back in, so the fine fluxes sum to the coarse flux only if the edges do. It runs from AverageDownTo behind remora.check_cf_metrics, so a regrid re-checks, and aborts past remora.check_cf_tol. Measured: 0 on Advection's ratio-2 grid, 1.4e-16 on DogboneAnalytic's ratio 3. That settles open question 1 from the plan for analytic grids. It is not guaranteed on the NetCDF path, where a finer level interpolates its metrics from the parent's and rescales by the refinement ratio, which need not preserve a sum -- which is the case the check exists for. The plan's other Tier 2 item, a per-coarse-face flux residual, is deliberately not added. face_cons_linear_interp preserves the face average, so the residual it would report is bounded by the edge-tiling residual above and would read 1e-16 for the same reason rather than for an independent one; the global statement it is reaching for -- that the flux across the perimeter balances -- is what DogboneAnalytic_ML_conservation already measures through volume. A third lane reporting a number the other two determine would look like coverage without being any. Source/REMORA.H Source/REMORA.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_cf_metrics/Advection_ML_cf_metrics.i commit d8eac049e569b1780c121e9947d87b2a30ad0ffe Author: Hannah Klion Date: Thu Sep 3 12:07:20 2026 -0700 Add Tier 1 conservation tests Four lanes on the two closed cases -- Advection is doubly periodic, DogboneAnalytic is walled on all four sides -- asserting that the integrated totals hold. sum_integrated_quantities already computed the right quantities: volWgtSumMF weights by Hz/(pm*pn) and masks coarse cells under finer ones, so its sums are totals over the hierarchy. Only a comparison script was missing. Every bound comes from measurement, and the numbers are worth recording: tracer mass, Advection, 20 steps single level exact to 12 digits subcycled+reflux exact to 12 digits subcycled, no reflux 7.8e-5 volume, DogboneAnalytic, 20 steps single level exact subcycled 3.1e-10 lockstep 2.0e-6 So refluxing recovers tracer conservation completely here, and the barotropic mass-flux interface conserves volume about 6500 times better than the ubar interpolation the lockstep driver still uses. Both are the first direct evidence that Phases 3 and 5 do what they were built to do rather than merely changing the answer. One lane asserts drift must EXCEED a bound: the same run with refluxing off. A conservation test that only ever asserts smallness passes just as well when the case has nothing left to conserve -- no interface, no gradient across it, a correction gone quietly no-op -- which is the failure this work kept producing. The control fails in exactly that situation and says so. Also widen the data log columns. datwidth was fixed at 14 while the precision is settable, so at 12 digits volume and max_vel ran together and the log stopped being parseable at precisely the precision that makes it worth parsing. Source/REMORA_SumIQ.cpp Tests/CTestList.cmake Tests/check_conservation.sh commit 6c778ed93476fdaf023b1ada3da02c1b48c2f1db Author: Hannah Klion Date: Thu Sep 3 11:34:58 2026 -0700 Say what index-safe meant in the AverageDownTo comments Source/REMORA.cpp commit fc261396b8a2fa3b3a4c17cafa707d90f70ee4da Author: Hannah Klion Date: Thu Sep 3 11:30:58 2026 -0700 Record why ubar and vbar are averaged down but zeta is not Source/REMORA.cpp commit d52ed0557fda802028393e3c241d8640cc098e98 Author: Hannah Klion Date: Thu Sep 3 11:21:17 2026 -0700 Drop the zeta average-down and its knew index map Phase 4 averaged the child's newest zeta onto the parent's newest zeta, tracking last_2d_knew so the two levels' leapfrog slots could be mapped onto each other the way ROMS does with Dindex2d and Rindex2d. In REMORA that work is unobservable. setup_step calls set_zeta_to_Ztavg, which overwrites all three zeta components from Zt_avg1 at the top of the next step, and stretch_transform reads Zt_avg1 rather than zeta. So nothing reads what the average-down wrote, and Zt_avg1 -- already averaged down, since before this work -- is what actually carries the free surface from child to parent. ROMS's set_zeta covers only components 1 and 2, which is presumably why it still has something to transfer. Confirmed rather than argued: DogboneAnalytic_ML_subcycle is bit-identical with the block removed. That also disposes of the caveat that the index map was never exercised. It was not exercised because it never needed to exist, and removing it takes with it a fragile dependency on advance_2d's internal index arithmetic. ubar and vbar are still averaged down; those use components 0 and 1, which update_massflux_3d makes index-safe, and they do real work. Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit 844f8f85b14c36927988eb1a913493ce5106bb42 Author: Hannah Klion Date: Thu Sep 3 11:12:34 2026 -0700 Add remora.reflux_clamp, defaulting to ROMS behaviour ROMS applies the tracer flux correction as Tvalue = MAX(0, t - cff*(TFF-TFC)) in correct_tracer_tile, over every tracer including temperature and salinity. REMORA called Reflux raw, so a large correction could drive a positive tracer negative. reflux_clamp restores ROMS's behaviour and is on by default. The clamp is not free, which is why it is an option rather than fixed: it puts back exactly the mass the correction removed, so any step that clamps is not conservative. Positivity and conservation cannot both hold here and ROMS picks positivity. Worth knowing too that clamping at zero suits a concentration but not temperature in Celsius, which is legitimately negative in polar water -- ROMS clamps it regardless, and matching that is what was asked for. Only cells the correction actually changed are clamped, so a value that was already negative beforehand is left alone. That needs a copy of the tracers taken before refluxing, allocated only when the option is on. Not exercised by any current test: on DogboneAnalytic temp and salt sit far from zero, and on Advection the dye is flat wherever it is near zero, so the flux mismatch there vanishes too. Both cases give bit-identical answers with the clamp on and off. Making it fire needs a sharp tracer front crossing the interface, which is a purpose-built case rather than an existing one. Docs/sphinx_doc/Inputs.rst Source/REMORA.H Source/REMORA.cpp commit 8e348f1340b12295f1b6c508730c6e564e34e68b Author: Hannah Klion Date: Wed Sep 2 16:21:30 2026 -0700 Drop the misleading zeta caveat from the do_substep warning The message implied the free surface at the contact points was a deficiency. It is not. setup_step calls set_zeta_to_Ztavg, which sets all three zeta components to Zt_avg1 over the grown box at the top of every baroclinic step, so what a finer level interpolates there is already the parent's fast-time average -- zeta and Zt_avg1 are the same field at that point. ROMS does the same thing, with set_zeta at main3d.F:527 running ahead of the put_refine call at 590, and set_zeta_tile assigning zeta(i,j,1) and zeta(i,j,2) from Zt_avg1. That also explains why the rejected experiment on experiment/2d-coarse-time-interp was the wrong idea twice over: it tried to add time interpolation ROMS does not do, to a field that is already an average. The remaining caveat is only that nothing tests conservation. Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp commit 4fa6860acd67ff8bf129b1269ad72d12fea8a9e4 Author: Hannah Klion Date: Wed Sep 2 16:09:19 2026 -0700 Sync the stream after adding tile fluxes to the register, as ERF does Source/TimeIntegration/REMORA_advance_3d.cpp commit 35de5a87276034c32987e7a1efc91fc3516323a2 Author: Hannah Klion Date: Wed Sep 2 16:01:54 2026 -0700 Correct the do_substep caveat: zeta is filled at contact points Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp commit 6fa3d90948c30fd86be59813c992f8cf139a31d0 Author: Hannah Klion Date: Wed Sep 2 15:32:09 2026 -0700 Update the do_substep warning now that the coupling is in place Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp commit b44490743858684e8503ff15d9f03b1ab326a0f2 Author: Hannah Klion Date: Wed Sep 2 15:30:55 2026 -0700 Reflux the tracer across the coarse-fine interface ROMS accumulates the finer level's perimeter advective tracer flux over its substeps and subtracts the mismatch against the coarse flux from the coarse ring (correct_tracer, nesting.F). YAFluxRegister is the same construction and advflux_reg was already allocated, but nothing fed it and the Reflux call had been commented out since it was written. rhs_t_3d now emits its FX and FE to the register alongside applying them, scaled so the register's internal dt/dx reproduces REMORA's dt*pm*pn. Because that divergence uses the receiving cell's metric rather than a face one, the face weight is an average of the two cells: exact where pm and pn are uniform. advance_3d does CrseAdd on the coarse step and FineAdd on each fine substep; Advance resets the register at the start of the parent step, and post_timestep refluxes before AverageDownTo, since averaging down overwrites what refluxing just corrected. The register holds the correction in Hz*t units, the form the tracer is advanced in, so post_timestep weights by Hz across the call. Two lifecycle bugs surfaced. The registers were only built in InitData for levels that existed then, so a level appearing later through tagging had none -- segfault on its first step. define_flux_register now runs from make_new_level alongside the fill patchers, and takes its layout from the MultiFabs rather than grids/dmap, which AmrCore has not set yet at that point. Second, Hz has one component and the tracers have ncons, so MultiFab::Multiply read past the end; the weighting is now an explicit loop that also leaves zero-thickness land cells alone instead of dividing by zero. remora.do_reflux, default 1, needs amr.do_substep and two-way coupling to do anything. Advection_ML_subcycle_identity now runs with remora.do_reflux=0. Refluxing is a correction the lockstep driver never applies, so leaving it on would compare a feature rather than the drivers. It moves the tracer by 3e-4 there -- and only the tracer, since temp and salt are uniform in that case and so have no flux mismatch to correct. Docs/sphinx_doc/Inputs.rst Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i commit 2c1a69ceed369db798082669aa03049eacee45d1 Author: Hannah Klion Date: Wed Sep 2 14:34:05 2026 -0700 Average the 2D state down to the parent under subcycling AverageDownTo covered cons, Zt_avg1 and the three face velocities, but not ubar, vbar or zeta. ROMS's fine2coarse replaces the coarse 2D state, not just the free surface average, and without it a child drifts from its parent over nsubsteps steps with nothing pulling it back. Measured on DogboneAnalytic_ML_subcycle: the coarse ubar under the fine patch moves by up to 0.018 m/s. Components 0 and 1 of ubar and vbar are index-safe -- update_massflux_3d has just set both to the same vertically integrated velocity. zeta is not: it keeps a leapfrog history and the rotation is per level, so last_2d_knew records which component each level considers newest and the average maps one onto the other, as ROMS does with Dindex2d and Rindex2d. Those two indices coincide in every case tested so far, so the mapping itself is not yet exercised; the comment says so. Gated on do_substep. The omission is arguably a bug in the lockstep path too, but fixing it there moves blessed answers, which is a separate call. Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit 6e470bf8576909d882e9acceb20fff3682370b94 Author: Hannah Klion Date: Wed Sep 2 09:28:28 2026 -0700 Set subcycled 2D contact points from the parent's mass flux ROMS's put_refine2d, ported. A finer level's normal barotropic velocity on the coarse-fine interface comes from the parent's fast-time-averaged mass flux rather than its interpolated ubar: ubar_f = Dubar_c / D_f, D_f = 0.5*(h + zeta)_{i-1} + 0.5*(h + zeta)_i Dubar is DU_avg2/on_u, the flux per unit cell edge length. A fine face multiplies its own edge length back in, so the fine fluxes sum to the coarse flux they replace whenever the fine edges tile the coarse edge. Interpolating ubar loses that, which is what the do_substep warning has been about. One thing came out backwards first. ROMS sets a contact point once per baroclinic step and holds it, because the point sits on the finer grid's physical perimeter. Here the interface faces are interior to the fine level and the barotropic solver rewrites them every fast step, so skipping the refill removes the only mechanism that imposes anything. set_2d_cf_bcs therefore runs after each FillPatch inside advance_2d and overwrites the faces the patchers just wrote. What is held constant over the step is the flux, not the act of imposing it. remora.time_interp_flux, default off, matches ROMS not defining TIME_INTERP_FLUX: holding the step average conserves mass over the parent interval, interpolating between two averages does not. Advection_ML cannot test any of this. Its bottom is flat, so D is the same either side of the interface and the flux form reduces exactly to the interpolation it replaces -- measured at 2e-16, i.e. this whole change is a no-op there, and the ratio-1 identity lane keeps passing for that reason. DogboneAnalytic has varying bathymetry and the correction reaches 0.02 m/s, so DogboneAnalytic_ML_subcycle is added as the lane that actually exercises it. Both facts are recorded in the inputs. Not included: the zeta and Zt_avg1 contact fill. cf_set_width is 0, and BuildMask only special-cases node directions, so a cell-centred FillSet marks nothing and is a no-op by construction. Turning on a nonzero cf_set_width changes the mask geometry for every variable and has never been exercised. CMake/BuildREMORAExe.cmake Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_set_2d_cf_bcs.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i Tests/test_files/DogboneAnalytic_ML_subcycle/DogboneAnalytic_ML_subcycle.i commit 3b8eeaaf164c2146d105074a8081840c07ffb4bd Author: Hannah Klion Date: Tue Sep 1 16:14:12 2026 -0700 Time-interpolate coarse data for subcycled levels; move dt_ref_ratio to remora amrex owns the amr namespace, so the new option is remora.dt_ref_ratio. amr.do_substep keeps its name: it predates this work and inputs already use it. FillPatch and FillPatchNoBC take an optional coarse old/new pair. Both passed mfs[lev-1] twice to FillPatchTwoLevels, so the coarse contribution was whatever buffer the caller handed in, at any requested time. That is harmless while the levels march together and wrong once they do not: a subcycled child asks for times strictly inside its parent's step. setup_step and advance_3d_ml now pass the real pair for cons and the three velocities. Gated on do_substep so timeStepML is untouched -- the guard goes away when the lockstep path does. Effect is visible: at dt_ref_ratio = 2 the tracer moves 2e-4 against the same run before this change, while the ratio-1 identity test still matches lockstep and all 33 tests pass. Nothing to do for the plan's third Phase 2 item. advance_3d_ml already fills at t_old[lev], which is per level and correct; the blanket-t_old concern is advance_2d filling at the baroclinic time rather than the barotropic sub-time, and Phase 3 freezes that interface for the whole fast loop instead. Also: document remora.dt_ref_ratio, and correct the Inputs table and notes, which still said amr.do_substep triggers an assert. Docs/sphinx_doc/Inputs.rst Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_scale_rhs_vars.cpp Source/TimeIntegration/REMORA_setup_step.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i commit d8c3cf1770cf7a5ae7152089de24759b17e0b919 Author: Hannah Klion Date: Tue Sep 1 15:56:22 2026 -0700 Make subcycled bookkeeping per level and pin the ratio-1 invariant scale_rhs_vars and scale_rhs_vars_inv now take a level. Both looped over every level internally while timeStep called them once per level, so a subcycled run divided and remultiplied an untouched level's ru/rv once per parent step -- not an identity in floating point. timeStepML calls them in a loop, so its answers do not move. Add amr.dt_ref_ratio, mirroring erf.dt_ref_ratio and ROMS reading RefineSteps separately from RefineScale: the timestep ratio need not equal the spatial one. It takes one value for all levels or one per level, and factoring the two duplicated constructor blocks into set_nsubsteps gives it one home. Setting it to 1 runs the recursive driver with the levels in lockstep, which is the check that the restructuring itself changed nothing. Advection_ML_subcycle_identity runs the input twice, through timeStepML and through timeStep at ratio 1, and requires the plotfiles to agree; they do, to 1e-15 relative on both levels. Neither run is a baseline, so it needs no gold file -- add_test_r_selfcompare. At ratio 2 the same comparison differs by 3e-4 in the tracer, so the test discriminates. That test uses half of Advection_ML's dt. At dt = 100 with dt_ref_ratio = 1, level 1 runs the coarse barotropic step on a twice-finer grid and goes unstable, which tests the CFL limit rather than the drivers. Also: fill-patch the coarse level before regrid in timeStep, as ERF does -- regrid interpolates that data to build the finer level, so its ghost cells have to be current. Unreachable from the lockstep path, which never regrids through timeStep. And assert a child stays inside its parent's time interval, which REMORAFillPatcher also checks but from where the message cannot say which level ran ahead. Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_scale_rhs_vars.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle_identity/Advection_ML_subcycle_identity.i commit 84f28372bcd2f81ff2842eb341035b18444c859a Author: Hannah Klion Date: Tue Sep 1 12:37:08 2026 -0700 Enable amr.do_substep as an opt-in subcycled AMR path Route Evolve to the recursive timeStep when amr.do_substep is set, so a refined level takes nsubsteps[lev] steps of dt[lev-1]/nsubsteps[lev] per parent step instead of marching in lockstep with timeStepML. The default stays 0, so every existing multi-level answer is untouched. The coarse-to-fine coupling that lockstep got for free is not here yet. In timeStepML all levels share one barotropic loop, so a fine level reads its contact-point ubar/vbar from a coarse level standing at the same fast step and never interpolates in time. register_coarse_data now hands each level's completed step to the fill patchers as the bracket its child interpolates within, which is enough for the 3D state and enough to satisfy the patcher's in-bracket assert, but the 2D mode is registered piecewise-constant and does not conserve mass across the interface. Turning the flag on prints a warning saying so. Also: - print_timestep_hierarchy reports the per-level slow/fast timestep table once at startup and again whenever finest_level changes. Nothing else showed the derived hierarchy, and no test exercises estTimeStep because every input sets remora.fixed_dt. - Fix the regrid dt reset in timeStepML, which divided by nsubsteps[lev] (the outer loop variable) rather than nsubsteps[k]; and switch timeStep's copy from MaxRefRatio to nsubsteps, which agree under subcycling but not without it. - Add Advection_ML_subcycle, which asserts the subcycled driver runs and that level 1 receives dt[0]/2. No gold file: those answers are not yet worth blessing. Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Tests/CTestList.cmake Tests/test_files/Advection_ML_subcycle/Advection_ML_subcycle.i commit 3291303bf34fefe2e35577eb8a30a28995fa84ea Merge: 47466020 60046e61 Author: Hannah Klion Date: Thu Sep 10 15:18:48 2026 -0700 Merge pull request #674 from hklion/worktree-mask-refinement Land-sea masking across refinement levels commit 60046e61712067879ef13b081d3a6e67237e3c41 Author: Hannah Klion Date: Thu Sep 10 14:54:45 2026 -0700 set up psi-point mask as in ROMS always, not just for NetCDF Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit 97ded82532c3da705e1b20479a5be8a72af3da33 Author: Hannah Klion Date: Thu Sep 10 12:56:09 2026 -0700 correct errors about refinement near coastline and improve wording Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/RegressionTests.rst Tests/test_files/DogboneAnalytic_MLmask/DogboneAnalytic_MLmask.i Tests/test_files/DogboneAnalytic_MLmask_rr2/DogboneAnalytic_MLmask_rr2.i commit 38b169eca05ce3880e2c96aa0eeb915aca9bf5e7 Author: Hannah Klion Date: Thu Sep 10 10:50:22 2026 -0700 for clarity reword added instances of the word lane Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/RegressionTests.rst Exec/IdealMiniGrid/inputs_synth_hires Source/Initialization/REMORA_make_new_level.cpp Source/Prob/REMORA_InitAnalyticBathymetry_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/REMORA.cpp Tests/CTestList.cmake commit 1224f22e190012b1780a3fb63ab83ce158fcdc89 Merge: 7ff08179 47466020 Author: Hannah Klion Date: Thu Sep 10 10:16:45 2026 -0700 Merge remote-tracking branch 'upstream/development' into worktree-mask-refinement commit 474660204522f7336254c21c66e105d409f8c6c6 Merge: fa6c39dd 7cab64f2 Author: Hannah Klion Date: Thu Sep 10 10:15:36 2026 -0700 Merge pull request #675 from hklion/worktree-issue-662-dstart Record the simulation start time as `dstart`, not an uninitialized `start_time` commit 7cab64f221c8271dd9af57353e51162be4dbc3fd Author: Hannah Klion Date: Thu Sep 10 10:15:04 2026 -0700 adjust comments Source/Utils/REMORA_DateClock.H commit 2db1c09c3808cf5c32e27b8c03206c52e9d0b2d4 Author: Hannah Klion Date: Thu Sep 10 10:00:03 2026 -0700 shorten docs section on unit tests Docs/sphinx_doc/testing.rst commit 75588dbd310b9c4244f28b961b42669dba8762b8 Merge: 083154ee fa6c39dd Author: Hannah Klion Date: Tue Sep 8 22:13:38 2026 -0700 Merge remote-tracking branch 'upstream/development' into worktree-issue-662-dstart commit 7ff0817983985eb772dcc2d70ab392c95d49f0e1 Merge: 1d8d8060 fa6c39dd Author: Hannah Klion Date: Tue Sep 8 22:12:35 2026 -0700 Merge remote-tracking branch 'upstream/development' into worktree-mask-refinement commit 1d8d8060330af4bdfc9504f5e15d3f383cd7f8ca Author: Hannah Klion Date: Tue Sep 8 22:09:54 2026 -0700 update inputs_generic Exec/Generic/inputs_generic commit 083154eea3424e7179d42b6d28bdb1190843bfba Author: Hannah Klion Date: Tue Sep 8 21:46:06 2026 -0700 Add a unit test for the date clock REMORA_DateClock.H had no test. It is a header of pure functions ported from ROMS dateclock.F -- the easiest kind of code to test directly, and the hardest to check through a regression lane, since a gold file only says the answer has not moved, not that the calendar is right. Tests/Unit/REMORA_DateClock_test.cpp covers remora_yearday, remora_datenum, remora_ref_clock, remora_ref_datenum, remora_datevec, remora_caldate, remora_ref_calendar, remora_ref_date_string and both time_ref guards, in 2535 checks. It runs as the ctest lane DateClock under a new "unit" label, so `ctest -L unit` runs it alone and `ctest -LE unit` skips it. Expected values come from outside the implementation, so a failure means the port is wrong rather than that it changed: day numbers are Matlab datenum values, the anchors and reference dates are the ones dateclock.F states in its own comments, calendar names come off the four branches of ROMS ref_clock, and days of the year are Gregorian arithmetic. The round-trip checks are properties rather than tables -- datevec must invert datenum, which needs no authority and covers far more inputs. A yyyymmdd.dd reference date needs eight exact digits, so cases passing one are gated on remora_time_ref_is_representable and skipped in a single-precision build. Tests/Unit is new, with no framework: a unit test is a main() returning nonzero on failure, the contract ctest already uses for every other lane. The target links AMReX for amrex::Real and the inline and GPU qualifiers, and goes through the device compiler in a CUDA build as Source/ does. testing.rst documents the pattern. The dead add_test_u in CTestList.cmake, an amr-wind leftover naming an undefined variable and never invoked, is left for a separate cleanup. Docs/sphinx_doc/testing.rst Tests/CMakeLists.txt Tests/Unit/CMakeLists.txt Tests/Unit/REMORA_DateClock_test.cpp commit 3d2db76fa000edc13ba76bea4ceecc78c38a9f28 Author: Hannah Klion Date: Tue Sep 8 21:50:09 2026 -0700 fix CUDA build Source/REMORA.H Source/REMORA.cpp commit 8ebf879fe9a3330f136b955b76058fdac20da182 Author: Hannah Klion Date: Tue Sep 8 15:58:34 2026 -0700 move comments Source/Utils/REMORA_MaskedAverageDown.H commit fa6c39dd80057466f021340868667ef6dac3c5b6 Merge: 0d7b97bf 45005084 Author: Hannah Klion Date: Tue Sep 8 15:38:32 2026 -0700 Merge pull request #673 from hklion/worktree-issue-657-particle-tiling Make particle init consistently per-tile (fixes #657) commit 450050843c0263ae6744633ec90b9e55b4988fc5 Author: Hannah Klion Date: Tue Sep 8 14:26:59 2026 -0700 Make particle init consistently per-tile (fixes #657) The second MFIter loop in initializeParticlesUniformDistributionInBox mixed per-grid and per-tile quantities: it took the prefix sum over the whole num_particles fab (numPts()/dataPtr()) and sized the particle tile from that grid-wide total, while the ParallelFor that fills the particles only visited mfi.tilebox(). The two agree only because ParticleContainerBase::do_tiling defaults to false, giving one tile per grid. With particle tiling on, every tile of a grid allocated the whole grid's particle count but filled only its own cells, so a grid split into N tiles wrote N times too many particles, all but 1/N of them uninitialized. Each tile also recomputed the same grid-wide prefix sum and wrote the entire shared offsets fab, racing under OpenMP. The corruption was silent: TotalNumberOfParticles() skips invalid ids, so REMORA printed the right count while writing 4x that many into the checkpoint. Run the scan over mfi.tilebox() instead, writing offsets only into that tile's region, so np, the offsets, the resize and the fill all describe the same box. Box::atOffset supplies the index decode; it walks with i fastest, matching the linear layout the old dataPtr() scan relied on, so with one tile per grid the traversal order is unchanged. Also skip tiles with no particles. &particle_tile.GetArrayOfStructs()[0] on an empty tile forms &m_data[0] on a null pointer, which UBSan flags. This is not new -- np was already 0 for any grid lying entirely outside particle_init_domain -- but tiling makes empty regions far more common. Bailing right after the resize also skips a serializing omp critical on NextID and a wasted kernel launch. Nothing in CI or CTest builds the particle code, so this was verified by hand with Exec/ParticleAdvectionFlat at amr.max_grid_size = 16 (15 grids, 1600 particles, 4 tiles per grid once tiling is forced on). Counts read from chk00000/tracer_particles/Header, at OMP_NUM_THREADS 1/2/4/8: build checkpoint total distinct (id,cpu) before, tiling off 1600 1600 before, tiling forced on 6400 1601 (4799 duplicates) after, tiling off 1600 1600 after, tiling forced on 1600 1600 With tiling on the fix reproduces the same 1600 particles at the same positions as the tiling-off baseline. With tiling off (the shipping configuration, since do_tiling has no input-file knob) the chk00080 checkpoint of an 80-step run is bit-for-bit identical to a binary built from the parent commit. Source/Particles/REMORA_PC_Init.cpp commit 25cab00c7595bce94afe17cd7459361e890c9aed Author: Hannah Klion Date: Tue Sep 8 14:50:18 2026 -0700 nd->ndir for spellcheck reasons Source/REMORA.cpp commit 0b2c6ca93a066e8474237594acd9c1a40df5716c Author: Hannah Klion Date: Tue Sep 8 14:17:55 2026 -0700 move implementation detail comments into function Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 562c7590cb23fe45623f2f5d04491e26810079b2 Author: Hannah Klion Date: Tue Sep 8 14:04:22 2026 -0700 move initialization block to the right spot between bathymetry and masks, and fix mask consistency checking Source/REMORA.cpp commit 06647ac787413f3f5c83338a275f75c9d143ff64 Author: Hannah Klion Date: Tue Sep 8 13:34:57 2026 -0700 Record the simulation start time as dstart, not an uninitialized start_time REMORA::start_bdy_time had no initializer and no assignment: aef1964 deleted REMORA_ReadFromBdryNetcdf.cpp, which held its only write, and left the declaration and the one read behind. That read published an indeterminate value to every NetCDF history file and plotfile as the start_time global attribute, so it held a different denormal on every run and varied with rank count. Fixes #662. Drop the attribute and the member. The start time now goes out as ROMS does, in the scalar variable dstart: remora.start_time in days on the model clock, with ROMS's long_name, units of "days since ", and a calendar attribute. It is NC_DOUBLE regardless of the build's Real, since days since year 1 needs more than a float's seven significant digits. ocean_time's units were hardcoded to "seconds since 0001-01-01 00:00:00", the epoch of only the default time_ref = 0. Both time stamps now take their reference date and calendar from remora.time_ref, so a file with time_ref set no longer contradicts itself, and ocean_time = dstart * 86400 + elapsed reads as the clock ROMS writes. Producing those strings is ROMS ref_clock, split out of remora_ref_datenum as remora_ref_clock and joined by the host-only remora_ref_calendar and remora_ref_date_string. remora_ref_datenum now calls it instead of repeating the yyyymmdd.dd arithmetic, bit for bit unchanged across that range and all three sentinel calendars. Also remove bdy_time_interval and the #if 0 block in FillCoarsePatchMap that was its only mention, as #662 notes; that block declares ctime twice and would not compile if re-enabled. Docs/sphinx_doc/Inputs.rst Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.H Source/Utils/REMORA_DateClock.H commit 2ac790b312c1f6be6777a14dd760c69f90be0045 Author: Hannah Klion Date: Tue Sep 8 12:48:41 2026 -0700 cache refined coarse masks Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 9ea4382d5249d9aebcd557bd360ad8df9711454d Author: Hannah Klion Date: Tue Sep 8 11:58:34 2026 -0700 docs clarity Docs/sphinx_doc/Inputs.rst commit 2f2035f177c1271f45fbedaeb3dd0f2979108b9c Author: Hannah Klion Date: Tue Sep 8 11:58:11 2026 -0700 make zeta_bump option clearer Source/Prob/REMORA_InitAnalyticZeta_DogboneAnalytic.H Source/TimeIntegration/REMORA_TimeStepML.cpp commit 3f03cde9e800dabc619a10591ff27dc26727867f Author: Hannah Klion Date: Fri Sep 4 15:49:23 2026 -0700 Document that only the rho-point mask is read Inputs.rst still said the netcdf path reads mask_rho, mask_u and mask_v. It reads only mask_rho now; the staggered masks are derived from it. Docs/sphinx_doc/Inputs.rst commit bf404fcb92477ecad6d59fdfbec3a79ea654e96b Author: Hannah Klion Date: Fri Sep 4 15:48:57 2026 -0700 Read only the rho-point mask, and derive the rest A grid file's mask_u and mask_v were read alongside mask_rho at level 0, while every other path in the code derives them. That left two sources of truth for the same thing, so verify_file_nodal_masks existed purely to assert they agreed. Now only mask_rho is read, anywhere: the level-0 reader matches the high-resolution one, which already took mask_rho alone. The u-, v- and psi-point masks come from update_nodal_masks, which applies ROMS set_masks.F's rule and, for a netcdf run, its 0/1/2 psi variant. verify_file_nodal_masks is gone -- what it checked is now structural rather than asserted. Verified against idmini_grd_masked_v1_classic64.nc, which carries mask_rho, mask_u, mask_v and mask_psi: the derived masks reproduce the file's exactly, and four steps of Exec/IdealMiniGrid/inputs are bit-identical before and after. That is also the answer to whether the derivation is right -- a well-formed ROMS grid file satisfies the product rule by construction, and one that does not was previously an abort and is now simply corrected. The face-mask derivation in average_down_with_grow_cells moves into a named derive_face_mask helper. It stays derived rather than stored: only the full-domain average-down wants these, at most once per level during initialization, so keeping a pair of full-domain face-mask arrays in step with the rho mask would buy nothing measurable. Factoring it out states the rule in one place and shortens the branch that uses it. All 33 lanes pass in both a NetCDF and a non-NetCDF build. Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit d3b1ce821106877319141ccfaefb4e80e78e9e21 Author: Hannah Klion Date: Fri Sep 4 15:41:08 2026 -0700 Average down every component of a face-centered field average_down_with_grow_cells hardcoded a component count of 1 in both face-centered branches while the cell-centered one used nComp(). Correct today, since vec_xvel_full_domain and vec_yvel_full_domain are the only face arrays that reach it and both carry one component, but it would silently drop components if a multi-component face field were ever passed. All four ParallelFor sites now take nComp(). No behaviour change: the count is 1 for every face array in the tree. The masked branch loses its nodality ternary along with it. Source/REMORA.cpp commit a31c4f7cb0084612ca40abb10c04d0ece1113dc2 Author: Hannah Klion Date: Fri Sep 4 14:53:45 2026 -0700 Trim the land-mask comments and fix a stale one The comments added for the mask work ran at 25 per cent of the lines against 16 per cent for the rest of REMORA.cpp, so they were noticeably heavier than their surroundings. This cuts 22 lines of them without losing anything load-bearing: what goes is history that belongs in commit messages, and restatements of what the code below already says. Kept in full: why set_masks_averaged_down must not FillPatch, why the arithmetic in REMORA_MaskedAverageDown.H is written the way it is, and why the face masks are derived rather than stored. Those are the constraints a future edit would otherwise break. check_mask_consistency's doc still offered remora.mask_consistency = ignore, which stopped existing when the separate check_mask_consistency flag replaced it. It now names the flag and the two values that remain. Also drops "block" as a term for the fine cells under a coarse one -- it reads too close to AMReX's blocking_factor -- and fixes a continuation line that was misaligned by a space. Source/REMORA.cpp Source/Utils/REMORA_MaskedAverageDown.H commit 74233db6be1f746d7139eb46ee69b02a56eebd40 Author: Hannah Klion Date: Fri Sep 4 12:29:57 2026 -0700 Share the refinement-ratio setup between the two constructors Both constructors wrote out the same loop over ref_ratio -- print it, reject a vertical ratio, accumulate cum_ref_ratios -- and the explicit REMORA(rb, max_level, n_cell, ...) constructor had been left without the accumulation. cum_ref_ratios therefore stayed empty, and every index into it read past the end of an empty Vector: average_down_with_grow_cells, both full-domain allocators, the high-resolution NetCDF readers, and the mask and bathymetry coarsening kernels added on this branch. Latent, because nothing in the tree uses that constructor. main.cpp takes the default one; the explicit one is there for an external driver to embed REMORA, which is also why no test can reach this. Fixed by extracting init_ref_ratios() and calling it from both, rather than copying the missing lines into the second one: having the loop written twice is what let them drift apart. It asserts cum_ref_ratios is empty on entry, so a second call cannot silently double the vector. The print and the abort text move verbatim and now exist in one place instead of two. All 33 lanes pass unchanged in both a NetCDF and a non-NetCDF build. Source/REMORA.H Source/REMORA.cpp commit 76a44543ebee3b75f343f82728f0a69ef79439f2 Author: Hannah Klion Date: Fri Sep 4 12:05:54 2026 -0700 Document the land/sea mask inputs in the IdealMiniGrid hires lane The lane's own comments explained that masks were off because they would need a level-0 grid file. That stopped being true when the mask got its own hires_grid_level lane, and hires_grd.nc now carries mask_rho, so the reasoning was actively misleading. mask_type stays "none" so the lane still covers the unmasked path; the comment now says to override it to netcdf, which is what the nightly suite does. Coriolis stays off for the reason that does still apply -- it wants `f` from a level-0 grid file this lane does not have. The VOLUME note gains both reference values. volWgtSumMF does not mask, so at t = 0, where sum_k Hz == zeta + h, VOLUME reads out the coarsened bathymetry and hence the mask weighting: mask_type = none 9522606688.290653 mask_type = netcdf 9506731758.713726 Both were computed independently from the two NetCDF files and match the model to 15 digits, so whoever flips mask_type has a number to assert rather than a plotfile to bless. The note also records how to rederive them, since the pm/pn-divided-by-the-refinement-ratio step is easy to miss. check_mask_consistency is turned on: inert while mask_type is none, and exactly what you want alongside the override. Exec/IdealMiniGrid/inputs_synth_hires commit 24d4bf4df5a405df558a0a1d24c95998e2e74b9f Author: Hannah Klion Date: Fri Sep 4 10:55:34 2026 -0700 Emit a land mask in the high-resolution test data generator hires_grd.nc carried only h, pm and pn, so mask_type = netcdf could not be exercised on the hires lane and Exec/IdealMiniGrid/inputs_synth_hires had to set mask_type = none. Now that the mask has its own hires lane, that restriction is only about the data. mask_rho puts land along the southern edge with the coastline one fine row above the coarse cell face at y = 2*dx. The offset is the point: it leaves the coarse row straddling it (r-1)/r water, so the mask-weighted coarsening of the bathymetry and of the initial state has something to do. A coastline on a coarse face would make every block wholly wet or wholly dry and the weighting would be untestable. The geometry is deliberately the simplest that achieves that -- a wavier coast risks a coarse face that is open with no open fine face beneath it, which check_mask_consistency rejects. mask_u and mask_v are not written: the hires reader derives them from mask_rho the way ROMS set_masks.F defines them. At n_cell = 10 10 4 and ref_ratio 3 this gives 10 partly-wet coarse cells and 20 fully dry ones, and moves the t = 0 VOLUME diagnostic from 9522606688.290653 to 9506731758.713726, a relative 1.7e-3. Both values were computed independently from the two NetCDF files and match the model to 15 digits. Regenerating hires_grd.nc in the REMORA-data repository is a separate commit there; hires_ini.nc is byte-identical. Tests/tools/make_hires_test_data.py commit ba780d2a81fe184f588a9e23fe8e9e8e9ac9b250 Author: Hannah Klion Date: Thu Sep 3 12:15:55 2026 -0700 Weight the high-resolution initial state coarsening by the mask The last mask-blind coarsening on the hires path. Initial temperature, salinity, velocity and free surface specified at hires_init_level were averaged down with a plain mean, so a coarse cell only partly covered by water started from a value mixed with whatever the file holds under land. average_down_with_grow_cells now takes a use_mask flag. It defaults off, which keeps pm and pn mask-blind on purpose: a cell size is perfectly well defined under land, and masking the metrics would corrupt them. The four state call sites pass true. When set it applies AverageDownTo's formula rather than the bathymetry one -- wet-only mean, gated by the coarse mask, zero where the block is all land -- so the initial state and the running state agree about what a land point holds. Face masks for the velocity components are derived per call from the rho mask by the ROMS set_masks.F product rule rather than stored alongside it. Nothing else needs them, and a derived mask cannot drift out of sync with the one it comes from. ensure_full_domain_masks makes the mask exist as high as hires_init_level, which may sit above hires_grid_level. It follows the rules the rest of the mask machinery already uses: levels up to hires_grid_level are coarsened down from it, levels above are injected piecewise constant as set_masks does for a refined level, and level 0 is seeded from the per-level mask when there is no high-resolution grid at all. Verified in a PnetCDF build, the whole path being NetCDF-only: Exec/IdealMiniGrid/inputs_synth_hires against a locally regenerated hires_grd.nc carrying a mask_rho whose coastline sits one fine row off a coarse cell face. Disabling the weighting moves x-velocity 2.3 per cent relative within two steps. All 33 lanes pass in both a NetCDF and a non-NetCDF build. No CI lane covers it: the checked-in hires_grd.nc has no mask_rho, and adding one means committing data to the separate REMORA-data repository. Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit feb71f1505a444cf0d36f072081c16dfa327b54b Author: Hannah Klion Date: Thu Sep 3 11:40:17 2026 -0700 Set the masks before the level-creation FillPatch calls MakeNewLevelFromCoarse and RemakeLevel filled every state variable before installing the level's real mask, so the ~20 FillPatch calls in between ran against the all-water placeholder init_masks leaves. FillPatch hands the mask to the physical-BC functor, which uses it to mask domain-boundary ghost cells, so those were left unmasked until the mask was set afterwards. set_grid_scale and set_masks now precede the fills in both functions. In RemakeLevel init_stuff moves up with them, because set_grid_scale reallocates nothing but depends on init_stuff having reallocated vec_pm/vec_pn/vec_xr. All 33 lanes are unchanged, which was measured before landing rather than hoped for: the boundary ghosts are recomputed with the correct mask by the next FillPatch of the timestep, before anything reads them. Dogbone's land reaches the y-domain boundary, so the masked-BC path is genuinely exercised. This is therefore legibility, not a bug fix. Two ordering constraints that were undocumented and easy to trip over are now recorded in the comments: set_grid_scale must follow init_stuff, which reallocates the coordinate arrays it fills; and set_masks must follow set_grid_scale, since an analytic mask hook may read those coordinates. Dogbone's no longer does, but the contract holds for the next one. Source/Initialization/REMORA_make_new_level.cpp commit 40fef1103112f1c5aeac9443084f79d3f5480205 Author: Hannah Klion Date: Thu Sep 3 11:16:01 2026 -0700 Weight the high-resolution bathymetry coarsening by the mask The mask lane added earlier coarsens the mask by the any-wet rule, but the bathymetry it goes with was still coarsened by a plain mean. So a coarse cell that is wet because some of its fine cells are wet took a depth mixed with whatever the grid file holds under land -- on a ROMS grid, a fill value with no physical meaning. coarsen_bathymetry_with_grow_cells replaces average_down_with_grow_cells for vec_h_full_domain: the wet-only mean where the block holds any water, and the plain mean where it is all land, since h still has to hold something there. A block that is wholly wet or wholly land reproduces the old result bit for bit, which is why no lane moves. The four hires initialization blocks are consolidated into one, because the order now matters: the mask cascade has to run before the bathymetry cascade that reads it. Consolidating also fixes a latent ordering hole -- mask_type and ic_type are set independently, so ic_type = netcdf with mask_type = analytic previously filled the mask after the bathymetry, which the new dependency would have broken. Also fixes the Dogbone analytic bathymetry hook, which read vec_xr/vec_yr and so could not be evaluated on the full-domain MultiFab -- the same defect the mask hook had, leaving remora.prob.traditional = false broken on the hires lane independently of this change. It now derives coordinates from the Geometry. Verified by hand: with traditional = false over a partially-masked coarse cell, forcing the coarsening mask-blind moves the velocities 0.4 to 1.3 per cent relative within two steps. No registered lane covers it -- the MLmask lanes need flat h for their stationarity argument, and non-flat h is not at rest, so a lane would need a self-blessed gold file. The same mask-blind coarsening remains on the hires_init_level path for the initial state. That needs masks at hires_init_level, which vec_mskr_full_domain is not sized for, so it is a design question rather than a substitution. Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Prob/REMORA_InitAnalyticBathymetry_DogboneAnalytic.H Source/REMORA.H Source/REMORA.cpp commit 0d7b97bfbe57f7db9890111f4711664d650d15d1 Merge: fad39dad c0be8585 Author: Hannah Klion Date: Thu Sep 3 10:55:43 2026 -0700 Merge pull request #672 from hklion/lane-provenance record which forcing inputs deck named, let withheld ones fall back commit 927570fdf3b3887c73f1944573cb2f7d65c40522 Author: Hannah Klion Date: Wed Sep 2 15:27:33 2026 -0700 Document the land/sea mask inputs remora.mask_type was undocumented, and the two new options had nowhere to go. Adds a Land/Sea Masking section to Inputs.rst covering all three, placed after Mesh Refinement since most of what there is to say is about how the mask crosses levels. The prose covers what was implicit before: the mask is specified exactly once -- at level 0, or on hires_grid_level over the whole domain -- and every other level is derived, so no two levels can disagree about the coastline; coarsening takes a cell as land only if all its fine cells are; and the two-way average is weighted so a partly-covered coarse cell takes the mean of the water under it rather than a value pulled toward zero by the land beside it. It also says when to reach for the high-resolution lane: without it a refined level inherits a coastline resolved only as well as level 0 resolves it, even where the bathymetry is high-resolution. remora.check_mask_consistency is marked as a debug option and described as checking the machinery rather than user input -- worth turning on when bringing up a new grid, not worth paying for in production, and on for the whole regression suite. remora.mask_consistency is documented as only being read when that check is on. MeshRefinement.rst's masked-region section links to the new one. Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst commit a1064f4aaf496a2644a044c4c0c41f1dedeb3b5f Author: Hannah Klion Date: Wed Sep 2 14:43:33 2026 -0700 Test the mask-weighted average-down on a partially-masked cell Nothing in the suite had a coarse cell that is partly land and partly water, which is the case the wet-only average-down exists for. Producing one needs two things together: hires_grid_level, so the coastline is resolved on the refined level rather than injected from level 0, and a static refinement box over the coast, since velocity-tagged refinement never covers it -- masked cells and the land-sea boundary are untagged. Offsetting the coast one fine cell off a coarse cell face then leaves coarse rows covered by blocks that are 6 water of 9 at ratio 3, or 2 of 4 at ratio 2. DogboneAnalytic_MLmask and DogboneAnalytic_MLmask_rr2 do that with rest as their exact solution -- flat bathymetry and free surface, uniform temperature and salinity, no initial velocity, no Coriolis -- so plt00010 must equal plt00000 and no gold file has to be blessed. Under the wet-only mean the partially-masked coarse cells keep exactly T = 10 and S = 35. Under a plain arithmetic mean the fine land cells, which advance_3d_ml zeroes every step, drag them off those values and the run stops being stationary. Confirmed to be a correctness test rather than a change detector: forcing the divisor back to the full block count breaks stationarity by about 1e-2 in salinity and velocity in both lanes, against a 1e-14 tolerance. Three prob knobs make this configurable, all defaulting to what the existing lanes already do: mask_x_lo/x_hi/y_lo/y_hi for the coastline, zeta_bump for a flat free surface, temp_west for a uniform temperature. add_test_0, unused until now, also loses the leftover erf.input_sounding_file argument it carried from ERF. What is still untested is check_mask_consistency firing. With a single mask specification coarsened downward, an inconsistency cannot be produced from inputs alone, so it was verified by hand rather than in CI. Docs/sphinx_doc/RegressionTests.rst Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticZeta_DogboneAnalytic.H Tests/CTestList.cmake Tests/test_files/DogboneAnalytic_MLmask/DogboneAnalytic_MLmask.i Tests/test_files/DogboneAnalytic_MLmask_rr2/DogboneAnalytic_MLmask_rr2.i commit 84e6a6513753c44c8972192d2c778394432ef2b9 Author: Hannah Klion Date: Wed Sep 2 09:28:34 2026 -0700 Weight the two-way average-down by the land mask Two-way nesting averaged the fine level onto the coarse one with a plain arithmetic mean. Fine land cells hold zero -- advance_3d_ml zeroes them every step -- so a coarse cell only partly covered by water had its tracers pulled toward zero in proportion to the land under it. At the coast that is a large error in the wrong direction. Source/Utils/REMORA_MaskedAverageDown.H ports the ROMS wet-only mean from fine2coarse2d/fine2coarse3d in Nonlinear/nesting.F: sum the fine values times the fine mask, divide by the count of WET fine points rather than the number of points in the block, then apply the coarse mask. Land no longer dilutes the coarse value, and the coarse mask still has the final say on wet or dry. This is not conservative, and ROMS makes the same trade deliberately. Cell-centered fields take the whole block; face-centered fields take only the fine faces in the coarse face's own plane, the amrex_avgdown_faces stencil, so "wet" means the flow really does cross there. Which mask goes with which field follows the ROMS call sites: rmask for the free surface and tracers, umask and vmask for the momenta. A fully wet block reproduces amrex_avgdown and amrex_avgdown_faces bit for bit, which is what keeps every existing multilevel answer unchanged. That needs AMReX's block order, the mask multiplying the value before it is accumulated, and the division written as a multiplication by the reciprocal -- num/den would differ in the last bit. A wet coarse point with no wet fine point beneath it has nothing to divide by. check_mask_consistency rules that out, so the kernels write zero rather than trying to diagnose it from a device kernel. That check is now gated on remora.check_mask_consistency, off by default since it validates machinery rather than user input, and turned on for every ctest lane through RUNTIME_OPTIONS. Verified both directions: all 31 lanes pass bit-identically, and with a static fine grid placed over a deliberately offset coastline the wet-only divisor differs from a full-block divisor by exactly the expected dilution -- salt relative error 0.3333 at level 0, from blocks that are 6 wet of 9. Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/Utils/Make.package Source/Utils/REMORA_MaskedAverageDown.H Tests/CTestList.cmake commit ef1e08437c6b29cdb2cb03a07e3d4b11e0579f28 Author: Hannah Klion Date: Tue Sep 1 16:11:12 2026 -0700 Check the land-sea masks for what the solver assumes about them The wet-only average-down coming next divides by the number of wet fine points under a coarse one, so a coarse water point over an all-land fine block has no value to take. Coarsening by "wet if any fine cell is wet" makes that unreachable for cell centers, but not for faces: a coarse u-face is open whenever both its cells are wet, and their water can all sit away from the shared plane. Closing it would contradict the coarsening rule, so the only fix is to move the refined grids -- which means the code has to say so rather than silently produce a zero. check_mask_consistency runs after initialization or restart and after every regrid, and checks, per level pair over the refined footprint, that no coarse water cell, u-face or v-face sits over land alone. The coarse masks are pulled onto the coarsened-fine layout through a sentinel value, so an incomplete ParallelCopy is reported as itself instead of being read as coarse land and quietly passing. It also checks two per-level properties that nothing guarded before: that the masks hold only 0 and 1 (psi also 2), since mask_arrays_for_write decides what to blank by comparing them against 0 exactly and a fractional mask would silently stop masking; and that no water cell has a non-positive depth, which stretch_transform turns into quiet garbage rather than a crash. remora.mask_consistency selects abort (default), warn or ignore. Verified by breaking it on purpose: a fractional level-0 mask reports 630 bad values, and an all-land level 1 reports 15 coarse water cells plus 15 u- and 15 v-faces, caught at the regrid where level 1 first appears. All 31 ctest lanes pass unchanged, so no existing configuration trips any of the checks. Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit 0822e0582972e78cc7b11052f8459241b8bb2776 Author: Hannah Klion Date: Tue Sep 1 15:56:54 2026 -0700 Make the derived masks uniform across levels and fill their ghosts The psi mask had two definitions and which one a level got depended on how it was built: the level-0 netcdf read used update_mskp, ROMS set_masks.F's rule, which yields 2 at a free-slip corner; every other path used the plain product, which yields 0 or 1. So free-slip treatment at the coast changed between levels. New update_nodal_masks rebuilds msku/mskv/mskp from mskr and keys the psi rule off mask_type, so it is uniform. Every mask lane in set_masks uses it. The nodal masks also only ever had one of their three ghost rings written, the rest left at the all-water value init_masks sets. calculate_nodal_masks and update_mskp now write NGROW rings -- their stencil reaches mskr(i-1,j-1) and mskr carries NGROW+1 -- and fill_3d_masks writes NGROW+1, having no stencil. update_nodal_masks FillBoundarys all three afterwards, and vec_mskr now gets a FillBoundary after the analytic hook, which previously had none at all. What is left at 1 is the outermost ring outside a physical boundary, as before. verify_file_nodal_masks checks a grid file's mask_u and mask_v against the mask_rho product ROMS defines them as. Only the level-0 read takes them from a file; every other lane derives them, so this pins the assumption rather than letting the two disagree about where a face is closed. NetCDF-only, so not exercised by any registered test. All 31 ctest lanes pass bit-identically, so none of the widened ghost values reach the solution in these configurations. Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 33b6d70a3e580072ca7b144834ade53f851f75e0 Author: Hannah Klion Date: Tue Sep 1 15:41:03 2026 -0700 Select the mask lane on the regrid paths too MakeNewLevelFromCoarse and RemakeLevel injected the coarser level's mask directly instead of calling set_masks, so a refined level never saw the high-resolution mask added in the previous commit: the hires lane improved level 0 only. Both now call set_masks(lev), which picks the same lane level 0 does. A level above hires_grid_level still gets the FillCoarsePatchPC injection, so the no-hires cases are unchanged; a level at or below it now takes the high-resolution mask. set_grid_scale moves above the call in both, since an analytic mask reads the grid coordinates it fills. RemakeLevel's second init_masks goes away as redundant -- the one further up already allocated the masks on the new BoxArray, which is what set_bathymetry_averaged_down needs, and set_masks overwrites the values anyway. set_masks also runs fill_3d_masks, which these paths never did, so vec_mskr3d is no longer stale on a regridded level. That only matters at max_level >= 2, where ErrorEst's mask derefinement criteria read it for levc >= 1. Verified by tracing which branch each lane takes: DogboneAnalytic_MLhires now takes the hires lane at levels 0 and 1, DogboneAnalytic_MLvel still injects at level 1. All 31 ctest lanes pass bit-identically -- the Dogbone coastline is coarse-aligned, so the high-resolution mask and the injected one agree. Source/Initialization/REMORA_make_new_level.cpp commit c0be858555ff04f8b702a16ce9a387904089415e Author: Hannah Klion Date: Tue Sep 1 14:57:32 2026 -0700 generic inputs Exec/Generic/inputs_generic commit 3f7c30357f3e4f92a71af0a124642ae2ba07b675 Author: Hannah Klion Date: Tue Sep 1 14:41:38 2026 -0700 record which forcing inputs deck named, let withheld ones fall back Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_setup_step.cpp commit 0dc94329fb8ccc531400402921e8bae807f9e5e1 Author: Hannah Klion Date: Tue Sep 1 12:22:33 2026 -0700 Add a high-resolution lane for the land-sea mask The mask was the one grid variable with no hires_grid_level lane. With hires_grid_level > 0, h/pm/pn came from the high-resolution grid file covering the whole domain and were averaged down, but the mask was still read from the level-0 grid file -- so a run could have high-resolution depths under a coarse-resolution coastline, and needed a level-0 grid file purely to supply that coarse mask (which is why Exec/IdealMiniGrid/inputs_synth_hires has to set mask_type = none). set_masks now has the same shape as set_bathymetry: the mask is specified exactly once, on level 0 or at hires_grid_level, and every other level is derived from that one specification. No level reads its own independent mask, so the levels cannot disagree about where the coastline is. lev == 0, hires_grid_level < 0 analytic hook, or nc_grid_file[0] lev == 0, hires_grid_level >= 0 copied from the coarsened full-domain mask lev > hires_grid_level FillCoarsePatchPC from lev-1, as before lev <= hires_grid_level copied from the full-domain mask Coarsening uses a new coarsen_masks_with_grow_cells rather than average_down_with_grow_cells: an arithmetic mean of a partially-wet block gives a fractional value, and the mask has to stay exactly 0 or 1 (REMORA_Plotfile.cpp compares it against 0 with ==). It takes "a coarse cell is land only if every fine cell under it is land", which also means the coarse level never declares land where the fine grid found water. Only mask_rho is read from the hires file; the u-, v- and psi-point masks are derived from it the way ROMS set_masks.F defines them, so a coarsened level's staggered masks stay consistent with its rho-mask. set_masks moves after set_bathymetry in init_only. It has to follow the full-domain reads, and an analytic mask needs the grid coordinates that set_bathymetry -> set_grid_scale fills on the netcdf path. Nothing between the old and new call sites reads a mask. set_masks_averaged_down deliberately uses FillBoundary rather than the FillPatch its bathymetry and grid-variable analogues use: FillPatch would interpolate uncovered ghost cells from the coarser level with a non-piecewise-constant interpolater, putting fractional values in the mask. The Dogbone analytic mask hook now derives coordinates from the Geometry instead of remora.vec_xr/vec_yr, matching set_grid_coords_from_grid_scale's (i + 1/2) * dx convention. The per-level coordinate arrays cannot be indexed on the full-domain MultiFab, which is not built on grids[lev]. It also now writes every grow cell rather than NGROW of them, since the full-domain array carries as many as the cumulative refinement ratio needs and any left unwritten would coarsen down as water. Refined levels do not pick up the hires mask yet: they are created by MakeNewLevelFromCoarse, which still injects from the coarser level rather than calling set_masks. Wiring that up is the next step; for now the hires lane improves level 0. Verified that the lane runs -- with DogboneAnalytic_MLhires the analytic mask is evaluated at level 1 and coarsened onto level 0. All 31 ctest lanes pass bit-identically, the Dogbone coastline being coarse-aligned so the coarsened mask equals the directly-evaluated one. Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/REMORA.H Source/REMORA.cpp commit fad39dad8041bfd3096ca5f46271bd62215ddee7 Merge: 3a74e11c 1766633c Author: Hannah Klion Date: Tue Sep 1 09:57:44 2026 -0700 Merge pull request #671 from hklion/plotfile_mask only output plotfile variable warning on IO processor commit 1766633c832d56e546f3339010c80e8e307c0ef8 Author: Hannah Klion Date: Tue Sep 1 09:56:41 2026 -0700 only output plotfile variable warning on IO processor Source/IO/REMORA_SetPlotVars.cpp commit 3a74e11c8a804ee390c9e779a6fc968e6387e96e Merge: fa056def bbde6014 Author: Hannah Klion Date: Mon Aug 31 16:23:29 2026 -0700 Merge pull request #670 from hklion/fix-cuda-set-cuda-architectures Fix CUDA configure after AMReX removed set_cuda_architectures commit bbde60141dec8df990b45100d9c43eee11181108 Author: Hannah Klion Date: Mon Aug 31 16:20:33 2026 -0700 Fix CUDA configure after AMReX removed set_cuda_architectures AMReX's CUDA-architecture rework replaced the set_cuda_architectures() helper (formerly in Tools/CMake/AMReXUtils.cmake) with Tools/CMake/AMReXCUDAArchs.cmake, which resolves the architectures into the standard CMAKE_CUDA_ARCHITECTURES cache variable before enable_language(CUDA). REMORA picked that helper up via CMAKE_MODULE_PATH, so once the AMReX submodule was bumped past the rework (7181df4, pin f2cbba4) every CUDA configure failed with CMake Error at CMake/SetREMORACompileFlags.cmake:38 (set_cuda_architectures): Unknown CMake command "set_cuda_architectures". Drop the call. AMReX still exports the architectures it was built for as AMREX_CUDA_ARCHS (AMReXCUDAOptions.cmake for the submodule build, AMReXConfig.cmake.in for an external install), so the target keeps being built for the same set; guard it so a build against an AMReX that does not export them inherits CMAKE_CUDA_ARCHITECTURES instead of getting an empty property. Also drop the adjacent set(CMAKE_CUDA_FLAGS ${NVCC_ARCH_FLAGS}), which was dead: NVCC_ARCH_FLAGS is never defined and a plain set() inside a function is function-scoped. Switch cuda-ci.yml to -DCMAKE_CUDA_ARCHITECTURES=80; AMReX_CUDA_ARCH still works but is deprecated and warns, and the modern interface wants the integer form. Update the unsupported-architecture warning in CMakeLists.txt to name the option that is now in use. .github/workflows/cuda-ci.yml CMake/SetREMORACompileFlags.cmake CMakeLists.txt commit fa056defbb60a59f613c6debc77519be4b7809a3 Merge: 100b90cd 57c7c744 Author: Hannah Klion Date: Mon Aug 31 15:40:50 2026 -0700 Merge pull request #669 from hklion/plotfile_mask generic inputs commit 57c7c7442097c71f566deff954146f9b963b3dbb Author: Hannah Klion Date: Mon Aug 31 15:38:49 2026 -0700 generic inputs Exec/Generic/inputs_generic commit 100b90cd5f586afe7a4e582dd5114d11f86479e6 Merge: 7181df4f 04abfa76 Author: Hannah Klion Date: Mon Aug 31 15:36:10 2026 -0700 Merge pull request #668 from hklion/plotfile_mask add mask variables to plotfiles commit 04abfa7647465750d4051e4fc582bd3160a76a5b Author: Hannah Klion Date: Mon Aug 31 15:35:37 2026 -0700 add mask variables to plotfiles Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp commit 7181df4fb13ced2b20ed8d2bda6aa2004949bad8 Author: Hannah Klion Date: Mon Aug 31 11:28:29 2026 -0700 bump AMReX version Submodules/AMReX commit 667c47cb41ca99c620486b252db472eb48f49c16 Merge: b4aee960 ada5adae Author: Hannah Klion Date: Mon Aug 31 11:17:21 2026 -0700 Merge pull request #666 from hklion/rho_eos_alpha_beta guard against null dereference of alpha and beta in nonlinear EOS commit b4aee960020080c61303dfffe54a23229e0c441c Merge: bba5d548 0c3bbf0b Author: Hannah Klion Date: Fri Aug 28 16:12:44 2026 -0700 Merge pull request #667 from hklion/worktree-issue-598-zphysnd-shift Fix z_phys_nd nodal stencil shifted one cell in +x/+y commit ada5adaeaa6efb55898e2e31f068b6f10a24c6b5 Author: Hannah Klion Date: Fri Aug 28 16:07:15 2026 -0700 fix name of calc_alpha_beta flag Source/TimeIntegration/REMORA_rho_eos.cpp commit bba5d5488ec6904c973ecd49df25a1baeeb79320 Merge: 24c79cd8 c1f17291 Author: Hannah Klion Date: Fri Aug 28 15:39:41 2026 -0700 Merge pull request #665 from hklion/zero_evap_suvstr zero evap and s{u|v}str variables where needed commit 24c79cd8dffd177e28f24fb877e14a847410cc1f Merge: ef72a6d4 b6f491fc Author: Hannah Klion Date: Fri Aug 28 15:39:20 2026 -0700 Merge pull request #664 from hklion/worktree-issue-599-ndtfast-tests Cover the barotropic substep count with regression tests (#599) commit ad05f6e42b3d348d301f3bd9ad62155667ed669a Author: Hannah Klion Date: Fri Aug 28 15:38:44 2026 -0700 guard against null dereference of alpha and beta in nonlinear EOS Source/TimeIntegration/REMORA_rho_eos.cpp commit 0c3bbf0b43d23d821ecdb5bed0da5663b88e050a Author: Hannah Klion Date: Fri Aug 28 14:47:25 2026 -0700 Fix z_phys_nd nodal stencil shifted one cell in +x/+y stretch_transform averaged z_w over cells (i..i+1, j..j+1), which is the cell-centred average belonging to node (i+1,j+1), so the nodal terrain field was shifted one cell in +x and +y relative to the low-corner nodal convention that every consumer assumes: the plotfile z_cc (REMORA_Plotfile.cpp), the particle bilinear column interpolation (REMORA_PC.H update_location_idata) and particle initialization (REMORA_PC_Init.cpp) all reconstruct cell (i,j,k) from nodes (i..i+1, j..j+1, k..k+1). Average instead the four water columns that actually surround node (i,j) -- cells (i-1,j-1) through (i,j) -- which is the psi-point stencil ROMS uses in set_depth/metrics and that REMORA already uses for om_p/on_p in uv3dmix. This matches ERF, where make_zcc uses z_cc(i,j,k) = 0.125*sum(z_nd(i..i+1, j..j+1, k..k+1)) and the analogous cell-centred-to-nodal conversion of the WRF geopotential (ERF_InitFromWRFInput.cpp) averages (i-1..i, j-1..j) with clamped indices. Adopt that same clamped-index form here, which drops the special-case branch: a node on the edge of the array now picks up the correct one-sided value instead of a single corner column. Also loop over a fully nodal box so that the outermost node in x and y is filled rather than left uninitialized; z_w carries NGROW+1 ghost cells, so every read stays in bounds. Source/Utils/REMORA_DepthStretchTransform.H commit c1f172918757569fa44a18f29570eccda00a9d60 Author: Hannah Klion Date: Fri Aug 28 14:30:04 2026 -0700 zero evap and s{u|v}str variables where needed Source/Initialization/REMORA_make_new_level.cpp commit ef72a6d4b56381fa15fa7aca769d9ef3afbb914f Merge: 75e2bfdf 8d9ef0a6 Author: Hannah Klion Date: Fri Aug 28 14:25:01 2026 -0700 Merge pull request #661 from hklion/worktree-remove-2gb-netcdf-limit Remove the 2GB NetCDF history file limit commit b6f491fcc5f592fd2950b55586b164eb8815944a Author: Hannah Klion Date: Fri Aug 28 12:51:47 2026 -0700 Cover the barotropic substep count with regression tests (#599) Issue 599 reported the substep count being derived at two sites that had drifted apart: ReadParameters truncated fixed_dt / fixed_fast_dt and compared it to the integer exactly, while set_weights had the fallback inverted and so produced ndtfast = 0 on every path that did not set both time steps -- a division by zero and an out-of-bounds read of the barotropic weight vectors, which amrex::Vector does not bounds-check. Both defects are already fixed: fc6b5a2 removed fixed_fast_dt outright, so there is no derivation left to get wrong, and made a positive ndtfast a parse-time requirement on every path, the CFL-driven one included. That commit records the behavior as verified by hand, and nothing in the suite holds it. These tests do. Channel_Test_ndtfast_unset_abort leaves the count unset and pins the abort, which is the F066 path. Channel_Test_fixed_fast_dt_abort names the removed input and pins that it is rejected rather than ignored, since amrex does not abort on unused inputs. Channel_Test_ndtfast_alias pins that the deprecated fixed_ndtfast_ratio spelling still delivers the count it names, by agreeing with the same run under the current spelling -- agreement cannot pass for the wrong reason here, because a run that ignored the alias would be left at zero and abort rather than agree. Channel_Test_ndtfast_both_abort pins that naming the count under both spellings is an error. Each guard was disabled in turn to confirm the tests are discriminating: removing the ndtfast <= 0 abort, the fixed_fast_dt rejection, or the both-names abort fails exactly the corresponding test. Removing the whole alias block fails the alias test and the both-names test together, since the latter's check is nested inside it. All 31 tests pass unmutated; no source file is touched. Tests/CTestList.cmake Tests/test_files/Channel_Test_fixed_fast_dt_abort/Channel_Test_fixed_fast_dt_abort.i Tests/test_files/Channel_Test_ndtfast_alias/Channel_Test_ndtfast_alias.i Tests/test_files/Channel_Test_ndtfast_alias/Channel_Test_ndtfast_named.i Tests/test_files/Channel_Test_ndtfast_both_abort/Channel_Test_ndtfast_both_abort.i Tests/test_files/Channel_Test_ndtfast_unset_abort/Channel_Test_ndtfast_unset_abort.i commit 75e2bfdfcec0f9da21a54455f561d16ae18f1b98 Merge: 3f6dc9a8 bf277029 Author: Hannah Klion Date: Fri Aug 28 12:21:27 2026 -0700 Merge pull request #663 from hklion/worktree-issue-602-pm-pn-timestep Worktree issue 602 pm pn timestep commit bf277029494f5c82016005df4b34ef5e4b575e8d Author: Hannah Klion Date: Fri Aug 28 11:34:23 2026 -0700 Drop stale "Baratropic timestep size" comment from remora.ndtfast These 37 trailing comments were copy-pasted from the removed remora.fixed_fast_dt lines, which really were a barotropic timestep in seconds. remora.ndtfast is a dimensionless substep count, so the comment described the wrong quantity and the wrong units (and misspelled "barotropic"). Remove the comment and keep the setting. The inputs that carry the accurate "Ratio of baroclinic to barotropic time step" comment are left alone. All 29 regression tests pass. Exec/Advection/inputs Exec/Advection/inputs_ml Exec/BlankProblem/inputs Exec/CoupleToERF/inputs Exec/Dogbone/inputs Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/inputs_orlanski_mask Exec/DoublyPeriodic/inputs Exec/GulfRefinementTest/inputs_cf_orlanski Exec/GulfRefinementTest/inputs_outflow Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Exec/IdealMiniGrid/inputs_frc Exec/IdealRivGrid/inputs Exec/ParticleAdvectionFlat/inputs Exec/Seamount/inputs Tests/test_files/Advection/Advection.i Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Seamount_hires/Seamount_hires.i Tests/test_files/Seamount_hires_grid_max_abort/Seamount_hires_grid_max_abort.i Tests/test_files/Seamount_hires_grid_zero_abort/Seamount_hires_grid_zero_abort.i Tests/test_files/Seamount_hires_init_abort/Seamount_hires_init_abort.i Tests/test_files/Seamount_hires_init_max_abort/Seamount_hires_init_max_abort.i Tests/test_files/Seamount_hires_r4/Seamount_hires_r4.i commit fc6b5a244a252afabcabfdafae97723e9da3b1b5 Author: Hannah Klion Date: Fri Aug 28 12:02:49 2026 -0700 Remove use_barotropic and fixed_fast_dt; rename ndtfast Three input-interface changes: remora.use_barotropic is removed. The barotropic (2D) mode is always on -- the false branch was debug-only, and the fast step it skipped is what the mode-split timestep estimate assumes exists. Advance and timeStepML lose the conditional around the 2D substep loop. remora.fixed_fast_dt is removed. It only ever served to infer the number of barotropic substeps, and only when remora.fixed_dt was also given, which left the ratio at zero on every other path -- including any CFL-driven run, where dt is not known until run time. The two cases that relied on that inference (Exec/Upwelling, Exec/Upwelling_Coupling) now state remora.ndtfast = 30 outright, which is the value that was being inferred. This also retires the inverted fallback in set_weights (fixed_fast_dt / fixed_dt). remora.fixed_ndtfast_ratio becomes remora.ndtfast. The old name is kept as a deprecated alias that warns and still works; setting both is an error. The C++ static member is renamed to match, and set_weights now uses it directly rather than shadowing it with a local. amrex does not abort on unused inputs by default, so both removed names are rejected explicitly rather than silently ignored -- a stale use_barotropic = false would otherwise run different physics than the input file asks for. Both are tested with ParmParse::contains rather than query, so the schema scraper behind Exec/Generic does not re-advertise a parameter that no longer exists. ndtfast is now required to be positive at parse time, which replaces the narrower check added with the issue 602 fix. All 63 input files under Exec/ and Tests/test_files/ are converted, and Exec/Generic/inputs_generic plus remora_value_hints.json are regenerated. Gold-file job_info records are left alone: they are snapshots of the runs that produced the reference data, not inputs. All 29 regression tests pass with unchanged answers. Verified by hand that the deprecated alias warns and runs, that setting both names aborts, that use_barotropic, fixed_fast_dt and ndtfast <= 0 each abort with their intended message, and that the issue 602 CFL path still reports dt = 442.48 s on Upwelling. Docs/sphinx_doc/Inputs.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/BioToy/inputs Exec/BlankProblem/inputs Exec/BoundaryLayer/inputs Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/CoupleToERF/inputs Exec/Dogbone/inputs Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/inputs_orlanski_mask Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/Generic/inputs_generic Exec/Generic/remora_value_hints.json Exec/GulfRefinementTest/inputs_cf_orlanski Exec/GulfRefinementTest/inputs_outflow Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Exec/IdealMiniGrid/inputs_frc Exec/IdealMiniGrid/inputs_synth_hires Exec/IdealRivGrid/inputs Exec/ParticleAdvectionFlat/inputs Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_fennel Exec/Upwelling/inputs_fennel_hires Exec/Upwelling/inputs_gls Exec/Upwelling_Coupling/inputs Exec/Upwelling_ML/inputs Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_set_weights.cpp Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/BC_inflow_no_value/BC_inflow_no_value.i Tests/test_files/BC_per_variable/BC_per_side.i Tests/test_files/BC_per_variable/BC_per_variable.i Tests/test_files/BoundaryLayer/BoundaryLayer.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/Channel_Test_hires/Channel_Test_hires.i Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Seamount_hires/Seamount_hires.i Tests/test_files/Seamount_hires_grid_max_abort/Seamount_hires_grid_max_abort.i Tests/test_files/Seamount_hires_grid_zero_abort/Seamount_hires_grid_zero_abort.i Tests/test_files/Seamount_hires_init_abort/Seamount_hires_init_abort.i Tests/test_files/Seamount_hires_init_max_abort/Seamount_hires_init_max_abort.i Tests/test_files/Seamount_hires_r4/Seamount_hires_r4.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_Fennel/Upwelling_Fennel.i Tests/test_files/Upwelling_Fennel_hires_init/Upwelling_Fennel_hires_init.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit 0cdd2c90366e3f99b719ad96f91b3512f72b43f8 Author: Hannah Klion Date: Fri Aug 28 10:08:13 2026 -0700 Fix estTimeStep returning bogus_large_value from rest (#602) estTimeStep limited dt by advective velocity alone, so a quiescent start (u = v = w = 0, the standard spinup IC) reduced to zero and left estdt_lowM at its bogus_large_value sentinel. ComputeDt's change_max cap is inert on the first call -- dt[] is itself seeded to bogus_large_value -- so the sentinel reached dt[0] intact when stop_time was unset, or was laundered into stop_time - t_new[0] when it was set. Either way the run took a single step and produced NaN with no warning. Fold the external gravity wave speed into the estimate, and take the metric terms from vec_pm/vec_pn (the per-cell 1/dx and 1/dy) rather than the geometry's uniform cell size, so stretched and curvilinear grids are handled. This was the last physics use of geom.InvCellSizeArray() in Source/. dt is now the smaller of two limits, each a max over the wet cells: dt_adv = cfl / max( |u|*pm, |v|*pn, |w|/Hz ) dt_grav = cfl * ndtfast / max( sqrt(g*|h|) * sqrt(pm^2 + pn^2) ) dt_grav is the Courant quantity ROMS forms as Cg_max in metrics.F. Because REMORA is mode-split, the barotropic constraint is applied to the fast step and multiplied back up by ndtfast rather than imposed on the slow step directly, which would be roughly ndtfast times stricter than necessary. ndtfast is 1 when use_barotropic is false. Other changes: - The reduction now needs six FabArrays (ccvel, Hz, h, pm, pn, mskr) and amrex::ReduceMax's FabArray overloads take at most three, so it is driven through ReduceOps/ReduceData directly. Unlike amrex::ReduceMax, ReduceOps::eval has no host fallback in a GPU build, so no LaunchSafeGuard. - Land (mskr <= 0.5) is skipped, matching how ROMS forms Cg_max over water points; h there is a fill depth, not a real one. - The vertical term uses the true layer thickness Hz instead of the uniform dz, which is the thickness of a sigma level rather than of a cell. - estTimeStep aborts on the CFL path if neither limit is defined, instead of handing ComputeDt the sentinel; ComputeDt asserts dt_0 is positive, finite and below bogus_large_value. - ReadParameters now requires fixed_ndtfast_ratio when use_barotropic is set. It is inferred only when both fixed_dt and fixed_fast_dt are given, so a CFL-driven run left it at 0 and Advance divided by it. This also makes the inverted fallback in set_weights (fixed_fast_dt / fixed_dt) unreachable on every path; that expression is left alone as out of scope. Every Exec/*/inputs and Tests/test_files/*.i sets fixed_dt, so estTimeStep returns fixed_dt there and all 29 regression tests are unchanged. Verified by hand on Upwelling (uniform grid, dt = 442.48 s where the old code gave DT = 1e+150 and NaN) and BoundaryLayer (stretched grid, dt = 1390.298869 s, matching an independent calculation from the analytic dx(i) and h(x) to all printed digits). Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp commit 8d9ef0a65c00dfa1561a70a77c75b59ee048956a Merge: b8dfa20f 3f6dc9a8 Author: Hannah Klion Date: Fri Aug 28 10:24:29 2026 -0700 Merge branch 'development' into worktree-remove-2gb-netcdf-limit commit 3f6dc9a8c08fc8e172fbacd8b9dc44464ca088dd Merge: 5d1322f7 3a8c61b7 Author: Hannah Klion Date: Fri Aug 28 10:23:31 2026 -0700 Merge pull request #658 from hklion/worktree-ocean-time-unlimited NetCDF improvements commit 3a8c61b76a313226235d491ab8b9796766d03580 Merge: caf2944b 5d1322f7 Author: Hannah Klion Date: Fri Aug 28 10:16:35 2026 -0700 Merge upstream/development into worktree-ocean-time-unlimited development's 18f5fe9 ("Fix NetCDF plotfile GPU sync and ocean_time length (#606)") fixed the same ocean_time defect this branch does, the opposite way: it kept the dimension fixed-length, corrected the sizing to a ceiling form that counts the extra record WriteAtFinalTime writes, and made the fixed length safe by constraining inputs -- history output required an explicit max_step and plot_int > 0, and aborted at startup when plot_int_time was set. An unlimited dimension is never sized from max_step or plot_int, so it fixes that same case without predicting the record count, and none of the three restrictions have a basis any more. Drop them, along with max_step_specified, which the branch had already removed the other use of. plot_int_time and a stop_time-driven run once again write history files. Resolutions: - The nt sizing block in WriteNCPlotFile_which stays deleted, along with the two aborts 18f5fe9 added to it. - The four scaled-flux blocks (qnet, latent, sensible, lwrad) take both sides: 18f5fe9's Gpu::streamSynchronize() moved after the async mult(Hscale), plus this branch's collector staging. That fix is still needed -- VarnCollector::add() reads the pinned buffer on the host as it stages, so the sync has to precede it just as it preceded the old put(). - The history-file size warning keeps this branch's plot_int > 0 guard, since the estimate is meaningless under a time-based cadence, and takes 18f5fe9's ceiling form inside it. Verified on the merged tree: the F020 case 18f5fe9 targeted (plot_int=3, max_step=10) writes 5 records at steps 0, 3, 6, 9 and 10; plot_int_time-only and stop_time-only runs both write history files instead of aborting; collective output runs at 4, 8 and 16 ranks and with one box across 4 ranks; 27 of 27 ctest cases pass. Nothing outside this branch's five files differs from development -- the flat-bathymetry removal, the ErrorEst ghost-cell fix and the particle fixes are all intact. commit 5d1322f7e892b3ecbe34841f9197224f50263919 Merge: 0022816c b4922726 Author: Hannah Klion Date: Fri Aug 28 09:54:50 2026 -0700 Merge pull request #659 from hklion/worktree-issue-596-errorest-ghosts fix ghost cell reads in ErrorEst for z_velocity and vorticity commit 0022816c9c5be362fde4fb132c8153902acf0f20 Merge: 47fa3f7b 18f5fe90 Author: Hannah Klion Date: Fri Aug 28 09:54:34 2026 -0700 Merge pull request #660 from hklion/worktree-issue-606-ncplotfile-fixes Fix NetCDF plotfile GPU sync and ocean_time length (#606) commit b8dfa20f60b582146882fad2c088038ec2af326a Author: Hannah Klion Date: Thu Aug 27 16:12:27 2026 -0700 Remove the 2GB NetCDF history file limit REMORA already writes CDF-5 history files (NC_64BIT_DATA) and its ncutils put/get API is MPI_Offset-based, so neither the format nor REMORA imposed a 2GB ceiling. The auto-sizing heuristic in ReadParameters was vestigial, and inaccurate besides: it sized output from the fixed NC3D/NC2D/NCH2D macros, which undercounted biology tracers, forcing fields, vorticity, visc2 and staggered velocities. Drop the heuristic and both 2GB warnings; the default is now a single unbounded history file. chunk_history_file and steps_per_history_file stay opt-in, but chunking without a positive step count now aborts instead of producing misnumbered files. Also default NCFile::create to NC_64BIT_DATA. It was NC_MPIIO (classic CDF-1, genuinely 2GB-limited); no caller relied on the default, but one that omitted the flag would have silently gotten a 2GB-limited file. The remaining 2GB exposure belongs to the MPI-IO layer in older MPI builds, so the docs keep it as a build caveat pointing at building.rst. Verified: both builds compile; Channel_Test/inputs_orlanski with plotfile_type=netcdf writes one CDF-5 file with all 11 ocean_time records; steps_per_history_file=2 gives correct per-chunk times; chunking without a value aborts; 29/29 ctests pass; sphinx builds with no new warnings. Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCInterface.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_IndexDefines.H commit 47fa3f7bc51dd34af16836030d4176674408830a Merge: e12d649d 7e356ded Author: Hannah Klion Date: Thu Aug 27 16:07:54 2026 -0700 Merge pull request #656 from hklion/worktree-issue-593-particle-init fix particle init OpenMP race and duplicated corner in cell-center z commit caf2944b764f79f9120b6376cc1e4ab5f179ad71 Author: Hannah Klion Date: Thu Aug 27 16:02:18 2026 -0700 Write NetCDF history files with collective I/O The history writer put every hyperslab through ncmpi_begin_indep_data() and the independent ncmpi_put_vara_* calls, so MPI-IO never got to aggregate the many small scattered writes each rank makes. Switch the bulk writes to ncmpi_put_varn_*_all(). Two things made the obvious conversions fail: Blocking put_all() cannot be dropped into the existing loops. MPI collectives must be called the same number of times, in the same order, by every rank, but the puts sit inside MFIter loops guarded by subdomain.contains(bx). Upwelling has 6 boxes at level 0, so 4 ranks get {2,2,1,1} and 8 ranks leave two ranks with none at all. The nonblocking iput() + wait_all() approach, whose remnants were still in the file as a commented-out wait_all() and a vanished irq/requests pair, is worse than it looks. ncmpi_iput_* does not reliably copy the user buffer: classic NetCDF is big-endian, so on x86 every double write needs a byte swap, and ncmpio_i_getput.m4 only allocates its own buffer when the request is at or under NC_BYTE_SWAP_BUFFER_SIZE (4096 bytes). Above that it aliases the caller's buffer, swaps it in place, and does not read it until wait_all(). Every write here stages through a block-scoped FArrayBox from The_Pinned_Arena() that is destroyed at the closing brace, and every real write is far above 4 KB -- zeta alone is 28 KB. That is a use-after-free into arena memory the next box immediately reuses. A standalone repro confirms it: at 8192 bytes per request all 4096 elements come back wrong while wait_all() and the per-request status both report NC_NOERR. Small enough test grids stay under the threshold and pass, which is why this looks intermittent. ncmpi_put_varn_*_all() takes all of a rank's subarrays for one variable in a single collective call and tolerates counts that differ between ranks, including zero, so it fits the MFIter structure directly. The loops now stage hyperslabs into a VarnCollector, which copies the data on add() -- callers can reuse their staging buffer immediately -- and issues one collective call per variable on flush(). Ranks stage different variables because they own different boxes, so flush() agrees on the variable set with a reduction over a touched-variable mask before issuing any collective call, then walks that set in ascending varid order to give every rank the same call sequence. It runs at each of the four MFIter loop boundaries rather than once at the end, so only one loop's data is held at a time. Also make NCFile::wait_all() check both the return code and the per-request statuses. It discarded both, which is how the earlier attempt corrupted data without a word. The IO-processor-only header scalars stay on the independent path. Collective writes keep numrecs synced as they go, so the explicit ncmpi_end_indep_data() before close is no longer needed. Verified against a pre-change binary on Upwelling: ncmpidiff reports every compared variable identical at 4, 8 and 16 ranks, and with a single box across 4 ranks so three ranks stage nothing at all. Chunked history files and the plot_int_time-only case still produce the right records, and all 29 ctest cases pass. Source/IO/REMORA_NCInterface.H Source/IO/REMORA_NCInterface.cpp Source/IO/REMORA_NCPlotFile.cpp commit 18f5fe90b7696365abbc287d91a64ebb7b04a0ad Author: Hannah Klion Date: Thu Aug 27 15:15:56 2026 -0700 Fix NetCDF plotfile GPU sync and ocean_time length (#606) Two defects in WriteNCPlotFile_which. F003: in the four scaled-flux blocks (qnet, latent, sensible, lwrad) the streamSynchronize() sat between the async copy into pinned host memory and the async mult(Hscale), so the host-side put() raced the scaling kernel. Move the sync after the mult; both share a stream, so one still covers each and no extra synchronization is added. F020: ocean_time was sized max_step / min(plot_int, max_step) + 1, omitting the extra record WriteAtFinalTime writes when max_step is not a multiple of plot_int. With plot_int=3 and max_step=10 REMORA writes at steps 0, 3, 6, 9 and 10 but declared ocean_time = 4, so the final write aborted with "Index exceeds dimension bound" and that output was lost. Use the ceiling form. The same expression went negative under plot_int_time, since plot_int stays -1. A time-based cadence cannot be predicted from max_step, and ocean_time is fixed length, so history output now requires max_step and plot_int > 0 and rejects plot_int_time. ReadParameters checks this so the run fails at startup rather than mid-run inside PnetCDF; write_history_file=false still supports a time-based cadence, one file per output step. The replaced guard "is_history && max_step < 0" was unreachable: max_step defaults to numeric_limits::max(), so an unset max_step built a garbage dimension length. Track whether it was set explicitly instead. F019 from the same issue was already fixed by the arbitrary-tracer work. Verified with a PnetCDF build of Exec/BoundaryLayer: plot_int=3, max_step=10 aborts before the change and gives ocean_time = 5 after; plot_int=5 gives exactly 3 records; chunking splits 5 records 2+2+1 with every dimension filled; the scaled fluxes sum consistently in W/m2. All 29 CPU regression tests pass. Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.H Source/REMORA.cpp commit 7e356dedcc18a1659bad5043dda4ff728a979c2d Author: Hannah Klion Date: Thu Aug 27 15:29:17 2026 -0700 fix particle init OpenMP race and duplicated corner in cell-center z The second MFIter loop in initializeParticlesUniformDistributionInBox runs under omp parallel, but DefineAndReturnParticleTile grows m_particles[lev], a std::map, and the NextID()/NextID(pid+np) pair is not atomic (the getter is, the setter is not). Concurrent map growth aborts with map::at out_of_range on 4+ threads, and the overlapping reservations give duplicate (id,cpu). Define the tiles in a serial pre-pass as AMReX's addParticles does, look them up with ParticlesAt inside the region, and serialize the reserve with omp critical. Separately, the 8-corner nodal-to-cell-center average of z_phys_nd repeated height_arr(i+1,j+1,k) and omitted height_arr(i+1,j+1,k+1), biasing the z used to test particle_init_domain.contains() low by Hz/8. Restore the eighth corner, matching z_cc in REMORA_Plotfile.cpp. Fixes #593. Source/Particles/REMORA_PC_Init.cpp commit 7bff71c4323e78f1036d3661b8966b02813b32ca Author: Hannah Klion Date: Thu Aug 27 15:29:08 2026 -0700 Make ocean_time an unlimited dimension in NetCDF history files The time dimension was a fixed-length dimension sized up front from max_step and plot_int. That estimate is wrong whenever output is not driven by plot_int: with plot_int at its -1 default (output driven by plot_int_time) the computation yields a negative length and ncmpi_def_dim fails with "NetCDF: Invalid dimension size", and with max_step left at its INT_MAX default it yields a dimension of roughly INT_MAX/plot_int. Declare ocean_time as NC_UNLIMITED instead so the record count reflects what was actually written, and drop the sizing block along with the "Need to know max_step if writing history file" abort it required. Nothing in the PnetCDF layer blocked this: def_dim already forwards its length straight to ncmpi_def_dim, ocean_time is already the leading dimension of every time-varying variable, and PnetCDF permits independent blocking puts to record variables. The one real change is that PnetCDF does not prefill record variables, so the variables declared with def_var_fill no longer get a pass of netcdf_fill_value at enddef. That is safe here because mask_arrays_for_write already writes the fill value into land cells before each put, and the write loops grow each box at subdomain boundaries so every element is covered each step. Also in this path: - Sync numrecs by ending independent data mode before ncf.close(). The header previously only picked up new records inside ncmpi_close, so a crash mid-output left a file whose header understated the record count. This cannot go where the commented-out call sat: every put after it is an independent, rank-dependent write. - Only the IO processor writes ocean_time. Every rank was independently writing the same 8 bytes to the same offset. - Guard the history-file size warning against plot_int <= 0, which was a divide-by-zero or a negative step count on the same inputs. Verified against a pre-change binary on Upwelling over 4 MPI ranks: ncmpidiff reports the data identical for every compared variable, the header now reads "ocean_time = UNLIMITED ; // (6 currently)", the plot_int_time-only case that aborts on the reference now runs, chunked history files still land records at the right index, and all 29 ctest cases pass. Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.cpp commit b4922726508d292d90e6c691b1abca659a6688e2 Author: Hannah Klion Date: Thu Aug 27 15:29:03 2026 -0700 fix ghost cell reads in ErrorEst for z_velocity and vorticity Closes #596 (findings F033 and F064; F034 was already fixed). zvel_new has no ghost cells in z, so copying it into the tagging scratch MultiFab with a scalar nghost of 1 made amrex::Copy iterate the destination's growntilebox(1), reading one z-plane below the nodal source FAB. Ask for IntVect(1,1,0) instead, matching the mask branch. The vorticity branch averaged the face velocities with the default ngrow of 0, so only valid cells of mf_cc_vel were written, and FillBdyCCVels fills just domain-boundary and same-level ghosts. At levc > 0 the coarse/fine ghosts were left uninitialized and remora_dervort read them. FillPatch the face velocities first, as the velocity branches already do, then average into one lateral ghost layer -- the same sequence Plotfile.cpp uses for this computation. Also fill the tagging MultiFab's own ghosts before the criteria difference across them, which closes the long-standing TODO: remora_dervort only writes valid cells, so its lateral ghosts were read uninitialized at physical and coarse/fine boundaries. The two ghost fills are hoisted into file-local helpers and reused by the mask branch. Verified: the z_velocity criterion aborts with an out-of-bounds Array4 index under -DAMREX_BOUND_CHECK before this change and runs clean after; a vorticity criterion at levc=1 spuriously created level-2 grids from garbage before and no longer does, while still tagging normally at a lower threshold. All 29 ctest regression tests pass. Source/REMORA_Tagging.cpp commit e12d649da99f563e7f6b24948b00c8687579d7be Merge: 84a442ea 811550bc Author: Hannah Klion Date: Thu Aug 27 15:16:28 2026 -0700 Merge pull request #654 from hklion/fix-particlesoverseamount-flat-bathy ParticlesOverSeamount -> ParticleAdvectionFlat commit 811550bc5967bc2309302b4a209ca2aec80c4fb6 Author: Hannah Klion Date: Thu Aug 27 14:53:15 2026 -0700 rename ParticlesOverSeamount to ParticleAdvectionFlat There is no seamount in this problem. Its README already describes it as advection of tracer particles on a flat domain, and its bathymetry is a flat bottom at the base of the domain, so the name only ever described the DoublyPeriodic shelf profile it was mistakenly wired to. Renames the Exec case directory, prob_name, the five analytic Prob headers, and the doc references. The RST section label becomes particleadvectionflat. NOTE: the external nightly regression config still names this test ParticlesOverSeaMount and points buildDir at the old Exec directory. It has to be updated in the same pass, or those two tests will fail to find their inputs. Docs/sphinx_doc/Particles.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Exec/ParticleAdvectionFlat/README Exec/ParticleAdvectionFlat/inputs Exec/REMORA_Prob.cpp Source/Prob/Make.package Source/Prob/REMORA_InitAnalyticBathymetry_ParticleAdvectionFlat.H Source/Prob/REMORA_InitAnalyticHMix_ParticleAdvectionFlat.H Source/Prob/REMORA_InitAnalyticProb_ParticleAdvectionFlat.H Source/Prob/REMORA_InitAnalyticSMFlux_ParticleAdvectionFlat.H Source/Prob/REMORA_InitAnalyticVMix_ParticleAdvectionFlat.H commit 84a442ead3b0e3355c8797b01f20d26c0130cdbd Merge: 84628f38 ebdd17af Author: Hannah Klion Date: Thu Aug 27 14:44:21 2026 -0700 Merge pull request #653 from hklion/worktree-issue-592-nctimeseriesboundary-gpu-sync sync stream before host touches pinned boundary fabs commit fbdea97390622134e90f953f2da498ebd82c7cec Author: Hannah Klion Date: Thu Aug 27 14:01:57 2026 -0700 run ParticlesOverSeamount over a flat bottom again Removing remora.flat_bathymetry made this problem's analytic hook live for the first time: the dispatch had it spelled "particles" until 91faaf0, and the flag short-circuited set_bathymetry before that hook ran, so its shelf profile had never executed. That profile shoals to 27 m at the periodic x edges while the domain floor stays at 150 m, so the terrain-following grid no longer fills the domain box. Particles are seeded through the full column in the deep middle, drift onto the shelf, and end up under the sea floor, where AdvectWithFlow has no bed reflection and mac_interpolate_mapped_z extrapolates off the end of the z column. The particle then leaves the domain and Redistribute aborts in locateParticle. It reproduces at step 27 with 4 ranks. Restore the flat bottom this problem has always run with. Fixing the particle bed handling instead would let the shelf profile be used here, but that is a change to the particle advection, not to what this case has been testing. Source/Prob/REMORA_InitAnalyticBathymetry_ParticlesOverSeamount.H commit ebdd17af8627a34fda39c6c74dab3a0b29cb5aa2 Author: Hannah Klion Date: Thu Aug 27 13:37:37 2026 -0700 sync stream before host touches pinned boundary fabs NCTimeSeriesBoundary holds its boundary fabs in The_Pinned_Arena on GPU builds, so interp_fab's ParallelFor reads them in place and returns before the kernel has run. read_in_at_time then host-overwrote those fabs with the interp kernels still queued, and the pinned arena is not stream- ordered, so the crse_* locals could also be freed mid-kernel. Sync at the top of read_in_at_time and at the end of each lev>0 branch. No-op on CPU builds. Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit 84628f3875550f2e7835b0f2f6d3a8f465047b1d Merge: 3fb50f46 7516256f Author: Hannah Klion Date: Thu Aug 27 12:59:52 2026 -0700 Merge pull request #652 from hklion/remove-flat-bathymetry remove the flat bathymetry path commit 7516256fc5db4c6b19caeabf59a5653a21ae6526 Author: Hannah Klion Date: Thu Aug 27 11:12:40 2026 -0700 remove the flat bathymetry path remora.flat_bathymetry short-circuited set_bathymetry at level 0, bypassing the problem's analytic bathymetry hook entirely, and separately selected a different horizontal tracer advection formula in rhs_t_3d and prestep_t_advection. Drop the option and both code paths. Bathymetry now always comes from the problem's analytic hook or from NetCDF. The flat branches of the Seamount, DoublyPeriodic and ParticlesOverSeamount hooks are gone, so those problems use their designed analytic profile. CoupleToERF had no bathymetry hook at all and relied on the flag, so it gets an explicit flat one; Advection already had a flat hook, which is now the live path. Both guard the write to h's second component, which vec_h_full_domain does not have. The retained tracer advection formula is the one that matches ROMS: the flat branch added the upstream3/centered4 correction term where ROMS subtracts it. Advection and Advection_ML change only in the passive tracer field (~0.1% relative); their gold files are regenerated. Every other field is bit identical, which confirms the new Advection hook reproduces the bathymetry the flag used to install. Tests/test_files/DoublyPeriodic and DoublyPeriodic_bathy differed only by this flag, so they are now the same case: keep DoublyPeriodic and move the _bathy gold onto it. Seamount_hires_flat_abort covered an incompatibility that no longer exists and is removed. Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/RegressionTests.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/BioToy/inputs Exec/BoundaryLayer/inputs Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/CoupleToERF/inputs Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/inputs_orlanski_mask Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/Generic/inputs_generic Exec/Generic/remora_value_hints.json Exec/GulfRefinementTest/inputs_cf_orlanski Exec/GulfRefinementTest/inputs_outflow Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Exec/IdealMiniGrid/inputs_frc Exec/IdealRivGrid/inputs Exec/ParticlesOverSeaMount/inputs Exec/REMORA_Prob.cpp Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_fennel Exec/Upwelling/inputs_fennel_hires Exec/Upwelling/inputs_gls Exec/Upwelling_Coupling/inputs Exec/Upwelling_ML/inputs Source/Prob/Make.package Source/Prob/REMORA_InitAnalyticBathymetry_Advection.H Source/Prob/REMORA_InitAnalyticBathymetry_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticBathymetry_ChannelTest.H Source/Prob/REMORA_InitAnalyticBathymetry_CoupleToERF.H Source/Prob/REMORA_InitAnalyticBathymetry_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticBathymetry_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Seamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_ML.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection/job_info Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/job_info Tests/REMORA_Gold_Files/BoundaryLayer/job_info Tests/REMORA_Gold_Files/Channel_Test/job_info Tests/REMORA_Gold_Files/DogboneAnalytic/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info Tests/REMORA_Gold_Files/DoubleGyre/job_info Tests/REMORA_Gold_Files/DoublyPeriodic/Header Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_H Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoublyPeriodic/job_info Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Header Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_H Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount/job_info Tests/REMORA_Gold_Files/Seamount_hires/job_info Tests/REMORA_Gold_Files/Seamount_hires_r4/job_info Tests/REMORA_Gold_Files/Upwelling/job_info Tests/REMORA_Gold_Files/Upwelling_GLS/job_info Tests/REMORA_Gold_Files/Upwelling_NLEOS/job_info Tests/REMORA_Gold_Files/Upwelling_logdrag/job_info Tests/REMORA_Gold_Files/Upwelling_qdrag/job_info Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/BC_inflow_no_value/BC_inflow_no_value.i Tests/test_files/BC_per_variable/BC_per_side.i Tests/test_files/BC_per_variable/BC_per_variable.i Tests/test_files/BoundaryLayer/BoundaryLayer.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/Channel_Test_hires/Channel_Test_hires.i Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Seamount_hires/Seamount_hires.i Tests/test_files/Seamount_hires_flat_abort/Seamount_hires_flat_abort.i Tests/test_files/Seamount_hires_grid_max_abort/Seamount_hires_grid_max_abort.i Tests/test_files/Seamount_hires_grid_zero_abort/Seamount_hires_grid_zero_abort.i Tests/test_files/Seamount_hires_init_abort/Seamount_hires_init_abort.i Tests/test_files/Seamount_hires_init_max_abort/Seamount_hires_init_max_abort.i Tests/test_files/Seamount_hires_r4/Seamount_hires_r4.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_Fennel/Upwelling_Fennel.i Tests/test_files/Upwelling_Fennel_hires_init/Upwelling_Fennel_hires_init.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit 3fb50f46e93cc2d5c1c369e05b024bafde75590f Merge: 686245cc 44995860 Author: Hannah Klion Date: Thu Aug 27 10:24:18 2026 -0700 Merge pull request #648 from hklion/fix-river-vshape-tracers apply river_Vshape only to river_transport, not to tracers commit 686245cc612db04161c351e4dac3810b39d4e8a5 Merge: 076598e6 a533b9d8 Author: Hannah Klion Date: Thu Aug 27 10:23:34 2026 -0700 Merge pull request #651 from hklion/plotfile_fixes Plotfile fixes commit 076598e62f08e6e4eeaed1074a9dd135c99c0f08 Merge: 10e12c2b 9a11e3b9 Author: Hannah Klion Date: Thu Aug 27 10:23:16 2026 -0700 Merge pull request #649 from hklion/issue-601-clim-nudg-box compare clim-nudging box hi end to the nodal index, not dhi commit a533b9d86af1129e0a166b75d2166371d804fe37 Author: Hannah Klion Date: Wed Aug 26 15:21:43 2026 -0700 only write nu_nd header if outputting data Source/IO/REMORA_Plotfile.cpp commit 4cf6ab446fa4853c5b0b45ec7c55b0c77fa6ea96 Author: Hannah Klion Date: Wed Aug 26 15:21:13 2026 -0700 move {x|y|z}_cc before vorticity so header and data order match Source/IO/REMORA_Plotfile.cpp commit 71b8076cae9557156daad22d3f008ff4f50eecc4 Author: Hannah Klion Date: Wed Aug 26 15:18:37 2026 -0700 output ubar and vbar in amrex plotfiles rather than DU/DV Source/IO/REMORA_Plotfile.cpp commit 08ae2d02520a96691264b01cd1f861661aecceeb Author: Hannah Klion Date: Wed Aug 26 15:08:26 2026 -0700 do fill value masking in outer plotfile call Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp commit 10e12c2bd9bdac706a99a50535c0500862e85446 Merge: 487719d8 4f5a7b95 Author: Hannah Klion Date: Wed Aug 26 15:22:44 2026 -0700 Merge pull request #650 from hklion/checkpoint_level_overruns Checkpoint file level checks commit 4f5a7b95099bec261e34b80c5591f36639c907b0 Author: Hannah Klion Date: Wed Aug 26 14:43:08 2026 -0700 Checkpoint file level checks - Aborts if checkpoint file has more levels than current max_level - Doesn't let loop over levels overrun vector when reading in step and dt info from checkpoint Source/IO/REMORA_Checkpoint.cpp commit 487719d82e6d378930d4f1a1afc49001e79126e6 Merge: a57fe59a f235c9da Author: Hannah Klion Date: Wed Aug 26 14:40:19 2026 -0700 Merge pull request #647 from hklion/upwelling_bathy_cell_size use correct cell size when calculating upwelling bathymetry commit 9a11e3b93304d970dc1910e9b290278c8c5bc76d Author: Hannah Klion Date: Wed Aug 26 13:50:44 2026 -0700 compare clim-nudging box hi end to the nodal index, not dhi The momentum climatology-nudging boxes in setup_step (3D ru/rv) and advance_2d (2D rhs_ubar/rhs_vbar) tried to reproduce the ROMS nudging loops i=IstrU..Iend, j=JstrV..Jend, which exclude the u-face on the west and east domain edges and the v-face on the south and north edges. Two things kept them from doing that: - The high-side test compared the ubound of an x/y-nodal box against the cell-centered domain hi. MFIter::nodaltilebox calls surroundingNodes and only strips the high node when the tile stops short of the valid high end, so a box on the domain high edge ends at dhi+1 and `xbx_hi.x == dhi.x` never matched there. The eastern and northern edge faces were nudged while the western and southern ones were excluded. The test did match a grid whose last cell is dhi.x-1, wrongly dropping an interior face and making the result depend on the grid decomposition. - The lo and hi adjustments were chained with `else if`, so a box spanning the domain in a direction -- the single-grid case -- could only ever shed its low face. Fold the adjustment into one REMORA::clim_nudg_momentum_box helper, since the block was byte-identical in the two files, and have it compare the high side against domain.bigEnd(dir)+1 with independent lo/hi tests. In a periodic direction it returns the box untouched: ROMS sets IstrU=Istr under EW_PERIODIC and nudges every face, and the previous code wrongly dropped the west/south face there. The boxes are now built inside the existing REMORA_USE_NETCDF / do_m*_clim_nudg blocks, which are their only consumer. Verified against amrex::MFIter directly: for the IdealMiniGrid clim-nudging domain (10x16x20) the old boxes covered u-faces 1..10 and v-faces 1..16; they now cover 1..9 and 1..15, matching ROMS. The Exec/IdealMiniGrid inputs_clim_nudg case is bit-identical over 10 steps before and after, because its all-boundary orlanski_rad/Flather conditions overwrite the edge faces before the tendency reaches the state -- so no clim-nudging baseline moves here, contrary to what the issue anticipated. All 29 registered ctests pass. Fixes #601 Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 449958606813ab6bfb3dc15016ddde8b36790ab7 Author: Hannah Klion Date: Wed Aug 26 13:28:06 2026 -0700 apply river_Vshape only to river_transport, not to tracers river_Vshape is ROMS's Qshape: set_ngfldr/ana_psource form Qsrc(is,k) = Qbar(is)*Qshape(is,k) for the transport only, while Tsrc comes straight from river_temp/river_salt as a per-level concentration. NCTimeSeriesRiver applied the Vshape multiply to any field that was 2D in the file, inferring the field's kind from its rank. A tracer given as (river_time, river) was therefore stored as conc*Vshape, so with Nz levels and a uniform Vshape the injected concentration came out a factor of Nz too small, with a spurious vertical profile on top. The consumers want it unscaled: advance_3d sets u from river_transport (Vshape already applied), then prestep_t_advection and rhs_t_3d form FX = Huon * river_source. Give the class an explicit is_transport flag instead, set only for the two river_transport objects. When it is false and the file variable is 2D, broadcast the concentration over k, and skip the river_Vshape read so a file without Vshape still works for tracers. Warn when a tracer arrives without an s_rho dimension, since ROMS's rivers.cdl declares river_temp/river_salt as (river_time, s_rho, river). Files with 3D tracers, including the IdealRivGrid regression data, take the same path as before and are unaffected. Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/REMORA.cpp commit f235c9da935d187f66c45205c38a0e4d7778c432 Author: Hannah Klion Date: Wed Aug 26 13:26:38 2026 -0700 was using perpendicular cell size when calculating upwelling bathymetry Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_ML.H commit a57fe59adff0a639113a417c452904755d26a5ff Merge: b09e3b56 64325581 Author: Hannah Klion Date: Wed Aug 26 13:00:59 2026 -0700 Merge pull request #645 from hklion/ghost_cell_rad_bc_mask Ghost cell rad bc mask commit b09e3b567d9800825711bd603e25d114c97abdaf Merge: 1d392d40 91faaf0b Author: Hannah Klion Date: Wed Aug 26 11:31:02 2026 -0700 Merge pull request #646 from hklion/part_over_seamount_bathy correctly dispatch particlesoverseamount bathymetry calculation commit 91faaf0b1cc93182f1eb3b3d8ab38cea66238c0c Author: Hannah Klion Date: Wed Aug 26 11:30:34 2026 -0700 correctly dispatch particlesoverseamount bathymetry calculation Exec/REMORA_Prob.cpp commit 1d392d40fcffd388ee895a6e5928b1762095119d Merge: 50643163 b079d66f Author: Hannah Klion Date: Wed Aug 26 11:20:40 2026 -0700 Merge pull request #644 from hklion/worktree-fillbdyccvels-signflip Generalize velocity sign flip in FillBdyCCVels commit 64325581190953ef0cc6db009d18843d8c56f390 Author: Hannah Klion Date: Wed Aug 26 10:43:08 2026 -0700 mask east orlanski_rad gradients at dom_hi.x, not dom_lo.x The high-x branch of impose_cons_bcs took both of its transverse differences in column dom_hi.x but masked them with mskv(dom_lo.x, ...), so the west boundary column's land mask was applied at the east boundary. The three sibling branches already mask at the column the difference is taken in. The wrong column is also out of range. mskv carries 3 ghost cells, so on any domain decomposed in x the east-boundary fab's mskv box does not reach dom_lo.x and the Array4 offset lands outside the fab; AMReX_ASSERTIONS is forced off here, so nothing traps. BoundaryLayer is the only lane using orlanski_rad and it puts it on the east face, but it runs with mask_type defaulting to none, so every mask entry is 1.0 and the stray reads cannot change its answer. Exec/DogboneAnalytic/inputs_orlanski_mask is the configuration this was measured on: Dogbone cut to x = 5600 so its land block reaches the radiating face. There the two indexings differ by about 20% in salt and temp. It is not wired up as a regression lane because the radiating face also drives salt above its initial uniform value, independently of the masking; the header records the numbers. Also, while in init_bcs: the four-entry per-variable type list was guarded by AMREX_ASSERT, which is compiled out in this build, so a short list indexed a std::vector out of bounds instead of reporting anything. Abort with the input name instead. And add_test_equiv dropped stderr, so an abort in either of its two runs left the reason out of the logs it attaches on failure. Exec/DogboneAnalytic/inputs_orlanski_mask Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/Initialization/REMORA_init_bcs.cpp Tests/CTestList.cmake commit 50643163e81b0f4d565277a651ff8df143ec542f Merge: 9dde762a 70b02fb3 Author: Hannah Klion Date: Tue Aug 25 16:14:07 2026 -0700 Merge pull request #640 from hklion/netcdf_abort error if using initial condition netcdf without compiling with PnetCDF commit 9dde762a3d7948b9bb8f328032be13553133c5d7 Merge: 90983264 5719bb1d Author: Hannah Klion Date: Tue Aug 25 16:13:58 2026 -0700 Merge pull request #642 from hklion/restart_dt don't reset dt on reset and store last check/plot times commit 909832640a58af16cf03cb44349b43ef3bf429ed Merge: 66593879 1e53d53b Author: Hannah Klion Date: Tue Aug 25 16:13:48 2026 -0700 Merge pull request #643 from hklion/pr608 Land per-variable BCs on the right faces, and read inflow values for every tracer commit 5e18f902d13822f986c48877627932758c8600c0 Author: Hannah Klion Date: Tue Aug 25 16:11:29 2026 -0700 mask BC gradients as in ROMS Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp commit 1e53d53bb7eb97116af6a3be46e265b8c71b205f Author: Hannah Klion Date: Tue Aug 25 16:08:55 2026 -0700 get rid of {x|y}{lo|hi}.value BC suffix Docs/sphinx_doc/BoundaryConditions.rst Exec/Generic/inputs_generic Source/Initialization/REMORA_init_bcs.cpp Tests/test_files/BC_per_variable/BC_per_side.i commit b079d66f6c04279cd575710bb0a68759cdfead7b Author: Hannah Klion Date: Tue Aug 25 15:42:30 2026 -0700 Generalize velocity sign flip in FillBdyCCVels Port the generalization ERF made in its FillBdyCCVels (upstream f9af0f06, "fix for plotting vorticity with multiple levels"). REMORA still carried the older form, which used a single multiplier that flipped only for no_slip_wall and wrote just the two tangential components at each face. The sign now comes from a helper taking the BC type and whether the component is normal to the face: a component normal to a slip wall, no-slip wall or symmetry plane vanishes there and so reflects oddly, while only a no-slip wall also flips the tangential components. Three consequences: - The normal component is now filled. It never was, so in the vorticity tagging path, where the MultiFab is allocated without a setVal, those ghost cells held uninitialized memory. - Each component consults its own BC. phys_bc_type is indexed by variable as well as by face, unlike ERF's, so with remora.boundary_per_variable = true u, v and w can each carry a different type on one face; the old code read only the face-normal velocity's type and applied it to the others. - Drops a stray negation on w at the high-y face, which made that face inconsistent with the other five. It came in with the original port and is the same typo ERF fixed in the commit above. WritePlotFile now calls FillBdyCCVels rather than relying on setVal(zero), so plotted and tagged vorticity agree at a physical boundary. Its cell-centered velocities carry no ghost cell in z, so each direction is guarded on the available ghost width -- without that guard this call writes out of bounds. Corners are still left unfilled, as the vorticity stencil reads only face-adjacent ghost cells. Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_Plotfile.cpp commit 7805ba5b304c867c6ba527faf83ca42b5782abc8 Author: Hannah Klion Date: Tue Aug 25 15:40:59 2026 -0700 fix boundary condition side issues and test inflow bcs Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/testing.rst Exec/Generic/inputs_generic Source/Initialization/REMORA_init_bcs.cpp Tests/CTestList.cmake Tests/test_files/BC_inflow_no_value/BC_inflow_no_value.i Tests/test_files/BC_per_variable/BC_per_side.i Tests/test_files/BC_per_variable/BC_per_variable.i commit 5719bb1d44aa21203008985809b578ca276e1daa Author: Hannah Klion Date: Tue Aug 25 13:54:52 2026 -0700 don't reset dt on reset and store last check/plot times Source/REMORA.cpp commit 665938797d506d8a2b2c943854958c685e6c6c40 Merge: 11e953ee 7e58ee58 Author: Hannah Klion Date: Tue Aug 25 13:44:42 2026 -0700 Merge pull request #641 from hklion/remove_remora_math remove remora_math since contained function was unused commit 7e58ee58b454210cc8eaf2a9849f95c54f53dbb0 Author: Hannah Klion Date: Tue Aug 25 13:44:19 2026 -0700 remove remora_math since contained function was unused Source/REMORA.H Source/Utils/Make.package Source/Utils/REMORA_Math.H commit 70b02fb31614c517a3ab5026e5d11ec2b309b0e3 Author: Hannah Klion Date: Tue Aug 25 13:37:19 2026 -0700 error if using initial condition netcdf without compiling with PnetCDF Source/REMORA.cpp commit 11e953ee250e3783fceb752e27a8434e6d3b1902 Merge: 56687e9f c40665a6 Author: Hannah Klion Date: Tue Aug 25 11:50:13 2026 -0700 Merge pull request #639 from hklion/remove_cmakelists remove cmakelists commit c40665a6d4a9fed5e80328fc5fb5ad16b9fd3051 Author: Hannah Klion Date: Tue Aug 25 11:49:33 2026 -0700 remove cmakelists Exec/Advection/CMakeLists.txt Exec/BlankProblem/CMakeLists.txt Exec/BoundaryLayer/CMakeLists.txt Exec/Channel_Test/CMakeLists.txt Exec/CoupleToERF/CMakeLists.txt Exec/Dogbone/CMakeLists.txt Exec/DogboneAnalytic/CMakeLists.txt Exec/DoubleGyre/CMakeLists.txt Exec/DoublyPeriodic/CMakeLists.txt Exec/IdealMiniGrid/CMakeLists.txt Exec/IdealRivGrid/CMakeLists.txt Exec/ParticlesOverSeaMount/CMakeLists.txt Exec/Seamount/CMakeLists.txt Exec/Upwelling/CMakeLists.txt Exec/Upwelling_Coupling/CMakeLists.txt Exec/Upwelling_ML/CMakeLists.txt commit 56687e9f03c4f02f9dfd6981c9efec7032bbd0f3 Merge: 025cedf9 546b52b5 Author: Hannah Klion Date: Tue Aug 25 11:43:20 2026 -0700 Merge pull request #638 from hklion/docs_tweaks Docs tweaks commit 546b52b58eef7d10c7be8736d7742e462381853c Merge: f8534166 025cedf9 Author: Hannah Klion Date: Tue Aug 25 11:43:01 2026 -0700 Merge branch 'development' into docs_tweaks commit f853416636983bc00887a7b5fc7a9e04432eeb6e Author: Hannah Klion Date: Tue Aug 25 11:39:38 2026 -0700 add biotoy readme and add to verification tests Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Exec/BioToy/README.rst commit 025cedf97bf2469a9030e049120f8a43dfdb25a9 Merge: 02850c11 16bfdd44 Author: Hannah Klion Date: Tue Aug 25 11:00:16 2026 -0700 Merge pull request #636 from hklion/regtest_docs update docs for regtest commit 2e8bcd5f168331a850c7613608b4348fc859b4d9 Author: Hannah Klion Date: Tue Aug 25 10:51:44 2026 -0700 adjust grid calculation loops to better accomodate tiling Source/Initialization/REMORA_make_new_level.cpp commit 16bfdd44166aae79fccbed5efa2224ab65df9f30 Author: Hannah Klion Date: Tue Aug 25 10:05:41 2026 -0700 update docs for regtest Docs/sphinx_doc/RegressionTests.rst commit 02850c1198dc19c82a43c9dabcd34a67af4bfeb8 Merge: 8972999e db709432 Author: Hannah Klion Date: Tue Aug 25 09:14:47 2026 -0700 Merge pull request #634 from hklion/fix-surface-state-null-multifabs Avoid null MultiFab references in set_surface_state commit 8972999ecc8f8bf54d181ab27cbc16300f6b0509 Merge: 354420b5 e1d198c3 Author: Hannah Klion Date: Tue Aug 25 09:14:35 2026 -0700 Merge pull request #635 from hklion/coriolis_offset fix coriolis offset in beta plane commit e1d198c39520b70c255f0f8f75aeb85b24d0cba6 Author: Hannah Klion Date: Mon Aug 24 17:30:46 2026 -0700 fix coriolis offset in beta plane Docs/sphinx_doc/Inputs.rst Source/Initialization/REMORA_init.cpp commit db709432146a29ebd1acf0e02b0dd0062e3ac1bc Author: Hannah Klion Date: Mon Aug 24 16:20:59 2026 -0700 Avoid null MultiFab references in set_surface_state Fixes #611. Source/REMORA.cpp commit 354420b56cb923ca545e8cb7a850b46bfa610575 Author: Hannah Klion Date: Mon Aug 24 14:54:56 2026 -0700 lower time step on synth_hires so it can run for 100 steps Exec/IdealMiniGrid/inputs_synth_hires commit d7902cb7a7f92a5a6323e33653e180c299cd6f49 Author: Hannah Klion Date: Mon Aug 24 14:47:33 2026 -0700 output plotfiles for BioToy Exec/BioToy/inputs commit 968a8bf6eaa0c7a4fa6ac2ecaaab20902ae65580 Author: Hannah Klion Date: Mon Aug 24 14:16:38 2026 -0700 add biotoy inputs Exec/BioToy/inputs commit da79c6eb3e13551fcb061606a6e33bcc99b51e60 Author: Hannah Klion Date: Mon Aug 24 10:25:10 2026 -0700 move synthetic hires test to IdealMiniGrid Exec/IdealMiniGrid/inputs_synth_hires commit 9ab21a7fe67dab7e936826b37c6d74ab852d939d Author: Hannah Klion Date: Mon Aug 24 09:34:04 2026 -0700 add fennel upwelling test input files Exec/Upwelling/inputs_fennel Exec/Upwelling/inputs_fennel_hires commit a92478b831c45dfec4897442fb01ce4923e24769 Merge: eed0f3ff 117aeecc Author: Hannah Klion Date: Sat Aug 22 22:04:46 2026 -0700 Merge pull request #633 from hklion/pressure_grad use solverChoice rho0 to calculate pressure gradient commit 117aeecc6b7a34cff56c7bd10df3b693a8503aa7 Author: Hannah Klion Date: Sat Aug 22 22:00:36 2026 -0700 use solverChoice rho0 to calculate pressure gradient Source/TimeIntegration/REMORA_advance_2d.cpp commit eed0f3ff3d71fb3072da7760419c280eb26d8bfd Merge: e8c52fad d3bfb393 Author: Hannah Klion Date: Sat Aug 22 21:58:06 2026 -0700 Merge pull request #632 from hklion/curvilinear_terms_correction Curvilinear terms correction commit d3bfb3933faaf0dd4f15eb8feecd47c11f3111d7 Author: Hannah Klion Date: Sat Aug 22 21:57:33 2026 -0700 remove redundant convert Source/Initialization/REMORA_make_new_level.cpp commit f295bbc31019eca44008fedb4fcca7481f274d0f Author: Hannah Klion Date: Sat Aug 22 21:52:44 2026 -0700 patch wrong curvilinear calculation and make it on rho points Source/Initialization/REMORA_make_new_level.cpp commit e8c52fad2e7cb4a8a070e9620c9a259dc1189406 Merge: b7956733 57718aca Author: Hannah Klion Date: Sat Aug 22 21:34:36 2026 -0700 Merge pull request #631 from hklion/has_var_int make has_var an int in QueryNetCDFVarAttrStr commit b79567339cb6af5e9efedfee4c0cc35f708936cd Merge: 61ab6a21 c7ab33f4 Author: Hannah Klion Date: Sat Aug 22 17:52:54 2026 -0700 Merge pull request #630 from hklion/der_var_2d_3d check for 2d and 3d derived variables separately in plotfile var lists commit 61ab6a217b378ecdcd9ef6c4dc6bb3c2b44f7c1d Merge: 060e5c0c 52250423 Author: Hannah Klion Date: Sat Aug 22 17:52:43 2026 -0700 Merge pull request #629 from seahorce-scidac/moab_mesh_cell_center InitMOABMesh writes out cell centers commit 57718aca04dc65aa7676f7b40310c310aacdc223 Author: Hannah Klion Date: Sat Aug 22 17:51:38 2026 -0700 has_var result defined at every rank Source/IO/REMORA_NCFile.cpp commit c7ab33f4c8c11b967edecf9ecc7ab6714e54aa5c Author: Hannah Klion Date: Sat Aug 22 17:22:28 2026 -0700 check for 2d and 3d derived variables separately in plotfile var lists Source/IO/REMORA_SetPlotVars.cpp Source/REMORA.H commit 5225042343589a7a0ba3c3a52dcbc73fc9ebdb21 Author: Hannah Klion Date: Sat Aug 22 17:06:00 2026 -0700 InitMOABMesh writes out cell centers Source/REMORA_MOAB.cpp commit 060e5c0c3b9301d831d20f09d9097004c442ecf1 Author: Hannah Klion Date: Fri Aug 21 22:15:22 2026 -0700 bump advection test files and remove unused spatial_oder param from input files .gitignore Tests/REMORA_Gold_Files/Advection/Header Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00003 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Advection/job_info Tests/REMORA_Gold_Files/Advection_ML/Header Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/Advection_ML/job_info Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/Channel_Test_hires/Channel_Test_hires.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Seamount_hires/Seamount_hires.i Tests/test_files/Seamount_hires_flat_abort/Seamount_hires_flat_abort.i Tests/test_files/Seamount_hires_grid_max_abort/Seamount_hires_grid_max_abort.i Tests/test_files/Seamount_hires_grid_zero_abort/Seamount_hires_grid_zero_abort.i Tests/test_files/Seamount_hires_init_abort/Seamount_hires_init_abort.i Tests/test_files/Seamount_hires_init_max_abort/Seamount_hires_init_max_abort.i Tests/test_files/Seamount_hires_r4/Seamount_hires_r4.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_Fennel/Upwelling_Fennel.i Tests/test_files/Upwelling_Fennel_hires_init/Upwelling_Fennel_hires_init.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit b8e64e3a68f732b2f1dad17ff37812ca7580da9b Merge: 2791795c d18e019f Author: Hannah Klion Date: Fri Aug 21 21:01:21 2026 -0700 Merge pull request #628 from jmsexton03/impl/issue-12 Brings `ApplyConservativeRemap` to parity with its ERF-side twin commit d18e019f5e04112562fc00dbc3fb262b1dd4b0bb Author: Jean M. Sexton Date: Thu Aug 20 15:45:06 2026 -0700 Bring ApplyConservativeRemap to parity with its ERF twin - Add fallback_val parameter defaulting to zero, matching ERF - Return fallback for destination cells with no stencil (idx < 0) - Blend toward fallback instead of scaling by fractional mask - Land test now != 0, so ImmersedForcing buildings read as land Source/REMORA_Coupling.cpp commit 5a0b803282d0c32ef8b65887e8e3be380700e92e Author: Jean M. Sexton Date: Thu Aug 20 15:43:18 2026 -0700 Add .gitattributes pinning C++ sources to LF - REMORA_Coupling.cpp was once committed CRLF, since normalized - Prevents recurrence that made diffs read as whole-file rewrites - Scoped to sources: make.bat wants CRLF, gold files are binary - Verified git add --renormalize produces no tree churn .gitattributes commit 2791795c5fa8d6971dddbb0b8f6d3a6042a910c0 Merge: 2b758fe5 77f1ccf3 Author: Hannah Klion Date: Thu Aug 20 14:21:05 2026 -0700 Merge pull request #626 from seahorce-scidac/dependabot/github_actions/development/actions/setup-python-7 Bump actions/setup-python from 5 to 7 commit 2b758fe541160fcc0c20e250612463e2fa65c1b3 Merge: 2d7a9552 48001758 Author: Hannah Klion Date: Thu Aug 20 14:18:28 2026 -0700 Merge pull request #627 from seahorce-scidac/dependabot/github_actions/development/actions/checkout-7 Bump actions/checkout from 4 to 7 commit 48001758bfae56008fcca7d428a516b825390c92 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 20 21:05:17 2026 +0000 Bump actions/checkout from 4 to 7 Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] .github/workflows/generic-inputs-validate.yml commit 77f1ccf314a5ab60f7ce23ff6e97f767e361f222 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 20 21:04:58 2026 +0000 Bump actions/setup-python from 5 to 7 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 7. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v5...v7) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] .github/workflows/generic-inputs-validate.yml commit 2d7a95527a70752ef3ce998a14e34c8301cb352c Merge: ccc97136 d08935ed Author: Hannah Klion Date: Wed Aug 19 15:45:35 2026 -0700 Merge pull request #621 from seahorce-scidac/biology Fennel biology model, and a runtime-sized tracer block commit ccc971367918732cefefdf9ee5655b21d79b6b64 Merge: 1691c5da 39953ed1 Author: Hannah Klion Date: Wed Aug 19 15:27:41 2026 -0700 Merge pull request #625 from hklion/whitespace whitespace commit 39953ed1483b2a54f881e11f85da5ded38a50c13 Author: Hannah Klion Date: Wed Aug 19 15:26:55 2026 -0700 whitespace Source/REMORA_Coupling.cpp commit 1691c5dabf4291976dc6959a4dbbcfcd47738beb Merge: 6156e4f8 8623b4d3 Author: Hannah Klion Date: Wed Aug 19 15:24:32 2026 -0700 Merge pull request #624 from hklion/SetLongwaveFromDriver add SetLongwaveFromDriver commit 8623b4d3ebde54aa9c62fd42a16d5633f8165445 Author: Hannah Klion Date: Wed Aug 19 15:24:02 2026 -0700 add SetLongwaveFromDriver Source/REMORA.H Source/REMORA_Coupling.cpp commit d08935ed882e358e52ef294750b3dc7ae291705e Author: Hannah Klion Date: Wed Aug 19 15:16:38 2026 -0700 fill ghost cells in k Source/REMORA_Tagging.cpp commit 0ff34b02f54ceef0de37847270389b45e983da3b Author: Hannah Klion Date: Wed Aug 19 14:24:02 2026 -0700 style Source/Biology/REMORA_Biology.cpp Source/IO/REMORA_NCInterface.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA_DataStruct.H Source/Utils/REMORA_DateClock.H commit d415a5ad1b02b25e3ff66000a4921ee41ef699b4 Author: Hannah Klion Date: Wed Aug 19 14:03:25 2026 -0700 catch a missing file Source/REMORA.cpp commit edb749340b5958d7c32a5ee7361c42af869e28b9 Author: Hannah Klion Date: Wed Aug 19 14:03:06 2026 -0700 fix cyclic time series files Source/IO/REMORA_NCTimeSeries.cpp commit 2aebe455c9e44d2e03f0f5fa8baac65a79362d3e Author: Hannah Klion Date: Wed Aug 19 14:02:37 2026 -0700 check for positive pCO2air Source/Biology/REMORA_Biology.cpp commit 633a143115c8c588b1bcf2df6cf1e439a3a341eb Author: Hannah Klion Date: Wed Aug 19 14:00:41 2026 -0700 remove tracer plot request from problems that zero it out anyway Exec/Channel_Test/inputs Exec/CoupleToERF/inputs Exec/Upwelling_ML/inputs commit 05ebd231b4e31aaa1a4b21740ceda8f5508e9c71 Merge: c73f4202 a3fe0ddd Author: Hannah Klion Date: Wed Aug 19 13:05:48 2026 -0700 Merge branch 'biology_modules' into biology commit c73f420275b74033239c4e758d96ff2deed9c583 Author: Hannah Klion Date: Wed Aug 19 12:58:07 2026 -0700 test hires_grid_level/hires_init_level, and fix what that exposed Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/testing.rst Exec/GulfRefinementTest/README.rst Exec/GulfRefinementTest/inputs_cf_orlanski Exec/GulfRefinementTest/inputs_outflow Exec/GulfRefinementTest/inputs_synth_hires Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Prob/REMORA_InitAnalyticBathymetry_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticBathymetry_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticBathymetry_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Seamount.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_SumIQ.cpp Tests/CMakeLists.txt Tests/CTestList.cmake Tests/REMORA_Gold_Files/Seamount_hires/Header Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Cell_H Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Seamount_hires/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount_hires/job_info Tests/REMORA_Gold_Files/Seamount_hires_r4/Header Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Cell_H Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Seamount_hires_r4/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount_hires_r4/job_info Tests/check_extrema.sh Tests/reference/hires_volume_reference.py Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/Channel_Test_hires/Channel_Test_hires.i Tests/test_files/DogboneAnalytic_MLhires/DogboneAnalytic_MLhires.i Tests/test_files/Seamount_hires/Seamount_hires.i Tests/test_files/Seamount_hires_flat_abort/Seamount_hires_flat_abort.i Tests/test_files/Seamount_hires_grid_max_abort/Seamount_hires_grid_max_abort.i Tests/test_files/Seamount_hires_grid_zero_abort/Seamount_hires_grid_zero_abort.i Tests/test_files/Seamount_hires_init_abort/Seamount_hires_init_abort.i Tests/test_files/Seamount_hires_init_max_abort/Seamount_hires_init_max_abort.i Tests/test_files/Seamount_hires_r4/Seamount_hires_r4.i Tests/test_files/Upwelling_Fennel_hires_init/Upwelling_Fennel_hires_init.i Tests/tools/make_hires_test_data.py commit cbbcd5cf84ea42e27a55c678d857864658079438 Author: Hannah Klion Date: Tue Aug 18 16:01:02 2026 -0700 dyes - dye ICs now actually read from init NetCDF file - per-side BC special-casing for tracers (incl. biology) now removed so they act like salt and temp - dye is now opt-in regardless of whether biology is off or on Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Plotfiles.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/BlankProblem/inputs Exec/Generic/inputs_generic Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 311d96dc7c793141e41cf4f6aa3b7bfdedac291c Author: Hannah Klion Date: Tue Aug 18 14:32:18 2026 -0700 fix gpu access issues for Akt_bak in gls Source/TimeIntegration/REMORA_gls.cpp commit cc131fcb00531e5d7bb71a5f2d6dfd3d76878766 Author: Hannah Klion Date: Tue Aug 18 14:32:05 2026 -0700 add single precision check around time_ref Source/REMORA_DataStruct.H Source/Utils/REMORA_DateClock.H commit 1e270adfcc5579affdd17d9cc8f76d2260649310 Author: Hannah Klion Date: Tue Aug 18 14:31:17 2026 -0700 better handle whether we're setting dye variable in analytic initializtion Source/Prob/REMORA_InitAnalyticProb_Advection.H Source/Prob/REMORA_InitAnalyticProb_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_CoupleToERF.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticProb_Seamount.H Source/Prob/REMORA_InitAnalyticProb_Upwelling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/REMORA.H commit 4d5ad9db2b377e581ba7f2c0d9ca1e5c1439e581 Author: Hannah Klion Date: Tue Aug 18 14:30:00 2026 -0700 fix nudging coefficient variable indexing Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp commit 9b338ae20a242167188d424060a4b3d4e97cd626 Author: Hannah Klion Date: Tue Aug 18 14:29:29 2026 -0700 type on need_data pointer Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/Initialization/REMORA_init_from_netcdf.cpp commit 04e786f954315dbdc757ec0d587d262dd2c32e82 Author: Hannah Klion Date: Tue Aug 18 14:16:25 2026 -0700 skip masked cells for biology Source/Biology/REMORA_Biology.cpp commit d9be82f9ed934bb45b57082c37fa942c9b3e5dfd Author: Hannah Klion Date: Tue Aug 18 11:16:36 2026 -0700 Add in remaining physics options from fennel.h - nonconservative alkalinity - river DON - time-varying atmospheric CO2: this also required porting over the ROMS "time ref" logic as well as the calendar date functions from ROMS - Wanninkhof gas transfer Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Exec/Generic/inputs_generic Source/Biology/Fortran/REMORA_FennelBridge.cpp Source/Biology/Fortran/REMORA_Fennel_Fortran_Interface.H Source/Biology/Fortran/REMORA_fennel_roms.F Source/Biology/REMORA_Biology.H Source/Biology/REMORA_Biology.cpp Source/Prob/REMORA_InitAnalyticBiology_BioToy.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/Utils/Make.package Source/Utils/REMORA_DateClock.H commit a3fe0ddd7f093fe2852a892047f50905f13cdb6c Author: Hannah Klion Date: Tue Aug 18 12:26:16 2026 -0700 add additional fennel options to the regtest Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/RegressionTests.rst Source/Biology/REMORA_Biology.H Tests/REMORA_Gold_Files/Upwelling_Fennel/Header Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_H Tests/test_files/Upwelling_Fennel/Upwelling_Fennel.i commit 873762c8ae6ab59f9e01db79d8a7f5245bd09f0e Author: Hannah Klion Date: Tue Aug 18 11:16:36 2026 -0700 Add in remaining physics options from fennel.h - nonconservative alkalinity - river DON - time-varying atmospheric CO2: this also required porting over the ROMS "time ref" logic as well as the calendar date functions from ROMS - Wanninkhof gas transfer Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Exec/Generic/inputs_generic Source/Biology/Fortran/REMORA_FennelBridge.cpp Source/Biology/Fortran/REMORA_Fennel_Fortran_Interface.H Source/Biology/Fortran/REMORA_fennel_roms.F Source/Biology/REMORA_Biology.H Source/Biology/REMORA_Biology.cpp Source/Prob/REMORA_InitAnalyticBiology_BioToy.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/Utils/Make.package Source/Utils/REMORA_DateClock.H commit a302648203870f1e362afbb3f28e508589a240c0 Merge: 8c9af986 6156e4f8 Author: Hannah Klion Date: Mon Aug 17 17:25:01 2026 -0700 Merge branch 'development' into biology commit 6156e4f85555d052cafb1c0917bac87d5b1ec66e Merge: 21be7ddb 0133130a Author: Hannah Klion Date: Mon Aug 17 17:23:27 2026 -0700 Merge pull request #623 from hklion/eminusp_correction only do eminusp correction during an evolution step commit 8c9af9867bde7fb8c3c3c6ee3fc377beb2494193 Author: Hannah Klion Date: Mon Aug 17 16:01:20 2026 -0700 updated generic inputs Exec/Generic/inputs_generic commit 666c9b4358eda7c3e51da3f951e0ecd4c6f5b531 Author: Hannah Klion Date: Mon Aug 17 16:00:39 2026 -0700 resolve sometimes uninitialized warning Source/Prob/REMORA_InitAnalyticBiology_BioToy.H commit e0fc8a095134a198c9ba13a72eaf50fdd4735949 Author: Hannah Klion Date: Mon Aug 17 15:58:00 2026 -0700 Match ROMS behavior re: vertical mixing coeffs for passive tracers - Passive tracers now use the salt vertical mixing coefficients instead of being keyed with their own keywords. This is done solely to match ROMS. Treating them all separately would be straightforward. - Horizontal mixing coefficients are still per-variable for all variables Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst Exec/REMORA_Prob.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Prob/REMORA_InitAnalyticVMix_Advection.H Source/Prob/REMORA_InitAnalyticVMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticVMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticVMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticVMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticVMix_Seamount.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling.H Source/Prob/REMORA_InitAnalyticVMix_UpwellingML.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling_ML.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp commit 0133130a7ff78786163c384783d12fe699a5b554 Author: Hannah Klion Date: Mon Aug 17 15:50:53 2026 -0700 only do eminusp correction during an evolution step Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit f205b4058cdc4dd57a8b4bed4383b5f57f7e8fc2 Author: Hannah Klion Date: Mon Aug 17 15:34:34 2026 -0700 add test for Upwelling + biology and some other patches Docs/sphinx_doc/Fennel.rst Source/Biology/Fortran/README.md Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_SetPlotVars.cpp Tests/REMORA_Gold_Files/Upwelling_Fennel/Header Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_Fennel/Level_0/Nu_nd_H Tests/test_files/Upwelling_Fennel/Upwelling_Fennel.i commit 35ab3592c2595c2693ae23a9a18606e767aefa08 Author: Hannah Klion Date: Mon Aug 17 15:30:37 2026 -0700 Akt is now a vector over cons components Docs/sphinx_doc/Inputs.rst Exec/REMORA_Prob.cpp Source/Initialization/REMORA_init.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_gls.cpp Tests/CTestList.cmake commit 21be7ddba12159cc5aed1088b4bf3885715c35cb Merge: 7f805d4c d73592b8 Author: Hannah Klion Date: Mon Aug 17 15:04:45 2026 -0700 Merge pull request #622 from hklion/null_calc_arr_fix_2 avoid null dereference and foextrap bathymetry commit 3d7b4087d5e1fac9decee286b50a6f5847ce7b2e Author: Hannah Klion Date: Mon Aug 17 14:40:15 2026 -0700 fix schema file to catch remora_prefix as a prefix var name Exec/Generic/build_schema_remora.py commit d73592b81851b12be5676ec585603c1e83d3de7e Author: Hannah Klion Date: Mon Aug 17 14:34:34 2026 -0700 fix fillpatches for bathymetry to foextrap_perioidc Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit cb7fbc30d56179e971514e014a5e3015af4b0e68 Author: Hannah Klion Date: Mon Aug 17 14:07:16 2026 -0700 update generic inputs Exec/Generic/inputs_generic commit de853c2944c0104095b6005221ba261583e81807 Author: Hannah Klion Date: Mon Aug 17 14:04:48 2026 -0700 remove unused var Exec/REMORA_Prob.cpp commit eb272d1ee87db0027153d5bce7e89812385f3898 Author: Hannah Klion Date: Mon Aug 17 13:57:38 2026 -0700 try again to not check fortran dir .codespellrc commit d086dc5249a7dce5ae58ce730fb88f22897aafaa Author: Hannah Klion Date: Mon Aug 17 13:55:09 2026 -0700 avoid null dereference and foextrap bathymetry Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/Initialization/REMORA_make_new_level.cpp commit 9f600ecadfdfff6fed4da777ffb7ae63bf8f162e Author: Hannah Klion Date: Mon Aug 17 13:54:01 2026 -0700 fix spelling errors and don't check Fortran subdir .codespell-ignore-words Source/IO/REMORA_NCTimeSeries.cpp commit fe69dcc59a8cc97d2e0c30a3ce548c8b20de950a Author: Hannah Klion Date: Mon Aug 17 13:49:45 2026 -0700 biology tracers work for rivers Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp Source/REMORA_DataStruct.H commit 7a29227e00085ced97191d5e5a8f59de8902ac43 Author: Hannah Klion Date: Mon Aug 17 10:56:49 2026 -0700 patch plotfile nanchecking Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_Plotfile.cpp commit 4e6eea07933bed07f1f6e49a5b131c6b2bb78f76 Author: Hannah Klion Date: Mon Aug 17 10:48:22 2026 -0700 Expand arbitrary tracer capability - Refine on arbitrary tracers - Integrated quantity sums are given for all tracers - NetCDF plotfile nanchecking works for all tracers Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_NCPlotFile.cpp Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp commit 7860ea90739a57c0d47b49ae1a48dae608f7b795 Author: Hannah Klion Date: Mon Aug 17 10:31:53 2026 -0700 ntracer now unconstrained - Previously, ntracer had to be >= 1 and, if biology was on, then it had to equal the number of biology fields. This is no longer the case. - ntracer now controls the number of dye variables, and can be equal to zero or any number, with or without biology enabled Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Exec/REMORA_Prob.cpp Source/Biology/Fortran/REMORA_FennelBridge.cpp Source/Biology/REMORA_Biology.H Source/Biology/REMORA_Biology.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_SetPlotVars.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Prob/REMORA_InitAnalyticProb_Advection.H Source/Prob/REMORA_InitAnalyticProb_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_CoupleToERF.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticProb_Seamount.H Source/Prob/REMORA_InitAnalyticProb_Upwelling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticVMix_Advection.H Source/Prob/REMORA_InitAnalyticVMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticVMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticVMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticVMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticVMix_Seamount.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling.H Source/Prob/REMORA_InitAnalyticVMix_UpwellingML.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling_ML.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp commit f3ecdebaa38d069db067454295cb0662e5f61263 Author: Hannah Klion Date: Fri Aug 14 16:43:21 2026 -0700 fix potential erroneous error message about nscalar Source/IO/REMORA_Checkpoint.cpp commit 4a8a9bbc6a05caec3c492e34e8ef23d60c60b463 Author: Hannah Klion Date: Fri Aug 14 16:30:27 2026 -0700 Add climatology for biology Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_3d.cpp commit 7f307dbad68a07a12f08f0d82222e7bb02b73c36 Author: Hannah Klion Date: Fri Aug 14 15:55:18 2026 -0700 Biology variable boundary conditions - Biology variables now have the same boundary condition options as other scalar variables Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit ce94818fe573bfc0b99cc241118cb53721678a52 Merge: 490f230d 7f805d4c Author: Hannah Klion Date: Fri Aug 14 14:27:15 2026 -0700 Merge branch 'development' into biology commit 490f230d054e7da8c5ae89c64245a9b254501efc Author: Hannah Klion Date: Fri Aug 14 14:12:47 2026 -0700 Updates to biology - Finally actually add the biology file, which now has compiled-in debug tags - Added in infrastructure and documentation for validation of REMORA's Fennel C++ implementation against ROMS's - Updated documentation - Firmed up initialization path for analytic biology CMake/BuildREMORAExe.cmake CMakeLists.txt Docs/sphinx_doc/Fennel.rst Docs/sphinx_doc/Inputs.rst Exec/Make.REMORA Source/Biology/Fortran/Make.package Source/Biology/Fortran/REMORA_FennelBridge.cpp Source/Biology/Fortran/REMORA_Fennel_Fortran_Interface.H Source/Biology/Fortran/REMORA_fennel.h Source/Biology/Fortran/REMORA_fennel_mod.h Source/Biology/Fortran/REMORA_fennel_roms.F Source/Biology/Fortran/remora_bio_cppdefs.h Source/Biology/Fortran/set_bounds.h Source/Biology/Fortran/tag_map.md Source/Biology/Fortran/tile.h Source/Biology/Make.package Source/Biology/REMORA_Biology.H Source/Biology/REMORA_Biology.cpp Source/Initialization/REMORA_init.cpp Source/Prob/REMORA_InitAnalyticBiology_BioToy.H Source/REMORA.H Source/REMORA.cpp commit 7f805d4c98f9066c480e4fe171ee30a571211bff Merge: 8bf3cef7 f6a0ca86 Author: Hannah Klion Date: Fri Aug 14 14:02:48 2026 -0700 Merge pull request #618 from jmsexton03/mapping changes for realistic erf commit 8bf3cef7a473ca0ef65b82dd23ad17225b7df84b Merge: 574653c1 92f56a00 Author: Hannah Klion Date: Fri Aug 14 13:40:43 2026 -0700 Merge pull request #619 from hklion/prestep_river_source_cons2 hoist river_source_cons update in prestep to outside fo mfiter to prevent hang on boxless ranks commit 92f56a0034d5d7202cb13b778e43643f961ab032 Author: Hannah Klion Date: Fri Aug 14 11:09:14 2026 -0700 hoist river_source_cons update in prestep to outside fo mfiter to prevent hang on boxless ranks Source/TimeIntegration/REMORA_prestep.cpp commit 574653c1b6e1f71dc569b765f2dfe4dc4076e34b Merge: ffbcf4a7 5840c98f Author: Hannah Klion Date: Fri Aug 14 10:55:54 2026 -0700 Merge pull request #580 from seahorce-scidac/fix-build-executables-gate Gate remora_exec on REMORA_BUILD_EXECUTABLES commit ffbcf4a7da74bbbcda9b459cf37cd7825f869131 Merge: 581f1f85 897702ea Author: Hannah Klion Date: Fri Aug 14 10:29:21 2026 -0700 Merge pull request #579 from seahorce-scidac/fix-river-position-validation Validate river metadata sizes commit 581f1f8591b1f91cb20d25fb4f0fd416c5a10117 Merge: 4922eb22 41f74abc Author: Hannah Klion Date: Fri Aug 14 10:28:50 2026 -0700 Merge pull request #616 from jmsexton03/inputs_docs Adds docs on agentic tools and inputs commit 4922eb22f3b7d28bc0c18b937db1bbb4f3ed1f35 Merge: 4cb853ca 58d0b490 Author: Hannah Klion Date: Fri Aug 14 10:27:28 2026 -0700 Merge pull request #617 from seahorce-scidac/dependabot/github_actions/development/JamesIves/github-pages-deploy-action-4.9.0 Bump JamesIves/github-pages-deploy-action from 4.8.0 to 4.9.0 commit f6a0ca86b37ee861f1101a9bc6e3bb229d32d4a1 Author: Jean M. Sexton Date: Fri Aug 14 10:06:36 2026 -0700 codespell .codespell-ignore-words commit 41f74abc29939f7cf7c05278ee66783531b37588 Author: Jean M. Sexton Date: Thu Aug 13 16:30:41 2026 -0700 Find parameter defaults beyond a fixed line window extract_default only scanned 180 lines back from the ParmParse call for the assignment holding the default. Variables declared at file scope are often assigned their default in a different function, so the distance is incidental: AMReX 26.07 inserted nine lines into Amr::InitAmr and every amr bool assigned in that prologue silently became , at a measured distance of 187 where 178 had fit. Scan to the start of the file instead. The first match walking backwards wins, so this cannot change a default that was already found; it resolves 41 that were previously unknown. Exec/Generic/build_schema_remora.py Exec/Generic/inputs_generic commit 80d7dea274c8311cb191c069fec63a69593ca4fd Merge: a5b39217 4cb853ca Author: Jean M. Sexton Date: Thu Aug 13 16:20:22 2026 -0700 Merge branch 'development' into inputs_docs commit a5b39217ead5e1b2d45855ae090b9a7dd36d286e Author: Jean M. Sexton Date: Thu Aug 13 16:17:44 2026 -0700 Make generic inputs check actionable and machine independent Record the schema path relative to the repo root so the rendered file does not embed an absolute path, which made the CI comparison fail on any machine other than the one that generated it. Move the staleness check into .github/workflows/style/check_generic_inputs.sh so a failure prints the regenerate command and an annotation, matching check_trailing_whitespaces.sh. Source line number shifts now warn instead of fail; added, removed, or changed parameters still fail and are listed. .github/workflows/generic-inputs-validate.yml .github/workflows/style/check_generic_inputs.sh Docs/sphinx_doc/GenericInputs.rst Exec/Generic/inputs_generic Exec/Generic/render_inputs_generic.py commit 871215254687a3917fd3e2c16b11dbe5e2bd37ec Author: Hannah Klion Date: Thu Aug 13 15:51:38 2026 -0700 allow netcdf time series reader to accept cyclic data, and all netcdf files to be case-insensitive about field names Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCInterface.cpp Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp commit fe2cb31daa25a163abb51f55a4f7d8dbebb30bca Author: Hannah Klion Date: Thu Aug 13 15:50:16 2026 -0700 Biology updates - Plotfile alias fennel = all activated fennel variables - Initialize biology tracers from netcdf Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/IO/REMORA_SetPlotVars.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 58d0b490da27b9d5c0bea1205cda47d960259103 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 13 21:06:40 2026 +0000 Bump JamesIves/github-pages-deploy-action from 4.8.0 to 4.9.0 Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.8.0 to 4.9.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.8.0...v4.9.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-version: 4.9.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] .github/workflows/docs.yml commit c37c351c1c3cb62f79288676209699709489585a Author: Jean M. Sexton Date: Thu Aug 13 13:22:52 2026 -0700 seventh pass CMake/BuildREMORAExe.cmake Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCFile.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA_Coupling.cpp commit bdf397d372bc3b13ad7cd5943524ddcc25c2f9dd Author: Hannah Klion Date: Tue Aug 11 15:16:57 2026 -0700 patch analytic bio initialization Exec/REMORA_Prob.cpp Source/Prob/REMORA_InitAnalyticBiology_BioToy.H commit 55f13096a4d4c3420f34a611cb1021b8b935424c Author: Hannah Klion Date: Tue Aug 11 14:42:09 2026 -0700 initial commit of biology CMake/BuildREMORAExe.cmake Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/index.rst Exec/Make.REMORA Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Source/IO/REMORA_NCPlotFile.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_prob_common.H Source/Prob/REMORA_InitAnalyticBiology_BioToy.H Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d.cpp commit 5840c98f8f51b6286c9ddea16c58552977aabe91 Author: Hannah Klion Date: Fri Aug 7 16:34:04 2026 -0700 Gate remora executable target Exec/CMakeLists.txt commit 897702ea0972786c7b4e041b21468c7d29358124 Author: Hannah Klion Date: Fri Aug 7 16:15:02 2026 -0700 Validate river metadata sizes Source/Initialization/REMORA_init_from_netcdf.cpp commit 4cb853caea5d304a44fdcd938f5cffdd6c25bbd4 Merge: e1289019 315d8f13 Author: Hannah Klion Date: Fri Aug 7 15:52:27 2026 -0700 Merge pull request #578 from seahorce-scidac/fix-external-amrex-precision Fix external AMReX precision selection commit 315d8f13bd7428206abfe19c7b860e1e5efc3501 Author: Hannah Klion Date: Fri Aug 7 15:48:35 2026 -0700 Fix external AMReX precision selection CMakeLists.txt commit e1289019a135264ae0840208c85612644932ab98 Merge: e3719410 e4a52aca Author: Hannah Klion Date: Fri Aug 7 14:35:37 2026 -0700 Merge pull request #576 from emmashie/level1_source Added implementing river point source to higher levels commit e4a52acae674c3eb5842ad4d3814bb8b7574ee31 Author: Hannah Klion Date: Fri Aug 7 14:30:44 2026 -0700 Change river debug printing logic based on verbosity Source/Initialization/REMORA_init_from_netcdf.cpp commit e3719410a6032bd315f2b1f46bfb6cb88964c3ee Merge: cb9dc554 3ae43a51 Author: Hannah Klion Date: Fri Aug 7 12:25:33 2026 -0700 Merge pull request #577 from hklion/update_tag_block Update tag block docs and inputs commit 3ae43a51bd355e18f8effba8ac675aed53047a2c Author: Hannah Klion Date: Fri Aug 7 11:46:24 2026 -0700 spelling Docs/sphinx_doc/MeshRefinement.rst commit 42aae9fd60b9fec6b23d93e951de8494b2180f1b Author: Hannah Klion Date: Fri Aug 7 11:43:40 2026 -0700 update docs to reflect changes in tagging and blocking and update inputs to make regtest pass Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst Exec/Advection/inputs_ml Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad commit 228df9c25deb6489894a576520164a07a07a512d Author: Nuss Date: Fri Aug 7 09:49:03 2026 -0700 Added implementing river point source to higher levels Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp commit cb9dc554947f72564ba745f69e7c25dc52a3faa5 Merge: bcf2a395 b6d3c9b2 Author: Hannah Klion Date: Fri Aug 7 07:33:40 2026 -0700 Merge pull request #575 from hklion/update_tag_block Update tagging and blocking commit b6d3c9b22f0ea9e623caeb1a8220cdd2d6fb2006 Author: Hannah Klion Date: Thu Aug 6 16:16:25 2026 -0700 Update tagging and blocking - Untag sea-land boundaries, so that we no longer erroneously tag regions when using gradient refinement conditions - Tag full vertical column when any cell is tagged - Blocking factor is set to large in z, bypassing AmrCore input checks - Two prior points mean that there should no longer be domain decomposition in the z-direction on refined levels - n_error_buf is now overridable by inputs; was previously set to 0 Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp Source/REMORA_Tagging.cpp Source/main.cpp Tests/test_files/Advection_ML/Advection_ML.i commit 282390cb569b047a8861a6555506ae31cd46bde3 Author: Jean M. Sexton Date: Thu Aug 6 12:35:42 2026 -0700 sixth pass Source/REMORA.H Source/REMORA_Coupling.cpp commit 4a94044699309a6394e2107f588a2064f99471d6 Author: Jean M. Sexton Date: Thu Aug 6 09:02:57 2026 -0700 fourth pass Source/REMORA.H commit df2a376ba5b6f304955668b619e4bd7759a081bd Author: Jean M. Sexton Date: Thu Aug 6 07:48:52 2026 -0700 Third pass Source/REMORA.H Source/REMORA_Coupling.cpp commit 3118cd09a06ecc991177fd724d42a46ea22d7d52 Author: Jean M. Sexton Date: Wed Aug 5 14:47:44 2026 -0700 Next pass Source/REMORA_Coupling.cpp commit 88aae58e3f99127dbf5880e4b54b81cc8e3d6f16 Author: Jean M. Sexton Date: Wed Aug 5 14:30:50 2026 -0700 First pass Source/REMORA_Coupling.cpp commit bcf2a395e5ae73a6a46b2c4f698e94452faeda5b Author: Ann Almgren Date: Sat Aug 1 09:20:55 2026 -0700 Update submodule amrex Submodules/AMReX commit 4a8744abb5e0682cc4c080ed67ee10bd61576b45 Merge: 74ed6981 189a8f5f Author: Hannah Klion Date: Thu Jul 30 14:16:16 2026 -0700 Merge pull request #574 from hklion/fillpatch_fillset flip default value of fill_set in FillPatch and FillPatchNoBC and only fill_set on u, v, w, cons, ubar, vbar commit 189a8f5ffad70894ea5b4c9815f6c06d2124fa61 Author: Hannah Klion Date: Thu Jul 30 13:52:06 2026 -0700 flip default value of fill_set in FillPatch and FillPatchNoBC Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 74ed6981990e629b945f7d2231c8c5b1eaeaa00b Author: Hannah Klion Date: Tue Jul 28 13:19:38 2026 -0700 add single/multilevel integrated quantities and fix MPI bug Source/REMORA_SumIQ.cpp commit e8d2b6d7a24e9e670cd482a959055909988f9433 Merge: 56cdf0d7 1a2ea1ae Author: Hannah Klion Date: Sat Jul 25 09:49:20 2026 -0700 Merge pull request #572 from hklion/make_amrex_real Make conversion to amrex::Real consistent in preparation for single precision testing commit 56cdf0d70c1cc5625c200c3acaa6491fed7cb0e8 Merge: ac0eeda5 a72a3f06 Author: Hannah Klion Date: Sat Jul 25 09:49:04 2026 -0700 Merge pull request #573 from jmsexton03/add_cuda_arch_ci Use cuda arch cmake flag in gh action commit a72a3f06abc4483fc83f8523887bb5d2606acaa2 Author: Jean M. Sexton Date: Sat Jul 25 07:36:47 2026 -0700 Add warning for arch CMakeLists.txt commit 06248709f9bc6201828b4c8f3934028a133683e9 Author: Jean M. Sexton Date: Sat Jul 25 07:26:53 2026 -0700 Use cuda arch cmake flag in gh action .github/workflows/cuda-ci.yml commit 1a2ea1ae16355a99053b17c6fc69b8aacb7c04e1 Author: Hannah Klion Date: Fri Jul 24 14:37:48 2026 -0700 fix GPU build Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_t3dmix.cpp commit 75ff8f28d6242f5976fae9d81e6ed3a138404970 Author: Hannah Klion Date: Fri Jul 24 14:13:33 2026 -0700 revert half to 0.5 Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Particles/REMORA_PC_Init.cpp Source/Prob/REMORA_InitAnalyticBathymetry_Seamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticGridScale_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_Advection.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticSMFlux_DoubleGyre.H Source/REMORA.H Source/REMORA_Constants.H Source/REMORA_Derive.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_bulk_flux_test.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_curvilinear.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 3940db0095666b1959f3b8546c4d53fa9414f33f Author: Hannah Klion Date: Fri Jul 24 10:27:03 2026 -0700 last cleanup Exec/REMORA_Prob.cpp Source/Initialization/REMORA_init_bcs.cpp Source/REMORA.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 439f0d65e820479ee266be54aeb69d850f908681 Author: Hannah Klion Date: Fri Jul 24 10:10:05 2026 -0700 convert reals in TimeIntegration routines Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_bulk_flux_test.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_curvilinear.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp commit 8e30c0399a90561d1319302af60f575027d386a2 Author: Hannah Klion Date: Thu Jul 23 11:58:44 2026 -0700 convert prob files Source/Prob/REMORA_InitAnalyticBathymetry_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticBathymetry_ChannelTest.H Source/Prob/REMORA_InitAnalyticBathymetry_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticBathymetry_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticBathymetry_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Seamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticGridScale_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticHMix_Advection.H Source/Prob/REMORA_InitAnalyticHMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticHMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticHMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticHMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticHMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticHMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticHMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticHMix_Seamount.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_Advection.H Source/Prob/REMORA_InitAnalyticProb_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_CoupleToERF.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticProb_Seamount.H Source/Prob/REMORA_InitAnalyticProb_Upwelling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticSMFlux_ChannelTest.H Source/Prob/REMORA_InitAnalyticSMFlux_DoubleGyre.H Source/Prob/REMORA_InitAnalyticSMFlux_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticSMFlux_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticSMFlux_Upwelling.H Source/Prob/REMORA_InitAnalyticSMFlux_UpwellingML.H Source/Prob/REMORA_InitAnalyticSurfaceVar_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_Advection.H Source/Prob/REMORA_InitAnalyticVMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticVMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticVMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticVMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticVMix_Seamount.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling.H Source/Prob/REMORA_InitAnalyticVMix_UpwellingML.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticZeta_DogboneAnalytic.H commit c03ceb01a6d65c1652dc3eb70cb7abe26b8a5825 Author: Hannah Klion Date: Wed Jul 22 16:26:30 2026 -0700 convert Particles Source/Particles/REMORA_PC.H Source/Particles/REMORA_PC_Init.cpp Source/Particles/REMORA_PC_Utils.cpp commit 94a33a686a10e653c345b84b5295f9f70945445f Author: Hannah Klion Date: Wed Jul 22 16:14:26 2026 -0700 conversions for files in IO directory Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_writeJobInfo.cpp commit 351d852ae880ccf22b9908107f096e717836f11b Author: Hannah Klion Date: Wed Jul 22 15:46:04 2026 -0700 convert files in Initialization directory Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp commit d88582548c7c0948ab0d51525653c352333a102d Author: Hannah Klion Date: Wed Jul 22 15:40:42 2026 -0700 add missing include constants Source/BoundaryConditions/REMORA_FillPatcher.H Source/BoundaryConditions/REMORA_TimeInterpolatedData.H commit 7f4db626fb3a3dacb36e538533e57c570899d3c7 Author: Hannah Klion Date: Wed Jul 22 15:34:45 2026 -0700 more conversions Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.H Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/BoundaryConditions/REMORA_TimeInterpolatedData.H commit 52923ad6223d8b7ba775a37f885a5486b9daae79 Author: Hannah Klion Date: Wed Jul 22 15:24:12 2026 -0700 further real conversion Source/REMORA.H Source/REMORA_Constants.H Source/REMORA_DataStruct.H Source/REMORA_Derive.cpp Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp commit 1f16be22bae9c7acc485c6ad3bc4a1c116b85c49 Merge: 7e14d158 ac0eeda5 Author: Hannah Klion Date: Wed Jul 22 14:53:40 2026 -0700 Merge branch 'development' into make_amrex_real commit 7e14d158e3aabe6c189ba236b2c258f979932e76 Author: Hannah Klion Date: Wed Jul 22 14:45:27 2026 -0700 start converting all doubles to amrex real and standardizing on Real() syntax vs. _rt Source/REMORA.cpp Source/REMORA_Constants.H Source/REMORA_Coupling.cpp commit ac0eeda512c731c02013ced34d9948573b4055b9 Author: Jean M. Sexton Date: Wed Jul 15 11:44:15 2026 -0700 Add extra logic to remove unneeded copies and fix print Source/REMORA_Coupling.cpp commit ffa7005eac6c538bc96da96cc132b5c3f7739cf7 Author: Hannah Klion Date: Mon Jul 20 16:19:48 2026 -0700 flip sign on surface stress when ingesting from ERF Source/REMORA_Coupling.cpp commit 94385b73933eac054d99ba9aadeabc476f43019c Author: Hannah Klion Date: Mon Jul 20 16:18:33 2026 -0700 add NetCDF files in Exec directories to gitignore .gitignore commit 927b96cb769b066548bf1df4936e4a9d559f53d4 Author: Hannah Klion Date: Wed Jul 15 10:59:58 2026 -0700 initialize derived flux variables to zero when they will be computed so that plotfile 0 works Source/Initialization/REMORA_make_new_level.cpp commit 8c3eb01e870a11d980f4b062de13098df23b666e Merge: 60a3255a a2fe1739 Author: Ann Almgren Date: Wed Jul 15 09:55:07 2026 -0700 Merge branch 'development' of github.com:seahorce-scidac/REMORA into development commit 60a3255ac2266f1053af64251a8d42fbfd30e4ff Author: Ann Almgren Date: Wed Jul 15 09:55:01 2026 -0700 update required cmake to 3.20 CMakeLists.txt commit a2fe17397cee54cbf4983746ffc200ee372fbba5 Merge: 2212430f 76239f4a Author: Jean M. Sexton Date: Wed Jul 15 09:50:42 2026 -0700 Merge pull request #571 from jmsexton03/update_badm_flag_passing Update badm flag passing commit 76239f4ac35060e3cd17969fb97856d9f970d2f6 Merge: 8d2948c1 2212430f Author: Jean M. Sexton Date: Wed Jul 15 09:47:29 2026 -0700 Merge remote-tracking branch 'upstream/development' into update_badm_flag_passing commit 2212430f9bdb9a6d27111c040fcad1c3d645597c Author: Hannah Klion Date: Wed Jul 15 09:22:35 2026 -0700 fix flag on flux/state in setup_step and remove tab Source/TimeIntegration/REMORA_setup_step.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 33835b0ff3f1777d282181048362497d5189105e Author: Ann Almgren Date: Wed Jul 15 09:17:45 2026 -0700 Fix box on which depth transform stuff operates Source/REMORA_Coupling.cpp commit 8d2948c150581e3053574db34b8df85ab25c8fd5 Author: Jean M. Sexton Date: Wed Jul 15 08:21:58 2026 -0700 Add getters and set function Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp commit c379dc0da99055bb7109fdafc4ecb3e2fa0ce544 Author: Jean M. Sexton Date: Wed Jul 15 07:17:08 2026 -0700 Split mfiters for coupling apply Source/REMORA_Coupling.cpp commit 44afd025f9be9070f4c0240e1aaf9999062d7c59 Merge: 04e385cd a47ab057 Author: Jean M. Sexton Date: Tue Jul 14 15:02:20 2026 -0700 Merge pull request #570 from jmsexton03/coupling_flux_pass_tau_edits Update for nodal tau and flags commit a47ab0573f85db424a7ca994356d13c087764b39 Author: Jean M. Sexton Date: Tue Jul 14 14:57:09 2026 -0700 Update for nodal tau and flags Source/REMORA.H Source/REMORA_Coupling.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 04e385cd7ddac63a3f14f959693b6538fdeb0c1d Author: Hannah Klion Date: Tue Jul 14 10:56:34 2026 -0700 fix undefined behavior in DepthStretchTransform Source/Utils/REMORA_DepthStretchTransform.H commit 21b99faa37b5c1b598809f1e13cf83a951972ac2 Merge: 5a03418b 0b6780fe Author: Hannah Klion Date: Mon Jul 13 19:04:59 2026 -0700 Merge pull request #569 from hklion/bulk_flux_input_analytic enable bulk flux surface variables to come in via analytic functions and clean up initialization path commit 0b6780fe5ee5bd18676cd27eb81377f31e96b1fb Author: Hannah Klion Date: Mon Jul 13 17:46:50 2026 -0700 fix GPU build Source/REMORA_Coupling.cpp commit 0d8230dd4195c23b99cbcdaff9d76653fad567e0 Author: Hannah Klion Date: Mon Jul 13 17:27:05 2026 -0700 enable bulk flux surface variables to come in via analytic functions and clean up initialization path Docs/sphinx_doc/Inputs.rst Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/Prob/REMORA_InitAnalyticSurfaceVar_BoundaryLayer.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 5a03418bb09dae0caaed87fd95bade965c6b883d Merge: b8cc16de 7689ca18 Author: Hannah Klion Date: Fri Jul 10 12:31:29 2026 -0700 Merge pull request #568 from jmsexton03/coupling_flux_pass Add imported atm->ocn flux mode commit 7689ca187e94a693c70e56200ad678377b249abe Author: Jean M. Sexton Date: Fri Jul 10 12:16:31 2026 -0700 Add flux-apply validation in coupling - fill stflux boundaries before downstream use - print imported stress and surface-flux extrema after flux apply - expose Temp and Salt forcing assembled from ATM->OCN flux lanes Source/REMORA_Coupling.cpp commit b5932323f496dd47c7abfa96f162ad8282a7b91a Author: Jean M. Sexton Date: Thu Jul 9 16:47:24 2026 -0700 Add imported atm->ocn flux mode - Add atm2ocn_flux_mode and allocate forcing arrays outside bulk_fluxes. - Add ApplyAtmosphericFluxes to ingest lanes and assemble stflux. - Skip bulk_fluxes/set_smflux overrides while keeping flux diagnostics writable. Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA_Coupling.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/TimeIntegration/REMORA_setup_step.cpp commit b8cc16de2da584e60a533a4e2020997322f2ad3f Merge: 15fa7532 6c829b4a Author: Hannah Klion Date: Tue Jul 7 14:02:38 2026 -0700 Merge pull request #567 from hklion/radiation_tracer_flux_to_plotfile add surface scalar fluxes and radiation fluxes to plotfile commit 6c829b4a6334c1bc2263275fe44c0610c4e3d2a1 Author: Hannah Klion Date: Tue Jul 7 13:49:50 2026 -0700 add surface scalar fluxes and radiation fluxes to plotfile Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp commit 15fa753272c091aa27cecde7e8402c446b0be15b Merge: 9c550000 cde725f0 Author: Hannah Klion Date: Tue Jul 7 08:48:56 2026 -0700 Merge pull request #566 from hklion/curvgrid_advection add curvilinear terms to advection commit 9c5500006ddb6e034b5ac4106056d9b6da05f494 Merge: ad72501c 9e7a8a29 Author: Hannah Klion Date: Tue Jul 7 08:48:41 2026 -0700 Merge pull request #565 from seahorce-scidac/dependabot/submodules/Submodules/AMReX-1546c1c Bump Submodules/AMReX from `3c3bbaa` to `1546c1c` commit cde725f07158149b87acef488d2233356980be20 Author: Hannah Klion Date: Mon Jul 6 15:59:52 2026 -0700 actually add curvilinear terms Source/TimeIntegration/REMORA_curvilinear.cpp commit 9ade2ee52e1973a7d3144786c42e4ba6a23e8a98 Author: Hannah Klion Date: Mon Jul 6 15:53:24 2026 -0700 add curvilinear terms to advection CMake/BuildREMORAExe.cmake Docs/sphinx_doc/Inputs.rst Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA_DataStruct.H Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit ad72501c2acc415e99e8ecb82ef8d5d5c5d79023 Author: Hannah Klion Date: Wed Jul 1 15:35:30 2026 -0700 initialize hmix coeffs for upwelling coupling Exec/REMORA_Prob.cpp commit aff9e3f23018b00fe0f00731cadcfbd9f2d243b4 Author: Hannah Klion Date: Wed Jul 1 14:38:57 2026 -0700 make double gyre init cleaner Source/Prob/REMORA_InitAnalyticSMFlux_DoubleGyre.H commit 9e7a8a29857fcf77afe27cecc083994ca755c399 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed Jul 1 21:09:19 2026 +0000 Bump Submodules/AMReX from `3c3bbaa` to `1546c1c` Bumps [Submodules/AMReX](https://github.com/amrex-codes/AMReX) from `3c3bbaa` to `1546c1c`. - [Release notes](https://github.com/amrex-codes/AMReX/releases) - [Commits](https://github.com/amrex-codes/AMReX/compare/3c3bbaa34cd3423fe96e6cc601a33b42bfd5238d...1546c1ccbf41c704a33790f4bf445a2fcee1372e) --- updated-dependencies: - dependency-name: Submodules/AMReX dependency-version: 1546c1ccbf41c704a33790f4bf445a2fcee1372e dependency-type: direct:production ... Signed-off-by: dependabot[bot] Submodules/AMReX commit 2268b98d8ae092fac092e8d923e93b60372076bc Author: Hannah Klion Date: Wed Jul 1 13:19:56 2026 -0700 get prob_lo within parallel for in double gyre smflux init Source/Prob/REMORA_InitAnalyticSMFlux_DoubleGyre.H commit c15e1df948f5e734fadaacceb7ee60b9db4be29f Merge: 47a41284 aafc42f3 Author: Ann Almgren Date: Tue Jun 30 19:30:15 2026 -0700 Merge pull request #564 from seahorce-scidac/update_docs Update docs for new build paradigm commit aafc42f3c5c701a8941ac0a00319abae212b601d Author: Ann Almgren Date: Tue Jun 30 16:25:28 2026 -0700 Update docs for new build paradigm Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/Particles.rst Docs/sphinx_doc/ProblemSetup.rst Docs/sphinx_doc/building.rst Tests/CTestList.cmake commit 47a412847135b55c8a102baf5b1f0c1eb258a9e8 Merge: f2c4b90a ed76acfa Author: Ann Almgren Date: Tue Jun 30 13:53:50 2026 -0700 Merge pull request #563 from jmsexton03/remove_library_prob_flag Remove fatal error for no longer relevant flag commit f2c4b90a4fe4d3c57ce8cf3d03e59869509006c0 Merge: fafb43e7 e1e0fba2 Author: Ann Almgren Date: Tue Jun 30 13:46:51 2026 -0700 Merge pull request #560 from seahorce-scidac/exec_changes First steps towards single executable commit e1e0fba2a43e7bd6c0b7af0c3f0ba096ac5fc3e7 Author: Ann Almgren Date: Tue Jun 30 13:32:05 2026 -0700 remove whitespace Exec/REMORA_Prob.cpp commit e76a0e2be47ea48c089d0c7adbe27f8476e3a537 Author: Ann Almgren Date: Tue Jun 30 13:28:17 2026 -0700 fix whitespace Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H commit bd485fb9e6507d3e1d232483e2418bd18116df9c Author: Ann Almgren Date: Tue Jun 30 13:26:53 2026 -0700 Add Upwelling_Coupling files Exec/REMORA_Prob.cpp Source/Prob/Make.package Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticSMFlux_UpwellingCoupling.H commit 6eb074190e4752abe6defc2732b0c72174a1df09 Author: Ann Almgren Date: Tue Jun 30 13:14:14 2026 -0700 fix for windows Tests/CTestList.cmake commit 2523c31658db42f7fc359e56f21a99066d7c877b Author: Ann Almgren Date: Tue Jun 30 12:45:40 2026 -0700 remove debugging hack Source/Prob/REMORA_InitAnalyticSMFlux_DoublyPeriodic.H commit 84f6509bc04a5fd3726d5fc51550e63e23fee08e Author: Ann Almgren Date: Tue Jun 30 12:38:20 2026 -0700 remove unused Source/Prob/REMORA_InitAnalyticVMix_Upwelling_ML.H commit c4dda54760375612521cf3ae663148bd77b87c6a Author: Ann Almgren Date: Tue Jun 30 12:37:29 2026 -0700 fix white space Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H commit 46393e99cbc66c82af2a089a7b3ab9cf2cae2460 Merge: f17558db 4f3f4032 Author: Ann Almgren Date: Tue Jun 30 12:32:23 2026 -0700 Merge branch 'exec_changes' of github.com:seahorce-scidac/REMORA into exec_changes commit f17558db4266be2aedff4768d16b3b0fd96ed43b Author: Ann Almgren Date: Tue Jun 30 12:31:56 2026 -0700 update prob files Exec/REMORA_Prob.cpp Source/Prob/REMORA_InitAnalyticBathymetry_Advection.H Source/Prob/REMORA_InitAnalyticBathymetry_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticHMix_Advection.H Source/Prob/REMORA_InitAnalyticHMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticHMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticHMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticHMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticHMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticHMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticHMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticHMix_Seamount.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticSMFlux_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_Advection.H Source/Prob/REMORA_InitAnalyticVMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticVMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticVMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticVMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticVMix_Seamount.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling.H Source/Prob/REMORA_InitAnalyticVMix_UpwellingML.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling_ML.H commit 4f3f403207ff6898125cf80f4d4a3899bcea2d6f Author: Hannah Klion Date: Tue Jun 30 12:25:08 2026 -0700 turn of pnetcdf by default Exec/GNUmakefile commit ed76acfa9b10c69fcde7749511f9f6eb91cce339 Author: Jean M. Sexton Date: Tue Jun 30 12:23:33 2026 -0700 Remove fatal error for no longer relevant flag CMake/BuildREMORAExe.cmake commit 657d90730585d94ec53a932bf023a05ff9f3addf Author: Hannah Klion Date: Tue Jun 30 11:40:20 2026 -0700 fix prob name in IdealRivGrid inputs Exec/IdealRivGrid/inputs commit a6a379bd5e1c332df6fa15755f994faf2dab5a3b Author: Hannah Klion Date: Tue Jun 30 10:41:02 2026 -0700 remove ERF-specific make flags and swap netcdf with pnetcdf Exec/GNUmakefile commit d79a143ea1084c8ad36f10e23ae90135d6dd6754 Author: Ann Almgren Date: Tue Jun 30 09:37:26 2026 -0700 Update ctest .i files Tests/CTestList.cmake Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/BoundaryLayer/BoundaryLayer.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit fafb43e760a0b39ce66f294f5c31933e506d2120 Merge: 26cae8cc 50890374 Author: Hannah Klion Date: Tue Jun 30 09:30:24 2026 -0700 Merge pull request #561 from ffmares/updates_to_prob Updates to prob for coupled upwelling problem commit 50890374dddffad4f744499f3c1f29a40c50da0b Author: Feranmi Falodun Date: Tue Jun 30 09:19:55 2026 -0700 Updated prob.cpp Exec/Upwelling_Coupling/prob.cpp commit e7055b5bde2752476629f9b5d7ccfe30952ff8c8 Author: Ann Almgren Date: Tue Jun 30 09:02:58 2026 -0700 this now builds Exec/Make.REMORA Exec/REMORA_Prob.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 3396ef8d5ad96d7460b99ec30bd24d38a4a1d7a7 Author: Feranmi Falodun Date: Tue Jun 30 07:59:52 2026 -0700 Updated prob.cpp and prob.H, along with the inputs file Exec/Upwelling_Coupling/inputs commit 7824e0305df43367b9f3b21572ac05f2c7bd40db Author: Ann Almgren Date: Mon Jun 29 21:20:05 2026 -0700 cmake update Exec/CMakeLists.txt commit 756dd2f94dd5bf14fd44cc6248c01681fda8ab1a Author: Ann Almgren Date: Mon Jun 29 21:03:49 2026 -0700 This almost builds ... Exec/Advection/GNUmakefile Exec/Advection/Make.package Exec/Advection/inputs Exec/Advection/inputs_ml Exec/Advection/prob.H Exec/Advection/prob.cpp Exec/BlankProblem/GNUmakefile Exec/BlankProblem/Make.package Exec/BlankProblem/inputs Exec/BlankProblem/prob.H Exec/BlankProblem/prob.cpp Exec/BoundaryLayer/GNUmakefile Exec/BoundaryLayer/Make.package Exec/BoundaryLayer/inputs Exec/BoundaryLayer/prob.H Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/GNUmakefile Exec/Channel_Test/Make.package Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/Channel_Test/out Exec/Channel_Test/prob.H Exec/Channel_Test/prob.cpp Exec/CoupleToERF/GNUmakefile Exec/CoupleToERF/Make.package Exec/CoupleToERF/inputs Exec/CoupleToERF/prob.H Exec/CoupleToERF/prob.cpp Exec/Dogbone/GNUmakefile Exec/Dogbone/Make.package Exec/Dogbone/inputs Exec/Dogbone/prob.H Exec/Dogbone/prob.cpp Exec/DogboneAnalytic/GNUmakefile Exec/DogboneAnalytic/Make.package Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/prob.H Exec/DogboneAnalytic/prob.cpp Exec/DoubleGyre/GNUmakefile Exec/DoubleGyre/Make.package Exec/DoubleGyre/inputs Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/GNUmakefile Exec/DoublyPeriodic/Make.package Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/prob.H Exec/DoublyPeriodic/prob.cpp Exec/GNUmakefile Exec/IdealMiniGrid/GNUmakefile Exec/IdealMiniGrid/Make.package Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Exec/IdealMiniGrid/inputs_frc Exec/IdealMiniGrid/prob.H Exec/IdealMiniGrid/prob.cpp Exec/IdealRivGrid/GNUmakefile Exec/IdealRivGrid/Make.package Exec/IdealRivGrid/inputs Exec/IdealRivGrid/prob.H Exec/IdealRivGrid/prob.cpp Exec/Make.REMORA Exec/ParticlesOverSeaMount/GNUmakefile Exec/ParticlesOverSeaMount/Make.package Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Exec/Seamount/GNUmakefile Exec/Seamount/Make.package Exec/Seamount/inputs Exec/Seamount/prob.H Exec/Seamount/prob.cpp Exec/Upwelling/GNUmakefile Exec/Upwelling/Make.package Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Exec/Upwelling_Coupling/GNUmakefile Exec/Upwelling_Coupling/Make.package Exec/Upwelling_Coupling/inputs Exec/Upwelling_Coupling/prob.H Exec/Upwelling_Coupling/prob.cpp Exec/Upwelling_ML/GNUmakefile Exec/Upwelling_ML/Make.package Exec/Upwelling_ML/inputs Exec/Upwelling_ML/prob.H Exec/Upwelling_ML/prob.cpp Source/Prob/Make.package Source/Prob/REMORA_InitAnalyticBathymetry_Advection.H Source/Prob/REMORA_InitAnalyticBathymetry_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticBathymetry_ChannelTest.H Source/Prob/REMORA_InitAnalyticBathymetry_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticBathymetry_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticBathymetry_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Seamount.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticBathymetry_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticGridScale_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticHMix_Advection.H Source/Prob/REMORA_InitAnalyticHMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticHMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticHMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticHMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticHMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticHMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticHMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticHMix_Seamount.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling.H Source/Prob/REMORA_InitAnalyticHMix_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticMasks_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_Advection.H Source/Prob/REMORA_InitAnalyticProb_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticProb_ChannelTest.H Source/Prob/REMORA_InitAnalyticProb_CoupleToERF.H Source/Prob/REMORA_InitAnalyticProb_DogboneAnalytic.H Source/Prob/REMORA_InitAnalyticProb_DoubleGyre.H Source/Prob/REMORA_InitAnalyticProb_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticProb_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticProb_Seamount.H Source/Prob/REMORA_InitAnalyticProb_Upwelling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_Coupling.H Source/Prob/REMORA_InitAnalyticProb_Upwelling_ML.H Source/Prob/REMORA_InitAnalyticSMFlux_ChannelTest.H Source/Prob/REMORA_InitAnalyticSMFlux_DoubleGyre.H Source/Prob/REMORA_InitAnalyticSMFlux_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticSMFlux_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticSMFlux_Upwelling.H Source/Prob/REMORA_InitAnalyticSMFlux_UpwellingCoupling.H Source/Prob/REMORA_InitAnalyticSMFlux_UpwellingML.H Source/Prob/REMORA_InitAnalyticVMix_Advection.H Source/Prob/REMORA_InitAnalyticVMix_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticVMix_ChannelTest.H Source/Prob/REMORA_InitAnalyticVMix_DoubleGyre.H Source/Prob/REMORA_InitAnalyticVMix_DoublyPeriodic.H Source/Prob/REMORA_InitAnalyticVMix_IdealMiniGrid.H Source/Prob/REMORA_InitAnalyticVMix_IdealRivGrid.H Source/Prob/REMORA_InitAnalyticVMix_ParticlesOverSeamount.H Source/Prob/REMORA_InitAnalyticVMix_Seamount.H Source/Prob/REMORA_InitAnalyticVMix_Upwelling.H Source/Prob/REMORA_InitAnalyticVMix_UpwellingML.H Source/Prob/REMORA_InitAnalyticWind_BoundaryLayer.H Source/Prob/REMORA_InitAnalyticZeta_DogboneAnalytic.H Submodules/AMReX commit 5d996b52b53554776f289cd73516385c35278f9a Author: Ann Almgren Date: Mon Jun 29 13:07:14 2026 -0700 First steps towards single executable Exec/Advection/prob.H Exec/Advection/prob.cpp Exec/BlankProblem/prob.H Exec/BlankProblem/prob.cpp Exec/BoundaryLayer/prob.H Exec/BoundaryLayer/prob.cpp Exec/CMakeLists.txt Exec/Channel_Test/prob.H Exec/Channel_Test/prob.cpp Exec/CoupleToERF/prob.H Exec/CoupleToERF/prob.cpp Exec/Dogbone/prob.H Exec/Dogbone/prob.cpp Exec/DogboneAnalytic/prob.H Exec/DogboneAnalytic/prob.cpp Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.H Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.H Exec/IdealMiniGrid/prob.cpp Exec/IdealRivGrid/prob.H Exec/IdealRivGrid/prob.cpp Exec/Make.package Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp Exec/REMORA_Prob.H Exec/REMORA_Prob.cpp Exec/Seamount/prob.H Exec/Seamount/prob.cpp Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Exec/Upwelling_Coupling/prob.H Exec/Upwelling_Coupling/prob.cpp Exec/Upwelling_ML/prob.H Exec/Upwelling_ML/prob.cpp commit 26cae8cccc4c704a58a4c7ca917bdaadeb447310 Author: Ann Almgren Date: Mon Jun 29 12:04:29 2026 -0700 update prob* Exec/Upwelling_Coupling/prob.H Exec/Upwelling_Coupling/prob.cpp commit 89d56b4469cad730f1d2c9f39615a9451940937b Merge: ea48b442 60327221 Author: Ann Almgren Date: Sun Jun 28 10:51:52 2026 -0700 Merge pull request #559 from emmashie/pltfile_nodal_output added true/false flag for nodal data output in plotfiles commit 60327221ee761e1eb306ec672519acea2de80d2d Author: Nuss Date: Fri Jun 26 15:39:09 2026 -0700 fixed reading in string from inputs file for staggered vel and nodal data options Source/REMORA.H Source/REMORA.cpp commit eaa6cf217776a4d517fb4a415e7db6c56765551f Author: Nuss Date: Fri Jun 26 15:02:55 2026 -0700 switched nodal flag to bool and changed multifab allocation for nodal data Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 2d0ec6fa1f45d6ce972cf554e6a4d8ddb5391e49 Author: Nuss Date: Fri Jun 26 14:02:09 2026 -0700 added true/false flag for nodal data output in plotfiles Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit ea48b442569915ac6819805773a066b0f0987e28 Merge: d9e878b1 864bab11 Author: Ann Almgren Date: Fri Jun 26 10:30:59 2026 -0700 Merge pull request #558 from emmashie/eminusp_fix Updated handling of evap minus precipitation commit 864bab116c662544fb58728a19560eb8d0c75fd2 Author: Emma Nuss Date: Fri Jun 26 09:36:56 2026 -0700 fixed handling of evap minus precip Docs/sphinx_doc/Inputs.rst Source/Initialization/REMORA_make_new_level.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp commit d9e878b1373d67d185abbce02111a0700fd03464 Merge: 5b91ac01 527627c1 Author: Ann Almgren Date: Thu Jun 25 09:00:39 2026 -0700 Merge pull request #552 from seahorce-scidac/dependabot/submodules/Submodules/AMReX-e95d50b Bump Submodules/AMReX from `7674e50` to `e95d50b` commit 5b91ac01e60fcf4e90d6514093bc7858778020a0 Merge: 3e860356 b93d4a7d Author: Ann Almgren Date: Thu Jun 25 09:00:19 2026 -0700 Merge pull request #553 from seahorce-scidac/dependabot/github_actions/development/actions/upload-artifact-7 Bump actions/upload-artifact from 4 to 7 commit 3e860356ac4d3b08dbbdd6e7c08e6cc78ad2e26c Merge: 87588712 8373c7b6 Author: Ann Almgren Date: Thu Jun 25 09:00:03 2026 -0700 Merge pull request #554 from seahorce-scidac/dependabot/github_actions/development/actions/cache-6 Bump actions/cache from 4 to 6 commit 875887122ad195961eefeae5160e4653ef6cc705 Merge: ae63c578 13380d8f Author: Ann Almgren Date: Thu Jun 25 08:59:47 2026 -0700 Merge pull request #555 from seahorce-scidac/dependabot/github_actions/development/JamesIves/github-pages-deploy-action-4.8.0 Bump JamesIves/github-pages-deploy-action from 4.1.5 to 4.8.0 commit ae63c578753356206d9e26ed35f7101b2780aeca Merge: dd134558 1849a344 Author: Ann Almgren Date: Thu Jun 25 08:59:32 2026 -0700 Merge pull request #556 from seahorce-scidac/dependabot/github_actions/development/styfle/cancel-workflow-action-0.13.1 Bump styfle/cancel-workflow-action from 0.6.0 to 0.13.1 commit dd1345584b989b78779cc8fbf5479572104d0619 Merge: e510fbcb 45326d21 Author: Ann Almgren Date: Thu Jun 25 08:59:19 2026 -0700 Merge pull request #557 from seahorce-scidac/dependabot/github_actions/development/actions/checkout-7 Bump actions/checkout from 4 to 7 commit 45326d21389acdb5d806b0dbe32c8ba45dded9dc Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Jun 25 15:58:33 2026 +0000 Bump actions/checkout from 4 to 7 Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] .github/workflows/ci.yml .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/codespell.yml .github/workflows/cuda-ci.yml .github/workflows/docs.yml .github/workflows/draft-pdf.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/style.yml .github/workflows/sycl.yml .github/workflows/windows.yml commit 1849a3444ff71fa4d0dec28e4023b055ec339108 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Jun 25 15:58:28 2026 +0000 Bump styfle/cancel-workflow-action from 0.6.0 to 0.13.1 Bumps [styfle/cancel-workflow-action](https://github.com/styfle/cancel-workflow-action) from 0.6.0 to 0.13.1. - [Release notes](https://github.com/styfle/cancel-workflow-action/releases) - [Commits](https://github.com/styfle/cancel-workflow-action/compare/0.6.0...0.13.1) --- updated-dependencies: - dependency-name: styfle/cancel-workflow-action dependency-version: 0.13.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] .github/workflows/cuda-ci.yml commit 13380d8fb6ebab8df04086a45134cf18093da0c2 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Jun 25 15:58:27 2026 +0000 Bump JamesIves/github-pages-deploy-action from 4.1.5 to 4.8.0 Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.1.5 to 4.8.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/4.1.5...v4.8.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-version: 4.8.0 dependency-type: direct:production update-type: version-update:semver-minor ... 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Signed-off-by: dependabot[bot] .github/workflows/draft-pdf.yml .github/workflows/hip.yml commit 527627c1cbc458cad1f436408009833f9b761dde Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Jun 25 15:58:21 2026 +0000 Bump Submodules/AMReX from `7674e50` to `e95d50b` Bumps [Submodules/AMReX](https://github.com/amrex-codes/AMReX) from `7674e50` to `e95d50b`. - [Release notes](https://github.com/amrex-codes/AMReX/releases) - [Commits](https://github.com/amrex-codes/AMReX/compare/7674e50aff30ae8d06e2d60ea4cc04466bd5d1a9...e95d50b2b42429431ef60feb4a6158a2fa60db00) --- updated-dependencies: - dependency-name: Submodules/AMReX dependency-version: e95d50b2b42429431ef60feb4a6158a2fa60db00 dependency-type: direct:production ... Signed-off-by: dependabot[bot] Submodules/AMReX commit e510fbcb0c431baafb15083ffe13383852ab4e10 Merge: 21efc252 e1f49917 Author: Ann Almgren Date: Thu Jun 25 08:57:48 2026 -0700 Merge pull request #551 from seahorce-scidac/add_dependabot add dependabot.yml to keep github actions updated commit e1f4991798180a458911145bd09ab3eb872c5837 Author: Ann Almgren Date: Thu Jun 25 08:57:15 2026 -0700 add dependabot.yml to keep github actions updated .github/dependabot.yml commit 21efc252e25c25677f896bf7148bedc3b82c0a46 Merge: f6904455 7f11038f Author: Ann Almgren Date: Wed Jun 24 17:32:56 2026 -0700 Merge pull request #550 from seahorce-scidac/fix_compiler_warnings fixes to quiet compiler warnings commit 7f11038f05a6f07542aa591a7d7342817e93eb3c Author: Ann Almgren Date: Wed Jun 24 16:54:49 2026 -0700 fixes to quiet compiler warnings Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init_bcs.cpp commit f6904455f54e27623b9f06d06eb03cd07cc71f47 Merge: 4c07cf1b 3866fe52 Author: Hannah Klion Date: Wed Jun 24 16:24:52 2026 -0700 Merge pull request #548 from hklion/helper_functions_write_plotfile add helper functions for writing intermediate and final plotfiles commit 3866fe5246aeff858838ffb5ccbac93745301e2f Author: Hannah Klion Date: Wed Jun 24 16:23:44 2026 -0700 add helper functions for writing intermediate and final plotfiles Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp commit 4c07cf1b1577db77d108a860e9a6419e01685b45 Merge: f665f2bd 42eb015c Author: Hannah Klion Date: Thu Jun 18 16:14:59 2026 -0700 Merge pull request #547 from hklion/boundary_condition_errors improve documentation and error messages about boundary conditions commit 42eb015ce7aff20616562e50ad806fe532121484 Author: Hannah Klion Date: Thu Jun 18 16:14:07 2026 -0700 improve documentation and error messages about boundary conditions Docs/sphinx_doc/BoundaryConditions.rst Source/Initialization/REMORA_init_bcs.cpp commit f665f2bdb6a9beca0ad0805adaa757ea830821f0 Merge: c5721aab ffc77661 Author: Hannah Klion Date: Wed Jun 17 14:52:12 2026 -0700 Merge pull request #545 from hklion/hires_init_data revert changes to inputs commit ffc776614bc5a05a1106a02c97b0324e99c5812e Author: Hannah Klion Date: Wed Jun 17 14:29:17 2026 -0700 revert changes to inputs Exec/Upwelling/inputs commit c5721aabda2c775d5ba98d6e3bc56bd710f590f6 Merge: 3b71c66a c9288719 Author: Hannah Klion Date: Wed Jun 17 13:09:35 2026 -0700 Merge pull request #544 from hklion/hires_init_data Enable initialization with averaged-down high-resolution data commit c9288719a7a6090efa6d2ada1027e2750b2533aa Author: Hannah Klion Date: Mon Jun 15 19:17:26 2026 -0700 remove unused function and move check for analytic + high resolution initialization Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.cpp commit 8e9ab201f46e9b29a89410732693e3395b816ada Author: Hannah Klion Date: Mon Jun 15 18:55:21 2026 -0700 make progress toward analytic high-res initialization but note it is NOT fully implemented Source/Initialization/REMORA_init.cpp Source/REMORA.H commit 548cd2569d7a06a3c3611b1f35643343d38e2b11 Author: Hannah Klion Date: Mon Jun 15 11:13:42 2026 -0700 high resolution initial data working for netcdf initialization Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 67f751ee7d1ed16543bac9d55cfeea2bcc20dbf2 Author: Jean M. Sexton Date: Thu Jun 11 07:13:50 2026 -0700 working docs in progress Docs/sphinx_doc/AgenticWorkFlow.rst Docs/sphinx_doc/Context7.rst Docs/sphinx_doc/index.rst commit 3b71c66af2433a7af2ad6c727acfec52948f7b09 Merge: dca93bec c0afb174 Author: Ann Almgren Date: Tue Jun 9 12:52:35 2026 -0700 Merge pull request #543 from seahorce-scidac/add_coupling_test New exec directory for coupling problem commit c0afb17461ed2774ddef775f63b60395ac7451c0 Author: Ann Almgren Date: Tue Jun 9 12:34:15 2026 -0700 update remora_exe_name Exec/Upwelling_Coupling/CMakeLists.txt Exec/Upwelling_ML/CMakeLists.txt commit b3d59c5a22390392d71c3b13106c41a0aa465597 Author: Ann Almgren Date: Tue Jun 9 12:20:58 2026 -0700 New exec directory for coupling problem Exec/Upwelling_Coupling/CMakeLists.txt Exec/Upwelling_Coupling/GNUmakefile Exec/Upwelling_Coupling/Make.package Exec/Upwelling_Coupling/README.rst Exec/Upwelling_Coupling/inputs Exec/Upwelling_Coupling/prob.H Exec/Upwelling_Coupling/prob.cpp commit 9d8f2a597737e7c49b6ac8b072d4555465aacd9a Merge: e91b612b dca93bec Author: Hannah Klion Date: Tue Jun 9 10:36:53 2026 -0700 Merge branch 'development' into hires_init_data commit e91b612be5f05c6572e8119655d1436498a36a8b Author: Hannah Klion Date: Mon Jun 8 20:54:30 2026 -0700 Initial work for high resolution initial data - Average down or interpolate up as needed - No longer set zvel in analytic problem initialization - Make prob class methods override to catch call signature mismatches at compile time Exec/Advection/prob.H Exec/Advection/prob.cpp Exec/BlankProblem/prob.H Exec/BlankProblem/prob.cpp Exec/BoundaryLayer/prob.H Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.H Exec/Channel_Test/prob.cpp Exec/CoupleToERF/prob.H Exec/CoupleToERF/prob.cpp Exec/Dogbone/prob.H Exec/DogboneAnalytic/prob.H Exec/DogboneAnalytic/prob.cpp Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.H Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.H Exec/IdealRivGrid/prob.H Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.H Exec/Seamount/prob.cpp Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Exec/Upwelling_ML/prob.H Exec/Upwelling_ML/prob.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/REMORA.H Source/REMORA.cpp commit dca93becd79daf02d98a24a778451cc50beb5e13 Merge: 21ef9a9c bc2bed4c Author: Hannah Klion Date: Fri May 29 16:53:02 2026 -0700 Merge pull request #542 from jmsexton03/remora_erf_sst_remap_fix Remap SST slab for mismatched ERF resolution commit bc2bed4ccfd5dd04319fda1978389fde5b9614f0 Author: Jean M. Sexton Date: Fri May 29 16:29:11 2026 -0700 Ignore zstd broken link warning Docs/sphinx_doc/conf.py commit 5c56404a6016378a94954e9982f7c7adfc2fb53c Author: Jean M. Sexton Date: Thu May 28 17:43:37 2026 -0700 Remap SST slab for mismatched ERF resolution Source/REMORA_Coupling.cpp commit 21ef9a9cf3aeb993e90b9870d17dee8999f14eec Merge: 1faece4b 0379d3c8 Author: Hannah Klion Date: Thu May 28 17:31:18 2026 -0700 Merge pull request #541 from hklion/fix_netcdf_build fix build commit 0379d3c81c5620e43b557b4d53b9c04d267cd72f Author: Hannah Klion Date: Thu May 28 17:30:44 2026 -0700 fix build Source/REMORA.cpp commit 1faece4bf200f7d0a5d4d3814e04692bbf542ef8 Merge: 612f4746 1095c7a3 Author: Hannah Klion Date: Thu May 28 16:29:25 2026 -0700 Merge pull request #540 from hklion/fix_netcdf_build reorder params so that netcdf build works commit 1095c7a3e389bdbbb28dd895c81ffb5a869a1895 Author: Hannah Klion Date: Thu May 28 16:28:43 2026 -0700 reorder params so that netcdf build works Source/REMORA.cpp commit 612f47469f2773143c17746205055d351f614467 Merge: b48be2f4 9e09e9e2 Author: Hannah Klion Date: Tue May 26 11:47:09 2026 -0700 Merge pull request #539 from jmsexton03/update_remora_faceslab Add function and constructor for atmosphere coupling commit 9e09e9e2af8e7ead99376d2c9923a4e805e571ff Author: Jean M. Sexton Date: Tue May 26 10:27:18 2026 -0700 Document and enumerate atmospheric forcing indices - Add AtmosState enum to REMORA_IndexDefines.H with per-field unit annotations, replacing magic integer indices in ApplyAtmosphericStates - Expand driver_atmos_state_from_driver array size from hardcoded 9 to AtmosState::NumTypes - Add Doxygen @param docstrings to PackSurfaceState and ApplyAtmosphericStates in both the header and implementation Source/REMORA.H Source/REMORA_Coupling.cpp Source/REMORA_IndexDefines.H commit d0a6256935890448de0f88d3fe631d30c8d4ac88 Author: Jean M. Sexton Date: Thu May 21 13:58:27 2026 -0700 fix docs links Docs/sphinx_doc/coc.rst Docs/sphinx_doc/submodule.rst commit 64724b1afcb74189417a4b7f507f45c917c01a7e Author: Jean M. Sexton Date: Thu May 21 13:54:56 2026 -0700 remora: fix warning and whitespace Source/REMORA.cpp Source/REMORA_Coupling.cpp commit 054e029ac640752ab31f1db8848a31114904ae77 Author: Jean M. Sexton Date: Thu May 21 13:09:40 2026 -0700 Update unit conversion order and remove lambdas Source/REMORA_Coupling.cpp Source/TimeIntegration/REMORA_advance_3d.cpp commit 84cfc8de04ef7cf531bd4dd06a0a828be2f4f413 Author: Jean M. Sexton Date: Thu May 21 12:07:50 2026 -0700 remora: simplify fallback state handling Source/REMORA.cpp Source/REMORA_Coupling.cpp commit 719457778a33621bf87e308adb5a9b2cd9b74a40 Author: Jean M. Sexton Date: Tue May 19 12:54:59 2026 -0700 Preserve coupled atmospheric forcing lanes Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp commit a73896649be05b5c736fd13fdcab443f8faa80ed Author: Jean M. Sexton Date: Mon May 18 10:09:19 2026 -0700 coupling: add REMORA one-step evolve hook for driver loop Source/REMORA.H Source/REMORA_Coupling.cpp commit 42238175720038a3e2900ad53aac486aec89dd33 Author: Jean M. Sexton Date: Thu May 14 10:52:25 2026 -0700 Add timer print Source/REMORA.cpp commit 2b6674b7a65854707b0216aad98e71109b614493 Author: Jean M. Sexton Date: Thu May 14 06:50:25 2026 -0700 Fix removed variables Source/REMORA.cpp commit e1801ed80498bbf09a0b7efbd4cda131bda29281 Author: Jean M. Sexton Date: Thu May 14 03:54:19 2026 -0700 Minor cleanup Source/REMORA.H commit 5fc8256234ad91f55118a933742721dbb37ad2f0 Author: Jean M. Sexton Date: Wed May 13 14:22:47 2026 -0700 coupling: implement real PackSurfaceState and ApplyAtmosphericStates PackSurfaceState: extract SST from cons_new[0] at k=N (REMORA surface), convert Celsius to Kelvin, and ParallelCopy to the driver slab. ApplyAtmosphericStates: replace asserting copy_if_present with ParallelCopy-based safe_copy lambda. Add unit conversions at the boundary: Patm Pa→mb (×0.01), Tair K→°C (−273.15). Drop unused copy helpers. Source/REMORA_Coupling.cpp commit 7caba759a325268988606f99abbde43134cde34f Author: Jean M. Sexton Date: Wed May 13 13:18:22 2026 -0700 ReadParameters: fix body scope; remove explicit-construction guard; update CoupleToERF inputs Fix a duplicate ReadParameters() body that leaked at global scope (from commit 7a02d88). Restore full NETCDF/particles param reads and the boxes_at_level setup unconditionally. Remove the if (!explicit_construction) guard around amr.* queryAdd calls; the driver now removes those keys from the ParmParse table before constructing REMORA in coupled mode. Add ic_type=analytic and grid_scale_type=constant to CoupleToERF/inputs. Exec/CoupleToERF/inputs Source/REMORA.cpp commit bb4f8a9a3b6e5e17312eaeaefb61da53d8031a52 Merge: 4fdbcb5c b48be2f4 Author: Jean M. Sexton Date: Wed May 13 11:46:45 2026 -0700 Merge remote-tracking branch 'origin/development' into update_remora_faceslab commit 4fdbcb5c53f4d8296ca42013bce820289da6f5cf Author: Jean M. Sexton Date: Wed May 13 07:32:58 2026 -0700 remora: add explicit-construction constructor taking RealBox + n_cell args Source/REMORA.H Source/REMORA.cpp commit b48be2f4c08c1ca44f8962f0cdcf5494601b1128 Merge: befc8d41 f7efaf61 Author: Hannah Klion Date: Tue May 12 11:01:58 2026 -0700 Merge pull request #537 from hklion/base_prob_erf_coupling add base problem for testing coupling to ERF commit f7efaf610e2bf7ae4b590cd7642a80f015bf904d Author: Hannah Klion Date: Mon May 11 20:59:52 2026 -0700 remove unused Exec/CoupleToERF/prob.H commit 4b9179d58ec8867c416a18f0f6760546754feb22 Author: Hannah Klion Date: Mon May 11 17:33:28 2026 -0700 comment out lev Exec/CoupleToERF/prob.cpp commit d1afe0357fee8a866bf36e3ac606213ff22bdb71 Author: Hannah Klion Date: Mon May 11 17:24:39 2026 -0700 don't build the ERF coupling problem automatically CMakeLists.txt commit 7e9e2cc634afc7d79ddcb71cf1375a9e55a7c1c6 Author: Hannah Klion Date: Mon May 11 17:17:04 2026 -0700 add to cmakelists CMakeLists.txt Exec/CMakeLists.txt commit 488659188c3bc5b5afb8c6ab1910b4b64a4c4a4c Author: Hannah Klion Date: Mon May 11 17:14:36 2026 -0700 add base problem for testing coupling to ERF Exec/CoupleToERF/CMakeLists.txt Exec/CoupleToERF/GNUmakefile Exec/CoupleToERF/Make.package Exec/CoupleToERF/inputs Exec/CoupleToERF/prob.H Exec/CoupleToERF/prob.cpp commit 3569b2a6ca19d262e714bbb223cd1eedd7bbc012 Author: Jean M. Sexton Date: Mon May 11 13:45:42 2026 -0700 coupling: map ERF slabs into REMORA 2D forcing planes Source/REMORA_Coupling.cpp commit befc8d41041b1716423b216c7a0e1a2cd4588d6b Merge: 849339fb 6f1c6764 Author: Hannah Klion Date: Mon May 11 10:11:15 2026 -0700 Merge pull request #536 from jmsexton03/prereview/remora-coupling-api Prereview/remora coupling api commit 849339fbbea2ceecb9ae1935cef75d2bed15af1b Merge: 980fc71b 564554c5 Author: Hannah Klion Date: Mon May 11 10:09:28 2026 -0700 Merge pull request #535 from jmsexton03/prereview/remora-build-link REMORA CMake variable tweaks and library build commit 6f1c6764b7fcd839257a6971da850bd342931bba Merge: 08e81a4f 564554c5 Author: Jean M. Sexton Date: Fri May 8 11:57:06 2026 -0700 Merge remote-tracking branch 'jmsexton03/prereview/remora-build-link' into prereview/remora-coupling-api commit 08e81a4f4d595359b6638e70bee0924d731418b3 Author: Jean M. Sexton Date: Fri May 8 11:53:20 2026 -0700 cleanup: remove unused BCNames in REMORA.cpp Source/REMORA.cpp commit 564554c525d27ec957c202ff025ada768b750ab4 Author: Jean M. Sexton Date: Fri May 8 11:13:37 2026 -0700 cmake: add library-mode problem selector for remora_api CMake/BuildREMORAExe.cmake CMakeLists.txt commit d72cbafbe7f79c9b1d84e096608f76456a585c74 Author: Jean M. Sexton Date: Fri May 8 11:00:52 2026 -0700 cmake: restore main.cpp when building example executables CMake/BuildREMORAExe.cmake commit a86f52d856ca68c9a25fb26c72170f578a4982b0 Author: Jean M. Sexton Date: Fri May 8 09:21:47 2026 -0700 coupling: simplify stage checks with AMReX-native reductions Source/REMORA_Coupling.cpp commit c9e03939424855ef4afaa971abb3e3434356cfb8 Author: Jean M. Sexton Date: Fri May 8 09:01:17 2026 -0700 coupling: prioritize COAWST references in stage-0 comments Source/REMORA_Coupling.cpp commit 1b2f27d7b235902447f4e73fb3c702118da6a005 Author: Jean M. Sexton Date: Thu May 7 11:37:50 2026 -0700 coupling: add stage-0 surface/atmosphere exchange API Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Coupling.cpp commit ffc174dbf60fab5bca77bdab94f4347e11c4c5f5 Author: Jean M. Sexton Date: Fri May 8 10:25:15 2026 -0700 cmake: guard REMORA_Coupling.cpp on non-coupling branches CMake/BuildREMORAExe.cmake commit cc91569fd9db977e8d4e9b0622937dd6bcc001a4 Author: Jean M. Sexton Date: Fri May 8 05:59:25 2026 -0700 cmake: prefix Problem/SolverChoice symbols in library-only mode CMake/BuildREMORAExe.cmake commit 8736e78a084455b8458dd3ab78fb0b69f2070a95 Author: Jean M. Sexton Date: Thu May 7 17:17:44 2026 -0700 cmake+blankprob: enable library-only probinit and fix header declarations CMake/BuildREMORAExe.cmake Exec/BlankProblem/prob.H commit 54448c96f03cca7529eb7dcc12bdf8f10f26e4b5 Author: Jean M. Sexton Date: Thu May 7 11:37:45 2026 -0700 cmake: support parent-superbuild AMReX and library-only mode CMake/BuildREMORAExe.cmake CMakeLists.txt Exec/CMakeLists.txt commit 980fc71be833411f33922d880d6ddcd84bd41f0f Merge: f912cc71 b26569dd Author: Hannah Klion Date: Thu May 7 16:23:20 2026 -0700 Merge pull request #534 from hklion/dont_read_2dvel_netcdf Don't read in 2D vel from initial data NetCDF commit b26569dde68ee9802e72fd924004ae2fcf6e52ac Author: Hannah Klion Date: Thu May 7 15:53:04 2026 -0700 Don't read in 2D vel from initial data NetCDF - 2D velocities are calculated from 3D state so no need to read in from file Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp commit f912cc71d1d5f340e5e93df8d092639cf702c4cd Merge: 402a0a39 f0dded40 Author: Hannah Klion Date: Thu May 7 09:11:13 2026 -0700 Merge pull request #532 from hklion/hires_bathy_fix Fix high resolution bathymetry commit f0dded405b3ec55b72f090c825053a72c41f3410 Merge: 63108958 402a0a39 Author: Hannah Klion Date: Wed May 6 16:12:58 2026 -0700 Merge branch 'development' into hires_bathy_fix commit 631089584b3d2762ac8c04efc1a340a7d5e21414 Author: Hannah Klion Date: Wed May 6 16:11:12 2026 -0700 update Upwelling bathymetry setup to accomodate arbitrary number of grow cells Exec/Upwelling/prob.cpp commit 2003e4e0f6053e2ce9ef17b1e95de4b4a33c3cd0 Author: Hannah Klion Date: Wed May 6 16:10:18 2026 -0700 fix bugs in high resolution bathymetry feature and do pm/pn from high res files Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 402a0a390db7d0e2ea35d7cb4d26713601b30ffa Merge: 40997e77 84ff84f2 Author: Hannah Klion Date: Mon May 4 15:10:38 2026 -0700 Merge pull request #531 from hklion/update_tests update tests for more precise consts values commit 84ff84f2b8f12ab724fab1d16db30bfdb94192d1 Author: Hannah Klion Date: Mon May 4 14:46:02 2026 -0700 update tests for more precise consts values Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_H Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/BoundaryLayer/job_info Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_H Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Channel_Test/job_info Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Cell_H Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoubleGyre/job_info Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Header Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_H Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/job_info Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_H Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount/job_info Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling/job_info Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/job_info Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/job_info Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_logdrag/job_info Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_qdrag/job_info commit 40997e7730a77a6e9df9e589aa1a07c0ac27f28e Merge: 3679f11a 0f2e7100 Author: Hannah Klion Date: Mon May 4 14:44:59 2026 -0700 Merge pull request #529 from dylanschlichting/update_constants updates constants precision commit 3679f11ae8a1b61769af8285c142c7075c508765 Merge: a968ad9b 3e150cdf Author: Hannah Klion Date: Mon May 4 10:55:45 2026 -0700 Merge pull request #528 from dylanschlichting/add_geomix_docs Add geomix docs commit a968ad9b214e915056368eb1f7be63fbc1d57ea6 Merge: 42f51cbe a3d3f539 Author: Hannah Klion Date: Mon May 4 09:44:45 2026 -0700 Merge pull request #530 from hklion/geopotential_typo fix typo in geopotential commit a3d3f5398610f3894f1fd57a602a60481a93fb55 Author: Hannah Klion Date: Mon May 4 09:43:37 2026 -0700 fix typo in geopotential Source/TimeIntegration/REMORA_t3dmix.cpp commit 0f2e7100e69ac1c015fdd655f08b2e62a7c20bad Author: Dylan Schlichting Date: Sun May 3 07:14:04 2026 -0700 updates constant precision Source/REMORA_Constants.H commit 3e150cdfc5b9aed8ebffa8d256c0be8d81dea5ba Author: Dylan Schlichting Date: Fri May 1 08:10:51 2026 -0700 fixed whitespace Docs/sphinx_doc/Inputs.rst commit 1132edc131f6d05e35153bfc610e11face977514 Author: Dylan Schlichting Date: Fri May 1 07:59:05 2026 -0700 second update to docs Docs/sphinx_doc/Inputs.rst commit 42f51cbe2a395a0936bd6542aed22c7967dc88ae Merge: 3d262a35 605f2b5c Author: Hannah Klion Date: Wed Apr 29 15:21:30 2026 -0700 Merge pull request #514 from hklion/hires_bathy Initialize bathymetry in mesh refinement by averaging down high resolution data commit 605f2b5cedbff75b9e2c2de0c0535d3859d017b1 Author: Hannah Klion Date: Wed Apr 29 14:52:11 2026 -0700 fix GPU build Source/REMORA.H Source/REMORA.cpp commit 05a747e0795a796e358b1dfd3f81363fd991d9a4 Author: Hannah Klion Date: Wed Apr 29 13:19:35 2026 -0700 typo Source/Initialization/REMORA_init.cpp commit e19e7bdd81d0f44988899d847013ef4bef090dd1 Author: Hannah Klion Date: Wed Apr 29 13:14:05 2026 -0700 Enable higher-resolution grid levels for analytic initialization And fix errors with netcdf initialization Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/ProblemSetup.rst Source/IO/REMORA_NCFile.H Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 718b4ce6a937c56bbee86e440cf4bb45372cfd9c Author: Jean M. Sexton Date: Mon Apr 27 13:17:57 2026 -0700 Refine agentic docs tone and soften LLM admonition Docs/sphinx_doc/AgenticWorkFlow.rst Docs/sphinx_doc/GenericInputs.rst commit 97d4fd67af3712a024a8ea1ee4460d80297cb7ef Author: Jean M. Sexton Date: Mon Apr 27 06:01:42 2026 -0700 Add composed schema-based generic inputs generator and validation CI .github/workflows/generic-inputs-validate.yml Docs/sphinx_doc/AgenticWorkFlow.rst Docs/sphinx_doc/GenericInputs.rst Docs/sphinx_doc/index.rst Exec/Generic/.gitignore Exec/Generic/build_schema_remora.py Exec/Generic/build_schema_remora.sh Exec/Generic/inputs_generic Exec/Generic/remora_value_hints.json Exec/Generic/render_inputs_generic.py Exec/Generic/tests/test_build_schema_remora.py commit 40aa78e00abfd3592f0dcd2e09ab9aefaea0fd47 Author: Dylan Schlichting Date: Tue Apr 21 15:10:18 2026 -0700 initial update of geopotential mixing docs Docs/sphinx_doc/Inputs.rst commit cefc6e3b5d28696aaaae9ab4275829436d602deb Author: Hannah Klion Date: Mon Apr 20 14:55:32 2026 -0700 fix build issues Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit a910a7980ea30ded225562f16b478ea30abbcb43 Merge: d425a787 3d262a35 Author: Hannah Klion Date: Mon Apr 20 14:48:37 2026 -0700 Merge branch 'development' into hires_bathy commit 3d262a35ae95cc8020027a3bf37817a5aa588e1c Merge: df2ccb1f bb0c059e Author: Hannah Klion Date: Sun Apr 19 11:27:08 2026 -0700 Merge pull request #519 from emmashie/add_f_plot2d added functionality to output Coriolis parameter to 2d plotfiles commit df2ccb1f06952eb2ddecada1ff62eccb4e73b204 Merge: 91881197 f040e343 Author: Hannah Klion Date: Sun Apr 19 11:26:16 2026 -0700 Merge pull request #521 from hklion/geopotential_mixing Geopotential-aligned diffusion commit f040e3433c7b583caa0959a95e3a3b2d0b864ff9 Author: Hannah Klion Date: Sat Apr 18 21:09:24 2026 -0700 tweak docs Docs/sphinx_doc/Inputs.rst commit bf65076e9cb230d6b7d1bc78c85c81fdc8ef8fad Author: Hannah Klion Date: Sat Apr 18 21:06:37 2026 -0700 add docs Docs/sphinx_doc/Inputs.rst commit d9c08f30371224e510dcdfefd66ba41644bd83c5 Merge: a441fde8 91881197 Author: Hannah Klion Date: Sat Apr 18 21:04:13 2026 -0700 Merge branch 'development' into geopotential_mixing commit a441fde8006daad28b53e883ba586334ab8f14b5 Author: Hannah Klion Date: Sat Apr 18 21:03:38 2026 -0700 add option to align harmonic mixing with geopotential surfaces Source/REMORA.H Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp commit 91881197be03fd431c3e6cf9ea581a9f75c0837a Merge: e8807ef7 e9b6b4f3 Author: Hannah Klion Date: Sat Apr 18 21:01:49 2026 -0700 Merge pull request #520 from hklion/doc_fix fix inputs table formatting commit e9b6b4f37c61199861f0b9d857b9ca6526fba353 Author: Hannah Klion Date: Sat Apr 18 20:58:03 2026 -0700 fix inputs table formatting Docs/sphinx_doc/Inputs.rst commit bb0c059e0852b05ef5846a8aafdd00a19e0d40c9 Author: Emma Nuss Date: Fri Apr 17 10:28:17 2026 -0700 added functionality to output Coriolis parameter to 2d plotfiles Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp commit e8807ef76f79ab23ac42e9c86ad42616c2683acc Merge: 72b773fb ecfddcc6 Author: Hannah Klion Date: Thu Apr 16 11:29:03 2026 -0700 Merge pull request #517 from hklion/clima_rivers_multiple_files time series in NCTimeSeries and NCTimeSeriesRiver can be split over multiple files commit 72b773fbe49df9634abf40a30a274b7e6b9d3b50 Merge: 0003e96b 4ff3e67e Author: Hannah Klion Date: Thu Apr 16 11:27:24 2026 -0700 Merge pull request #513 from seahorce-scidac/add_multiple_scalars Allow us to set remora.nscalar at runtime commit 0003e96b2ee4f31466a2e1f0787cdae1d33abf81 Merge: d116c196 70ee7562 Author: Hannah Klion Date: Thu Apr 16 11:18:26 2026 -0700 Merge pull request #516 from jmsexton03/hdf5_remove Remove HDF5 support and legacy Cori build scripts commit ecfddcc6bfe7f3a251e1045193ab95054fabca6e Author: Hannah Klion Date: Thu Apr 16 11:05:19 2026 -0700 update docs Docs/sphinx_doc/Climatology.rst Docs/sphinx_doc/Inputs.rst commit 2f455b33f9f4bde12f1aca574245f1abd8078924 Author: Hannah Klion Date: Thu Apr 16 11:04:56 2026 -0700 enable NCTimeSeries and NCTimeSeriesRiver to take multiple data files as part of time series Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 70ee756211aa7fc883caf1b006e63f32f7276fb7 Author: Jean M. Sexton Date: Thu Apr 16 10:17:35 2026 -0700 Remove HDF5 support and legacy Cori build scripts * Remove HDF5 wiring from CMake and GNUmake build paths. * Remove HDF5 plotfile type handling from REMORA source code. * Delete Cori env script and clean NERSC build helpers. Build/clone_copy_build.sh Build/cmake_with_pnetcdf.sh Build/cori-env.sh Build/saul-env.sh CMake/BuildREMORAExe.cmake CMake/SetAmrexOptions.cmake Exec/Make.REMORA Source/IO/REMORA_Plotfile.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H commit d116c196b97b73260270a98e438c8f6036f6358d Merge: dcfd9dcb 3038fd78 Author: Hannah Klion Date: Wed Apr 15 15:58:26 2026 -0700 Merge pull request #515 from jmsexton03/minor_cmake_fix PNetCDF/HDF5 build fixes and config guards commit d425a787dd2993b278a0aa943aa61e4d59ebaf25 Author: Hannah Klion Date: Wed Apr 15 14:08:37 2026 -0700 add docs Docs/sphinx_doc/Inputs.rst commit 3038fd78a33a9c3c7b75b45411e8df0013072b59 Author: Jean M. Sexton Date: Wed Apr 15 13:51:18 2026 -0700 Check for amrex built in hdf5 plotfile path Source/REMORA.cpp commit dd69f163d069fa058b3ff7449c0179ec53d842d9 Author: Jean M. Sexton Date: Wed Apr 15 13:52:01 2026 -0700 Add missing module load for now Build/cmake_with_pnetcdf.sh Build/saul-env.sh commit b47d839821b181685a650e822fb2836c4a4dcd1c Author: Jean M. Sexton Date: Wed Apr 15 13:34:36 2026 -0700 Add error for using netcdf instead of pnetcdf CMakeLists.txt commit f289a7965913125aeb81d474515e7ee4d90dcf4f Author: Jean M. Sexton Date: Wed Apr 15 13:30:17 2026 -0700 Swap flag, remove old file target Build/cmake_with_pnetcdf.sh CMake/BuildREMORAExe.cmake commit 304571ab29db792809ab9285206926541e33d1f6 Author: Jean M. Sexton Date: Wed Apr 15 13:08:07 2026 -0700 Need pnetcdf cmake flag Build/cmake_with_pnetcdf.sh commit b7b2c2b8dfa34f71c676c0058e548e1f4121addd Author: Jean M. Sexton Date: Wed Apr 15 11:42:22 2026 -0700 Fix typo and add interpreter directive Build/cmake.sh Build/cmake_with_netcdf.sh Build/cmake_with_particles.sh commit 89f37f4f83956ba5268fbb5c1f0783d5eb4a9f1a Author: Hannah Klion Date: Wed Apr 15 12:21:56 2026 -0700 fix typo Source/REMORA.H commit c2f1127a508da83c6c9092e6d4f8a378f19befb5 Author: Hannah Klion Date: Wed Apr 15 12:16:54 2026 -0700 remove print statements and adjust initialization logic Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H commit 4ff3e67e7b743103bfa70184c8a8a67ec1110c7b Author: Ann Almgren Date: Wed Apr 15 12:01:01 2026 -0700 remove unused Source/Initialization/REMORA_init_bcs.cpp commit 1591580ab3f849db457208a3ea16919607fd43a1 Author: Ann Almgren Date: Wed Apr 15 11:58:18 2026 -0700 more changes to support multiple scalars Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init_bcs.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_gls.cpp commit a5e4848ecff49c040072b11b46fd158edb17d2d6 Author: Ann Almgren Date: Wed Apr 15 10:32:38 2026 -0700 Allow us to set remora.nscalar at runtime Docs/sphinx_doc/Inputs.rst Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit 05399c4eae07e180f7a95c618127911b35ab3d1f Merge: ec313a92 dcfd9dcb Author: Hannah Klion Date: Tue Apr 14 14:17:49 2026 -0700 Merge branch 'development' into hires_bathy commit dcfd9dcb9cf5b7c8e8c0a7570981571d3040da31 Merge: 729ffebe a6a42bc5 Author: Hannah Klion Date: Tue Apr 14 14:09:37 2026 -0700 Merge pull request #511 from hklion/extend_nudg_coeff_mf increase number of ghost cells in MFs for nudg_coeff to make Orlanski… commit a6a42bc5e60d330edd8f91b7f5f2b039d0f8147a Author: Hannah Klion Date: Tue Apr 14 14:09:06 2026 -0700 increase number of ghost cells in MFs for nudg_coeff to make Orlanski BCs work Source/Initialization/REMORA_make_new_level.cpp commit ec313a923faaf4aa71a9f2a6d10498cc8cb02be3 Author: Hannah Klion Date: Tue Apr 14 12:23:17 2026 -0700 initial commit initializing bathymetry at high resolution from netcdf and averaging down Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCFile.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 729ffebe6fd0789106b816df0c4238bbe52cfcf9 Merge: b2d2d3f7 8458acff Author: Hannah Klion Date: Mon Apr 13 12:17:15 2026 -0700 Merge pull request #509 from hklion/fix_2dvar_plotfile correct and improve error messages for plotfile fields commit 8458acff040af3c2ec91b056bedbcdd153e63937 Author: Hannah Klion Date: Mon Apr 13 10:26:45 2026 -0700 correct and improve error messages for plotfile fields Source/IO/REMORA_SetPlotVars.cpp commit b2d2d3f74d2f2a85a45e6c92aa62694ef8833260 Merge: 418cf947 f88ba775 Author: Hannah Klion Date: Mon Apr 13 08:31:16 2026 -0700 Merge pull request #497 from dylanschlichting/add_variable_hmix Adds laplacian mixing coefficients scaled to the grid size and refinement level commit 418cf947e7f8c3a7fcea45b125f38060e0e5f6ef Merge: 25f90d49 fe577323 Author: Hannah Klion Date: Fri Apr 10 11:19:09 2026 -0700 Merge pull request #506 from hklion/change_to_unique_ptr make netcdf data series and advective flux pointers into unique_ptr commit fe577323091bff86776a5c9a08d769d4572b1608 Author: Hannah Klion Date: Fri Apr 10 09:12:15 2026 -0700 make netcdf data series and advective flux pointers into unique_ptr Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit f88ba775f22395d9f984c71d7e395cc8a5e5e891 Author: Dylan Schlichting Date: Thu Apr 9 16:48:30 2026 -0700 made arrs 2D Source/IO/REMORA_Plotfile.cpp commit c167a18ae345a9c852ffe8496d3583783ef612b8 Author: Dylan Schlichting Date: Thu Apr 9 16:11:46 2026 -0700 gets rid of old plot erase + spaces Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp commit cd39bfe55cd7b54bc2c0bd440fd6cfb175508bf4 Author: Dylan Schlichting Date: Thu Apr 9 15:51:36 2026 -0700 reflects PR#501 now that coeffs are 2D Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.cpp commit 25f90d4909a172dc53038bf9449df21afa2ca3c3 Merge: b524e351 a72ef781 Author: Hannah Klion Date: Thu Apr 9 15:42:15 2026 -0700 Merge pull request #505 from hklion/ndarray_shared_ptr rewrite NDArray to use shared_ptr rather than doing memory management by hand commit d8616a715735405e2811715e14cea8abd2f7b337 Author: Dylan Schlichting Date: Thu Apr 9 14:25:23 2026 -0700 updates netcdf plotting code for bug fix Source/IO/REMORA_NCPlotFile.cpp commit c6d18b920af7fc7cc73f20d9b8c265944ce914c1 Merge: ed147122 b524e351 Author: Dylan Schlichting Date: Thu Apr 9 15:19:08 2026 -0600 Merge branch 'seahorce-scidac:development' into add_variable_hmix commit b524e351f0876f6c04e0d7082a654ab58d5a35fc Merge: 82edd141 b024a436 Author: Hannah Klion Date: Thu Apr 9 14:15:14 2026 -0700 Merge pull request #501 from hklion/visc_diff_2d make diff2, visc2_p and visc2_r 2D arrays commit a72ef781b88a60c037adbf38b25ea738708ac201 Author: Hannah Klion Date: Thu Apr 9 14:06:09 2026 -0700 rewrite NDArray to use shared_ptr rather than doing memory management by hand Source/IO/REMORA_NCFile.H commit b024a4369da97d2c0904f6406c63aa51b48ca479 Author: Hannah Klion Date: Thu Apr 9 13:57:54 2026 -0700 fix indexing Source/TimeIntegration/REMORA_t3dmix.cpp commit fd4ed0f9c2b7bc3c3b21826f3f2cf62d6b39fa51 Author: Hannah Klion Date: Thu Apr 9 12:41:52 2026 -0700 fix problem initialization of visc2 and diff2 Exec/Advection/prob.cpp Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/IdealRivGrid/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Exec/Upwelling_ML/prob.cpp commit 9cb1134095d06c73a70245262794cd199fd2da55 Author: Hannah Klion Date: Thu Apr 9 11:43:52 2026 -0700 make diff2, visc2_p and visc2_r 2D arrays Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_t3dmix.cpp commit ed1471229d1ff4d3f685a5dfff1e40650debbde6 Author: Dylan Schlichting Date: Wed Apr 8 14:59:28 2026 -0700 removed trailing space after par Source/REMORA.cpp commit 100b7b13fc22b8451c62e970e01c28ec9bef59a5 Author: Dylan Schlichting Date: Wed Apr 8 14:56:04 2026 -0700 fixed more unnecessary k loops Source/REMORA.cpp commit 7be5aefc511b76bb392fa0d866be5f59a4046db6 Author: Dylan Schlichting Date: Wed Apr 8 14:54:56 2026 -0700 fixed unnecessary k loops Source/REMORA.cpp commit 9f6e1dc7475f1fba4cde4dcce1d4607217480efe Author: Dylan Schlichting Date: Wed Apr 8 14:42:21 2026 -0700 fixed braces for style on loops/if statements Source/REMORA.cpp commit d3cee0583377fccbd39d35cbfb8a9449da234068 Author: Dylan Schlichting Date: Wed Apr 8 15:27:59 2026 -0600 Update Source/REMORA.cpp so k is 0 Co-authored-by: Hannah Klion Source/REMORA.cpp commit 40ba92dadccb33d14ee8716f01de12a6c58cc2e7 Author: Dylan Schlichting Date: Wed Apr 8 15:27:24 2026 -0600 Removed loop over k in remora.cpp Co-authored-by: Hannah Klion Source/REMORA.cpp commit d2613d99480df8ecbfb311442c3a960b9168b3d4 Author: Dylan Schlichting Date: Wed Apr 8 14:27:55 2026 -0600 Update Source/IO/REMORA_NCPlotFile.cpp Co-authored-by: Hannah Klion Source/IO/REMORA_NCPlotFile.cpp commit 82edd141a54d68b632810b1caca96be6541f6678 Merge: f5623066 f5a08857 Author: Hannah Klion Date: Wed Apr 8 12:56:47 2026 -0700 Merge pull request #500 from emmashie/update_docs Updated docs for AMR interpolation and bulk fluxes commit f5a08857b77b872b3c8f0db23b241c2cec8fede3 Author: Emma Nuss Date: Wed Apr 8 11:55:20 2026 -0700 ran trailing whitespace check Docs/sphinx_doc/Inputs.rst commit 9cde9c1e3f3d359e421862382a0791d21ccff6b8 Author: Emma Nuss Date: Wed Apr 8 11:47:46 2026 -0700 edited inputs docs formatting Docs/sphinx_doc/Inputs.rst commit 839e2b085cb577348f0e8c97027aec306834d572 Author: Dylan Schlichting Date: Wed Apr 8 12:02:47 2026 -0600 once again, fix whitespace Docs/sphinx_doc/Plotfiles.rst commit be9aadc69934361e8b9d4a634d702b81fcaf1202 Author: Dylan Schlichting Date: Wed Apr 8 11:59:06 2026 -0600 Updated plotfiles docs to remove old comment Docs/sphinx_doc/Plotfiles.rst commit 27188b0e338592eee7e867ddaa4a3e0bf95454f7 Author: Emma Nuss Date: Wed Apr 8 09:19:14 2026 -0700 Updated docs on interpolation from level0 to finer grids for AMR (climatology and forcing files) and bulk fluxes documentation Docs/sphinx_doc/Climatology.rst Docs/sphinx_doc/Inputs.rst commit 608e91754da1721d2e5410e7a62d3d5e0ef5ed35 Merge: 99ae9733 f5623066 Author: Dylan Schlichting Date: Tue Apr 7 15:09:45 2026 -0600 Merge branch 'development' into add_variable_hmix commit 99ae97337bec0d7825fd029b8bb6f9d66731f300 Author: Dylan Schlichting Date: Tue Apr 7 14:05:35 2026 -0700 added scaled mixing for AMR Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H commit f5623066324cc7d7546a08d98b910656d705ea7e Merge: 37b799d8 43faffeb Author: Hannah Klion Date: Tue Apr 7 13:35:09 2026 -0700 Merge pull request #499 from hklion/user_spec_fill_value allow user to specify fill value for masked arrays commit 43faffeb1fcff13a9c79924f2426f1e8114767b8 Author: Hannah Klion Date: Tue Apr 7 13:08:22 2026 -0700 allow user to specify fill value for masked arrays Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 40b7f8d30eddb9e360c0d44e5aca2c5a4a60bf34 Author: Dylan Schlichting Date: Tue Apr 7 10:15:02 2026 -0700 Fix trailing whitespace in Inputs docs Docs/sphinx_doc/Inputs.rst commit 49131de8138b2ad2e08dfdf4fc336641ddad3811 Author: Dylan Schlichting Date: Tue Apr 7 09:30:59 2026 -0700 updated print and doc statements for masks Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp commit b724a7965435ab0681b7efe3fbbe0de72c5797cc Author: Dylan Schlichting Date: Tue Apr 7 09:12:36 2026 -0700 modified coeffs to be 2D + updated docs Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp commit fbb900ea2c98406700010792751330fee9ef7abd Author: Dylan Schlichting Date: Tue Apr 7 07:54:49 2026 -0700 initial commit, compiles + runs Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H commit 37b799d8b29bfeac63eeea73b9df95238b508c7b Merge: 9cf524f9 0861ee05 Author: Hannah Klion Date: Mon Apr 6 15:53:28 2026 -0700 Merge pull request #490 from hklion/time_series_error_msg only do check for number of times on IO Processor commit 0861ee05ce86892f2d5130d988dadc94a4bd2151 Author: Hannah Klion Date: Mon Apr 6 15:03:34 2026 -0700 only do check on IOProc Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_NCTimeSeriesRiver.cpp commit 9cf524f9ac93b6f5e37e33c4556f238c18ecf1ea Merge: 43face64 be3bf34b Author: Hannah Klion Date: Fri Apr 3 10:48:30 2026 -0700 Merge pull request #484 from hklion/time_series_error_msg exit with error if there is only one point in a time series read from file commit be3bf34b0b2cf4812e6a46dc671276de32efe422 Author: Hannah Klion Date: Fri Apr 3 10:46:43 2026 -0700 exit with error if there is only one point in a time series read from file Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/REMORA_NCTimeSeriesRiver.cpp commit 43face64e28d6578cdb2fc8f987cc4dd336f63a3 Merge: 422c3758 de52bea6 Author: Hannah Klion Date: Thu Apr 2 16:42:17 2026 -0700 Merge pull request #482 from hklion/fix_qsea_small_value_guard add qsea small value guard and note that ROMS does not have it commit de52bea68ecf24d3b9e880f52dc2a4d0419685fe Author: Hannah Klion Date: Thu Apr 2 14:01:18 2026 -0700 add qsea small value guard and note that ROMS does not have it Source/TimeIntegration/REMORA_bulk_flux.cpp commit 422c37585deb64225fbeba4b7caab0c5c8b1c79a Merge: 34562959 dd5fe13c Author: Hannah Klion Date: Thu Apr 2 13:24:06 2026 -0700 Merge pull request #481 from hklion/fix_swapped_north_south swap north and south tags in BC application commit dd5fe13c0d98af847225c14713dedec2de98e8fa Author: Hannah Klion Date: Thu Apr 2 13:16:09 2026 -0700 swap north and south tags in BC application Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp commit 345629596baf06f0d8dc93b45357d6ba7616787e Merge: 4895fb0c 0531b629 Author: Hannah Klion Date: Thu Apr 2 12:00:24 2026 -0700 Merge pull request #479 from hklion/fix_yhigh_BC_branch_checks fix yhigh BC branch checks for Orlanski BCs commit 4895fb0c84758f37ff42dbaa322d7a347d4250c5 Merge: 6b975e3e 0eca1468 Author: Hannah Klion Date: Thu Apr 2 12:00:00 2026 -0700 Merge pull request #480 from hklion/fix_zhigh_ghost_fill fix z-high ghost fill being guarded by bx_zlo rather than bx_zhi commit 0eca146800782b096050771374acde72828faf8d Author: Hannah Klion Date: Thu Apr 2 10:49:34 2026 -0700 fix z-high ghost fill being guarded by bx_zlo rather than bx_zhi Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp commit 0531b6293c9a53843c6fa2590be3108d076c50ba Author: Hannah Klion Date: Thu Apr 2 10:40:49 2026 -0700 remove weirdly pasted makeSlab Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp commit 2752050db7be576a380a57a3c8cb606e4986ebb3 Author: Hannah Klion Date: Thu Apr 2 10:38:44 2026 -0700 fix yhigh BC branch checks for Orlanski BCs Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp commit 6b975e3e0b236f01fd461781487136865a17f8dc Merge: de0cf7f5 7e39e3ee Author: Ann Almgren Date: Mon Mar 30 18:27:26 2026 -0700 Merge pull request #478 from emmashie/net_lwrad added functionality for providing net lward, rather than just downward commit 7e39e3ee2e69bed01101601412db3024d0bbec5e Author: Emma Nuss Date: Mon Mar 30 09:42:47 2026 -0700 added functionality for providing net lward, rather than just downward Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit de0cf7f54083120433d7acf6f941c8e45cf5d238 Merge: 4f115f75 916639e1 Author: Ann Almgren Date: Sat Mar 28 19:43:55 2026 -0700 Merge pull request #477 from seahorce-scidac/fix_msg fix error message commit 916639e153c5e7532a408a77a05fb7697733ecd5 Author: Ann Almgren Date: Sat Mar 28 19:43:21 2026 -0700 fix error message Source/REMORA.cpp commit 4f115f750bc72eb2c1631212cc0f2807f79d1145 Merge: 4e899817 8cbcefaf Author: Ann Almgren Date: Sat Mar 28 19:39:57 2026 -0700 Merge pull request #476 from seahorce-scidac/better_error_message add a more informative error message commit 8cbcefafeaadc522b4f1b756680fa673b9c1f4e4 Author: Ann Almgren Date: Sat Mar 28 19:39:15 2026 -0700 add a more informative error message Source/REMORA.cpp commit 4e899817772766014f4caeab39f3a4dc8fcf5bb1 Merge: e89457dd 64d29d6c Author: Ann Almgren Date: Mon Mar 23 17:57:56 2026 -0700 Merge pull request #475 from seahorce-scidac/fix_bc_index_error fix index oops in bcs commit 64d29d6c2073e60a04c90b9babafe5885fb81e84 Author: Ann Almgren Date: Mon Mar 23 17:57:03 2026 -0700 fix index oops in bcs Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp commit e89457dd4d3addf1ea73aaa1078de4d234041957 Merge: 7bc1a0d5 d9c0d8c2 Author: Ann Almgren Date: Mon Mar 23 17:54:59 2026 -0700 Merge pull request #466 from seahorce-scidac/add_tagging_on_indices add tagging options commit d9c0d8c2d9359cdfec852fab1c28211711626903 Author: Ann Almgren Date: Mon Mar 23 17:51:15 2026 -0700 remove broken link Docs/sphinx_doc/Inputs.rst commit 7bc1a0d5b635233f5a536e75530839d6e5f29e8c Author: Ann Almgren Date: Mon Mar 23 17:50:17 2026 -0700 remove broken link Docs/sphinx_doc/Inputs.rst commit e3ae19e34230491f4167d05842c2ec0e01fd32f8 Author: Ann Almgren Date: Mon Mar 23 17:44:13 2026 -0700 fix typo identified in issue 470 Source/REMORA_Tagging.cpp commit 87e4466191e70d5e2440fc6347c0f51011b4ffda Author: Ann Almgren Date: Mon Mar 23 17:28:48 2026 -0700 add tagging options Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_Tagging.cpp commit 7c83a34d38d72f390252e5ccec0a8337c4e3621b Merge: 357e231d 703bcba9 Author: Ann Almgren Date: Sat Mar 14 17:48:12 2026 -0700 Merge branch 'development' of github.com:seahorce-scidac/REMORA into development commit 357e231d02692d58e20b9f62fd3f09ffef8f64b4 Author: Ann Almgren Date: Sat Mar 14 17:47:39 2026 -0700 remove c-linter .github/workflows/c-linter.yml commit 703bcba9b5cd9de049fcc21450c55bd09756b606 Merge: ef9fd9ce 4686cd48 Author: Ann Almgren Date: Thu Mar 12 09:28:38 2026 -0700 Merge pull request #465 from emmashie/level1_interp Interpolation from level0 to higher levels commit 4686cd480f37590197b1ce97acd7d3615a5b3ec3 Author: Emma Nuss Date: Wed Mar 11 17:21:53 2026 -0700 Added interpolation of surface forcing to higher levels for refinement with netcdf forcing Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit ef9fd9cebb82a992cf0af3769f0216dce76a42c3 Merge: 52a73476 580e8a01 Author: Ann Almgren Date: Fri Mar 6 07:07:23 2026 -0800 Merge pull request #464 from seahorce-scidac/fix_gmake default to no pnetcdf commit 580e8a01b9356b64aa0c15707ef3e75b63f42014 Author: Ann Almgren Date: Fri Mar 6 07:06:41 2026 -0800 default to no pnetcdf Exec/Channel_Test/GNUmakefile commit 52a734764995b04c4e630c48579a190483821cce Merge: 2d69fa62 d7d05d5c Author: Ann Almgren Date: Fri Mar 6 06:50:06 2026 -0800 Merge pull request #463 from seahorce-scidac/fix_inputs restore plotfile_type to amrex commit d7d05d5c6169a0935aca41f8e7e6f0676da882c9 Author: Ann Almgren Date: Fri Mar 6 06:49:31 2026 -0800 restore plotfile_type to amrex Exec/Channel_Test/inputs commit 2d69fa6264295686b56f3fe87ab1222609c450da Merge: 629a0ce7 136cdfd9 Author: Ann Almgren Date: Thu Mar 5 14:52:54 2026 -0800 Merge pull request #462 from seahorce-scidac/change_plts Change plts commit 136cdfd9fdfd07415731ca95f8fa3b728553aa02 Author: Ann Almgren Date: Thu Mar 5 14:49:49 2026 -0800 fix test on plotfile type Source/IO/REMORA_Plotfile.cpp commit 71ef57ee0bc983020bdf6576e7926a89014b0637 Author: Ann Almgren Date: Thu Mar 5 14:21:11 2026 -0800 two more fixes Source/IO/REMORA_Plotfile.cpp Source/REMORA_Tagging.cpp commit 455b4d54e762a4eca1be79d750529e25831fc810 Author: Ann Almgren Date: Thu Mar 5 13:16:47 2026 -0800 replace broken link Docs/sphinx_doc/Inputs.rst commit 2e122bd2033f84ca71564e38f6861bc1f65d7976 Author: Ann Almgren Date: Thu Mar 5 12:55:11 2026 -0800 update docs Docs/sphinx_doc/Visualization.rst Docs/sphinx_doc/coc.rst commit 5125417b287496c7eb303f0cbd86b96619e003a6 Author: Ann Almgren Date: Thu Mar 5 12:47:45 2026 -0800 update ctests Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i commit d6e948dc1509405ccaeed6811d590547674f5589 Author: Ann Almgren Date: Thu Mar 5 12:30:30 2026 -0800 address unused issues Source/IO/REMORA_Plotfile.cpp commit 40bdc51b82812a9a940356b55b5409e69b5270e6 Author: Ann Almgren Date: Thu Mar 5 12:23:18 2026 -0800 more fixes for netcdf write Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Submodules/AMReX commit d0ad121ef7a1e49dfbea51b8eff83922687bc52e Author: Ann Almgren Date: Thu Mar 5 10:26:23 2026 -0800 allow us to plot vorticity in netcdf plot Source/IO/REMORA_NCPlotFile.cpp commit 79ff9d1ad4b5f811f1999c1b66a4ac2bfd247984 Author: Ann Almgren Date: Thu Mar 5 09:50:59 2026 -0800 replaced scalar by tracer; Scalar_comp --> Tracer_comp Exec/Advection/README Exec/Advection/inputs Exec/Advection/inputs_ml Exec/Advection/prob.cpp Exec/BlankProblem/inputs Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/GNUmakefile Exec/Channel_Test/inputs Exec/Channel_Test/out Exec/Channel_Test/prob.cpp Exec/DogboneAnalytic/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/IdealRivGrid/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Exec/Upwelling_ML/inputs Exec/Upwelling_ML/prob.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_IndexDefines.H Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_setup_step.cpp Submodules/AMReX commit 6fee25bf1fc8974faf98f5fcfe1cf066580a8ef6 Author: Ann Almgren Date: Wed Mar 4 19:01:58 2026 -0800 pass plotMF from Plotfile to NCPlotfile rather than directly using cons_new Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.H commit 7beebbedf268484bea688af92b2a91679d110e6a Author: Ann Almgren Date: Wed Mar 4 16:51:32 2026 -0800 Move choice of type of plotfile into WritePlotfile Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit 629a0ce723c41d1951ea45243c11f179cee29f98 Merge: 6ae05d5a 71e5e0f8 Author: Ann Almgren Date: Tue Mar 3 08:58:24 2026 -0800 Merge pull request #460 from seahorce-scidac/update_docs Remove comment about being in beta mode commit 71e5e0f8ddd82bb68ee840dac3a6079f4835d982 Author: Ann Almgren Date: Tue Mar 3 08:57:47 2026 -0800 Remove comment about being in beta mode Docs/sphinx_doc/MeshRefinement.rst commit 6ae05d5a49a7ddc1007d900de2d2f73c13ee62a6 Merge: 6895e457 76e7bcfa Author: Ann Almgren Date: Tue Mar 3 06:27:02 2026 -0800 Merge pull request #459 from seahorce-scidac/update_amrex Update AMReX submodule commit 76e7bcfa9428cbe11f2044854eee42c2bdc3786a Author: Ann Almgren Date: Tue Mar 3 06:26:12 2026 -0800 Update AMReX submodule Submodules/AMReX commit 6895e457090b4e4bb9b90f5c65c75c1ebe20b530 Merge: a9e6f1c0 ffb57320 Author: Ann Almgren Date: Tue Mar 3 06:24:43 2026 -0800 Merge pull request #458 from seahorce-scidac/fix_for_cuda fix for cuda commit ffb57320dfce126405386c52e95c7acca55edcb7 Author: Ann Almgren Date: Tue Mar 3 06:24:01 2026 -0800 fix for cuda Source/IO/REMORA_NCPlotFile.cpp commit a9e6f1c08f8cdd55cdb3ff352f61481e3b2afd03 Merge: 262f4ce8 d8707d2e Author: Ann Almgren Date: Mon Mar 2 07:03:08 2026 -0800 Merge pull request #457 from dylanschlichting/add_forcing_outputs Outputs surface forcing to netcdf files commit d8707d2e654075cec264226719833fb174366ddc Merge: 631cf99d 262f4ce8 Author: Ann Almgren Date: Mon Mar 2 07:02:54 2026 -0800 Merge branch 'development' into add_forcing_outputs commit 262f4ce828ec205cebfe3d392ad28fb5578f686f Merge: db65ce07 eb8d1df4 Author: Ann Almgren Date: Sun Mar 1 19:44:01 2026 -0800 Merge pull request #456 from dylanschlichting/add_longwaveout Adds outgoing longwave parameterization commit 631cf99da44d5e4a069e2c3edf75e47959befe6e Author: Dylan Schlichting Date: Sun Mar 1 10:41:26 2026 -0800 adds rest of forcing to netcdf output Source/IO/REMORA_NCPlotFile.cpp commit f42beda105b81ad470c09cf1b26991f6194a48b1 Author: Dylan Schlichting Date: Fri Feb 27 09:43:28 2026 -0800 Initial commit with tair/pair, writes to netcdf Source/IO/REMORA_NCPlotFile.cpp Source/REMORA_DataStruct.H commit eb8d1df4f344a61ba3ddc7a623daffd1091d1726 Author: Dylan Schlichting Date: Fri Feb 27 08:38:33 2026 -0800 updates cff to test CI debugging Source/TimeIntegration/REMORA_bulk_flux.cpp commit c19c895c266ee3a1c22798ce2734d0a8f23ff8b4 Author: Dylan Schlichting Date: Thu Feb 26 16:00:42 2026 -0800 removed white spaces from datastruct.h Source/REMORA_DataStruct.H commit 1052fee825ee6e43934446882b0cbe7522ff2ff0 Author: Dylan Schlichting Date: Thu Feb 26 15:48:41 2026 -0800 Unless bulk fluxes is rewritten, CI warning can't be removed Source/TimeIntegration/REMORA_bulk_flux.cpp commit 36470c80508b6ddb0d1e8e68f95215653f391bbb Author: Dylan Schlichting Date: Thu Feb 26 15:42:56 2026 -0800 fixed CI warning in bulk fluxes Source/TimeIntegration/REMORA_bulk_flux.cpp commit 8b55621fbc18d9f33b2253f927804eeddf476cd3 Author: Dylan Schlichting Date: Thu Feb 26 13:46:24 2026 -0800 fixed netcdf read bug Source/REMORA.cpp Source/REMORA_DataStruct.H commit cde4e896c0d2819f31160df3d7e0befff77b8970 Author: Dylan Schlichting Date: Wed Feb 25 15:13:13 2026 -0800 initial commit for outward longwave par, compiles Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit db65ce07f5c37f04f2801963ca59f5a4f8a4a884 Merge: fdb2caa7 681859c1 Author: Ann Almgren Date: Fri Jan 30 18:10:37 2026 -0800 Merge pull request #454 from seahorce-scidac/fix_2d_plotting fix for 2d plotting commit 681859c1c05929faaa648e53c46bda24f91061e5 Author: Ann Almgren Date: Fri Jan 30 16:53:15 2026 -0800 fix for 2d plotting Source/IO/REMORA_Plotfile.cpp commit fdb2caa75b1734951288a3474371d34bf102e3db Merge: 74973bce fe1d8d12 Author: Rob Hetland Date: Wed Jan 28 17:00:25 2026 -0800 Merge pull request #453 from hetland/development Bugfix in dy calculation commit fe1d8d126225b130fd4954ab2fe98f1b519e0570 Author: Rob Hetland Date: Wed Jan 28 16:59:17 2026 -0800 Bugfix in dy calculation Source/REMORA_Derive.cpp commit 74973bce3c2404133e023baeb8a21d2a5f0bec28 Merge: f4d66019 f8a059b5 Author: Ann Almgren Date: Mon Jan 26 13:14:17 2026 -0800 Merge pull request #452 from emmashie/salt_flux Added spatially varying salt flux variables, i.e. eminusp, rain, etc commit f8a059b5d26aa4cd629807fe394a4e09eb6383ef Author: Nuss Date: Mon Jan 26 12:08:49 2026 -0800 Fixed srflux bug, code now uses defined variable rather than the array Source/TimeIntegration/REMORA_bulk_flux.cpp commit 3d59ebd1de17b48ccc35b64e92f010a903bb23f5 Author: Nuss Date: Mon Jan 26 10:53:04 2026 -0800 Added spatially varying salt flux variables, i.e. eminusp, rain, etc Docs/sphinx_doc/Inputs.rst Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp commit f4d660198c36463d1e8a949fd028d6411c70e0ff Merge: 106c494c c0bfa33e Author: Ann Almgren Date: Sun Jan 25 11:31:04 2026 -0800 Merge pull request #451 from WeiqunZhang/clean_ci_space Update SYCL.yml commit c0bfa33e3933de357d31666083edc34bf9baea18 Author: Weiqun Zhang Date: Sun Jan 25 09:54:47 2026 -0800 Change build type .github/workflows/sycl.yml commit 031990851037d3deed7abba4d0575c6ce9f4b0f3 Author: Ann Almgren Date: Sun Jan 25 08:13:14 2026 -0800 fix sycl .github/workflows/sycl.yml commit 18865d5245556284a9c513fdb83115738acb239a Author: Ann Almgren Date: Sat Jan 24 20:18:32 2026 -0800 remove tabs .github/workflows/sycl.yml commit 25d2cc89f1489ed487f831563b0cec5286e8877c Author: Ann Almgren Date: Sat Jan 24 20:17:10 2026 -0800 update sycl.yml .github/workflows/sycl.yml commit 106c494c7cab1eebe76154b061353af2d841daf6 Merge: 4000a485 d2f6d108 Author: Ann Almgren Date: Sat Jan 24 17:14:28 2026 -0800 Merge pull request #449 from seahorce-scidac/update_amrex update amrex version commit d2f6d1084670385b420b5df9dbc68be1091e731a Author: Ann Almgren Date: Sat Jan 24 15:51:54 2026 -0800 update amrex version Submodules/AMReX commit 4000a485dbbbdb6c7a3d2b5d209adc79d989f0c2 Merge: 1285f92b 9dd666c2 Author: Ann Almgren Date: Tue Jan 20 09:11:44 2026 -0800 Merge pull request #448 from seahorce-scidac/rx_should_be_int Rx should be int commit 9dd666c202b9a42a7bec95f35f4100be333b97b3 Author: Ann Almgren Date: Mon Jan 19 17:49:48 2026 -0800 remove trailing whitespace Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp commit 7344c66ce1bc33297e5e569923b7b7943055289a Merge: af31bccc 1285f92b Author: Ann Almgren Date: Mon Jan 19 17:48:29 2026 -0800 Merge branch 'development' into rx_should_be_int commit af31bccc364ef5030380c5308094063cec3b6d66 Author: Ann Almgren Date: Mon Jan 19 17:48:14 2026 -0800 Real rx should be int rx Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit 1285f92b7fb410841dcc25b7d4fef73b69347a81 Merge: 757227e9 c451e501 Author: Ann Almgren Date: Mon Jan 19 17:47:51 2026 -0800 Merge pull request #447 from emmashie/spatial_bulk_flux Spatial bulk flux commit c451e5017021284acce7f07c30bf579f14508008 Author: Nuss Date: Mon Jan 19 10:52:46 2026 -0800 updated documentation to reflect bulk flux changes Docs/sphinx_doc/Inputs.rst commit 88e1d1a7bfc4a843890e4298fb7f9acf426b608b Author: Nuss Date: Mon Jan 19 10:45:33 2026 -0800 removed extra print statements Source/REMORA.cpp commit c12f327c6bfdb85702e10de985e83a9614eaddc9 Author: Nuss Date: Mon Jan 19 10:43:40 2026 -0800 Added loading spatial bulk flux and surface forcing from netcdf and removed some extraneous print statements Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_2d.cpp commit 9cfb46cddffe541c3b63a0e69639e906432434da Author: Nuss Date: Mon Jan 19 10:34:37 2026 -0800 Added loading spatial bulk flux and surface forcing from netcdf Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 757227e9e451eca975adcca4ce6450e68662c0a6 Author: Rob Hetland Date: Fri Jan 9 13:19:06 2026 -0800 Removed unneeded ghost cells in 2D plotfile writes that was corrupting output. Source/IO/REMORA_Plotfile.cpp commit 7539b1df409532514c27c46d59b66120327e8512 Merge: 6748682d 5a2edc56 Author: Ann Almgren Date: Wed Oct 29 17:39:11 2025 -0700 Merge pull request #446 from seahorce-scidac/update_plotting update plotting of 2D vars commit 5a2edc565e26007b23621d664cebe5c7a9bf62c0 Author: Ann Almgren Date: Wed Oct 29 17:39:00 2025 -0700 remove unused Source/IO/REMORA_Plotfile.cpp commit a7c62e513241a9d09bd5723c80256cefa3a113b2 Author: Ann Almgren Date: Wed Oct 29 17:12:25 2025 -0700 update plotting of 2D vars CMake/BuildREMORAExe.cmake Docs/sphinx_doc/Plotfiles.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/BlankProblem/inputs Exec/BoundaryLayer/inputs Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/Dogbone/inputs Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/inputs_clim_nudg Exec/IdealMiniGrid/inputs_frc Exec/IdealRivGrid/inputs Exec/ParticlesOverSeaMount/inputs Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling_ML/inputs Source/IO/Make.package Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_SetPlotVars.cpp Source/REMORA.H Source/REMORA.cpp Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/BoundaryLayer/BoundaryLayer.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit 6748682dd0db8c305991931f00bd0e9780f769c4 Merge: d0ea2a1a 4cba1444 Author: Ann Almgren Date: Tue Oct 28 17:50:29 2025 -0700 Merge pull request #445 from seahorce-scidac/revert_previous_PR revert previous PR by me commit 4cba14449e3005b976a41eb0cdebf9915ca68f56 Author: Ann Almgren Date: Tue Oct 28 17:49:58 2025 -0700 revert previous PR by me Source/IO/REMORA_Plotfile.cpp commit d0ea2a1ad7eb6ffd62e74bd8dc5b13e2f29444e9 Merge: ad2c85b6 72e424ed Author: Hannah Klion Date: Tue Oct 28 17:32:39 2025 -0700 Merge pull request #442 from hetland/masked_derived Add masking to derived variables. commit 72e424ed69284658e76e9232356b8f92373a44c2 Merge: 32c84c69 ad2c85b6 Author: Rob Hetland Date: Tue Oct 28 15:29:25 2025 -0700 Merge branch 'seahorce-scidac:development' into masked_derived commit ad2c85b62395360162269e75c2f21aa60b1a18b6 Merge: e3423526 be78cb9c Author: Ann Almgren Date: Tue Oct 28 14:40:53 2025 -0700 Merge pull request #444 from seahorce-scidac/fix_2dplotting fix 2d plotting commit be78cb9c271e4f6abb0e5dee1663b928a0cf6d4f Author: Ann Almgren Date: Tue Oct 28 14:40:15 2025 -0700 fix 2d plotting Source/IO/REMORA_Plotfile.cpp commit e3423526f5c8d735ef82a4a268a63de0ec0085f2 Merge: 9ada4e7e 6c140f62 Author: Hannah Klion Date: Mon Oct 27 15:43:34 2025 -0700 Merge pull request #443 from hklion/fix_cuda fix CUDA build issues with netcdf commit 6c140f62de3b00186fd1b500e22f5ea4d16b5765 Author: Hannah Klion Date: Mon Oct 27 15:43:03 2025 -0700 fix CUDA build issues with netcdf Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit 32c84c69ca8c8ba11475c738798d4f05e62624d7 Merge: caa6e03b 9ada4e7e Author: Rob Hetland Date: Thu Oct 23 18:31:41 2025 -0700 Merge branch 'seahorce-scidac:development' into masked_derived commit caa6e03bbb34860d48d22b403784d72fb42be1da Author: Rob Hetland Date: Thu Oct 23 18:25:04 2025 -0700 Add masking to derived variables. Add masking to derived variables. Source/IO/REMORA_Plotfile.cpp Source/REMORA_Derive.H Source/REMORA_Derive.cpp Source/REMORA_Tagging.cpp commit 9ada4e7e85018ee989188dfc5dfefc46b40c94d3 Author: Hannah Klion Date: Thu Oct 23 14:05:26 2025 -0700 clean up Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit c715cd951bf9f674f98c1d9840936497834f8bc0 Merge: b24e090d f9220c21 Author: Hannah Klion Date: Wed Oct 22 15:58:02 2025 -0700 Merge pull request #439 from hklion/plotfile_2d_fields add 2d variables to plotfile at rho, u, and v points commit b24e090dd9d5f94a03113e1996a678fb692e4b3f Author: Ann Almgren Date: Wed Oct 22 13:57:58 2025 -0700 fix interpolation for rr != 2 Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit 38457027f7c11c66b797d728ac297c2d1ef91e87 Author: Ann Almgren Date: Wed Oct 22 13:45:30 2025 -0700 lessen memory usage Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/bkup/NEW commit 18983bd66576a4bd8ff0c6ecda235d2cb77b64e4 Author: Ann Almgren Date: Wed Oct 22 12:58:45 2025 -0700 This interpolates coarse boundary conditions to every finer level Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/IO/bkup/NEW Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d.cpp commit ebd60a937c09f5e18f61056ecf1de1e912361a5c Merge: 66997eaf 6956dcca Author: Hannah Klion Date: Tue Oct 21 19:24:42 2025 -0700 Merge pull request #441 from hklion/netcdf_mesh_refinement mesh refinement for realistic problems with refined patches not touching edge commit 6956dccaa1f3df8454cc4328c07fec2f84229710 Author: Hannah Klion Date: Tue Oct 21 17:40:40 2025 -0700 mesh refinement for realistic problems with refined patches not touching edge Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit 66997eaf7f9b5d1acfb05ebcae66a240ae3c0fb1 Merge: 53b5d46b e00442ed Author: Hannah Klion Date: Mon Oct 20 16:23:56 2025 -0700 Merge pull request #440 from hklion/queryadd add more things to jobinfo by using queryadd instead of query commit f9220c218bf1d6050e8a65d63547fe7d06fcf791 Author: Hannah Klion Date: Mon Oct 20 12:37:20 2025 -0700 output Dphi_avg1 for phibar and bottom/surface stresses to plotfile Docs/sphinx_doc/Plotfiles.rst Source/IO/REMORA_Plotfile.cpp commit 17f7bc1c76657fe44156ba574f7d3512f82a345b Author: Hannah Klion Date: Fri Oct 17 18:09:45 2025 -0700 typo_ Source/IO/REMORA_Plotfile.cpp commit e00442ed75c9c8296f2e94439c6a39313ef47b6b Author: Hannah Klion Date: Fri Oct 17 18:08:02 2025 -0700 add more things to jobinfo by using queryadd instead of query Source/Initialization/REMORA_init_bcs.cpp Source/Particles/REMORA_PC_Init.cpp Source/Particles/REMORA_Tracers.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H commit 1df9b45af5de5601b35f1184b40e6f5b2a10a8f8 Author: Hannah Klion Date: Fri Oct 17 17:53:05 2025 -0700 add 2d variables to plotfile at rho, u, and v points Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 53b5d46bbad38b6d224129f960529f7ab3d9988e Merge: 0da86e87 2db3bdd3 Author: Hannah Klion Date: Fri Oct 17 17:47:58 2025 -0700 Merge pull request #437 from seahorce-scidac/fix_tagging Need one ghost cell when tagging for refinement commit 2db3bdd3c6e750e9c506f5dff3c437cad595008e Author: Hannah Klion Date: Fri Oct 17 12:22:36 2025 -0700 clean up tagging so it shouldn't crash Source/REMORA_Tagging.cpp commit 0da86e8798a13c4b62ff529a020b8992a7a188d0 Merge: c5634605 793eee7a Author: Hannah Klion Date: Thu Oct 16 19:18:01 2025 -0700 Merge pull request #438 from jmsexton03/cuda_ci_space_force_run Fix CUDA CI disk space failures commit 807e62e46b5ca4a35dfb65b52fea0d692da11681 Author: Hannah Klion Date: Thu Oct 16 19:17:13 2025 -0700 add un-tagging for land-regions; still doesn't quite work Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Tagging.cpp commit 793eee7a5934fcb993ed05f656069f5732097dfa Author: Jean M. Sexton Date: Wed Oct 15 09:31:35 2025 -0700 Only add additional dispatch step .github/workflows/cuda-ci.yml commit d9b053520fc788d3b5eee1821adf6bdfc3dbfbba Author: Jean M. Sexton Date: Wed Oct 15 07:21:44 2025 -0700 Copy free action from ERF .github/actions/free-space-ubuntu/action.yml commit 8db2795d6c77c2820ecaa4e338f520692cccacbd Author: Jean M. Sexton Date: Wed Oct 15 07:19:16 2025 -0700 Force running ci .github/workflows/cuda-ci.yml commit d1ae1ad32e90d42e4f0585d03553a1a01fd8bf4b Author: Jean M. Sexton Date: Wed Oct 15 07:05:48 2025 -0700 Add prints and some additional free for cuda CI * Free up space before build * Use smaller ccache * Add option to trigger CI manually .github/workflows/cuda-ci.yml commit a967eb10e80b993805ae114b40bc5de86c3cdd3b Author: Ann Almgren Date: Tue Oct 14 19:22:57 2025 -0700 impose FillBoundary before tagging Source/REMORA_Tagging.cpp commit c4dcd19e0063f3a55c6ec2e3f2e87deb9b9043a4 Author: Ann Almgren Date: Tue Oct 14 18:39:44 2025 -0700 Need one ghost cell when tagging for refinement Source/REMORA_Tagging.cpp commit c5634605e32a7e632d5d4359c2de608dad91f948 Author: Hannah Klion Date: Tue Oct 14 10:24:01 2025 -0700 abort if doing rivers without netcdf Source/REMORA.cpp commit abd46e8cc19ded39bc7ddb0f12c56ec730112c62 Author: Hannah Klion Date: Fri Oct 10 17:27:36 2025 -0700 note we can do orlanski for 2d vars Docs/sphinx_doc/BoundaryConditions.rst commit 2023dd6b98efa2cd9031a0cc80699a25a2d1f80b Merge: e504cae5 827bb995 Author: Hannah Klion Date: Fri Oct 10 16:42:23 2025 -0700 Merge pull request #436 from hklion/skip_unused_boundary_data skip interpolating boundary data when a boundary is not used commit 827bb995b4f7ee7dfb0b2519b1e610da598f1c3f Author: Hannah Klion Date: Fri Oct 10 16:41:56 2025 -0700 skip interpolating boundary data when a boundary is not used Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit e504cae595592a277cfea5bbc49a76bf4df18d93 Merge: b51598b6 1aac15cd Author: Hannah Klion Date: Tue Oct 7 11:46:27 2025 -0700 Merge pull request #435 from hklion/orlanski_2d_vars add option to do orlanski and orlanski_rad for ubar/vbar/zeta commit 1aac15cd7d1baf67c6ba475b992d56015b7d0d0e Author: Hannah Klion Date: Tue Oct 7 10:32:41 2025 -0700 add option to do orlanski and orlanski_rad for ubar/vbar/zeta Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit b51598b6fb9163a4c2f52307a3e5c9d9320df2c9 Author: Hannah Klion Date: Tue Sep 30 11:37:48 2025 -0700 update docs to include units of climatology nudging coeffs Docs/sphinx_doc/Climatology.rst commit 9fedb17f534eb15f7b7be693f544bf7c792ec998 Merge: bf69fde5 03edef12 Author: Hannah Klion Date: Wed Sep 24 13:29:39 2025 -0700 Merge pull request #434 from hklion/1d_vert_vars_dtoh when outputting 1D vertical variables to netcdf, copy device-to-host rather than vice versa commit 03edef1243b4ed7caaee700b19f2f39a72fabf45 Author: Hannah Klion Date: Wed Sep 24 13:29:07 2025 -0700 when outputting 1D vertical variables to netcdf, copy device-to-host rather than vice versa Source/IO/REMORA_NCPlotFile.cpp commit bf69fde55c5fd30bd175b1be4f3c6d86669bedb0 Merge: 66fed12f 1eafeece Author: Hannah Klion Date: Tue Sep 23 16:46:48 2025 -0700 Merge pull request #433 from hklion/ic_type_docs fix docs saying ic_type is true/false commit 1eafeece9fed30ed1ad6d96d8024bb96557e26a8 Author: Hannah Klion Date: Tue Sep 23 16:46:21 2025 -0700 fix docs saying ic_type is true/false Docs/sphinx_doc/Inputs.rst commit 66fed12f5b4e4683d6f7b991a143443a26cc2db7 Merge: 3f639e08 dcc8cb51 Author: Hannah Klion Date: Tue Sep 23 16:44:27 2025 -0700 Merge pull request #432 from hklion/tagging_less_fragile make tagging by position less fragile by auto-expanding the tagged bo… commit dcc8cb51eb8a6126c56cf26394f5a0a752ef14e9 Author: Hannah Klion Date: Tue Sep 23 16:05:05 2025 -0700 make tagging by position less fragile by auto-expanding the tagged box so that entire coarse cells are tagged Docs/sphinx_doc/MeshRefinement.rst Source/REMORA_Tagging.cpp commit 3f639e080a207a6fed8fc6508a01d5c7dbf89de2 Merge: c329f798 39145636 Author: Hannah Klion Date: Fri Sep 12 14:48:42 2025 -0700 Merge pull request #431 from hklion/backticks remove extraneous backticks from documentation commit 39145636a23f8988b53b84f0be183f9b7be7fbf2 Author: Hannah Klion Date: Fri Sep 12 14:45:32 2025 -0700 remove extraneous backticks from documentation Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Climatology.rst Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/theory/VerticalMixing.rst commit c329f798f4ce2b00a2f73bb28c417b44934098b9 Merge: c3e09014 fbf45709 Author: Hannah Klion Date: Fri Sep 12 11:31:22 2025 -0700 Merge pull request #430 from hklion/vorticity fix bug in vorticity calc commit fbf45709e6e5f93cf8f6d0b6029a9c616605e654 Author: Hannah Klion Date: Fri Sep 12 11:26:51 2025 -0700 fix bug in vorticity calc Source/REMORA_Derive.cpp commit c3e0901420001f1de2326ae2bb761234a6996069 Merge: f2524223 bc576df0 Author: Hannah Klion Date: Fri Sep 12 11:11:26 2025 -0700 Merge pull request #429 from hklion/writing_ml_info add plotfile and grid info to ML stdout output commit bc576df0b19115ab8e2909bb7076164c043bec95 Author: Hannah Klion Date: Fri Sep 12 11:10:35 2025 -0700 add plotfile and grid info to ML stdout output Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_make_new_level.cpp commit f2524223b7240be652a82cd2b2753a8100d16907 Merge: f786f15d 6c934fea Author: Hannah Klion Date: Thu Sep 11 21:16:31 2025 -0700 Merge pull request #428 from hklion/docs_format Docs format commit 6c934fea2ad21e0ce696659a3adc6f74c6ae6050 Author: Hannah Klion Date: Thu Sep 11 21:14:44 2025 -0700 fix spelling Docs/sphinx_doc/Inputs.rst commit 9a773401ebda286fe88e7ff1e5c0911514465745 Author: Hannah Klion Date: Thu Sep 11 21:10:42 2025 -0700 update docs formatting Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Time_Stepping.rst commit a9502f1a000c49b1fd42058275444dfe509ae198 Author: Hannah Klion Date: Thu Sep 11 16:49:09 2025 -0700 rename hOfTheConfusingName to h Docs/sphinx_doc/Numerical_Solution_Technique.rst Exec/DoublyPeriodic/prob.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCPlotFile.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 26739e5f3d7613fc6264a605987d2a68d1cb6d7e Author: Hannah Klion Date: Thu Sep 11 16:17:17 2025 -0700 reformat table Docs/sphinx_doc/Inputs.rst commit b53eabb12ac6f84c245fc8cbf45f14e28dd80994 Merge: 45820fb2 f786f15d Author: Hannah Klion Date: Thu Sep 11 15:55:37 2025 -0700 Merge remote-tracking branch 'upstream' into docs_format commit 45820fb2c59e60a6dc9259438c2110fb23135540 Author: Hannah Klion Date: Thu Sep 11 09:48:36 2025 -0700 reformat tables in documentations Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Verification.rst Docs/sphinx_doc/building.rst commit f786f15d3c3d65bf98975838b437c11f1ed9b408 Merge: 50f1e6a9 e766e877 Author: Hannah Klion Date: Wed Sep 10 18:37:14 2025 -0700 Merge pull request #427 from jmsexton03/fix_report_save Fix warnings, CI configuration, and shared library builds commit e766e877b8f248257d389edbe64f926a741096ef Author: Jean M. Sexton Date: Wed Sep 10 12:15:47 2025 -0700 Don't use shared on macos .github/workflows/macos.yml commit 08236674f32884240e28e463fdc7f22a0ab36bc3 Author: Jean M. Sexton Date: Wed Sep 10 09:38:38 2025 -0700 Make srclib object library shared, fix typo Exec/CMakeLists.txt Source/IO/REMORA_Plotfile.cpp commit 5be8e0cac6d9b94a3ecee4df0ffa6f183391e334 Author: Jean M. Sexton Date: Wed Sep 10 08:36:34 2025 -0700 Compare to 0.0 for MultiFab mask Source/IO/REMORA_Plotfile.cpp commit e945a6d3ae8aa61abc0aa1bb6bb257de1055c30e Author: Jean M. Sexton Date: Wed Sep 10 08:33:48 2025 -0700 Fix unused and shadow Exec/Advection/prob.cpp Exec/BoundaryLayer/prob.H Exec/Channel_Test/prob.H Exec/DoubleGyre/prob.H Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.H Exec/Seamount/prob.H Exec/Upwelling/prob.H Source/IO/REMORA_Plotfile.cpp commit d903a6c1d679db60220b5f746aac781738d2dbb3 Merge: bd19382d 50f1e6a9 Author: Jean M. Sexton Date: Wed Sep 10 08:20:00 2025 -0700 Merge branch 'development' into fix_report_save commit bd19382d384d0ceda41c06c1052867e429133435 Author: Jean M. Sexton Date: Tue Sep 9 16:11:18 2025 -0700 First pass Exec/DoublyPeriodic/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp commit 50f1e6a93326229cde2446de2920b10beae85e5f Merge: 3ea3d287 9e6084f9 Author: Hannah Klion Date: Tue Sep 9 16:03:43 2025 -0700 Merge pull request #426 from hklion/ml_docs update docs with AMR commit e8530fb6184642277905c937273a8dc1714789d5 Author: Jean M. Sexton Date: Tue Sep 9 15:48:43 2025 -0700 MacOS ci warnings Exec/Seamount/prob.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_init_bcs.cpp Source/TimeIntegration/REMORA_gls.cpp commit 2704ce59514fab7b7694ac5daa22a8095bb40a38 Author: Jean M. Sexton Date: Tue Sep 9 15:15:55 2025 -0700 Unused Variables noted with maybe_unused Exec/Advection/prob.cpp Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.cpp Exec/DogboneAnalytic/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/Upwelling/prob.cpp Source/IO/REMORA_Plotfile.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/Utils/REMORA_DepthStretchTransform.H commit b6e93b3301fe526f10dbebd22f7d5ce57d5b4731 Author: Jean M. Sexton Date: Tue Sep 9 15:13:18 2025 -0700 Unused parameters fixes Exec/Advection/prob.cpp Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp commit cabbe3992226c3319fb66899562f787fca6754e4 Author: Jean M. Sexton Date: Tue Sep 9 15:04:22 2025 -0700 Fix report save .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/sycl.yml commit 9e6084f918f7411f49f25d78c93f6fa4e720e932 Author: Hannah Klion Date: Tue Sep 9 14:52:49 2025 -0700 update docs with AMR Docs/sphinx_doc/Inputs.rst commit 3ea3d287e4a1041dac681dcc9b4e70a2de345d1d Merge: 93542f8a ed0e9629 Author: Hannah Klion Date: Tue Sep 9 09:22:31 2025 -0700 Merge pull request #425 from hklion/boundary_as_needed fix MPI for boundary data reader commit ed0e9629e2ed02198c45173a6d3ce6bed3e10962 Author: Hannah Klion Date: Tue Sep 9 09:21:50 2025 -0700 fix MPI Source/IO/REMORA_NCTimeSeriesBoundary.cpp commit 93542f8a5173cd87298a3528a750e224372cad05 Merge: 1d577a54 d08804d0 Author: Hannah Klion Date: Mon Sep 8 17:14:45 2025 -0700 Merge pull request #424 from hklion/boundary_as_needed Boundary as needed commit d08804d06a0a10625a126c085b0bdac5f6ec4d64 Author: Hannah Klion Date: Mon Sep 8 17:06:17 2025 -0700 add docs Docs/sphinx_doc/Inputs.rst commit aef1964702124c35f5aa33ea71b1085051b3c2d2 Author: Hannah Klion Date: Mon Sep 8 16:46:53 2025 -0700 remove old boundary reading function Source/IO/REMORA_ReadFromBdryNetcdf.cpp commit 1aee268db2da90b9da1a9fd3ab01dcdf5d58c302 Author: Hannah Klion Date: Mon Sep 8 16:44:39 2025 -0700 add NCTImeSeriesBoundary class to read in boundary data as needed and allow different time axes for different variables CMake/BuildREMORAExe.cmake Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/Make.package Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCTimeSeriesBoundary.H Source/IO/REMORA_NCTimeSeriesBoundary.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 1d577a5439a918e8a73f5350a97e6d7d5520b19b Merge: 1cb8176d db972d3c Author: Hannah Klion Date: Fri Sep 5 10:27:47 2025 -0700 Merge pull request #423 from hklion/bc_dest_arr limit bc application to dest_arr in order to prevent out of bounds when level 1 boxes get too close to edge commit db972d3cc376b08b83ea316c316d8a01c14298f4 Author: Hannah Klion Date: Thu Sep 4 19:31:03 2025 -0700 limit bc application to dest_arr in order to prevent out of bounds when level 1 boxes get too close to edge Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp commit 1cb8176d13fdc7d6fb0eaa68a983391423c16af3 Merge: ad3ff881 03d8f164 Author: Hannah Klion Date: Wed Sep 3 16:17:35 2025 -0700 Merge pull request #422 from hklion/rhs_scale_single_level scale rhs u/v variables even if on single level commit 03d8f16455d16159dc3608a59de59922c0501520 Author: Hannah Klion Date: Wed Sep 3 16:16:34 2025 -0700 scale rhs u/v variables even if on single level Source/TimeIntegration/REMORA_TimeStep.cpp commit ad3ff8812fa2d7da0f7d8080b8bcc9960d8d625c Merge: 42f85e88 cd0eee92 Author: Hannah Klion Date: Fri Aug 29 14:32:37 2025 -0700 Merge pull request #421 from hklion/cons_linear_interp Change velocity interpolation to cons_linear_interp commit cd0eee92738a7f7a9ac18fecccc78dfec6765316 Merge: 4420e1bf 42f85e88 Author: Hannah Klion Date: Fri Aug 29 13:11:07 2025 -0700 Merge remote-tracking branch 'upstream/development' into cons_linear_interp commit 4420e1bf4f3c41214734b4557c11b7bdd1ee6fa8 Author: Hannah Klion Date: Fri Aug 29 13:09:18 2025 -0700 update amrex to fix bug in FaceConservativeLinear and update tests Submodules/AMReX Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info commit 42f85e88061666f53e6bfea6b8f097c6a6c13b93 Merge: 204f078e a7079e3b Author: Hannah Klion Date: Fri Aug 29 09:25:54 2025 -0700 Merge pull request #420 from jmsexton03/add_warnings_report Add warnings report commit a7079e3bd5152467069b981d3b503d06e80b483c Author: Jean M. Sexton Date: Fri Aug 29 07:20:12 2025 -0700 Make egrep for submodules case insensitive .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/sycl.yml commit defd1019188e4430a69837d82b1fb93b2278083a Author: Jean M. Sexton Date: Fri Aug 29 07:15:16 2025 -0700 Add warnings report block in CI like ERF .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/sycl.yml commit a387b2fa6d57e97175e71a15c912138c6d95d119 Author: Hannah Klion Date: Tue Aug 26 16:36:14 2025 -0700 use conservative linear interpolation on faces Source/BoundaryConditions/REMORA_FillPatch.cpp commit 204f078eaf42e1143de9f7521ebb902766c0b14a Merge: 70ded027 0bf57589 Author: Hannah Klion Date: Tue Aug 26 16:26:21 2025 -0700 Merge pull request #419 from hklion/cc_vels_grow calculate cell centered velocity on ghost cells commit 0bf57589c831273baa54fabc086c0383c79d452c Author: Hannah Klion Date: Tue Aug 26 16:25:04 2025 -0700 calculate cell centered velocity on ghost cells Source/IO/REMORA_Plotfile.cpp Submodules/AMReX commit 70ded027eac01b7416434c7c654623f874bffcd2 Merge: 2e55a3da 9c122b95 Author: Hannah Klion Date: Tue Aug 26 15:36:10 2025 -0700 Merge pull request #418 from hklion/patch_fp2d_plotfile patch grow cells in cc vels in plotfile commit 9c122b950804c6452d552e735f82bf5387e0ad28 Author: Hannah Klion Date: Tue Aug 26 15:29:48 2025 -0700 patch grow cells in cc vels in plotfile Source/IO/REMORA_Plotfile.cpp commit 2e55a3da0c95d445354ebc798f73b7b48209c6b4 Merge: 5190722b af31a86a Author: Hannah Klion Date: Tue Aug 26 14:59:28 2025 -0700 Merge pull request #417 from hklion/mr_docs update docs with new options and clarifying about refinement ratios commit af31a86a6082dd2038861a5e14fae44b4d17c64c Author: Hannah Klion Date: Tue Aug 26 14:51:50 2025 -0700 update docs with new options and clarifying about refinement ratios Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Plotfiles.rst commit 5190722b09186cdc58c94ccf8aea9a4bf0bcf413 Merge: a901a894 4ddd60f8 Author: Hannah Klion Date: Mon Aug 25 19:33:02 2025 -0700 Merge pull request #416 from hklion/ml_plotfiles ML plotfiles commit 4ddd60f8bff8e2c34bd3785aa4113750a24c9114 Author: Hannah Klion Date: Mon Aug 25 19:32:27 2025 -0700 fix spelling Source/IO/REMORA_Plotfile.cpp commit 14def888a0f7dece8a069bad8f8bf860311f990a Author: Hannah Klion Date: Mon Aug 25 19:18:30 2025 -0700 patch number of grow cells in cell centering velocities Source/IO/REMORA_Plotfile.cpp commit 43d24d676e5ed43e11357dd72cd684e6323dfe61 Author: Hannah Klion Date: Mon Aug 25 19:00:54 2025 -0700 fix header Source/REMORA.H commit 79bb73c1e94dcfa500733864d5c40558afcfb023 Author: Hannah Klion Date: Mon Aug 25 18:59:20 2025 -0700 fix geometry Source/IO/REMORA_Plotfile.cpp commit 456ed77ec38598401e625b281ba15f9e5b507839 Author: Hannah Klion Date: Mon Aug 25 16:27:00 2025 -0700 add uniform refratio to ML test input files Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i commit 5c5e8066c3f9e045b383c9465e4609c54aaf7adc Author: Hannah Klion Date: Mon Aug 25 16:16:47 2025 -0700 output multilevel plotfiles with bathymetry and add default false option for expanding z to uniform refinement Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit a901a89423fc645d4f230dc805bc479abc46b1ad Merge: 40b7be65 2338f13b Author: Hannah Klion Date: Wed Aug 20 14:57:35 2025 -0700 Merge pull request #415 from hklion/average_down_zeta Average down zeta commit 2338f13bfcb9284099aced5f4c7b8a480cf643bb Author: Hannah Klion Date: Wed Aug 20 14:54:35 2025 -0700 update tests Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit ea2db12e9527020f51705ca3c58932d5b5eae7e2 Author: Hannah Klion Date: Wed Aug 20 14:48:22 2025 -0700 recalculate Hz after zeta averaged down Source/REMORA.cpp commit 40b7be65b5f69df7ec6faf18064eeb2fb6927ccd Merge: 203a02f4 45b3ddb5 Author: Hannah Klion Date: Tue Aug 19 20:40:43 2025 -0700 Merge pull request #414 from hklion/average_down_zeta correctly average down Zt_avg1 rather than zeta commit 45b3ddb5b3ef405c4fca8b078f74b64e1044d095 Author: Hannah Klion Date: Tue Aug 19 20:38:58 2025 -0700 correctly average down Zt_avg1 rather than zeta Source/REMORA.cpp Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit 203a02f4efebb67ea6971df9e67c07d39b8c8362 Merge: 93e98ac7 977dd315 Author: Hannah Klion Date: Mon Aug 18 17:23:34 2025 -0700 Merge pull request #413 from seahorce-scidac/add_staggered_vels_to_plotfile add option (default false) to add staggered velocities to plotfiles commit 93e98ac7cd6af0d13dbc5108404b1410e47fda88 Merge: b4b915dd f53e40f3 Author: Hannah Klion Date: Sun Aug 17 21:36:05 2025 -0700 Merge pull request #412 from hklion/profiling Profiling commit f53e40f31401a58a4871bb6bbb3367866e70a0ca Author: Hannah Klion Date: Sun Aug 17 17:46:36 2025 -0700 get stretching coeffs in scope for GPU Source/Utils/REMORA_DepthStretchTransform.H commit 977dd31556e588c308c6f33f86ff001c0b12101e Author: Ann Almgren Date: Sat Aug 16 19:26:27 2025 -0700 add option (default false) to add staggered velocities to plotfiles Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 4dbda69aa1cb0c6d07afd09a14a152025aaa8c5d Merge: dc3f03db b4b915dd Author: Hannah Klion Date: Sat Aug 16 13:50:22 2025 -0700 Merge remote-tracking branch 'upstream' into profiling commit b4b915dd2b07f7fa6d8e05b55d731f5c585e0185 Merge: 9eacd122 ff315cb0 Author: Hannah Klion Date: Sat Aug 16 13:49:27 2025 -0700 Merge pull request #411 from hklion/fix_scale_rhs_boxes update DogboneAnalytic_MLvel commit dc3f03dbfc535cb959424c4f64e7d5679ae79471 Merge: e72d51e2 9eacd122 Author: Hannah Klion Date: Sat Aug 16 13:46:25 2025 -0700 Merge remote-tracking branch 'upstream' into profiling commit e72d51e25c9b8623cd918958795a5bc1cee2f8b1 Author: Hannah Klion Date: Fri Aug 15 17:28:13 2025 -0700 fix nodal z coords and fix compile warnings Source/Initialization/REMORA_init.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 48ecb759fb9efba6ab2db446e85fb28a61bd0592 Author: Hannah Klion Date: Fri Aug 15 16:37:30 2025 -0700 improve time to solution and add more profiling subregions Source/IO/REMORA_NCPlotFile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/REMORA_DepthStretchTransform.H commit ff315cb0c1504faac2b5ecd4d82f497b2225a98b Author: Hannah Klion Date: Fri Aug 8 17:56:08 2025 -0700 update DogboneAnalytic_MLvel Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info commit 9eacd1220fd2d52e37ba090d630724f2bfa52a62 Merge: 44517f3b e893bd78 Author: Hannah Klion Date: Fri Aug 8 16:48:51 2025 -0700 Merge pull request #410 from hklion/fix_scale_rhs_boxes fix boxes in scale_rhs_var commit e893bd78f6532bc25f892cea98882b3e33643eb6 Author: Hannah Klion Date: Fri Aug 8 16:44:22 2025 -0700 fix boxes in scale_rhs_var Source/TimeIntegration/REMORA_scale_rhs_vars.cpp Submodules/AMReX commit ca8b521b107792f7d5a423eaafd74ebb7abbfc26 Author: Hannah Klion Date: Thu Aug 7 12:53:05 2025 -0700 add more profilng regions Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 44517f3be52defd07ce0ef5e9d625628a9c39ff6 Merge: 141f7d92 cb0c1ab1 Author: Hannah Klion Date: Wed Aug 6 10:46:37 2025 -0700 Merge pull request #409 from hklion/dogbone_ml add modified dogbone problem commit cb0c1ab1b04c9a64f3a544ebb980fc0d06778280 Author: Hannah Klion Date: Wed Aug 6 10:45:08 2025 -0700 add modified dogbone problem Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_mid Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/prob.H Exec/DogboneAnalytic/prob.cpp commit 141f7d925d3c473ea9892c11bcc993c476ee37bf Merge: 3723e291 a3007e88 Author: Hannah Klion Date: Tue Aug 5 13:27:38 2025 -0700 Merge pull request #408 from hklion/dogbone_ml add middle refinement case commit a3007e8856760214f42c6ebdc64349e3e347f0b6 Author: Hannah Klion Date: Tue Aug 5 13:26:18 2025 -0700 add middle refinement case Exec/DogboneAnalytic/README.rst Exec/DogboneAnalytic/inputs_ml_mid commit 3723e2916cbdb614ca03ef829c624612624086a5 Merge: e0584bec 22854429 Author: Hannah Klion Date: Tue Aug 5 13:22:43 2025 -0700 Merge pull request #407 from hklion/dogbone_ml Dogbone test and multilevel commit 22854429313a266ef36beff6d816a05772c80bf8 Author: Hannah Klion Date: Mon Aug 4 19:27:31 2025 -0700 add dogbone analytic ctest cases Docs/sphinx_doc/RegressionTests.rst Exec/CMakeLists.txt Exec/DogboneAnalytic/CMakeLists.txt Exec/DogboneAnalytic/GNUmakefile Exec/DogboneAnalytic/Make.package Exec/DogboneAnalytic/README.rst Exec/DogboneAnalytic/inputs Exec/DogboneAnalytic/inputs_ml Exec/DogboneAnalytic/inputs_ml_quad Exec/DogboneAnalytic/prob.H Exec/DogboneAnalytic/prob.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/DogboneAnalytic/Header Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DogboneAnalytic/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLquad/job_info Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Header Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_0/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/Level_1/Cell_H Tests/REMORA_Gold_Files/DogboneAnalytic_MLvel/job_info Tests/test_files/DogboneAnalytic/DogboneAnalytic.i Tests/test_files/DogboneAnalytic_MLquad/DogboneAnalytic_MLquad.i Tests/test_files/DogboneAnalytic_MLvel/DogboneAnalytic_MLvel.i commit 4001e3df734187fd12b1c231c5cfb8acd15df585 Author: Hannah Klion Date: Fri Aug 1 18:19:34 2025 -0700 fix remake level and get boundary conditions right on FillCoarsePatch Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 507132e4d7b99c2a72fec3fc48bb82b9ea744634 Author: Hannah Klion Date: Fri Aug 1 18:16:13 2025 -0700 when checking for domain edge, use geometry at level, not at level=0 Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit e0584bece23c97783807d5ec042cb48c3e40be3d Merge: c9f6cecc 201f8ea2 Author: Hannah Klion Date: Mon Jul 28 09:52:00 2025 -0700 Merge pull request #406 from hklion/dogbone Patch multilevel to work at boundaries commit 201f8ea2d8d1f87eba312da562fa920395987854 Author: Hannah Klion Date: Sat Jul 26 09:48:14 2025 -0700 make FillCoarsePatch public for GPU Source/REMORA.H commit fc5d1325cebb49492694476f1b39c73e891c1c57 Author: Hannah Klion Date: Fri Jul 25 22:44:24 2025 -0700 add fillboundary on parent level before interpolating onto child levels Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_make_new_level.cpp commit 9744fb4f4cf70ec81bc533ba249b97f0d6005718 Author: Hannah Klion Date: Thu Jul 24 19:02:46 2025 -0700 analytic mask initialization and make multilevel work at boundaries Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_3d.cpp commit c9f6cecc8131959b8fd5558b5c776be365f74cd7 Merge: 546de8ad 60215c5d Author: Hannah Klion Date: Tue Jul 22 10:36:08 2025 -0700 Merge pull request #405 from jmsexton03/api_library Add remora_api library as an install target commit 60215c5d59d9008e056fc497a7b8d50595fcdcc8 Author: Jean M. Sexton Date: Tue Jul 22 06:47:42 2025 -0700 Adding file that was missed CMake/REMORAConfig.cmake.in commit e274612fc5359d76451dd1258635c876220a786a Author: Jean M. Sexton Date: Tue Jul 22 06:25:43 2025 -0700 Add remora_api.a as an install target * Minor updates to include directories for superbuild * Added install target * Added REMORAConfig.cmake generation Build/cmake.sh Build/cmake_with_netcdf.sh Build/cmake_with_particles.sh CMake/BuildREMORAExe.cmake CMakeLists.txt commit 546de8ad5371e03abfce03afe2ee52e100fd8e87 Merge: 7b4a7f06 50abd723 Author: Hannah Klion Date: Wed Jul 16 15:17:32 2025 -0700 Merge pull request #404 from hklion/dogbone Add dogbone problem commit 50abd723b86c1e8971ddff0b5eb93b5c0a70b33e Author: Hannah Klion Date: Wed Jul 16 15:16:54 2025 -0700 update tests to include dogbone Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst commit c02dcad5b6afe411f125725ccce4711d9e01d3eb Author: Hannah Klion Date: Wed Jul 16 15:15:11 2025 -0700 update netcdf file names Exec/Dogbone/inputs commit 5b9a296405bc45212cb54cc87aa0290ff17e94d0 Author: Hannah Klion Date: Tue Jul 15 17:20:31 2025 -0700 add dogbone problem Exec/Dogbone/CMakeLists.txt Exec/Dogbone/GNUmakefile Exec/Dogbone/Make.package Exec/Dogbone/README.rst Exec/Dogbone/inputs Exec/Dogbone/prob.H Exec/Dogbone/prob.cpp commit 5cf390e687376b3abfaf2ea70e9afcd7bc7940bf Merge: 4dce8674 7b4a7f06 Author: Hannah Klion Date: Tue Jul 15 15:56:09 2025 -0700 Merge remote-tracking branch 'upstream' into dogbone commit 4dce86746f4807cfb8205361c3d4c525bccd4f80 Author: Hannah Klion Date: Tue Jul 15 15:54:29 2025 -0700 change ic_bc_type to ic_type in docs Docs/sphinx_doc/Inputs.rst commit 7b4a7f0644e6b950e0d305a1ccd41db12c85f11b Merge: 5f27c47a f1b89d35 Author: Hannah Klion Date: Tue Jul 15 15:53:43 2025 -0700 Merge pull request #403 from hklion/netcdf_interface Netcdf quality of life changes commit 7fdc459776080be5909c9b4c6a07eb15cec020cf Author: Hannah Klion Date: Tue Jul 15 14:28:14 2025 -0700 rename ic_bc_type as ic_type. Whether BCs need netcdf is inferred from BC options Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_Checkpoint.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_3d.cpp commit 5f27c47a4fb3c53f1a7aeeedaa3a6f5755aff426 Merge: c2d41cf4 1cbb213f Author: Ann Almgren Date: Thu Jul 10 17:38:38 2025 -0700 Merge pull request #402 from seahorce-scidac/add_xamr_ref add pointer to xamr repo commit 1cbb213fb84be25d494ba3b32cf2e9501bb7f2e3 Author: Ann Almgren Date: Thu Jul 10 16:44:08 2025 -0700 add pointer to xamr repo Docs/sphinx_doc/Visualization.rst commit c2d41cf41bdcaa0bc45151ac1787b6d27b1ab813 Merge: efdde872 9d9c7ed6 Author: Hannah Klion Date: Wed Jul 9 14:26:15 2025 -0700 Merge pull request #401 from hklion/patch_ml adjust where we calculate fluxes commit f1b89d358c8cb60951875bd678e85fdf677765ae Author: Hannah Klion Date: Tue Jul 8 13:25:34 2025 -0700 fix orlanski name in documentation Docs/sphinx_doc/BoundaryConditions.rst commit 6a899283c84d926b7ea19152153bc2e6c6abee2f Author: Hannah Klion Date: Tue Jul 8 13:07:58 2025 -0700 add missing word to docs Docs/sphinx_doc/Inputs.rst commit 83a7be75e533bc7a9f8da4647114ec65e48c9bce Author: Hannah Klion Date: Tue Jul 8 12:29:48 2025 -0700 add comment that netcdf4 classic doesn't work Docs/sphinx_doc/Inputs.rst commit ffe5bbd6d107a1cb9cb9fd9ccfb95f6349b24bec Author: Hannah Klion Date: Tue Jul 8 12:28:38 2025 -0700 if variable not found, write out which variable is missing Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCFile.cpp commit f0c9fa395fc6414fb21092d44d3ff13a4c8bd6f7 Author: Hannah Klion Date: Tue Jul 8 12:14:55 2025 -0700 fix has_var and friends Source/IO/REMORA_NCInterface.cpp commit 9d9c7ed6254b9fcbaf221387e1bcb2fb24b33bc8 Author: Hannah Klion Date: Mon Jul 7 17:15:57 2025 -0700 adjust where we calculate fluxes Source/TimeIntegration/REMORA_setup_step.cpp commit efdde872fc7c191d90be17413bdcc6beafc32689 Merge: d0972826 f1b1b5b7 Author: Hannah Klion Date: Mon Jul 7 17:09:39 2025 -0700 Merge pull request #400 from hklion/fix_scale_rhs_tile Fix scale rhs w/tiling and remove OCCAMS problem commit f1b1b5b7d05411dccc3ee3220e3fa43869837db4 Author: Hannah Klion Date: Mon Jul 7 15:18:54 2025 -0700 fix scale_rhs_vars for tiling Source/TimeIntegration/REMORA_scale_rhs_vars.cpp commit ed166fc75065f0fac06ab57293b824f2214d40dc Author: Hannah Klion Date: Mon Jul 7 13:50:06 2025 -0700 remove OCCAMS problem Exec/OCCAMS/GNUmakefile Exec/OCCAMS/Make.package Exec/OCCAMS/inputs Exec/OCCAMS/prob.H Exec/OCCAMS/prob.cpp commit d097282662926c29174b2c6cfc598feeaf87e8b4 Merge: faa4920f cd2c9174 Author: Hannah Klion Date: Wed Jul 2 13:35:12 2025 -0700 Merge pull request #399 from hklion/flat_bathy when flat bathymetry is selected, override other bathymetry specification commit cd2c91741f278cd9a0517fe4ba05f5c11d37a009 Author: Hannah Klion Date: Wed Jul 2 11:03:46 2025 -0700 when flat bathymetry is selected, bathymetry function in prob.cpp not called Source/REMORA.H Source/REMORA.cpp commit faa4920f3f6d4903385472cebb01781305d14bd0 Merge: ce96fe05 382abe37 Author: Hannah Klion Date: Thu Jun 26 16:43:21 2025 -0700 Merge pull request #398 from hklion/rivers Bugfixes + river test docs commit 382abe37ef3203ed979db5a835a9f55bd7dd0d46 Author: Hannah Klion Date: Thu Jun 26 16:12:27 2025 -0700 fix compile bug for particles on GPU Exec/ParticlesOverSeaMount/prob.cpp commit 08930aa83f08fb20f32f6ad84371802c2fb17e5c Author: Hannah Klion Date: Thu Jun 26 15:00:49 2025 -0700 set temp/salt/scalar river flags to false when river flag is false Source/REMORA_DataStruct.H commit e475786150828baf01b2c9d7ff078809e1e2ed01 Author: Hannah Klion Date: Thu Jun 26 14:50:40 2025 -0700 add docs about IdealRivGrid Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Exec/IdealRivGrid/README.rst commit ce96fe0562ebf1bf6aaeb85de8fc6a2db80f57af Merge: edb105dd dfa95891 Author: Hannah Klion Date: Wed Jun 25 11:30:39 2025 -0700 Merge pull request #397 from hklion/rivers Add capability for rivers commit dfa95891d43d8352d7897a451349d2e1127e1600 Author: Hannah Klion Date: Tue Jun 17 16:57:38 2025 -0700 update inputs and GNUMakefile for prod runs Exec/IdealRivGrid/GNUmakefile Exec/IdealRivGrid/inputs commit 9fbb2e4c80745e2ac5ccc9ba213f2af674f39661 Author: Hannah Klion Date: Tue Jun 17 16:56:19 2025 -0700 make interp_array calculation in parallelfor for GPU Source/IO/REMORA_NCTimeSeriesRiver.cpp commit 0f229dff4c1239c5054ca52085f8409bbedf8277 Author: Hannah Klion Date: Tue Jun 17 14:13:17 2025 -0700 fix race-ish condition Source/Initialization/REMORA_init_from_netcdf.cpp commit 2fb94f684dd482de23fc38d0f301eaf6fc19376b Author: Hannah Klion Date: Tue Jun 17 13:24:27 2025 -0700 fix on GPU Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 3a0264cd723548795614a7e49f7bf38b71ad58a8 Author: Hannah Klion Date: Mon Jun 16 17:43:34 2025 -0700 add rivergrid problem Exec/IdealRivGrid/CMakeLists.txt Exec/IdealRivGrid/GNUmakefile Exec/IdealRivGrid/inputs Exec/IdealRivGrid/prob.H Exec/IdealRivGrid/prob.cpp commit edb105dd95188d1b34f53a566f4fb69cddfc58bc Merge: 1f83a209 2f9275d1 Author: Hannah Klion Date: Mon Jun 16 17:34:20 2025 -0700 Merge pull request #396 from hklion/update_amrex update amrex commit 86b4418ec953be69699ef508991bd8a295a92992 Author: Hannah Klion Date: Mon Jun 16 17:33:54 2025 -0700 fully fix for non-netcdf Source/TimeIntegration/REMORA_advance_3d.cpp commit d11259e019d95f4577a175c34050a5dd48fc6fd6 Author: Hannah Klion Date: Mon Jun 16 17:32:48 2025 -0700 add docs Docs/sphinx_doc/Inputs.rst commit 9fb57b653b99255f0daaf5392a02cb65f28b2d80 Author: Hannah Klion Date: Mon Jun 16 17:14:43 2025 -0700 rename var so no collision in codespell Source/IO/REMORA_ReadFromInitNetcdf.cpp commit df6e0fc62e517790824811395e6a3abdd29f38f9 Author: Hannah Klion Date: Mon Jun 16 17:11:41 2025 -0700 fix build for non-netcdf Source/REMORA.H commit 469f294c18cf4f4dbdf6b080d8f14525a8a106ab Merge: 57237552 1f83a209 Author: Hannah Klion Date: Mon Jun 16 16:57:04 2025 -0700 Merge remote-tracking branch 'upstream/development' into rivers commit 572375522b882e802a756a21a6ddc71f4704369a Author: Hannah Klion Date: Mon Jun 16 16:55:46 2025 -0700 fix bugs in rivers to agree with ROMS Source/IO/Make.package Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 2f9275d1138086d668a95ff489c1cd5894afd3ac Author: Hannah Klion Date: Thu Jun 12 13:59:45 2025 -0700 update amrex Submodules/AMReX commit 1f83a209921e77c17bcfbf9cd7905c3b4d629324 Author: Hannah Klion Date: Thu Jun 12 13:43:23 2025 -0700 Update README.rst README.rst commit 60705bd320a6c31cd0e17ba922b05574200bfcb2 Author: Hannah Klion Date: Thu Jun 12 13:36:20 2025 -0700 Update README.rst README.rst commit ed16ff148a8061e77f669ce8860aa32d25fcf3b4 Author: Hannah Klion Date: Mon Jun 9 11:03:37 2025 -0700 Update name of PNNL in paper affiliations and pub month paper/paper.md commit afb67cf9746d3925cee1ad162b7bb5fd2ed1f2ea Merge: 9f35d451 000b78ec Author: Hannah Klion Date: Mon Jun 9 10:23:35 2025 -0700 Merge pull request #395 from jatkinson1000/JOSS-editorial Minor changes in paper.md as part of the JOSS Editorial Process commit 000b78ec212575ad7913642d700a1135d015b009 Author: Jack Atkinson Date: Mon Jun 9 14:22:45 2025 +0100 Add citation of the Oceananigans software. paper/paper.bib paper/paper.md commit 6d36069d057e9e289e1213c75852d5d30a3e1546 Author: Jack Atkinson Date: Mon Jun 9 14:15:50 2025 +0100 Rename section 'Next development steps' to 'Future development'. paper/paper.md commit 7eee12079ebc598b2aabd23c7a0d16b38de4e79d Author: Jack Atkinson Date: Mon Jun 9 14:15:08 2025 +0100 Typographical change Replace 'adaptive mesh refinement' with 'AMR'. paper/paper.md commit 952bca191cff977430f592c7be871fd11f2c9028 Author: Jack Atkinson Date: Mon Jun 9 14:14:11 2025 +0100 Typographical change - remove parantheses. paper/paper.md commit 6d46810b5e3afebf083d42b2613f491132b10658 Author: Jack Atkinson Date: Mon Jun 9 13:53:58 2025 +0100 Spelling FORTRAN -> Fortran consistent with standards for Fortran 90. paper/paper.md commit f863edaf67baf68d88492772ff4da44c10571d31 Merge: 624716ab 9f35d451 Author: Hannah Klion Date: Fri Jun 6 17:58:03 2025 -0700 Merge branch 'development' into rivers commit 624716abc8273db929b77d64326f96c49fcfa79c Author: Hannah Klion Date: Fri Jun 6 17:55:17 2025 -0700 update rivers Exec/IdealRivGrid/Make.package Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCTimeSeriesRiver.H Source/IO/REMORA_NCTimeSeriesRiver.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H commit 9f35d4518cd36a56c7272921ffb43488d024837c Merge: 798cc264 d6ce4ba1 Author: Hannah Klion Date: Wed Jun 4 15:03:04 2025 -0700 Merge pull request #394 from hklion/plot_time_interval Add option to output plot and checkpoint files at simulation time interval commit d6ce4ba17ddba8e141b19de2b5107a6720079aaa Author: Hannah Klion Date: Wed Jun 4 14:08:06 2025 -0700 add option to output plot and checkpoint files at simulation time intervals Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Plotfiles.rst Source/REMORA.H Source/REMORA.cpp commit 798cc264745b0462b28c59e3b282abd16c90f63f Merge: b1e91baa bcfd85c9 Author: Hannah Klion Date: Wed Jun 4 10:56:11 2025 -0700 Merge pull request #393 from hklion/multiple_boundary_files add ability to specify multiple time-consecutive boundary data files commit bcfd85c913841af18fb9105024e16e42e60022a3 Author: Hannah Klion Date: Tue Jun 3 15:38:48 2025 -0700 add ability to specify multiple time-consecutive boundary data files Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit d21c34ea37c83098518536db10fd91b7895607f2 Author: Hannah Klion Date: Mon Jun 2 15:03:19 2025 -0700 start adding time controls for outputs Source/REMORA.cpp commit b1e91baad9ca385a6abd1a226b29bf475a12c315 Merge: 9211aeba 44980fcc Author: Hannah Klion Date: Fri May 30 18:06:13 2025 -0700 Merge pull request #392 from hklion/quickstart add a quickstart to docs and a few lines on amrvis commit 44980fcc1d8ae37286b3eb12084ace8dc80b29e3 Author: Hannah Klion Date: Fri May 30 18:03:22 2025 -0700 add a quickstart to docs and a few lines on amrvis Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/Visualization.rst Docs/sphinx_doc/building.rst commit 9211aeba08cdb58556633bc33e2953a9a7a5de76 Merge: 4677b227 75d5bdd0 Author: Hannah Klion Date: Fri May 30 16:53:47 2025 -0700 Merge pull request #391 from hklion/remora_summary_par add summary paragrpah about REMORA to docs commit 75d5bdd0ac8b8e4b3ecaae2f5d8b2f8aca458a63 Author: Hannah Klion Date: Fri May 30 16:45:05 2025 -0700 add summary paragrpah about REMORA to docs Docs/sphinx_doc/index.rst commit 4677b227fb56f091f2a1e37bff65115bf3ce8b40 Author: Hannah Klion Date: Fri May 30 16:38:33 2025 -0700 Update README.rst README.rst commit 876fa301cc9975f53c80c63b3047b625a12c534d Merge: 9f9d0c21 86843546 Author: Hannah Klion Date: Fri May 30 11:56:05 2025 -0700 Merge pull request #390 from hklion/bl_test_tol Increase tolerance for BoundaryLayer ctest and add a note to README commit 86843546a2ed4067c6bbef777efe8260eceeff9c Author: Hannah Klion Date: Thu May 29 15:35:37 2025 -0700 Increase tolerance for BoundaryLayer ctest and add a note to README Exec/BoundaryLayer/README Tests/CTestList.cmake commit 9f9d0c213275b0111273ba91e6495b8656ed2946 Merge: cd945251 4dfa68f2 Author: Hannah Klion Date: Tue May 20 19:59:47 2025 -0700 Merge pull request #389 from hklion/ocean_times ocean_times is now a vector and no longer hardcoded size commit 4dfa68f293cdfa755256c71780d562106ba93e3a Author: Hannah Klion Date: Tue May 20 18:58:37 2025 -0700 ocean_times is now a vector and no longer hardcoded size Source/IO/REMORA_ReadFromBdryNetcdf.cpp commit cd945251691ddc3d1922f50e7854ac141020bbe9 Merge: 0fe37cbb 3bfb5fac Author: Hannah Klion Date: Fri May 16 18:13:34 2025 -0700 Merge pull request #388 from hklion/paper_updates more citation formatting commit 3bfb5facb13e598bdb024047355f0cf22f62b075 Author: Hannah Klion Date: Fri May 16 18:11:36 2025 -0700 more citation formatting paper/paper.md commit 0fe37cbbd03489d7520da3f67b5e4f8dfff9cdf2 Merge: dcd749a8 e429f365 Author: Hannah Klion Date: Fri May 16 17:30:25 2025 -0700 Merge pull request #387 from hklion/paper_updates Another attempt at citations commit e429f365c28fcdc729ec38a25ad5d674e91369f2 Author: Hannah Klion Date: Fri May 16 17:23:04 2025 -0700 Another attempt at citations paper/paper.md commit dcd749a8887b7d86c9ea196863c314a1404211f6 Merge: 680752f1 a75d06b9 Author: Hannah Klion Date: Fri May 16 17:20:17 2025 -0700 Merge pull request #386 from hklion/paper_updates fix citations again commit a75d06b9af6a7d73b335cd3a8527c977cbea11ab Author: Hannah Klion Date: Fri May 16 17:19:16 2025 -0700 fix citations again paper/paper.md commit 680752f1ae03f2c4bfb3c726d6b15b851499ea13 Merge: e0940487 cc67bde4 Author: Hannah Klion Date: Fri May 16 16:49:49 2025 -0700 Merge pull request #385 from hklion/paper_updates fix paper citations commit cc67bde42faf72aef6462de0183d1a4bcd33e719 Author: Hannah Klion Date: Fri May 16 16:42:48 2025 -0700 fix paper citations paper/paper.md commit e0940487c786c04981d9dc139f4795afe6bcc2d6 Merge: ddd30f84 e66b75c1 Author: Hannah Klion Date: Fri May 16 16:39:47 2025 -0700 Merge pull request #384 from hklion/paper_updates paper updates for JOSS commit e66b75c1e2adf4b5468f08fdb71cbb4ce7ef9b08 Author: Hannah Klion Date: Fri May 16 16:34:56 2025 -0700 fix spelling and bib paper/paper.bib paper/paper.md commit 4b6c557ef3c1cfe0eb28ccf4d31f57db93918228 Author: Hannah Klion Date: Fri May 16 15:53:38 2025 -0700 paper updates for JOSS paper/paper.bib paper/paper.md commit ddd30f84f3e58440a42fa4cfbe123147f973aac7 Merge: e17506ef b61acf2c Author: Hannah Klion Date: Thu May 15 13:48:13 2025 -0700 Merge pull request #383 from hklion/mpi_comm_namespace make sure MPI_Comm in amrex namespace to match AMReX changes commit b61acf2c39af4f47753e0df49bcb3932239a115f Author: Hannah Klion Date: Thu May 15 12:35:35 2025 -0700 fix MPI_Comm issues for both MPI/non-MPI builds Source/IO/REMORA_console_io.cpp Source/REMORA.H commit e7e985feba9c3423e2664d4bcb803247cb6d2657 Author: Hannah Klion Date: Thu May 15 10:57:15 2025 -0700 make sure MPI_Comm in amrex namespace to match AMReX changes Source/IO/REMORA_console_io.cpp Source/REMORA.H Submodules/AMReX commit e17506ef464d1598105290eedf0fbc390255fa8d Merge: 88f5fde0 998f214b Author: Hannah Klion Date: Tue May 13 11:31:15 2025 -0700 Merge pull request #382 from hklion/patch_docs Patch docs commit 88f5fde0f21af112152fcf2a9efca55047308cc3 Merge: 93102698 03fdc47d Author: Hannah Klion Date: Tue May 13 11:23:46 2025 -0700 Merge pull request #381 from hklion/netcdf_patch patch netcdf write commit 03fdc47d1ee9ba41277b48bf3d36dc2a146ad3b5 Author: Hannah Klion Date: Tue May 13 11:23:04 2025 -0700 patch netcdf write Source/IO/REMORA_NCPlotFile.cpp commit 998f214b882025b6607c891ae5a290a1cb95dc3f Author: Hannah Klion Date: Mon May 12 18:47:17 2025 -0700 adjust none param annotation Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp commit f0da8673e03be37a1484258e54c7fd4ed67a02d6 Author: Hannah Klion Date: Mon May 12 17:57:21 2025 -0700 include netcdf in doxygen Docs/Doxyfile.in commit 93102698efee154d96145179172c0dc2810ae3e4 Merge: df66ea5b 91a4b4e5 Author: Hannah Klion Date: Mon May 12 14:09:43 2025 -0700 Merge pull request #380 from jmsexton03/docs_ci_fix Make docs workflow run both on push and pull_request commit 91a4b4e5abb9b1366c91991d91556e1c2834f7ca Author: Jean M. Sexton Date: Mon May 12 13:38:08 2025 -0700 Make docs workflow run both on push and pull_request .github/workflows/docs.yml commit df66ea5b5e4e2281218220d9951a56664c58088c Merge: 1559d03c 6b7b83ed Author: Hannah Klion Date: Mon May 12 09:46:38 2025 -0700 Merge pull request #379 from hklion/docstrings Docstrings commit 6b7b83edf6713db033522281d257d0d2806dcf4f Author: Hannah Klion Date: Sun May 11 20:18:14 2025 -0700 fix spelling Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/REMORA.H commit 2fd07334b3fcda8e66d30119550132274469401d Merge: 812d2334 1559d03c Author: Hannah Klion Date: Sun May 11 20:15:59 2025 -0700 Merge remote-tracking branch 'upstream/development' into docstrings commit 812d233453875c46340df9d5c35226881b024b0c Author: Hannah Klion Date: Sun May 11 20:06:46 2025 -0700 remove unused variables and update docstrings Docs/Doxyfile.in Exec/IdealMiniGrid/prob.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.H Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCFile.cpp Source/IO/REMORA_NCInterface.H Source/IO/REMORA_NCInterface.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/Particles/REMORA_PC_Evolve.cpp Source/Particles/REMORA_PC_Init.cpp Source/Particles/REMORA_PC_Utils.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_Derive.cpp Source/REMORA_IndexDefines.H Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/REMORA_DepthStretchTransform.H Source/Utils/REMORA_Math.H commit 1559d03c71ef432c19525ee2a50c1540164a8786 Merge: d1b6c858 0fe5018a Author: Hannah Klion Date: Fri May 9 20:23:02 2025 -0700 Merge pull request #378 from hklion/gpu_ctest add docs about GPU CTest commit 0fe5018a33ed56a82ef19e1ed5b3a6ea09590763 Author: Hannah Klion Date: Fri May 9 10:20:43 2025 -0700 add docs about GPU CTest Docs/sphinx_doc/testing.rst commit 5431f60b2d56abf0ab42e6567165b56dc05ac4ac Author: Hannah Klion Date: Tue Apr 29 17:15:56 2025 -0700 add docstrings to REMORA.H and do some cleanup of unused class members Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCFile.H Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit 21967cd3c6d00bf13887a9dd55f5dce51c86d9f0 Author: Hannah Klion Date: Tue Apr 29 10:58:54 2025 -0700 add header docstrings Source/REMORA.H commit d1b6c858d2fa5cb263cfcd5407830bf9ed254047 Merge: cb0e9e4d 20cb1264 Author: Hannah Klion Date: Mon Apr 28 14:05:27 2025 -0700 Merge pull request #377 from hklion/patch_netcdf_bdry add empty FABs to boundary condition data structures so the filler knows where to look commit 20cb1264e52f15b0a5eba3a7e36cffd8813b2cf8 Author: Hannah Klion Date: Mon Apr 28 14:04:38 2025 -0700 add empty FABs to boundary condition data structures so the filler knows where to look Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp commit cb0e9e4d19a27b2e05e10a661872a3c09ea60841 Merge: ff2fc72e 687d55bb Author: Hannah Klion Date: Fri Apr 25 19:14:33 2025 -0700 Merge pull request #376 from hklion/boundary_file only read in boundary data required by boundary config and fix floating point issue in dt check commit 7795b6325b809010771fec93f8a1e6729f300e38 Author: Hannah Klion Date: Fri Apr 25 18:54:21 2025 -0700 update subhead of doxygen Docs/Doxyfile.in commit 687d55bb627b746aeebe82cb9fbed22e673be709 Author: Hannah Klion Date: Fri Apr 25 16:58:52 2025 -0700 only read in boundary data required by bounday config and fix floating point issue in dt cheeck Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H commit ff2fc72ef08ae6c2c0c7eea4413db05d2c508528 Merge: 900585b3 3bfc65d5 Author: Hannah Klion Date: Mon Apr 21 16:17:40 2025 -0700 Merge pull request #374 from hklion/time_variable_names allow user to specify time variable name in netcdf file commit 3bfc65d5bbd6cc11a96d02ec0133142cf8a19a1d Author: Hannah Klion Date: Mon Apr 21 15:35:28 2025 -0700 allow user to specify time variable name in netcdf file Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp commit 900585b30d9382db3e6dbc018b351467f104e7eb Merge: 2c98abb3 c5e323b6 Author: Hannah Klion Date: Mon Apr 21 12:50:17 2025 -0700 Merge pull request #373 from emmashie/mask_loading removed mask_psi loading commit c5e323b68ac31ee649aec1adee2ef9b46b611065 Author: Hannah Klion Date: Mon Apr 21 12:49:20 2025 -0700 remove other references to mskp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp commit f4d8b4dd94c12c460d932752d5e18df9bd77da7e Author: Emma Nuss Date: Fri Apr 18 16:15:39 2025 -0700 removed mask_psi loading Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp commit 2c98abb3e3881e20c4e956ef2691c0c99da97b0c Merge: 1b01e334 c9a173da Author: Hannah Klion Date: Fri Apr 18 10:56:46 2025 -0700 Merge pull request #372 from hklion/docs_patch add notes to docs about netcdf error commit c9a173da1cff918a69dc06019e37cba387652f2e Author: Hannah Klion Date: Fri Apr 18 10:56:10 2025 -0700 add notes to docs about netcdf error Docs/sphinx_doc/Inputs.rst commit 1b01e334d5325d4061d1f83d826a3bc1156aab4a Merge: f511553b 152fad9d Author: Hannah Klion Date: Fri Apr 18 09:25:59 2025 -0700 Merge pull request #371 from seahorce-scidac/add_first_fortran Framework for calling Fortran functions commit 152fad9d30ea30e75320212fed62e27d06ff7a2a Author: Ann Almgren Date: Thu Apr 17 19:03:07 2025 -0700 Framework for calling Fortran functions Exec/Make.REMORA Source/TimeIntegration/FUNWAVE/Make.package Source/TimeIntegration/FUNWAVE/REMORA_funwave_Fortran_Interface.H Source/TimeIntegration/FUNWAVE/REMORA_funwave_advance.F90 Source/TimeIntegration/FUNWAVE/REMORA_funwave_isohelper.F90 Source/TimeIntegration/REMORA_Advance.cpp commit f511553bb194dd98c8fcfeab6e7fe0e1cc79997d Merge: baf5d100 df65e77f Author: Hannah Klion Date: Thu Apr 17 15:25:30 2025 -0700 Merge pull request #370 from seahorce-scidac/get_ready_for_fortran get build system ready to include fortran commit df65e77fd91ffc030050444cfffde307a7a523e0 Author: Ann Almgren Date: Thu Apr 17 10:34:56 2025 -0700 get build system ready to include fortran .codespellrc .github/workflows/hip.yml CMake/BuildREMORAExe.cmake CMake/SetAmrexOptions.cmake CMake/SetREMORACompileFlags.cmake CMakeLists.txt Exec/Make.REMORA commit baf5d100de30351be70af1baf50c6cab613eec1a Merge: 993b839a 3c041951 Author: Hannah Klion Date: Wed Apr 16 15:08:05 2025 -0700 Merge pull request #369 from hklion/climatology_docs fix typo commit 3c0419516c92abfe532177243abb8724e4d4afd5 Author: Hannah Klion Date: Wed Apr 16 15:07:01 2025 -0700 fix typo Docs/sphinx_doc/Climatology.rst commit 993b839a3e5b8f4af055df23b37d2455ee4f044b Merge: 8a6cebbf 4390e5f5 Author: Hannah Klion Date: Wed Apr 16 15:06:19 2025 -0700 Merge pull request #368 from hklion/climatology_docs actually add climatology page commit 4390e5f53071a3ac6d5e084e2e76950e1e1cf6a2 Author: Hannah Klion Date: Wed Apr 16 15:05:15 2025 -0700 actually add climatology page Docs/sphinx_doc/Climatology.rst commit 8a6cebbf27feedbe27b4a9f094270146dff9b1c3 Merge: 9e50592b 22890e92 Author: Hannah Klion Date: Wed Apr 16 14:35:21 2025 -0700 Merge pull request #367 from hklion/climatology_docs Climatology docs commit 22890e9275e911148d75dae83d95617889944304 Author: Hannah Klion Date: Wed Apr 16 14:34:48 2025 -0700 add info about climatology and wind regtests Docs/sphinx_doc/RegressionTests.rst Exec/IdealMiniGrid/README.rst commit 069497ceb641b8609d454bb3e207a93a9a6051f2 Author: Hannah Klion Date: Wed Apr 16 14:08:13 2025 -0700 add climatology documentation Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/index.rst commit 9e50592b965a01d4f1a556a1f8fc52a2cb4ffb92 Merge: 5355a978 168175db Author: Hannah Klion Date: Tue Apr 15 18:28:48 2025 -0700 Merge pull request #366 from hklion/add_Cs add Cs_r and Cs_w to netcdf files commit 168175db092ad7624a3c31bd58fc2385d2776457 Author: Hannah Klion Date: Tue Apr 15 18:23:14 2025 -0700 add Cs_r and Cs_w to netcdf files Source/IO/REMORA_NCPlotFile.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/Utils/REMORA_DepthStretchTransform.H commit 5355a9787bd915ed39aba4ba00ebec2a4db47e5c Merge: bd4f8405 a2aee12e Author: Hannah Klion Date: Tue Apr 15 16:08:34 2025 -0700 Merge pull request #365 from hklion/fix_gpu fix gpu build for climatology commit a2aee12e391b2df56056907b4b798b8537bfe3e3 Author: Hannah Klion Date: Tue Apr 15 16:08:05 2025 -0700 fix gpu build for climatology Source/IO/REMORA_NCTimeSeries.cpp commit bd4f8405c5b0b93ef609c8716c432f4242d9df80 Merge: 51c47ac8 a8a887ac Author: Hannah Klion Date: Tue Apr 15 13:15:20 2025 -0700 Merge pull request #364 from hklion/nudg_clim Add nudging to climatology commit a8a887ac792b8dc9a9219b13b5361786f10b7ab5 Author: Hannah Klion Date: Mon Apr 14 16:31:58 2025 -0700 Add nudging to climatology CMake/BuildREMORAExe.cmake Exec/IdealMiniGrid/inputs_clim_nudg Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCTimeSeries.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_apply_clim_nudg.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 51c47ac8d3b8d6af4206f0904534af3f08c2e8eb Merge: 70127358 c73e7804 Author: Hannah Klion Date: Thu Apr 3 19:49:01 2025 -0700 Merge pull request #363 from hklion/move_cons_bc move application of BCs to cons variables to advance_3d from advance_3d_ml commit c73e7804f2d6418c4a932a6725cce7394e29f738 Author: Hannah Klion Date: Thu Apr 3 19:46:59 2025 -0700 move application of BCs to cons variables to advance_3d from advance3d_ml Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit 70127358447e009dcdaf068427137318963b16d8 Merge: 1e5947b8 073d8d8d Author: Hannah Klion Date: Mon Mar 31 14:21:07 2025 -0700 Merge pull request #362 from hklion/error_out_nan_inf fix typos commit 073d8d8dde9b78c6c2cf200dfc84509f63d60b0f Author: Hannah Klion Date: Mon Mar 31 14:20:17 2025 -0700 fix typos Source/IO/REMORA_NCPlotFile.cpp commit 1e5947b8150a477191424f1b1b23c1d0065352d2 Merge: e6202a7a e04b30ad Author: Hannah Klion Date: Mon Mar 31 14:14:10 2025 -0700 Merge pull request #361 from hklion/error_out_nan_inf throw an error when finding nan or inf on writing output commit e04b30ad3337ceeef9b9f211d353c7925946b366 Author: Hannah Klion Date: Mon Mar 31 14:13:39 2025 -0700 throw an error when finding nan or inf on writing output Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp commit e6202a7a92ca5663d2ca91acfd04080f3892485d Merge: f8912fab faabbac3 Author: Hannah Klion Date: Fri Mar 28 15:14:47 2025 -0700 Merge pull request #360 from hklion/wind_from_netcdf Add framework to read in time series data from netcdf file commit faabbac3c52684971a1279870b7bc9ea6254c11f Author: Hannah Klion Date: Fri Mar 28 15:13:16 2025 -0700 add docs about time series winds and adjust time series name Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_NCTimeSeries.H Source/IO/REMORA_NCTimeSeries.cpp commit 2bdfc60ff4d50df2ebbe9b47e5862a0dda29accf Author: Hannah Klion Date: Wed Mar 26 15:21:58 2025 -0700 add inputs for netcdf forcing Exec/IdealMiniGrid/inputs_frc commit 39035d2968e37a0c4698248b73fd5974e7ab53e7 Author: Hannah Klion Date: Wed Mar 26 15:16:02 2025 -0700 add .cpp file Source/IO/REMORA_NCTimeSeries.cpp commit 153afb7e69e5fef7aa63c40d702255d09e98923d Author: Hannah Klion Date: Wed Mar 26 14:34:54 2025 -0700 add needed compile guards CMake/BuildREMORAExe.cmake Source/IO/Make.package Source/IO/REMORA_NCTimeSeries.H Source/REMORA.H Source/REMORA.cpp commit 9bc60e28ceccdf45a75c738d7cfadb2b55c0a812 Author: Hannah Klion Date: Wed Mar 26 12:39:28 2025 -0700 Add framework to read in time series data from netcdf file - NCTimeSeries reads in two time points and linearly interpolates - Adds option to read in winds from netcdf file Exec/IdealMiniGrid/inputs_frc Source/IO/Make.package Source/IO/REMORA_NCFile.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H commit f8912fabe418f31322363b6b35a11e27c1da6fc4 Merge: 2cf48430 85c01221 Author: Hannah Klion Date: Thu Mar 20 16:56:01 2025 -0700 Merge pull request #359 from hklion/rho_point_winds winds are defined at rho points commit 85c012213906313afa2ae9ea52660ee62b6884c7 Author: Hannah Klion Date: Thu Mar 20 16:53:55 2025 -0700 winds are defined at rho points Source/Initialization/REMORA_make_new_level.cpp commit 2cf48430ac1548bce57fd56ea83c16ae3144f481 Merge: 136ad9d2 25485f7e Author: Hannah Klion Date: Mon Mar 17 17:28:12 2025 -0700 Merge pull request #358 from hklion/buoy_bvf revert buoy2 test commit 25485f7ea5661353a255c83dd03c4888f343c212 Author: Hannah Klion Date: Mon Mar 17 17:27:27 2025 -0700 revert buoy2 test Source/TimeIntegration/REMORA_gls.cpp commit 136ad9d239b6d2131655fa7ad97b584d9c057a26 Merge: 9a2f06ca b9f1f161 Author: Hannah Klion Date: Mon Mar 17 16:40:39 2025 -0700 Merge pull request #357 from hklion/buoy_bvf Buoy bvf commit b9f1f1615eb9054dfba8574a5591ca4977259e56 Author: Hannah Klion Date: Mon Mar 17 16:40:01 2025 -0700 add comment Source/TimeIntegration/REMORA_gls.cpp commit d1212be9cc41ca162fcc3b57c73338223270395b Author: Hannah Klion Date: Mon Mar 17 16:39:12 2025 -0700 adjust buoy2 condition for BVF stability Source/TimeIntegration/REMORA_gls.cpp commit 9a2f06ca11929ff10be686880585bc80cd8f70f1 Merge: 7f2bb8e1 aa785b3b Author: Hannah Klion Date: Tue Mar 11 14:36:43 2025 -0700 Merge pull request #356 from hklion/drag_checkpoint add used rdrag2 or ZoBot to checkpoints when using commit aa785b3be0d0a153142b049bad94218d9d530b09 Author: Hannah Klion Date: Tue Mar 11 14:09:52 2025 -0700 add used rdrag2 or ZoBot to checkpoints when using Source/IO/REMORA_Checkpoint.cpp commit 7f2bb8e1321f56e70090dc38eb4ca1e6b61e8f8a Merge: 08616d34 318201a2 Author: Hannah Klion Date: Mon Mar 10 17:16:43 2025 -0700 Merge pull request #355 from hklion/prob_common modernize inputs commit 318201a2b95d25f251d35834da9be28746b8b989 Author: Hannah Klion Date: Mon Mar 10 17:14:45 2025 -0700 modernize inputs Exec/BoundaryLayer/inputs commit 08616d34427f959c0262ae4762b07e08fa36c2fd Merge: aa5727f2 f74aa72d Author: Hannah Klion Date: Mon Mar 10 16:32:16 2025 -0700 Merge pull request #354 from hklion/prob_common Prob common commit f74aa72da654a262a55bf57be54fa97613601f13 Author: Hannah Klion Date: Mon Mar 10 16:31:56 2025 -0700 plt name update Exec/BoundaryLayer/inputs commit 13706bff3d3cf57fab5d05e9e0a8c03796cea72c Author: Hannah Klion Date: Mon Mar 10 16:29:24 2025 -0700 remove tile size from inputs Exec/BoundaryLayer/inputs commit aa5727f271e02222e4e3d917eb3817bef8c5d72c Merge: 3dda41a9 bb380ab4 Author: Hannah Klion Date: Mon Mar 10 16:02:43 2025 -0700 Merge pull request #353 from hklion/prob_common Prob common commit bb380ab45d731aaebeb4c6be6a33d62729226b10 Author: Hannah Klion Date: Fri Mar 7 17:26:46 2025 -0800 added blankproblem and added to docs about analytic functions Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/ProblemSetup.rst Exec/BlankProblem/CMakeLists.txt Exec/BlankProblem/GNUmakefile Exec/BlankProblem/Make.package Exec/BlankProblem/amrvis.defaults Exec/BlankProblem/inputs Exec/BlankProblem/prob.H Exec/BlankProblem/prob.cpp commit 42255913ad542f2a2b71268eed325ba12ce2d4ee Author: Hannah Klion Date: Fri Mar 7 15:18:22 2025 -0800 tweaks in docs Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/theory/VerticalMixing.rst Source/TimeIntegration/REMORA_setup_step.cpp commit ced6a1aabd26f1cfa90fe957cd997e4868152069 Author: Hannah Klion Date: Fri Mar 7 15:13:51 2025 -0800 adjust custom to analytic in BoundaryLayer test inputs Tests/test_files/BoundaryLayer/BoundaryLayer.i commit 708b429a5c466857ea140ab9ec81bc526f1dc4cd Author: Hannah Klion Date: Fri Mar 7 15:12:29 2025 -0800 make rename custom to analytic and real to netcdf, but don't deprecate options yet Exec/BoundaryLayer/inputs Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_Checkpoint.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit bc08b05843aaf3a9d58f6e9ce82b4c8e324ae8ba Merge: 0ec6d922 6d48e224 Author: Hannah Klion Date: Thu Mar 6 17:31:31 2025 -0800 Merge remote-tracking branch 'upstream/bulk_fluxes' into prob_common commit 0ec6d9228adfa2e61cc1397a7834e04afb48213b Author: Hannah Klion Date: Thu Mar 6 17:25:50 2025 -0800 make a ProblemBase class and define virtual functions to be overriden by each problem where necessary Exec/Advection/prob.H Exec/Advection/prob.cpp Exec/BoundaryLayer/prob.H Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.H Exec/Channel_Test/prob.cpp Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.H Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.H Exec/IdealMiniGrid/prob.cpp Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.H Exec/Seamount/prob.cpp Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Exec/Upwelling_ML/prob.H Exec/Upwelling_ML/prob.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 6d48e22450b8fb4dc77a85684c3e47a36b8c54eb Author: Hannah Klion Date: Thu Mar 6 11:55:32 2025 -0800 make bulk fluxes work on GPU by making helper function static inline Source/REMORA.H Source/TimeIntegration/REMORA_bulk_flux.cpp commit 3af98a778e0eaf7112be29a87a68e810b1391728 Author: Hannah Klion Date: Tue Mar 4 17:48:40 2025 -0800 add docs about BL test Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Exec/BoundaryLayer/README commit d83f86ebc34ef0d16bcc4a39137e0de3242272fd Author: Hannah Klion Date: Tue Mar 4 17:40:07 2025 -0800 add test for bulk fluxes Exec/BoundaryLayer/CMakeLists.txt Exec/CMakeLists.txt Tests/CTestList.cmake Tests/REMORA_Gold_Files/BoundaryLayer/Header Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Cell_H Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/BoundaryLayer/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/BoundaryLayer/job_info Tests/test_files/BoundaryLayer/BoundaryLayer.i commit 5899ec5250c238621cffe3d7e589063584e0b024 Author: Hannah Klion Date: Tue Mar 4 17:26:37 2025 -0800 fix codespell .codespell-ignore-words Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp commit 291c88437f870334b9da46ac3d174a66d87be544 Author: Hannah Klion Date: Tue Mar 4 17:19:46 2025 -0800 add docs about bulk fluxes Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/theory/Equations.rst commit bcbe12aae9fbf08527f6e7366ea64fd6f0f61bbe Author: Hannah Klion Date: Tue Mar 4 15:58:26 2025 -0800 add bulk fluxes options to docs Docs/sphinx_doc/Inputs.rst commit 3dda41a96ca662193b56bfc2a67b535ed9113a13 Merge: 4f560e91 570be17c Author: Hannah Klion Date: Tue Mar 4 15:57:37 2025 -0800 Merge pull request #351 from hklion/warning_netcdf_file_size add warning about netcdf file size being too large commit 570be17c01360f6c964396cb71438f2bc3057f1a Author: Hannah Klion Date: Tue Mar 4 15:57:15 2025 -0800 add warning about netcdf file size being too large Source/REMORA.cpp commit 4f560e914c562687e0dd052a1b61d56c8aae8925 Merge: 14323ed6 80f09f6d Author: Hannah Klion Date: Tue Mar 4 15:05:50 2025 -0800 Merge pull request #350 from hklion/fix_typo fix typo commit 80f09f6deba51ed9205c51b67501d12e311e0597 Author: Hannah Klion Date: Tue Mar 4 15:05:25 2025 -0800 fix typo Docs/sphinx_doc/building.rst commit 14323ed6570b96822b4ced041764b08184911001 Merge: a7e859f3 661f930b Author: Hannah Klion Date: Tue Mar 4 14:00:02 2025 -0800 Merge pull request #349 from hklion/moab_docs add option to build with MOAB commit 661f930bd1a98503198888b363d4bbb9e3a36773 Author: Hannah Klion Date: Tue Mar 4 13:53:18 2025 -0800 add option to build with MOAB Docs/sphinx_doc/building.rst commit a7e859f3c32374d9a0bdb05dc252b85445171b93 Merge: 0f9ba2aa f08cb951 Author: Hannah Klion Date: Tue Mar 4 13:24:38 2025 -0800 Merge pull request #348 from hklion/scaling_docs update scaling plots and texts commit f08cb95190439c521705a1b84557ef213d025f05 Author: Hannah Klion Date: Tue Mar 4 13:21:36 2025 -0800 update scaling plots and texts Docs/sphinx_doc/Performance.rst Docs/sphinx_doc/figures/strong.png Docs/sphinx_doc/figures/weak.png Docs/sphinx_doc/figures/weak_scale.png commit 0f9ba2aa753a052685870ddcc90927c2d1d85941 Merge: e07fd80b 4dd8a1b5 Author: Hannah Klion Date: Mon Mar 3 15:57:26 2025 -0800 Merge pull request #347 from iulian787/iulian787/enable_moab Adapt build to link with MOAB commit 4dd8a1b525512d73810a839b7217ba9510b4ff6a Author: Iulian Grindeanu Date: Tue Jan 7 10:57:19 2025 -0600 change to pnetcdf build; also, use CDF-5 format for pnetcdf files Source/IO/REMORA_NCPlotFile.cpp Source/REMORA_MOAB.cpp commit b7df17bced777ac3ab400138a29bd10e2a1c081f Author: Iulian Grindeanu Date: Sun Sep 15 22:02:04 2024 -0500 add gmake changes, instance cell centers with MOAB CMake/BuildREMORAExe.cmake Source/Make.package Source/REMORA.H Source/REMORA.cpp Source/REMORA_MOAB.H Source/REMORA_MOAB.cpp commit 8494453e14a7897263c9f0fecd2dfac7041a6db8 Author: Iulian Grindeanu Date: Thu Sep 12 23:02:09 2024 -0500 modify user suffix for moab builds Exec/Make.REMORA commit 5a977f7b5207c0fe6429b2785cc0bad44baf727b Author: Iulian Grindeanu Date: Thu Aug 22 11:59:05 2024 -0500 add USE_MOAB option for gmake build in order to build with moab, we will use the pkgconfig file installed for moab, if moab was build with autotools to compile an executable with MOAB, we can use something like this cd Exec/Upwelling make MOAB_DIR=/nfs/gce/projects/climate/software/moab/devel/mpich-4.1.2/gcc-12.1.0 USE_MOAB=TRUE -j8 to run: mpiexec -np 2 ./REMORA3d.gnu.TEST.MPI.ex inputs to compile with debug on: make MOAB_DIR=/nfs/gce/projects/climate/software/moab/devel/mpich-4.1.2/gcc-12.1.0 USE_MOAB=TRUE DEBUG=TRUE -j8 It will actually create a different executable for debug: REMORA3d.gnu.DEBUG.MPI.ex careful about MOAB.pc, it has a @CGM reference unresolved; need to fix Exec/Make.REMORA commit 0fa0a05c0435e17dbb4bfa74e3cc1a86d129dad8 Author: Iulian Grindeanu Date: Thu Aug 22 10:53:32 2024 -0500 REMORA_USE_MOAB instead of REMORA_HAVE_MOAB CMake/BuildREMORAExe.cmake CMakeLists.txt Source/REMORA.H Source/REMORA.cpp commit c66dc6f664523d9a372bc538f802b737ec885fe1 Author: Iulian Grindeanu Date: Sun Aug 18 23:58:23 2024 -0500 first pass at adding moab dependency CMake/BuildREMORAExe.cmake CMakeLists.txt Source/REMORA.H Source/REMORA.cpp commit 78b608611fb61aa95ea3a4088063304931de6192 Author: Hannah Klion Date: Thu Feb 27 17:27:29 2025 -0800 fix evap with tiling Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 774c3f59398d4c0e42eebd9c497aa857f62e5b95 Author: Hannah Klion Date: Thu Feb 27 15:09:21 2025 -0800 add E-P Exec/BoundaryLayer/inputs Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit b498512730ca3c0932405478edc72dc52e17dce6 Author: Hannah Klion Date: Tue Feb 25 16:17:27 2025 -0800 adjust boundary handling in advection stencils Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 5cfd6cdd238fff9791913719cfb7aa99ecc9f875 Author: Hannah Klion Date: Wed Feb 19 18:29:08 2025 -0800 initial bulk flux commits, plus add things to constants file CMake/BuildREMORAExe.cmake Exec/Advection/prob.cpp Exec/BoundaryLayer/CMakeLists.txt Exec/BoundaryLayer/GNUmakefile Exec/BoundaryLayer/Make.package Exec/BoundaryLayer/inputs Exec/BoundaryLayer/prob.H Exec/BoundaryLayer/prob.cpp Exec/Channel_Test/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_Constants.H Source/REMORA_DataStruct.H Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_bulk_flux.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit e07fd80be68e8d3d2ccc9928c827aae26c0e95d1 Author: Weiqun Zhang Date: Tue Feb 11 21:54:34 2025 -0800 Update GitHub runner to ubuntu-24.04 (#346) GitHub will stop supporting 20.04 soon. Also update AMReX submodule to get access to the latest dependency scripts. .github/workflows/cuda-ci.yml .github/workflows/gcc.yml .github/workflows/hip.yml Submodules/AMReX commit 9ac1b9c4126fc6b129ea8abe67589f21321464c9 Merge: 4fa8760d e2030890 Author: Hannah Klion Date: Mon Feb 10 11:03:48 2025 -0800 Merge pull request #345 from hklion/mask_grow_cells_netcdf adjust boxes to avoid crash commit e2030890aef572a60754c07c8702b5d6b5c32033 Author: Hannah Klion Date: Mon Feb 10 10:56:12 2025 -0800 adjust boxes to avoid crash Source/IO/REMORA_Plotfile.cpp commit 4fa8760de282fd17d56d8475ce532c08bd8dfdc9 Merge: 03193ec0 cd65c48f Author: Hannah Klion Date: Thu Jan 30 18:08:11 2025 -0800 Merge pull request #344 from hklion/doc_updates update docs with scaling and mesh refinement commit cd65c48f4068c722133098b744180e17b469935a Author: Hannah Klion Date: Thu Jan 30 18:07:38 2025 -0800 update docs with scaling and mesh refinement Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Performance.rst Docs/sphinx_doc/figures/scalar_whitebg_circle_hr_00010.png Docs/sphinx_doc/figures/strong.png Docs/sphinx_doc/figures/weak.png Docs/sphinx_doc/figures/weak_scale.png commit 03193ec09dfb60815b1ec2819b171f9a094766fc Author: Hannah Klion Date: Thu Jan 30 14:37:07 2025 -0800 Update paper.bib paper/paper.bib commit 04027fd7a6f5d1cd77d0dab822a6c10658d469f5 Author: Hannah Klion Date: Thu Jan 30 13:45:36 2025 -0800 Update paper.md paper/paper.md commit 156bb0f66ba4600bf8cec76fe1d84c449ea959b5 Author: Hannah Klion Date: Thu Jan 30 13:32:24 2025 -0800 Update paper.md paper/paper.md commit 4e727e86553f908bcfd300dd8332f7cede33f455 Author: Hannah Klion Date: Thu Jan 30 13:24:08 2025 -0800 Update paper.bib paper/paper.bib commit 64a26a9658e088cc29cac92392f860cefdad7526 Author: Hannah Klion Date: Thu Jan 30 13:23:46 2025 -0800 Update paper.md paper/paper.md commit daa845056aba6ce4e23c24cd6916a26083a66e27 Author: Hannah Klion Date: Thu Jan 30 11:46:25 2025 -0800 Update paper.bib paper/paper.bib commit 050c1c3a06ca0aef80ac1ae521e88e5b9d15ce1d Merge: 8ca2470c 35849315 Author: Hannah Klion Date: Thu Jan 30 11:43:54 2025 -0800 Merge pull request #343 from seahorce-scidac/hklion-patch-2 Update paper.bib commit 35849315ea5fac51c32a2b3a19e2844ad9a793bb Author: Hannah Klion Date: Thu Jan 30 11:43:43 2025 -0800 Update paper.bib paper/paper.bib commit 8ca2470cc23f7cda03bf82d2e7c899028b8827f2 Author: Hannah Klion Date: Thu Jan 30 11:41:23 2025 -0800 Update paper.bib paper/paper.bib commit 01b21a0ad23e0ce64163c3c215138e83f3b71bb2 Merge: e5223f53 4d0015d9 Author: Hannah Klion Date: Wed Jan 29 16:22:06 2025 -0800 Merge pull request #342 from hklion/input_namespaces fix namespacing in documentation commit 4d0015d92d88e6301d9e42de0d57830fb2822970 Author: Hannah Klion Date: Wed Jan 29 16:21:43 2025 -0800 fix namespacing in documentation Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Checkpoint.rst commit e5223f53eee73e48dde09e1ee283a300786b687b Merge: 4f4ca83e aff69dcc Author: Hannah Klion Date: Wed Jan 29 13:32:58 2025 -0800 Merge pull request #341 from hklion/input_namespaces fix prob_lo/hi prefix in inputs_cf_orlanski commit aff69dcc0808d39e6068040d335dd308a200bcef Author: Hannah Klion Date: Wed Jan 29 13:26:54 2025 -0800 fix prob_lo/hi prefix in inputs_cf_orlanski Exec/IdealMiniGrid/inputs_cf_orlanski commit 4f4ca83e7f70baebf65be3d546761f91d5580d74 Author: Hannah Klion Date: Wed Jan 29 11:57:53 2025 -0800 Add DOIs to JOSS paper references paper/paper.bib commit 00b98c06eb4d486220f928bf8483b5a94ff8efef Merge: 999d2ba3 ec997dca Author: Hannah Klion Date: Wed Jan 29 11:47:01 2025 -0800 Merge pull request #340 from hklion/input_namespaces look for remora.bc.{varname} rather than bc.{varname} commit ec997dcad6723f92fbd87d6f6adc9441b822639a Author: Hannah Klion Date: Wed Jan 29 11:46:02 2025 -0800 look for remora.bc.{varname} rather than bc.{varname} Source/Initialization/REMORA_init_bcs.cpp commit 999d2ba3b80cbf8edfcf5abbe1af91cf9b58a5ef Merge: 9ce8bcbe 1acffd80 Author: Hannah Klion Date: Wed Jan 29 11:29:01 2025 -0800 Merge pull request #339 from hklion/input_namespaces ParticlesOverSeaMount bathymetry should be flat commit 1acffd801a126ac66bc14fc1d8694aa6a0188f9f Author: Hannah Klion Date: Wed Jan 29 11:23:37 2025 -0800 ParticlesOverSeaMount bathymetry should be flat Exec/ParticlesOverSeaMount/inputs commit 9ce8bcbe7a5b781cc7cae6a2c51b9b30db8fec6a Author: Hannah Klion Date: Tue Jan 28 18:25:21 2025 -0800 Remove extra . Exec/Advection/inputs commit 8b8cbdb9c9f6eea3923ceefb084b6fec46998f1c Merge: 3f29379a b03ca9b2 Author: Hannah Klion Date: Tue Jan 28 18:13:04 2025 -0800 Merge pull request #338 from hklion/input_namespaces Input namespaces commit 3f29379a4f783920d5e73f080ce4130024398ae1 Author: Hannah Klion Date: Tue Jan 28 18:02:29 2025 -0800 Update paper.md paper/paper.md commit b03ca9b21e299aafa8149e3e20ca9be50bb9260c Author: Hannah Klion Date: Tue Jan 28 17:56:05 2025 -0800 update inputs file namespaces Docs/sphinx_doc/Inputs.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/Advection/prob.cpp Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/inputs_ml Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/IdealMiniGrid/prob.cpp Exec/OCCAMS/inputs Exec/OCCAMS/prob.cpp Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/inputs_ml Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/inputs Exec/Seamount/prob.cpp Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling_ML/inputs Exec/Upwelling_ML/prob.cpp Source/Particles/REMORA_PC_Init.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/main.cpp Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit fefb572ab6e0be799029b6319e5428c9c36105d8 Author: Hannah Klion Date: Tue Jan 28 16:33:46 2025 -0800 Update paper.md paper/paper.md commit b103fc6f7081b8a00674160bc78d7d067684b84e Author: Hannah Klion Date: Mon Jan 27 11:36:00 2025 -0800 Update paper.md paper/paper.md commit 8d4fb103282a2dd94681afbc928ef47ce4726ac5 Author: Hannah Klion Date: Thu Jan 23 15:20:55 2025 -0800 remove spatial_order and fpe_trap_invalid Exec/Advection/inputs Exec/Advection/inputs_ml Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/inputs_ml Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/inputs_ml Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling_ML/inputs Source/REMORA_DataStruct.H commit 294ed5f962409634df6835536372acd755dab447 Author: Hannah Klion Date: Thu Jan 23 13:26:04 2025 -0800 bc. to remora.bc. Docs/sphinx_doc/BoundaryConditions.rst Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/DoubleGyre/inputs Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Source/Initialization/REMORA_init_bcs.cpp Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit e728be694033b29d27e8c8f2779dbbc47f0eb17f Merge: 1b99d104 0a6dd7ab Author: Hannah Klion Date: Thu Jan 23 10:25:13 2025 -0800 Merge pull request #337 from hklion/drag add in info about drag regression tests commit 0a6dd7ab704db878a9c43fd562fddb0292fa35e9 Author: Hannah Klion Date: Thu Jan 23 10:24:47 2025 -0800 add in info about drag regression tests Docs/sphinx_doc/RegressionTests.rst commit 1b99d104e1be7f58812324bc5140734ab1e9b9c9 Merge: 2c19cee0 db21f093 Author: Hannah Klion Date: Wed Jan 22 18:00:39 2025 -0800 Merge pull request #336 from hklion/drag Add options for logarithmic and quadratic drag commit db21f09391926779590e65fb63e41ed40a74541a Author: Hannah Klion Date: Wed Jan 22 17:18:39 2025 -0800 move solver choice outside for GPU reasons Source/TimeIntegration/REMORA_setup_step.cpp commit f4ce4283bdc59a7e0f126e73474c8144fced8ca8 Author: Hannah Klion Date: Wed Jan 22 16:49:39 2025 -0800 add ctests for drags Tests/CTestList.cmake Tests/REMORA_Gold_Files/Upwelling_logdrag/Header Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_logdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_logdrag/job_info Tests/REMORA_Gold_Files/Upwelling_qdrag/Header Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_qdrag/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_qdrag/job_info Tests/test_files/Upwelling_logdrag/Upwelling_logdrag.i Tests/test_files/Upwelling_qdrag/Upwelling_qdrag.i commit 2c19cee03cb160b4b4e7b76c5e9dd19f720d8308 Merge: f3242669 f6f5be68 Author: Hannah Klion Date: Tue Jan 21 17:13:44 2025 -0800 Merge pull request #335 from jmsexton03/fix_omp_ml Remove omp for growntilebox type loops commit 9ddeb0e85136d2d39e8229aad50728fa3ae05a86 Author: Hannah Klion Date: Tue Jan 21 15:23:59 2025 -0800 add docs for drag Docs/sphinx_doc/Inputs.rst commit 8ff1185329df7e152d3e96f4c25195f4278b102d Author: Hannah Klion Date: Tue Jan 21 14:40:17 2025 -0800 add changes to solverChoice Source/REMORA_DataStruct.H commit f6f5be689ca8a117fb033f89d52dd9db9e1d04c2 Author: Jean M. Sexton Date: Tue Jan 21 11:11:14 2025 -0800 Make codespell ignore indx variable .codespell-ignore-words commit 22a35f1cd307fca66d42d111b31f362c278dd3e5 Author: Jean M. Sexton Date: Tue Jan 21 10:55:53 2025 -0800 Remove some pragmas with potential overlaps Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/Utils/REMORA_DepthStretchTransform.H commit f00862e705561b1468d746ace7f59fc22bfed619 Author: Jean M. Sexton Date: Tue Jan 21 08:54:17 2025 -0800 Remove omp from fillpatcher Source/BoundaryConditions/REMORA_FillPatcher.cpp commit f3242669b8da260b1dc246b52edc9cdf505025c1 Merge: 7b9eec8e 8177a13f Author: Ann Almgren Date: Mon Jan 20 07:20:28 2025 -0800 Merge pull request #334 from seahorce-scidac/update_links add link to amrex in AMReX.rst commit 8177a13f7c492998b811d8ad8ad5b6a3804e5d4b Author: Ann Almgren Date: Mon Jan 20 07:19:51 2025 -0800 add link to amrex in AMReX.rst Docs/sphinx_doc/AMReX.rst commit 51eeb605945ae1b8bafc323e85b59404384bc2b6 Author: Hannah Klion Date: Fri Jan 17 17:29:37 2025 -0800 add options for quadratic and logarithmic drag Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 7b9eec8eb0d4c0d6b74c61f072ed5e1b83f49b77 Merge: 02051fef b4fc263a Author: Hannah Klion Date: Fri Jan 17 17:00:08 2025 -0800 Merge pull request #332 from jmsexton03/omp_add Add pragma omp parallel commit 02051fefc077f51b0c51ed52c9dbdb7175997e64 Author: Hannah Klion Date: Fri Jan 17 14:08:37 2025 -0800 fix typo in paper paper/paper.md commit 192ef940d818e5fd84a63bfd7d5b0678092a61fd Author: Hannah Klion Date: Fri Jan 17 13:06:56 2025 -0800 Update paper.md paper/paper.md commit 7afac892c27c4e5d3ff15f6349f44143933d6be8 Author: Hannah Klion Date: Fri Jan 17 13:02:15 2025 -0800 Remove commit part of draft paper action .github/workflows/draft-pdf.yml commit b69027680a3903e95d07e5fe63c8a5b25e4f60cb Author: Hannah Klion Date: Fri Jan 17 12:09:37 2025 -0800 Update paper.md paper/paper.md commit 2a4a86f36b46fee591684d58724d563cd1238af0 Author: Hannah Klion Date: Fri Jan 17 11:58:29 2025 -0800 Update paper.md paper/paper.md commit 165f1c29e21a25522ed9038ce2bddc0c2b917d5f Merge: 4b037048 35a7b41a Author: Hannah Klion Date: Fri Jan 17 09:53:50 2025 -0800 Merge pull request #333 from hklion/paper_workflow_action add draft pdf action commit 35a7b41aab9bcb706c3163f88796b5a1674976e1 Author: Hannah Klion Date: Fri Jan 17 09:53:05 2025 -0800 add draft pdf action .github/workflows/draft-pdf.yml commit b4fc263ab307efcee05f9251a11bdaf3f4fa1d7b Author: Jean M. Sexton Date: Thu Jan 16 18:53:46 2025 -0800 Add pragma omp parallel Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Particles/REMORA_PC_Init.cpp Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_scale_rhs_vars.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/Utils/REMORA_DepthStretchTransform.H commit 4b0370484ecbbb750ee4af53dcde1036071a92db Merge: 7ab6fd75 7b5e72ab Author: Hannah Klion Date: Wed Jan 15 17:16:43 2025 -0800 Merge pull request #331 from hklion/grid_scale_before_bathy only call set_pm_pn early if using IC_BC_Type=custom commit 7b5e72ab8fc19691948da9546404d8acdf8f9155 Author: Hannah Klion Date: Wed Jan 15 17:15:28 2025 -0800 only call set_pm_pn early if using IC_BC_Type=custom Source/REMORA.cpp commit 7ab6fd75b9d221bbfeb8a13635825daa813732f1 Merge: e7fe9e94 1ad7b115 Author: Hannah Klion Date: Wed Jan 15 13:58:11 2025 -0800 Merge pull request #329 from hklion/multiple_refinement patch FillFromCoarse so that it works with more than 1 refinement level commit e7fe9e94df1d1fe3ba7db86e5a9d4c3d0eeefb34 Merge: 70171a9d 9a1dc54e Author: Hannah Klion Date: Wed Jan 15 13:58:01 2025 -0800 Merge pull request #330 from hklion/grid_scale_before_bathy initialize grid scale arrays (pm and pn) before other initialization routines commit 9a1dc54e2ef42735993c02dd273b5d84dce96493 Author: Hannah Klion Date: Wed Jan 15 13:21:33 2025 -0800 initialize grid scale arrays (pm and pn) before other initialization routines Source/REMORA.cpp commit 1ad7b11548b48adf4b0f3605fd7ca75f3ec5e6c5 Author: Hannah Klion Date: Wed Jan 15 13:13:38 2025 -0800 patch FillFromCoarse so that it works with more than 1 refinement level Source/BoundaryConditions/REMORA_FillPatch.cpp commit 70171a9dc09c0d1ee31cfb99e124145f5ebbb7ce Merge: 47d715b4 c15b8ad3 Author: Hannah Klion Date: Mon Jan 13 13:36:42 2025 -0800 Merge pull request #328 from hklion/init_timer add timer for initialization commit 47d715b4bd4cf6b14818859990e287bf028d23ce Merge: 3e30ce22 42ae26e3 Author: Hannah Klion Date: Mon Jan 13 13:36:23 2025 -0800 Merge pull request #327 from hklion/ncplotfile_tracer_chunk NCplotfile tracer chunk commit c15b8ad3d1e9b074611f2cfa44baf31d5c11fd50 Author: Hannah Klion Date: Mon Jan 13 13:12:15 2025 -0800 add timer for initialization Source/main.cpp commit 42ae26e358a6f7e4ab114faaed6a03d3baa252a8 Author: Hannah Klion Date: Mon Jan 13 10:23:52 2025 -0800 add option to chunk netcdf history files to keep under 2GB Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/building.rst Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_IndexDefines.H commit 3e30ce22069546f955072b8a07df7eb3f145f76b Merge: 84816580 993e1a12 Author: Hannah Klion Date: Fri Jan 10 12:29:03 2025 -0800 Merge pull request #326 from seahorce-scidac/hklion-patch-1 Update README.rst commit 993e1a12a8630b09879c78a64911a9532c46efd4 Author: Hannah Klion Date: Fri Jan 10 12:28:54 2025 -0800 Update README.rst README.rst commit a7f610b49443d7f6e9c3e9bef67dc73c95b65665 Author: Hannah Klion Date: Thu Jan 9 17:25:43 2025 -0800 add passive tracer to NetCDF file Source/IO/REMORA_NCPlotFile.cpp commit 8481658083b9f7fce32201a3f38a920b33e2311e Author: Hannah Klion Date: Thu Jan 9 14:01:12 2025 -0800 Update paper.md paper/paper.md commit a4e2ed9645aff8c23e1610918c57934f40b453e7 Merge: ae87d7db b053de52 Author: Hannah Klion Date: Fri Dec 27 13:45:26 2024 -0800 Merge pull request #325 from hklion/plotfile_docs fix spelling commit b053de52361b07c85fe0bc10e398614d0727a752 Author: Hannah Klion Date: Fri Dec 27 13:42:34 2024 -0800 fix spelling Docs/sphinx_doc/Inputs.rst commit ae87d7db3baf0e8e812794481838c9276204b6ef Merge: 329a16bb ca9da09b Author: Hannah Klion Date: Fri Dec 27 13:41:12 2024 -0800 Merge pull request #324 from hklion/plotfile_docs Plotfile docs commit ca9da09be467289d4f90717a3e2c27839f14a6ed Author: Hannah Klion Date: Fri Dec 27 13:40:44 2024 -0800 add ncks conversion command Docs/sphinx_doc/Inputs.rst commit a9e3c18a1501d99ee03e31bde6f8a78f025ca87b Author: Hannah Klion Date: Fri Dec 27 13:22:14 2024 -0800 move min_file_digits docs to checkpoint and plotfile pages Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Plotfiles.rst commit 329a16bba08325bb1988a2209f681fb18209cca2 Merge: 7d00cf2f f1871841 Author: Hannah Klion Date: Thu Dec 26 19:20:59 2024 -0800 Merge pull request #323 from hklion/nonlin_eos add docs about EOS regtest commit f1871841c1813b2d0ecf76c00e97299a0c4160ff Author: Hannah Klion Date: Thu Dec 26 19:20:08 2024 -0800 add docs about EOS regtest Docs/sphinx_doc/RegressionTests.rst commit 7d00cf2fd04a4bb956aec3d53e1eabe012060fab Merge: 7cbd5b32 87e11e95 Author: Hannah Klion Date: Thu Dec 26 19:14:35 2024 -0800 Merge pull request #322 from hklion/nonlin_eos Add nonlinear equation of state option commit 87e11e9546115934e7242d421db44147a62450ba Author: Hannah Klion Date: Thu Dec 26 18:47:11 2024 -0800 add ctest Tests/CTestList.cmake Tests/REMORA_Gold_Files/Upwelling_NLEOS/Header Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_NLEOS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_NLEOS/job_info Tests/test_files/Upwelling_NLEOS/Upwelling_NLEOS.i commit 2992add83e21d47a6118cf766464239ca6783402 Author: Hannah Klion Date: Thu Dec 26 18:28:53 2024 -0800 add docs for EOS Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst commit 33d537e8fcb09b2b59beedcda395f6e3850529a6 Author: Hannah Klion Date: Thu Dec 26 18:15:20 2024 -0800 fix shadow declaration Source/TimeIntegration/REMORA_rho_eos.cpp commit 80c74ff55f7d90e3b4ffd4db2774475986c434eb Author: Hannah Klion Date: Thu Dec 26 18:12:11 2024 -0800 add nonlinear equation of state option Source/IO/REMORA_NCPlotFile.cpp Source/REMORA.H Source/REMORA_Constants.H Source/REMORA_DataStruct.H Source/TimeIntegration/REMORA_rho_eos.cpp commit 7cbd5b3262c8d2505b454bb7663517a82df61ed5 Merge: f416914b 3f663af7 Author: Hannah Klion Date: Fri Dec 20 19:22:14 2024 -0800 Merge pull request #321 from hklion/viz_nu add to viz docs and update plotfile so nu is corret commit 3f663af7850ff15acff94641e5bc495d20d70f46 Author: Hannah Klion Date: Fri Dec 20 19:16:13 2024 -0800 add to viz docs and update plotfile so nu is corret Docs/sphinx_doc/Visualization.rst Source/IO/REMORA_Plotfile.cpp commit f416914b6a47b82848021657f06430aadfc55c2a Merge: 9278e6d5 5c78c20d Author: Hannah Klion Date: Wed Dec 18 16:29:43 2024 -0800 Merge pull request #320 from hklion/docs doc tweaks commit 5c78c20dd1ff822aaa1b0b25c312e5ffb6279844 Author: Hannah Klion Date: Wed Dec 18 16:29:21 2024 -0800 doc tweaks Docs/sphinx_doc/building.rst Docs/sphinx_doc/testing.rst commit 9278e6d5b5dde3a7415bb05a78df1e9c30c87034 Author: Hannah Klion Date: Wed Dec 18 16:23:31 2024 -0800 Update paper.md typo paper/paper.md commit 76b73b4e68c3cf060af43d7b6242d76af4a0b185 Merge: 08915d39 c57394f6 Author: Hannah Klion Date: Wed Dec 18 16:22:49 2024 -0800 Merge pull request #319 from hklion/cmake_adjust remove fortran and c compilers from cmake command commit c57394f6bf82d53a9af94385598ebcb1bd82e2ae Author: Hannah Klion Date: Wed Dec 18 16:22:22 2024 -0800 remove fortran and c compilers from cmake command Build/cmake.sh Docs/sphinx_doc/building.rst Docs/sphinx_doc/testing.rst commit 08915d39bcf539bca39528d59b8d995b9b74032e Author: Rob Hetland Date: Wed Dec 18 15:54:39 2024 -0600 Update paper.md spell checking. paper/paper.md commit f6cd749fc020954dd6d410cf1a1039c803ccf960 Author: Rob Hetland Date: Wed Dec 18 15:50:57 2024 -0600 Update paper.md Finished capability list paper/paper.md commit c8719cc66eee1c362e2d408963fa211cd517996a Author: Rob Hetland Date: Wed Dec 18 14:53:34 2024 -0600 Update paper.bib Added Jackett and MacDougall reference paper/paper.bib commit 7917a89f53d765e4f00e731735d82be590657ac9 Author: Rob Hetland Date: Wed Dec 18 14:16:07 2024 -0600 Update paper.md Added to and revised the overview. paper/paper.md commit 951f5de14bd5113162afdd939c250f4d7af7f030 Author: Rob Hetland Date: Wed Dec 18 13:39:21 2024 -0600 Update paper.bib Added ROMS citations paper/paper.bib commit e5ce15b27b422b4dc80ee22dde5f65cb81c44c64 Merge: 5d19c751 8edf33af Author: Hannah Klion Date: Wed Dec 18 10:49:46 2024 -0800 Merge pull request #318 from hklion/docs add readmes to problems and tweak docs commit 8edf33af551afeb3e9afef25092ad01d8692e075 Author: Hannah Klion Date: Wed Dec 18 10:45:47 2024 -0800 add readmes to problems and tweak docs Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/Verification.rst Docs/sphinx_doc/index.rst Exec/Advection/README Exec/Channel_Test/README Exec/DoubleGyre/README Exec/DoublyPeriodic/README Exec/IdealMiniGrid/README.rst Exec/ParticlesOverSeaMount/README Exec/Seamount/README.rst Exec/Upwelling/README.rst commit 5d19c7516dbcaadd82c836833a2dcff75f07084d Merge: cfb041a6 e3c4c661 Author: Hannah Klion Date: Tue Dec 17 09:59:51 2024 -0800 Merge pull request #317 from hklion/docs documentation tweaks commit e3c4c66152028794a08999f3913aad732f1bfbd6 Author: Hannah Klion Date: Mon Dec 16 18:53:09 2024 -0800 documentation tweaks Docs/sphinx_doc/AMReX.rst Docs/sphinx_doc/Doxygen.rst Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/index.rst commit cfb041a6c78752da300e03bea1defe3ccee3565d Author: Hannah Klion Date: Mon Dec 16 10:05:35 2024 -0800 Update README.rst README.rst commit b7d11b62ee1cb6da7fd0c6024ec7bf6a2f7f517a Merge: 53467950 6d702aee Author: Hannah Klion Date: Mon Dec 16 09:58:49 2024 -0800 Merge pull request #316 from seahorce-scidac/paper Update paper.md commit 6d702aeeec591ed2c5c20ac23639f0237f3c23f2 Author: Hannah Klion Date: Mon Dec 16 09:58:36 2024 -0800 Update paper.md paper/paper.md commit 534679505a9cb670f961df123a9910a69cec8b6d Merge: d0b24561 968a9d57 Author: Hannah Klion Date: Fri Dec 13 17:50:17 2024 -0800 Merge pull request #315 from seahorce-scidac/paper-1 Update paper.bib commit 968a9d57ea57ab2707579c35e6faeab4599b4883 Author: Hannah Klion Date: Fri Dec 13 17:50:04 2024 -0800 Update paper.bib paper/paper.bib commit d0b24561a75079851019ec17787655b35b3b79c6 Merge: 93192b98 1dd04982 Author: Hannah Klion Date: Fri Dec 13 17:49:18 2024 -0800 Merge pull request #314 from seahorce-scidac/paper Paper commit 1dd049821ed49c5268141b854223d3b4bd89d2ae Merge: 654f4169 397a3c23 Author: Hannah Klion Date: Fri Dec 13 17:48:16 2024 -0800 Merge pull request #313 from seahorce-scidac/paper-1 Update paper.md commit 397a3c233a286d42820f09d7b94bbd653adb282b Author: Hannah Klion Date: Fri Dec 13 17:47:39 2024 -0800 Update paper.md paper/paper.md commit 654f41692457521b2d7868098af9b01a18f5b6f3 Author: Hannah Klion Date: Fri Dec 13 17:04:54 2024 -0800 Update paper.bib paper/paper.bib commit 93192b9899004fcc298966e5323bb960ef66e5a8 Author: Hannah Klion Date: Thu Dec 12 18:29:32 2024 -0800 Update paper.md paper/paper.md commit 11bcbaac55275ffb0531b91fd7dee4c49634b83f Merge: ac14df9f 78c0d81d Author: Hannah Klion Date: Tue Dec 10 18:24:32 2024 -0800 Merge pull request #312 from hklion/netcdf_history_default update docs about netcdf history default commit ac14df9f9f0af8e91d53003158ddd08cd51744ea Merge: ee3e7642 b7eaeaea Author: Hannah Klion Date: Tue Dec 10 18:23:49 2024 -0800 Merge pull request #311 from hklion/hmix update hmix parameters to be set more like in ROMS commit 78c0d81dfc4e054b0c8f7f4b36dd7519296fb2f6 Author: Hannah Klion Date: Tue Dec 10 18:23:28 2024 -0800 update docs Docs/sphinx_doc/Plotfiles.rst commit b7eaeaeada996be6026809f975f6a1928dce5cd0 Author: Hannah Klion Date: Tue Dec 10 18:22:58 2024 -0800 update hmix parameters to be set more like in ROMS Docs/sphinx_doc/Inputs.rst Source/REMORA.cpp Source/REMORA_DataStruct.H Tests/test_files/DoubleGyre/DoubleGyre.i commit ee3e76421e9fc3a54ed13d6ad88400901caff0bb Merge: 8d1ace0b e8cf68f8 Author: Hannah Klion Date: Mon Dec 9 14:45:16 2024 -0800 Merge pull request #310 from hklion/netcdf_history_default make netcdf history output the default commit e8cf68f8012b32bf12f22a2044b753b8dbca0a47 Author: Hannah Klion Date: Mon Dec 9 14:44:55 2024 -0800 make netcdf history output the default Source/REMORA.cpp commit 8d1ace0bb345f085be2b3b34d09604fb6754d9ca Merge: 5e851630 24abb48d Author: Hannah Klion Date: Mon Dec 9 14:39:16 2024 -0800 Merge pull request #309 from hklion/file_min_digits minimum number of digits in plotfile and checkpoints commit 5e85163015e8bbcae593abbe85e9e9823c861dd6 Author: Hannah Klion Date: Mon Dec 9 14:39:00 2024 -0800 Fix link Docs/sphinx_doc/theory/VerticalMixing.rst commit 24abb48d2c0226f83966a8678dc78d00adeebfb3 Author: Hannah Klion Date: Mon Dec 9 14:22:04 2024 -0800 semicolon Source/REMORA.cpp commit fecaee9288544da61a41ea78a7f86d94b50cf2d4 Author: Hannah Klion Date: Mon Dec 9 14:17:36 2024 -0800 minimum number of digits in plotfile and checkpoints Docs/sphinx_doc/Inputs.rst Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 51f38b12d2b5cc99d5afcc0773fbf2b33b77d19b Merge: 2ab8ece8 e69d93e2 Author: Hannah Klion Date: Fri Dec 6 15:35:28 2024 -0800 Merge pull request #308 from hklion/docs Docs commit e69d93e2d7a23d1dae74ade7b8e4219e7482e966 Merge: 0da91d0f 2ab8ece8 Author: Hannah Klion Date: Fri Dec 6 15:34:48 2024 -0800 Merge branch 'development' of github.com:seahorce-scidac/REMORA into docs commit 0da91d0f7ee3782373f6268ebebc3d7f8e415e76 Author: Hannah Klion Date: Fri Dec 6 15:34:17 2024 -0800 update docs Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Docs/sphinx_doc/theory/Equations.rst Docs/sphinx_doc/theory/VerticalMixing.rst commit 2ab8ece8f5c623753efb012d1d75c550a903ad55 Merge: b5813a5a b31f7121 Author: Hannah Klion Date: Fri Dec 6 14:01:10 2024 -0800 Merge pull request #307 from hklion/rename prepend REMORA_ onto all files commit b31f71218cb2ec68e9cdce43f050dad75e95d2e8 Author: Hannah Klion Date: Fri Dec 6 13:32:42 2024 -0800 prepend REMORA_ onto all files CMake/BuildREMORAExe.cmake CMake/SetAmrexOptions.cmake Exec/Advection/prob.cpp Exec/Channel_Test/prob.cpp Exec/DoubleGyre/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/OCCAMS/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Exec/Upwelling_ML/prob.cpp Source/BoundaryConditions/Make.package Source/BoundaryConditions/REMORA_BoundaryConditions_cons.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp Source/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/BoundaryConditions/REMORA_TimeInterpolatedData.H Source/EOS.H Source/IO/Make.package Source/IO/NCPlotFile.H Source/IO/REMORA_Checkpoint.cpp Source/IO/REMORA_NCFile.H Source/IO/REMORA_NCFile.cpp Source/IO/REMORA_NCInterface.H Source/IO/REMORA_NCInterface.cpp Source/IO/REMORA_NCPlotFile.H Source/IO/REMORA_NCPlotFile.cpp Source/IO/REMORA_Plotfile.cpp Source/IO/REMORA_ReadFromBdryNetcdf.cpp Source/IO/REMORA_ReadFromInitNetcdf.cpp Source/IO/REMORA_console_io.cpp Source/IO/REMORA_writeJobInfo.cpp Source/Initialization/Make.package Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init1d.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/REMORA_prob_common.H Source/Make.package Source/Particles/Make.package Source/Particles/REMORA_PC_Evolve.cpp Source/Particles/REMORA_ParticleData.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_DataStruct.H Source/REMORA_Derive.H Source/REMORA_Derive.cpp Source/REMORA_IndexDefines.H Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/Utils/Make.package Source/Utils/REMORA_DepthStretchTransform.H commit b5813a5a9ea236f04bf6b630d95e379e58a7c094 Merge: a131886c 91e3f2ea Author: Hannah Klion Date: Wed Dec 4 20:52:59 2024 -0800 Merge pull request #304 from seahorce-scidac/update_bdy_netcdf change to single component bc_ptr commit 91e3f2eaa89230c9832eb8cea96c3f78e06f5e95 Author: Hannah Klion Date: Wed Dec 4 17:07:22 2024 -0800 only work on one component at a time, so we don't need a vector of BCRs Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit a131886cbdd23fb78ad52faba9fb75a08f389056 Merge: 93cc30f0 26e54e8b Author: Hannah Klion Date: Wed Dec 4 11:27:49 2024 -0800 Merge pull request #306 from hklion/docs Docs commit 26e54e8b2e00633df64618e3cbcadc713896ae47 Author: Hannah Klion Date: Wed Dec 4 11:26:44 2024 -0800 fix link Docs/sphinx_doc/Verification.rst commit 5ce9325a4bcc59014c5d14090d47b6c5befbe201 Author: Hannah Klion Date: Wed Dec 4 11:13:57 2024 -0800 update docs Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/Verification.rst commit 93cc30f0747aef7fbd42a675c60154cda6042eb2 Merge: 8d956c5b 3b0271ef Author: Hannah Klion Date: Wed Dec 4 10:10:54 2024 -0800 Merge pull request #305 from hklion/docs update docs commit 3b0271efebf8eec0ccff765e6ab05ca9d6137fb9 Author: Hannah Klion Date: Wed Dec 4 10:10:10 2024 -0800 update docs Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Docs/sphinx_doc/building.rst Docs/sphinx_doc/index.rst Docs/sphinx_doc/perlmutter.rst commit 15da6086600e9774925a6e314b645ed38b96bf68 Author: Ann Almgren Date: Mon Dec 2 19:05:32 2024 -0800 change to single component bc_ptr Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 8d956c5b326dfaf514092951c454d575d2d56975 Merge: d9fbb357 b05f7dc8 Author: Hannah Klion Date: Wed Nov 27 18:07:21 2024 -0800 Merge pull request #303 from seahorce-scidac/bcs line breaks in table commit b05f7dc8cbb10ca4ce2c0051dcfdf0d082e92f07 Author: Hannah Klion Date: Wed Nov 27 18:06:31 2024 -0800 line breaks in table Docs/sphinx_doc/RegressionTests.rst commit d9fbb357092eb761f1f877337def1206651d4e77 Merge: 38518b29 63642a92 Author: Hannah Klion Date: Wed Nov 27 17:44:58 2024 -0800 Merge pull request #302 from hklion/more_bc_docs add more about regression tests commit 63642a92f8ff264548056bc15274c097f41c80d2 Author: Hannah Klion Date: Wed Nov 27 17:43:12 2024 -0800 add more about regression tests Docs/sphinx_doc/RegressionTests.rst commit 38518b292623b39de04f7497627bbf4b79f89a39 Merge: e857d921 b7d1cf20 Author: Hannah Klion Date: Sun Nov 24 10:20:28 2024 -0800 Merge pull request #301 from hklion/more_bc_docs update docs to better reflect bcs and nudging commit b7d1cf20cc12ac3a04488d38259bae67b8d2ecf3 Author: Hannah Klion Date: Sun Nov 24 10:17:38 2024 -0800 update docs to better reflect bcs and nudging Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Inputs.rst commit e857d92192e40d17c943e47a5702ef47ca407b04 Merge: 4d71d2d7 ed07455d Author: Hannah Klion Date: Fri Nov 22 17:12:31 2024 -0800 Merge pull request #300 from hklion/netcdf_attrs add attributes to netcdf file, as well as s_w commit ed07455d14617ce2fcc1d9360e14bd341ff2cf99 Author: Hannah Klion Date: Fri Nov 22 17:11:49 2024 -0800 add attributes to netcdf file, as well as s_w Source/IO/NCPlotFile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/Utils/DepthStretchTransform.H commit 4d71d2d734f9b1292535a5b45ad86e6d3f6384d3 Merge: 0a751a1e c6ba8fc5 Author: Hannah Klion Date: Fri Nov 22 11:46:11 2024 -0800 Merge pull request #299 from hklion/dx_gpu save dx and dy as Reals so they can be accessed on GPU commit c6ba8fc54b27d009597d99e0b5543e45004714bc Author: Hannah Klion Date: Fri Nov 22 11:44:57 2024 -0800 save dx and dy as Reals so they can be accessed on GPU Source/Initialization/REMORA_make_new_level.cpp commit 0a751a1eee16d1f458c282dc47bbf168be5372e5 Merge: c4a72ebd 3b24d7e9 Author: Hannah Klion Date: Thu Nov 21 16:29:46 2024 -0800 Merge pull request #298 from hklion/add_xy_grid add {x,y}_{rho,u,v,psi} commit 3b24d7e9fb8824d2cdab1b3e2f431a9beedcfeae Author: Hannah Klion Date: Thu Nov 21 15:09:36 2024 -0800 add {x,y}_{rho,u,v,psi} Source/IO/NCFile.H Source/IO/NCPlotFile.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit c4a72ebd4607621ba15e8e49140fafda01ac6bfa Merge: ce191ae8 021572d0 Author: Hannah Klion Date: Thu Nov 21 11:45:18 2024 -0800 Merge pull request #297 from iulian787/iulian787/pnetcdf_indep_writes replace nonblocking collective with independent commit 021572d0d3a2b96f121da94e52924486cdb694ce Author: Iulian Grindeanu Date: Thu Nov 21 13:36:49 2024 -0600 replace nonblocking collective with independent big reversal of strategy (self inflicted wound) until I figure out how to do correctly the collective writes, switch bach to independent writes it seems that the buffers with nonblocking collective "iput" were overwritten Need to investigate more Source/IO/NCPlotFile.cpp commit ce191ae8a1ce17ce108ddcf93ea257e129110b39 Author: Hannah Klion Date: Sat Nov 16 16:56:42 2024 -0800 fix bug in foextrap in netcdf Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 438b2d8968fe3434bfe70712c87186381ebeb958 Merge: c6cb1e4d 200117e1 Author: Hannah Klion Date: Thu Nov 14 14:57:15 2024 -0800 Merge pull request #296 from hklion/perl_pnetcdf remove missing header and adjust version info commit 200117e1e1161a6ca56e1081a3cd207c234e3e8f Author: Hannah Klion Date: Thu Nov 14 14:10:42 2024 -0800 remove missing header and adjust version info Source/IO/console_io.cpp commit c6cb1e4d91e8177fa07b05fcab72421274aa3a80 Merge: a9f970b5 c0f8423a Author: Hannah Klion Date: Wed Nov 13 17:11:57 2024 -0800 Merge pull request #295 from hklion/bc_docs BC docs commit c0f8423a0c86fe411876881badfe99de2ce2d4da Author: Hannah Klion Date: Wed Nov 13 17:11:18 2024 -0800 update documentation for boundary conditions Docs/sphinx_doc/BoundaryConditions.rst commit a9f970b51b95862c0d01a98528e7fe8fe04d15ae Merge: 2558f414 daec721b Author: Hannah Klion Date: Wed Nov 13 12:46:47 2024 -0800 Merge pull request #294 from hklion/bc_prefix add bc. prefix to bc options, and make zlo/zhi optional commit daec721b3c06754b5d4c404530c3dadf82516f37 Author: Hannah Klion Date: Wed Nov 13 12:18:12 2024 -0800 add bc. prefix to bc options, and make zlo/zhi optional Exec/Advection/inputs Exec/Advection/inputs_ml Exec/Channel_Test/inputs Exec/Channel_Test/inputs_orlanski Exec/DoubleGyre/inputs Exec/DoublyPeriodic/inputs Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/inputs_ml Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling_ML/inputs Source/Initialization/REMORA_init_bcs.cpp Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/Channel_Test/Channel_Test.i Tests/test_files/DoubleGyre/DoubleGyre.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i commit 2558f41412fa8ec26eda3caa23866a2d8581f115 Merge: 2204c4b6 476a4006 Author: Hannah Klion Date: Tue Nov 12 16:57:56 2024 -0800 Merge pull request #293 from hklion/perlmutter_pnetcdf pnetcdf working on perlmutter plus note in docs about mpich commit 476a400689cdc42af475069e2aa0a257c1da6a4a Author: Hannah Klion Date: Tue Nov 12 16:57:33 2024 -0800 pnetcdf working on perlmutter plus note in docs about mpich Build/saul-env.sh Docs/sphinx_doc/perlmutter.rst commit 2204c4b607791e17af79529cb778f32278defd71 Merge: 352686dd 73e0ae0a Author: Hannah Klion Date: Tue Nov 12 15:16:42 2024 -0800 Merge pull request #292 from hklion/make_classic_default make classic versions of netcdf input files the default commit 73e0ae0a848c4c6a219edca8d71be8d6d501b9c4 Author: Hannah Klion Date: Tue Nov 12 15:16:11 2024 -0800 make classic versions of netcdf input files the default Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather commit 352686dd166a1d0ee5886594577825f8b3a65069 Merge: 495f11ba 1abbaeb3 Author: Hannah Klion Date: Tue Nov 12 13:57:27 2024 -0800 Merge pull request #291 from hklion/unsignedlong change unsigned long to long long commit 1abbaeb38c01144f1327caacbd67527f88650cf5 Author: Hannah Klion Date: Tue Nov 12 13:56:58 2024 -0800 change unsigned long to long long Source/IO/NCPlotFile.cpp commit 495f11ba5d88370d35b75e57fbdf6bbaf5b427d5 Merge: cfd3a0bc d8cb1f47 Author: Hannah Klion Date: Tue Nov 12 13:12:02 2024 -0800 Merge pull request #290 from hklion/pnetcdf_docs typo commit d8cb1f47a79af29b663e37c364d95bbf242f6523 Author: Hannah Klion Date: Tue Nov 12 13:11:13 2024 -0800 typo Docs/sphinx_doc/building.rst commit cfd3a0bcd718b708b04bbfc4975d0f9188602422 Merge: 686a1385 17a31477 Author: Hannah Klion Date: Tue Nov 12 13:07:01 2024 -0800 Merge pull request #289 from hklion/pnetcdf_docs USE_NETCDF->USE_PNETCDF and added documentation commit 17a3147713bb818758c84305c550e5cc31f17e1d Author: Hannah Klion Date: Tue Nov 12 13:05:00 2024 -0800 USE_NETCDF->USE_PNETCDF and added documentation Docs/sphinx_doc/building.rst Exec/Advection/GNUmakefile Exec/Channel_Test/GNUmakefile Exec/DoubleGyre/GNUmakefile Exec/DoublyPeriodic/GNUmakefile Exec/IdealMiniGrid/GNUmakefile Exec/ParticlesOverSeaMount/GNUmakefile Exec/Seamount/GNUmakefile Exec/Upwelling/GNUmakefile commit 686a1385e2277db557629fd932a6c8300d9867bc Merge: 2fcd4fff 4805d4d1 Author: Hannah Klion Date: Tue Nov 12 12:32:01 2024 -0800 Merge pull request #278 from iulian787/iulian787/pnetcdf_support PNetCDF support commit 4805d4d1587e1f090e9132c5d947dd0ff92d4110 Author: Iulian Grindeanu Date: Tue Nov 12 10:35:58 2024 -0600 this is getting ridiculous :( Source/IO/NCInterface.H commit 0ba44eac331722cc5be121fc98419d5f84c5277f Author: Iulian Grindeanu Date: Tue Nov 12 10:33:03 2024 -0600 format NCInterface Source/IO/NCInterface.H Source/IO/NCInterface.cpp commit cea30bd52cdab01334e4a9edf4ee466feafb75c0 Author: Iulian Grindeanu Date: Tue Nov 12 10:29:42 2024 -0600 allow lines width up to 132 Source/IO/NCPlotFile.cpp commit 92aa5783250a3c981b8da33af574d445045e3206 Author: Iulian Grindeanu Date: Tue Nov 12 10:26:06 2024 -0600 format without tabs Source/IO/NCPlotFile.cpp commit 428900785b615cf2b10efefdd2500e4e6cad38cc Author: Iulian Grindeanu Date: Tue Nov 12 08:34:58 2024 -0600 add iput to the list of accepted words iput is used in pnetcdf to signal non-blocking writes there should be more iput methods added in NCInterface, for completeness .codespell-ignore-words commit 5ea5c9aa468ee41a1f437b891487725ede4e24c6 Author: Iulian Grindeanu Date: Mon Nov 11 16:07:09 2024 -0600 remove debug statements Source/IO/NCPlotFile.cpp commit e8ac047887e61fea66cdb357bb8e37b8db04a6f3 Author: Iulian Grindeanu Date: Mon Nov 11 16:01:29 2024 -0600 replace collective blocking calls when we write in parallel, number of iterations per task can be different we cannot use blocking calls in general need to use non-blocking calls Source/IO/NCInterface.H Source/IO/NCInterface.cpp Source/IO/NCPlotFile.cpp commit f44e7c5adcbe3677ab992f2c445b40e1c07c4b90 Author: Iulian Grindeanu Date: Fri Nov 1 18:29:23 2024 -0500 fix parallel read in fact, still read only on proc 0, and broadcast what is important Exec/IdealMiniGrid/inputs Source/IO/NCFile.H Source/IO/NCFile.cpp Source/IO/ReadFromBdryNetcdf.cpp commit 868bd4b08f943d169ccb1e9a09a0f54d29579ef7 Author: Iulian Grindeanu Date: Fri Nov 1 15:12:41 2024 -0500 fix pnetcdf read in serial actual read is in serial, on task 0 only need to fix read when it is actual in parallel Exec/CMakeLists.txt Exec/IdealMiniGrid/CMakeLists.txt Source/IO/NCFile.H Source/IO/NCFile.cpp Source/IO/NCInterface.cpp commit d91c6d6689b30f4f5ec363ccc3c983219465bd8d Author: Iulian Grindeanu Date: Thu Oct 31 17:11:51 2024 -0500 pnetcdf include and library CMake/BuildREMORAExe.cmake commit 30d053f02ed8cb43c94fed787c3d5b8c7df681a9 Author: Iulian Grindeanu Date: Wed Oct 30 22:57:05 2024 -0500 modify cmake to use pnetcdf user has to define PKG_CONFIG_PATH with the proper pnetcdf installation then a cmake command would work cmake -DCMAKE_INSTALL_PREFIX:PATH= \ -DCMAKE_CXX_COMPILER:STRING=mpicxx \ -DCMAKE_C_COMPILER:STRING=mpicc \ -DCMAKE_Fortran_COMPILER:STRING=mpifort \ -DCMAKE_BUILD_TYPE:STRING=Release \ -DREMORA_DIM:STRING=3 \ -DREMORA_ENABLE_MPI:BOOL=ON \ -DREMORA_ENABLE_TESTS:BOOL=ON \ -DREMORA_ENABLE_FCOMPARE:BOOL=ON \ -DREMORA_ENABLE_DOCUMENTATION:BOOL=OFF \ -DREMORA_ENABLE_PNETCDF:BOOL=ON \ -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \ CMake/BuildREMORAExe.cmake CMake/FindNetCDF.cmake CMake/FindPNetCDF.cmake CMakeLists.txt commit d4c3c55e3d32e172d264d4b3bd53e0ef56ef150e Author: Iulian Grindeanu Date: Wed Oct 30 20:53:39 2024 -0500 cmake fixes CMakeLists.txt commit 194406865c2e8d2b8e6020da836a727d27913ee0 Author: Iulian Grindeanu Date: Mon Oct 28 00:20:05 2024 -0500 add rest of collective calls add the strided versions, and float and integer put_all calls also, add all get_all calls, for doble, float, int, strided too Source/IO/NCInterface.H Source/IO/NCInterface.cpp commit 8b393a1147e5c6939a903ee7fdfd63101c743cc6 Author: Iulian Grindeanu Date: Sat Oct 12 19:18:37 2024 -0500 add independent data and put_all method this methd is collective, while some header data is written only on master task (descriptive data) still need to fix the coordinates data Source/IO/NCInterface.H Source/IO/NCInterface.cpp Source/IO/NCPlotFile.cpp commit e2fac2782d5a88a105664e9b256572cd5016a352 Author: Iulian Grindeanu Date: Tue Oct 1 20:14:17 2024 -0500 def mode change Source/IO/NCPlotFile.cpp commit 914564c9f96e3a0b27a27a4e4d7a48ee0561c959 Author: Iulian Grindeanu Date: Sun Sep 29 23:02:58 2024 -0500 replace netcdf with pnetcdf need to use make USE_PNETCDF=TRUE DEBUG=TRUE -j8 there is no par_access anymore collective calls will need to be made with *_all methods so far, everything is independent, which is not allowed Exec/Make.REMORA Source/BoundaryConditions/Make.package Source/IO/Make.package Source/IO/NCFile.H Source/IO/NCFile.cpp Source/IO/NCInterface.H Source/IO/NCInterface.cpp Source/IO/NCPlotFile.cpp commit ab736bfb60e3b4444a4e7638991832125e6651a0 Author: Iulian Grindeanu Date: Sat Sep 28 23:33:13 2024 -0500 remove first group references from NCInterface Source/IO/NCInterface.H Source/IO/NCInterface.cpp commit 2fcd4fffcb291852637ec0689495a0a32db10895 Merge: a844009c eedb58d7 Author: Hannah Klion Date: Fri Nov 8 16:14:43 2024 -0800 Merge pull request #288 from hklion/outflow_zvel Outflow zvel commit eedb58d7ebdd423a42db019cfe4101565112f567 Author: Hannah Klion Date: Fri Nov 8 16:13:55 2024 -0800 remove w bc from orlanski test Exec/Channel_Test/inputs_orlanski commit 06c7763cece2a92af9399140cd10c38ed5182855 Author: Hannah Klion Date: Fri Nov 8 16:12:45 2024 -0800 split out zvel so it's always foextrap Source/Initialization/REMORA_init_bcs.cpp commit 8d3c2aadf7a2edafcb78770e60b5b063e577f9e4 Author: Hannah Klion Date: Fri Nov 8 15:50:57 2024 -0800 zvel boundary conditions default to outflow Exec/IdealMiniGrid/inputs_cf_orlanski Exec/IdealMiniGrid/inputs_chapman_flather Source/Initialization/REMORA_init_bcs.cpp commit 2319981497dd0a53a9b076faebf0ed68af66da84 Author: Hannah Klion Date: Fri Nov 8 10:34:44 2024 -0800 start updating docs for boundary conditions Docs/sphinx_doc/BoundaryConditions.rst commit a844009c6f290a4cc618e871fff5460640cfe0ce Merge: a3b8886c 2f0bdb6b Author: Hannah Klion Date: Thu Nov 7 16:06:15 2024 -0800 Merge pull request #287 from hklion/extdir actually initialize extdir bc for {u,v}2d_simple_bc commit 2f0bdb6bc6dadd72b20ec6fce2cdd86cce7b5abe Author: Hannah Klion Date: Thu Nov 7 15:41:29 2024 -0800 actually initialize extdir bc for {u,v}2d_simple_bc Source/Initialization/REMORA_init_bcs.cpp commit a3b8886c74e7bae9cab28529812642ea7f602cd5 Merge: 0c876652 51af8fe7 Author: Hannah Klion Date: Thu Nov 7 15:12:05 2024 -0800 Merge pull request #286 from hklion/fix_bcs fix netcdf BCs so we aren't applying BCs to the entire box commit 51af8fe7efef95d7b7d7bb446b54576b6f87c3a4 Author: Hannah Klion Date: Thu Nov 7 15:11:02 2024 -0800 fix netcdf BCs so we aren't applying BCs to the entire box Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 9ca2961dd45518ed299be160c489da13d985243f Merge: 4c8c4cf9 0c876652 Author: Hannah Klion Date: Thu Nov 7 11:51:00 2024 -0800 Merge branch 'development' of github.com:seahorce-scidac/REMORA into development commit 0c876652081ac689841cb9f0f0f7870d0903b66d Merge: 4661a016 a6d0ba68 Author: Hannah Klion Date: Wed Nov 6 17:02:01 2024 -0800 Merge pull request #285 from hklion/gpu_orlanski update orlanski BCs so that edges are updated first, then copied to g… commit a6d0ba68e00314a363b583cca494be780d998f83 Author: Hannah Klion Date: Wed Nov 6 16:56:07 2024 -0800 update orlanski BCs so that edges are updated first, then copied to ghost zones Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp commit 4661a0168713d20b96dc93c7314a9552f0933352 Merge: b6ff77fb 07bb49b3 Author: Hannah Klion Date: Wed Nov 6 10:19:54 2024 -0800 Merge pull request #284 from hklion/fix_links remove extraneous files from documentation commit 07bb49b337f9b51282783f0e096fc638858aa174 Author: Hannah Klion Date: Wed Nov 6 10:17:23 2024 -0800 remove extraneous files Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/TimeAdvance.rst Docs/sphinx_doc/conf.py Docs/sphinx_doc/index.rst commit b6ff77fbd74a41afa81e5f97ab7226ccf75b3c49 Author: Hannah Klion Date: Tue Nov 5 20:58:55 2024 -0800 Define external dirichelet value for simplified 2d u and v BCs (#283) commit 4c8c4cf9756b39db75913cd790e0a1f8c5894280 Author: Hannah Klion Date: Tue Nov 5 20:50:10 2024 -0800 Revert "set external dirichelet value for u2d_simple and v2d_simple" This reverts commit 1c0238e831055f00e7455cbfb4ec81e65d3df892. Source/Initialization/REMORA_init_bcs.cpp commit 1c0238e831055f00e7455cbfb4ec81e65d3df892 Author: Hannah Klion Date: Tue Nov 5 20:45:22 2024 -0800 set external dirichelet value for u2d_simple and v2d_simple Source/Initialization/REMORA_init_bcs.cpp commit 84b782dcdeeb14ac203697339ae6d4b1f77aa8c1 Merge: 21ab88fb eab0973c Author: Hannah Klion Date: Fri Nov 1 15:41:10 2024 -0700 Merge pull request #282 from hklion/add_orlanski_inputs add chapman/flather/orlanski inputs file commit eab0973ceba5e38533f6fd426c5b33d28eceff16 Author: Hannah Klion Date: Fri Nov 1 15:40:40 2024 -0700 add chapman/flather/orlanski inputs file Exec/IdealMiniGrid/inputs_cf_orlanski commit 21ab88fbded4894a92af22783ddd54e8e9ea79fe Merge: 0498c892 c3e0878d Author: Hannah Klion Date: Fri Nov 1 12:10:31 2024 -0700 Merge pull request #281 from hklion/checkpoint_nofillpatch remove now-unnecessary FillPatch from Checkpoint commit c3e0878d0edc3319e0083b980e02c19c6576d89c Author: Hannah Klion Date: Fri Nov 1 11:14:19 2024 -0700 remove now-unnecessary FillPatch from Checkpoint Source/IO/Checkpoint.cpp Source/REMORA.cpp commit 0498c892c83f0602f0758d38b2d8898ab1e8e9e8 Author: Hannah Klion Date: Thu Oct 31 10:58:07 2024 -0700 note on where to find netcdf input files Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/inputs_chapman_flather commit 9e183d4cdc9d48fc997dd761b9d9189089bddec2 Author: Hannah Klion Date: Wed Oct 30 15:36:29 2024 -0700 patch so plotfile history will work correctly if max_step < plot_int Source/IO/NCPlotFile.cpp commit 3c5c0ae22a4a8487d2e5423a088a80a6d938b187 Merge: 5fd126c3 741c7fc8 Author: Hannah Klion Date: Tue Oct 29 12:21:52 2024 -0700 Merge pull request #280 from hklion/patch_orlanski patch some things in problem setup and BC application commit 741c7fc8f8f790011dadb2071ece3b837a48b33f Author: Hannah Klion Date: Tue Oct 29 12:14:04 2024 -0700 patch some things in problem setup and BC application Exec/Channel_Test/inputs_orlanski Exec/Channel_Test/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp commit 5fd126c37cd4075a6243ba02f7b49e300b2ab654 Merge: dffea468 6609680d Author: Hannah Klion Date: Mon Oct 28 18:11:17 2024 -0700 Merge pull request #279 from hklion/patch_orlanski add an inputs file to exercise orlanski radiation functionality witho… commit 6609680d643f0bbdd934fa3541699aa801a2c78d Author: Hannah Klion Date: Mon Oct 28 18:10:52 2024 -0700 add an inputs file to exercise orlanski radiation functionality without nudging Exec/Channel_Test/inputs_orlanski commit dffea4686f600f6fd7f488a2857ca31dc278cd36 Merge: 1eb50215 67f998a1 Author: Hannah Klion Date: Tue Oct 22 14:11:01 2024 -0700 Merge pull request #277 from hklion/patch_orlanski patches from orlanski bcs commit 67f998a106b49c72e219b24797b1ae1de11abaa4 Author: Hannah Klion Date: Tue Oct 22 11:57:25 2024 -0700 patches from orlanski bcs Exec/Channel_Test/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 1eb50215c2ed9bfeea40fa700efdf89b9ef522d1 Merge: 0f9f83c6 e1307910 Author: Hannah Klion Date: Fri Oct 18 11:04:34 2024 -0700 Merge pull request #276 from hklion/check_box_ok check on boxes being ok rather than empty commit e13079103d9b3c8c8dacdbc3eeb1ad62a0b87f50 Author: Hannah Klion Date: Fri Oct 18 11:03:33 2024 -0700 check on boxes being ok rather than empty Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 0f9f83c6f79498f06da70d1402bd38d23ebd6c01 Merge: 2c9b320e f8384359 Author: Hannah Klion Date: Thu Oct 17 17:55:03 2024 -0700 Merge pull request #275 from hklion/adjust_bounds_ncbounds add necessary braces commit f83843594037893a2cee6e264929765794c9bbcf Author: Hannah Klion Date: Thu Oct 17 17:54:06 2024 -0700 add necessary braces Source/Initialization/REMORA_init_bcs.cpp commit 2c9b320e035e287849f4bc835218ff01266f29fc Merge: d0342548 dcb0ca87 Author: Hannah Klion Date: Thu Oct 17 17:50:54 2024 -0700 Merge pull request #274 from hklion/adjust_bounds_ncbounds adjust bounds in netcdf boundary conditions commit dcb0ca87155c6a1bdb284791886e55be95522445 Author: Hannah Klion Date: Thu Oct 17 17:48:12 2024 -0700 adjust bounds in netcdf boundary conditions Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/Initialization/REMORA_init_bcs.cpp commit d03425484d6921ef9459561e6faf6ca5eacc85e1 Merge: 97f765ed 259734db Author: Hannah Klion Date: Thu Oct 17 11:10:15 2024 -0700 Merge pull request #273 from hklion/defaults_for_nudging set defaults for nudging params commit 259734db9e6a93012276f6f3da74df21d5c36da0 Author: Hannah Klion Date: Thu Oct 17 11:09:15 2024 -0700 set defaults for nudging params Source/DataStruct.H commit 97f765ed2580319c41cf6267c0823edceb496911 Author: Hannah Klion Date: Thu Oct 17 10:01:42 2024 -0700 update AMReX submodule Submodules/AMReX commit 32853bd78f728d8c92ba41a0863b9b35a269122b Merge: ebf32895 3f0988d5 Author: Hannah Klion Date: Wed Oct 16 16:56:22 2024 -0700 Merge pull request #272 from hklion/radiation_bc Add radiation BC for u/v/t commit 3f0988d512a737fa8fef826e0e9c6c6099c74b2f Author: Hannah Klion Date: Wed Oct 16 16:21:24 2024 -0700 fix spelling Source/DataStruct.H commit 213cf932abab244cb321a2e7dca96bbd0a36049b Author: Hannah Klion Date: Wed Oct 16 16:19:53 2024 -0700 add option for orlanski rad, with and without nudging. Only works for single grid Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/DataStruct.H Source/IndexDefines.H Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit ebf32895e8e1f72142211e705703ad8598461b6d Author: Hannah Klion Date: Tue Sep 24 10:04:36 2024 -0700 add commented out option for a donut of scalar in Advection Exec/Advection/prob.cpp commit 699333c77a52979ada1f3cf55ba84484eb103694 Merge: 4a36ab59 43852ed8 Author: Hannah Klion Date: Thu Sep 19 10:31:57 2024 -0700 Merge branch 'development' into radiation_bc commit 4a36ab59e40dbdb2bc990b13befd24febc8a9bb2 Author: Hannah Klion Date: Wed Sep 18 17:29:18 2024 -0700 add back FillBoundary in velocity Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit bf1990989c84652b910e02195c20822209955fb0 Author: Hannah Klion Date: Wed Sep 18 16:17:42 2024 -0700 added radiation bc condition and testing removal of some fillpatches Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 43852ed82998e8f2bad3dfe4bdb6e86da2c526bd Merge: 72766d6e 377b2d30 Author: Hannah Klion Date: Fri Sep 13 10:36:22 2024 -0700 Merge pull request #271 from hklion/patch_netcdf_init only read masks from netcdf when initializing from file commit 377b2d3005a5d008a9e0bdf978dca986a25d6116 Author: Hannah Klion Date: Fri Sep 13 10:35:38 2024 -0700 only read masks from netcdf when initializing from file Source/REMORA.cpp commit 72766d6e649b9002b73b9de77678a7ed3c8fccde Merge: 912c7094 cefeafd4 Author: Hannah Klion Date: Thu Sep 12 09:21:33 2024 -0700 Merge pull request #270 from hklion/chapman_flather add chapman-flather input file commit cefeafd4e74b27181f7f24a885fc3a507dd99455 Author: Hannah Klion Date: Thu Sep 12 09:20:13 2024 -0700 add chapman-flather input file Exec/IdealMiniGrid/inputs_chapman_flather Source/Initialization/REMORA_init_bcs.cpp commit 912c7094b7e54707246f4ec5a3774984a05727eb Merge: 63191919 73aea869 Author: Hannah Klion Date: Wed Sep 11 17:15:03 2024 -0700 Merge pull request #269 from hklion/chapman_flather add Chapman-Flather boundary conditions for ubar/vbar and zeta commit 73aea8695825f5b8d3f50361fd78a807b510e89a Author: Hannah Klion Date: Wed Sep 11 16:44:54 2024 -0700 add Chapman-Flather boundary conditions for ubar/vbar and zeta Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_init_bcs.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp commit 63191919b51b93793a55770968877ae518e89bd1 Merge: 2aef55b9 d839ed2c Author: Ann Almgren Date: Tue Sep 10 19:25:22 2024 -0700 Merge pull request #268 from jmsexton03/netcdf_cmake_saul Hack for perlmutter libraries commit d839ed2c3eeec7f69f31d124ce2a0b6441b2ee5e Author: Jean M. Sexton Date: Tue Sep 10 18:40:32 2024 -0700 Hack for perlmutter libraries Build/cmake_with_netcdf.sh commit 2aef55b90fd24167aab93a5064d1d42631e09f60 Merge: 05188ba8 28356016 Author: Ann Almgren Date: Tue Sep 10 13:51:34 2024 -0700 Merge pull request #266 from jmsexton03/docs_getting_started_update Update Getting Started and build parts of docs commit 05188ba88400c0cff9169c9e44b55740e923e9f0 Merge: 6ecdcd9b a272525a Author: Ann Almgren Date: Tue Sep 10 13:45:49 2024 -0700 Merge pull request #267 from seahorce-scidac/fix_req update theme commit a272525aa3c9bfd773ce764bc47e1a928e2812e2 Author: Ann Almgren Date: Tue Sep 10 13:45:12 2024 -0700 update theme Docs/requirements.txt commit 2835601638aa5b817d28d3093cd46a49bcee43a3 Author: Jean M. Sexton Date: Tue Sep 10 10:48:32 2024 -0500 Update Getting Started and build parts of docs Docs/sphinx_doc/InputFiles.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/building.rst Docs/sphinx_doc/testing.rst commit 6ecdcd9b8f6f54f6101c804705f5d201483776a9 Merge: e9aba338 8795dd90 Author: Hannah Klion Date: Fri Sep 6 16:47:09 2024 -0700 Merge pull request #265 from hklion/no_mask_w do not apply mask to z velocity when applying boundary conditions commit 8795dd9022fb455b6b5dab4ec868a1c5cf4d6396 Author: Hannah Klion Date: Fri Sep 6 16:46:32 2024 -0700 do not apply mask to z velocity when applying boundary conditions Source/BoundaryConditions/BoundaryConditions_zvel.cpp commit e9aba33895f2de890a03be3745d5f41944cfc8b0 Merge: 54fef6d1 3accc1ca Author: Hannah Klion Date: Fri Sep 6 13:20:49 2024 -0700 Merge pull request #264 from hklion/init_old_vels initialize *vel_old to zero to avoid math on unitialized data commit 3accc1ca033e2cce855b5b7affead3d0a899bfe6 Author: Hannah Klion Date: Fri Sep 6 13:19:56 2024 -0700 initialize *vel_old to zero to avoid math on unitialized data Source/REMORA.cpp commit 54fef6d16d464c0c54f95968544168b038eb9443 Merge: fbf325f7 022762a0 Author: Hannah Klion Date: Fri Sep 6 12:15:15 2024 -0700 Merge pull request #263 from hklion/foextrap_edges apply foextrap boundary on edges commit 022762a0807d8b0cdb6edad3f5e4e50c4aaac691 Author: Hannah Klion Date: Fri Sep 6 10:48:46 2024 -0700 apply foextrap boundary on edges Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp commit fbf325f7197d3b55b8907efe9f917bb6ff6d21d0 Author: Weiqun Zhang Date: Thu Sep 5 11:21:07 2024 -0500 Simplify cache cleanup actions (#262) 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/ci.yml .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/cuda-ci.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/post-pr.yml .github/workflows/sycl.yml commit 6785d5730be2a9671ec21289c5e7a37724b64fc7 Merge: e3d9e452 dee9a124 Author: Hannah Klion Date: Wed Sep 4 13:23:15 2024 -0700 Merge pull request #261 from hklion/adjust_corners swap east and west and add masking on velocity boundaries commit dee9a124b63646f7a19c85b846aa3df2002c2b94 Author: Hannah Klion Date: Wed Sep 4 13:10:43 2024 -0700 swap east and west and add masking on velocity boundaries Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/REMORA.cpp commit e3d9e45263ce337bb1ee6270a44ae0360bb8c857 Merge: 1ed6cd8b 9f0d9ef3 Author: Hannah Klion Date: Tue Sep 3 18:44:36 2024 -0700 Merge pull request #260 from hklion/adjust_corners only apply edge mass flux adjustment to corners once commit 9f0d9ef351e4b8433d1f6c76f443fa5414755b65 Author: Hannah Klion Date: Tue Sep 3 17:32:34 2024 -0700 only apply edge mass flux adjustment to corners once Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit 1ed6cd8b07f2be7629c9cf6c35dd4925f4720b9e Merge: 1408b076 2d2e8a4c Author: Hannah Klion Date: Fri Aug 30 22:22:48 2024 -0700 Merge pull request #258 from hklion/specify_bc_by_variable only update corners after doing all boundaries and change logic to be… commit 1408b076c698effb5a88fbbfc2516c5dbd038d8f Merge: bec87f92 d2691072 Author: Ann Almgren Date: Fri Aug 30 15:43:26 2024 -0700 Merge pull request #259 from seahorce-scidac/fix_docs fix docs commit d2691072497c571b406397884539908beba7af3a Author: Ann Almgren Date: Fri Aug 30 15:42:55 2024 -0700 fix docs Docs/sphinx_doc/RegressionTests.rst commit bec87f9292fa4f0d650927c1b9cf3ecff5bba887 Merge: 05023c4e 64413fca Author: Ann Almgren Date: Fri Aug 30 15:32:06 2024 -0700 Merge pull request #257 from seahorce-scidac/update_docs add new docs on regression tests commit 2d2e8a4cb7d6673461c32cfd45cd10b4c37f8434 Author: Hannah Klion Date: Fri Aug 30 15:30:53 2024 -0700 only update corners after doing all boundaries and change logic to be if not periodic Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit 64413fca226bd0d30f01d97160e64330f0e97e74 Author: Ann Almgren Date: Fri Aug 30 15:20:08 2024 -0700 add new docs on regression tests Docs/sphinx_doc/Performance.rst Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/Verification.rst Docs/sphinx_doc/index.rst commit 05023c4e6854276a3544a8673bf5a38db1124f23 Merge: 772e4dab 7bf2aac1 Author: Hannah Klion Date: Wed Aug 28 18:22:17 2024 -0700 Merge pull request #255 from hklion/specify_bc_by_variable Only apply netcdf BCs on clamped sides commit 7bf2aac17f98ee7791b3eb1fb15028a70aa2b1cd Author: Hannah Klion Date: Wed Aug 28 17:47:42 2024 -0700 Only apply netcdf BCs on clamped sides Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_3d.cpp commit 772e4dab7cb94278639ec99304651a68f1db99d1 Author: Hannah Klion Date: Wed Aug 28 15:38:50 2024 -0700 resize boundary condition arrays to be NCONS+SPACEDIM+5 to account for additional vars Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/Initialization/REMORA_init_bcs.cpp Source/REMORA.H commit 3ca2ac623767fb42dfd8dc9372275be43a0a71df Author: Hannah Klion Date: Wed Aug 28 15:25:14 2024 -0700 Revert "try reverting BCVars::ubar/vbar to BCVars::xvel/yvel" This reverts commit 0b572f0c284eff7ab28a345403424b144aaacb52. Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit 0b572f0c284eff7ab28a345403424b144aaacb52 Author: Hannah Klion Date: Wed Aug 28 12:49:11 2024 -0700 try reverting BCVars::ubar/vbar to BCVars::xvel/yvel Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit 8b1cc993696c86a8fe16d70ae5a1320f996860f3 Merge: 8732fa27 efb0f733 Author: Hannah Klion Date: Tue Aug 27 12:07:16 2024 -0700 Merge pull request #254 from hklion/specify_bc_by_variable add in more BCVar args commit efb0f7336e63a9b0905807d7939238c408860cae Author: Hannah Klion Date: Tue Aug 27 11:55:11 2024 -0700 add in more BCVar args Source/Initialization/REMORA_init.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 8732fa276ab4fe48b460659870ee0e6f5060a633 Merge: 31e526a2 ba756226 Author: Hannah Klion Date: Tue Aug 27 11:21:55 2024 -0700 Merge pull request #253 from hklion/specify_bc_by_variable added more BC options and add option to specify it by variable commit ba75622604e468108e6962d09f0e6ad72bbda574 Author: Hannah Klion Date: Tue Aug 27 11:20:06 2024 -0700 pass BCVar into FillPatch rather than inferring it Exec/IdealMiniGrid/inputs Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/Checkpoint.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 896b239f202cfd740c6ce47d0411d2bdcb8a9ba7 Author: Hannah Klion Date: Tue Aug 27 11:17:20 2024 -0700 call it clamped instead of outflow Source/Initialization/REMORA_init_bcs.cpp commit 8005fb368f6db8dbd5b6cf97feca5bf794783e0e Author: Hannah Klion Date: Mon Aug 26 14:10:38 2024 -0700 added more BC options and add option to specify it by varialbe, like in ROMS Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IndexDefines.H Source/Initialization/REMORA_init_bcs.cpp Source/REMORA.H commit 31e526a2c384a8d80b4f2e1a831b7f94956da5ca Merge: 6f67f28e f71e016c Author: Hannah Klion Date: Fri Aug 23 14:25:58 2024 -0700 Merge pull request #252 from hklion/double_gyre_test update double gyre input to not use netcdf commit f71e016cfcad2f3711d5d6b6f4062988e4d320a1 Author: Hannah Klion Date: Fri Aug 23 14:25:22 2024 -0700 update double gyre input to not use netcdf Exec/DoubleGyre/inputs commit 6f67f28e7ff7ba3db9d00a3a79985c5de7a58211 Merge: 29f4eda0 ce1072e3 Author: Hannah Klion Date: Fri Aug 23 09:56:27 2024 -0700 Merge pull request #251 from hklion/double_gyre_test add double gyre test commit ce1072e3aebca35f94c35fd0582dddf417ee0ec1 Author: Hannah Klion Date: Fri Aug 23 09:36:27 2024 -0700 add double gyre test Exec/CMakeLists.txt Exec/DoubleGyre/CMakeLists.txt Exec/DoubleGyre/GNUmakefile Exec/DoubleGyre/Make.package Exec/DoubleGyre/inputs Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Tests/CTestList.cmake Tests/REMORA_Gold_Files/DoubleGyre/Header Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Cell_H Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoubleGyre/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoubleGyre/job_info Tests/test_files/DoubleGyre/DoubleGyre.i commit 29f4eda00291c0bdba94cc5912dfa18ff75e46d0 Merge: 1d912d0f 4ac546b8 Author: Hannah Klion Date: Thu Aug 22 21:52:36 2024 -0700 Merge pull request #250 from hklion/corner_bcs fill boundary in velocity corners and overridesync winds commit 4ac546b85aef5fe990405655c71641d32deb9008 Author: Hannah Klion Date: Thu Aug 22 17:25:14 2024 -0700 fill boundary in corners and overridesync winds Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/REMORA.cpp commit 1d912d0f4f4529d855c75baf72caa9144df7bf63 Merge: 41830cf4 f0c7e552 Author: Hannah Klion Date: Wed Aug 21 10:55:08 2024 -0700 Merge pull request #249 from hklion/foextrap_bc_periodic apply physical boundary conditions if using foextrap_bc type commit f0c7e5525dfea43054ba7c81eeed79890ab3d30f Author: Hannah Klion Date: Wed Aug 21 10:49:34 2024 -0700 apply physical boundary conditions if using foextrap_bc type Source/BoundaryConditions/REMORA_PhysBCFunct.cpp commit 41830cf44c00dc410b802e3ccbd240c4be1740d0 Merge: b7f6019f 4c189a60 Author: Hannah Klion Date: Mon Aug 19 16:43:05 2024 -0700 Merge pull request #248 from hklion/override_sync_phibar move override sync for velocities to before ubar/vbar are calculated commit 4c189a600c922c7247ba31e1b6d3db188c1985c2 Author: Hannah Klion Date: Mon Aug 19 16:27:53 2024 -0700 move override sync for velocities to before ubar/vbar are calculated Source/REMORA.cpp commit b7f6019fac1d1cdd4f4a9a17acd1740fd04fe218 Merge: f97ca581 6c8f1e08 Author: Hannah Klion Date: Fri Aug 16 13:55:00 2024 -0700 Merge pull request #247 from hklion/mask_array_public make the mask array output public for GPU commit 6c8f1e086b40728ea9bd4129e1b5b50c99bf03e1 Author: Hannah Klion Date: Fri Aug 16 13:34:41 2024 -0700 make the mask array output public for GPU Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/REMORA.H commit f97ca58163db6c08ac9a489d237439cb32bd62df Merge: 3c89f16c 700b27cc Author: Hannah Klion Date: Thu Aug 15 16:33:40 2024 -0700 Merge pull request #246 from hklion/mask_land_netcdf Mask land in netcdf output commit 700b27ccebf8f3cf879f27baa6e0b8fdd0d9fd29 Author: Hannah Klion Date: Thu Aug 15 14:24:05 2024 -0700 actually mask output in netcdf plotfiles Source/IO/NCPlotFile.cpp Source/REMORA.H commit 0e955ef79bd966bb9749a80799a94f923fcd002f Author: Hannah Klion Date: Thu Aug 15 11:58:34 2024 -0700 add fill value to netcdf fields Source/IO/NCInterface.H Source/IO/NCInterface.cpp Source/IO/NCPlotFile.cpp commit 3c89f16cf4ea8728366d6169b0a1ea8f9abcfb18 Merge: fe531910 db4a6502 Author: Hannah Klion Date: Thu Aug 15 11:06:47 2024 -0700 Merge pull request #244 from hklion/gls_boundary_bugs Add Channel_Test -- compares with ROMS commit db4a65022c518e84c9ba9dab50bccf70ced7d78b Author: Hannah Klion Date: Thu Aug 15 10:32:51 2024 -0700 add gold file for Channel_Test Tests/REMORA_Gold_Files/Channel_Test/Header Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Cell_H Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Channel_Test/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Channel_Test/job_info commit f77a65ad49611bb4a8f0ab75733854cad3eb9f88 Author: Hannah Klion Date: Thu Aug 15 10:23:47 2024 -0700 actually add Channel_Test input file Tests/test_files/Channel_Test/Channel_Test.i commit 64ebe528b7508d655e503f238f032bd4564da9bd Merge: 39c9a4ab fe531910 Author: Hannah Klion Date: Thu Aug 15 10:07:35 2024 -0700 Merge branch 'development' into gls_boundary_bugs commit 39c9a4abd89f893d15274425c32daf000521b2a6 Author: Hannah Klion Date: Thu Aug 15 09:56:10 2024 -0700 remove tab Exec/Channel_Test/prob.cpp commit e87ae81c6ea1c53f0df52333217d0f85aca56bf6 Author: Hannah Klion Date: Thu Aug 15 09:53:37 2024 -0700 register Channel_Test with cmake Exec/CMakeLists.txt Exec/Channel_Test/CMakeLists.txt Tests/CTestList.cmake commit fe5319108a3d7d52b3b942764285520d2167e6a7 Merge: a02b366d 7416277f Author: Hannah Klion Date: Wed Aug 14 20:30:22 2024 -0700 Merge pull request #243 from seahorce-scidac/fix_netcdf_with_cuda add streamSynchronize after copies commit 7416277f8de0a85a0c091db74a76acee6829169e Author: Ann Almgren Date: Wed Aug 14 20:07:33 2024 -0700 add streamSynchronize after copies Source/IO/NCPlotFile.cpp commit 1b0fcf00b2a402e7a16de997892fd62b74adf8e8 Merge: 676183ab a02b366d Author: Hannah Klion Date: Wed Aug 14 17:26:06 2024 -0700 Merge branch 'development' into gls_boundary_bugs commit 676183ab0d7f14f493183fbffa62802ca0febfb5 Merge: d2865f0d 6a4ef4ed Author: Hannah Klion Date: Wed Aug 14 16:54:35 2024 -0700 Merge remote-tracking branch 'upstream/development' into gls_boundary_bugs commit a02b366db783fd25f48845d1d5bbe0fa5d41f76e Merge: 6a4ef4ed 2db07d23 Author: Hannah Klion Date: Wed Aug 14 16:51:32 2024 -0700 Merge pull request #242 from hklion/fix_plotfile don't apply BCs when FillPatching for plotfiles commit 2db07d23922aeb1d6e6e2ee0d8b32f7d8a941e1d Author: Hannah Klion Date: Wed Aug 14 15:38:10 2024 -0700 don't apply BCs when FillPatching for plotfiles Source/IO/Plotfile.cpp commit 6a4ef4edad7556b348090280a08e8580b822b346 Merge: aa1e7254 f510d967 Author: Hannah Klion Date: Wed Aug 14 14:41:48 2024 -0700 Merge pull request #241 from seahorce-scidac/fix_netcdf_write fix netcdf write and remove unused variables commit f510d967bbe315a4fc0886455ea605c94a4355a8 Author: Ann Almgren Date: Wed Aug 14 13:44:33 2024 -0700 fix netcdf write and remove unused variables Source/IO/NCPlotFile.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp commit d2865f0df3a3e3e135402f3fc5139d61715c71a3 Author: Hannah Klion Date: Tue Aug 13 17:19:04 2024 -0700 update Upwelling_GLS benchmark Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/job_info commit c569159a6696ccaeb8715a04fa9c8b2a037f5228 Author: Hannah Klion Date: Tue Aug 13 17:06:53 2024 -0700 add Channel_Test case Exec/Channel_Test/CMakeLists.txt Exec/Channel_Test/GNUmakefile Exec/Channel_Test/Make.package Exec/Channel_Test/inputs Exec/Channel_Test/prob.H Exec/Channel_Test/prob.cpp commit 61c686107d5d729132eba476e27a7212a2864770 Author: Hannah Klion Date: Tue Aug 13 16:32:26 2024 -0700 Fix bugs in GLS and output NetCDF as DOUBLE - Some indexing errors in GLS fixed - Add a BC var that unconditionally does foextrap, even if it's at a periodic boundary - OverrideSync for x and y velocities Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/DataStruct.H Source/IO/NCPlotFile.cpp Source/IndexDefines.H Source/Initialization/REMORA_init_bcs.cpp Source/TimeIntegration/REMORA_gls.cpp commit aa1e72549f0a6ce5d443ed4c1fa8003ff299a1ba Merge: 39cafda2 b8512cc4 Author: Hannah Klion Date: Fri Aug 2 19:26:26 2024 -0700 Merge pull request #240 from hklion/land_sea_mask initialize masks before they are used in remake levels commit b8512cc417e69d496c37f96d8c27b2b1d1393422 Author: Hannah Klion Date: Fri Aug 2 19:05:21 2024 -0700 initialize masks before they are used in remake levels Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit 39cafda264b982e9143d9da4aa3f35f596bbc312 Merge: 6c8e4e3a 6900b4c0 Author: Hannah Klion Date: Fri Aug 2 18:17:04 2024 -0700 Merge pull request #239 from hklion/land_sea_mask Land sea mask commit 6900b4c0efeb4fd321edebe428916f92fee42c7a Author: Hannah Klion Date: Fri Aug 2 17:18:35 2024 -0700 IdealMiniGrid agrees with ROMS - Recalculate psi mask as in ROMS - Make sure masks are actually read from file - When read from file, one ghost cell of bathymetry is maintained, to match with ROMS - Pass masks around as needed Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/IO/NCFile.H Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp commit df2cfbe16e8a205832f03dc14f408361bddaa1af Author: Hannah Klion Date: Tue Jul 30 09:57:55 2024 -0700 First pass at adding land/sea masking to evolution - Read masks in from the NetCDF grid file rather than initial file - Masks are set to 1 if ocean, 0 if land - Add psi-point masks Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp commit 6c8e4e3a6ae45d37844965c6beaae15253175082 Merge: b4025fe5 7c00ff4b Author: Hannah Klion Date: Fri Jul 26 17:13:07 2024 -0700 Merge pull request #238 from hklion/remove_atomic remove atomic when accumulating into rufrc and rvfrc. Instead loop through k's commit 7c00ff4b6f7084edc99feb4a0d11810923695cee Author: Hannah Klion Date: Fri Jul 26 16:26:50 2024 -0700 remove atomic when accumulating into rufrc and rvfrc. Instead loop through k's Source/TimeIntegration/REMORA_uv3dmix.cpp commit b4025fe5001b9ba96689973b4038752f2dbcd385 Merge: ef5f3cfc ac308596 Author: Hannah Klion Date: Wed Jul 24 15:40:43 2024 -0700 Merge pull request #237 from hklion/setup_docs_fillboundary add a paragraph to ProblemSetup about FillBoundary commit ac308596fa438f068dac3638d8bc9c70347b2859 Author: Hannah Klion Date: Wed Jul 24 14:29:39 2024 -0700 add a paragraph to ProblemSetup about FillBoundary Docs/sphinx_doc/ProblemSetup.rst commit ef5f3cfc01718a4e130f37bd0b838eee86af0087 Merge: 3de16924 d2e804a4 Author: Hannah Klion Date: Tue Jul 23 15:42:36 2024 -0700 Merge pull request #236 from hklion/AMReX_update update AMReX commit d2e804a43aa87250f70a181c6ac1cc25e1368516 Author: Hannah Klion Date: Tue Jul 23 15:20:08 2024 -0700 update AMReX Submodules/AMReX commit 3de16924a00a3f18428af686c19c490f97a9f29c Merge: 938c947d 5d4c2744 Author: Hannah Klion Date: Tue Jul 23 10:55:02 2024 -0700 Merge pull request #235 from hklion/remove_init remove redundant initialization commit 5d4c2744d2b9f345eccea9ceb2324de129539a98 Author: Hannah Klion Date: Tue Jul 23 10:34:38 2024 -0700 remove redundant initalization Source/REMORA.cpp commit 938c947d343bf4ecae5de45227af6f70a7b81820 Merge: af8f9950 8af3a990 Author: Hannah Klion Date: Tue Jul 23 09:37:35 2024 -0700 Merge pull request #234 from hklion/fix_checkpoint initialize GLS variables even when not used commit 8af3a9906d2b8289112f0582df4cabac95f4e45d Author: Hannah Klion Date: Tue Jul 23 09:17:24 2024 -0700 initialize GLS variables even when not used Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit af8f9950f2a343f04f9ab66b4595cf8166fd4846 Merge: 9e73a57e 4d3318ee Author: Hannah Klion Date: Mon Jul 22 14:24:59 2024 -0700 Merge pull request #233 from hklion/restart_gls checkpoint GLS variables commit 4d3318eeb74cf1d210f1f0bea43768f6bf60856f Author: Hannah Klion Date: Mon Jul 22 14:02:21 2024 -0700 checkpoint GLS variables Source/IO/Checkpoint.cpp commit 9e73a57eac443ccfa2e5b4b6a6b92d6a63f081ec Merge: e4f00827 ea493c2e Author: Hannah Klion Date: Fri Jul 19 09:05:02 2024 -0700 Merge pull request #232 from hklion/fillpatch_checkpoint add a FillPatch before writing checkpoint file commit ea493c2e6c3205c1e4386aa5872104fca0dd7c5c Author: Hannah Klion Date: Thu Jul 18 09:03:27 2024 -0700 add a FillPatch before writing checkpoint file. This appears to be necessary for correctness Source/IO/Checkpoint.cpp Source/REMORA.H commit e4f00827a8c8d36997f9a8b49c723fb502440c70 Merge: 438e9171 2e01e1e4 Author: Hannah Klion Date: Thu Jul 18 07:02:27 2024 -0700 Merge pull request #231 from seahorce-scidac/reorg_perl_docs update perlmutter docs commit 2e01e1e423766aa703fd52c9b75a9a5b934b8e1f Author: Hannah Klion Date: Thu Jul 18 07:00:13 2024 -0700 update perlmutter docs Docs/sphinx_doc/building.rst Docs/sphinx_doc/index.rst Docs/sphinx_doc/perlmutter.rst commit 438e9171e793a5f978fc50bf175ff4ac397d3a02 Merge: 21cce407 e118a5e6 Author: Hannah Klion Date: Thu Jul 18 06:40:32 2024 -0700 Merge pull request #230 from seahorce-scidac/smflux_ncplotfile initialize sustr and svstr when making new level commit e118a5e6c1c7acb3928302aa164d1270757df793 Author: Hannah Klion Date: Thu Jul 18 06:39:37 2024 -0700 initialize sustr and svstr when making new level Source/Initialization/REMORA_make_new_level.cpp commit 21cce40764a1eaf398ca32f3697ca8c89b6d2a8b Merge: 2a246894 2bc83852 Author: Hannah Klion Date: Thu Jul 18 06:32:56 2024 -0700 Merge pull request #229 from seahorce-scidac/smflux_ncplotfile add sustr and svstr to netcdf plotfile commit 2a246894f2ceead18cec5408e395d106fdbb5b63 Merge: f8a332f0 dcab91d7 Author: Hannah Klion Date: Thu Jul 18 05:30:34 2024 -0700 Merge pull request #228 from hklion/perl_docs tweak header formatting commit dcab91d7895de65cf6a3116f71bf00347d320608 Author: Hannah Klion Date: Wed Jul 17 11:50:39 2024 -0400 tweak header ormatting Docs/sphinx_doc/building.rst commit f8a332f07a924e95a86c9d59c94cf380a192dbf0 Merge: 86169a19 9dae5421 Author: Hannah Klion Date: Wed Jul 17 08:37:09 2024 -0700 Merge pull request #227 from hklion/perl_docs update docs for perlmutter commit 9dae5421f514f70ae836ce78f223b087a23a0b78 Author: Hannah Klion Date: Wed Jul 17 11:34:03 2024 -0400 update docs for perlmutter Docs/sphinx_doc/building.rst commit 2bc83852a8a380c1a7c0dcc4f0e7cf74537b856c Author: Hannah Klion Date: Wed Jul 17 07:54:08 2024 -0700 add sustr and svstr to netcdf plotfile Source/IO/NCPlotFile.cpp Source/REMORA.cpp commit 86169a19c913ae32627862caa9986e187129987f Merge: 1a59b261 cabdd0dd Author: Hannah Klion Date: Fri Jul 12 18:32:48 2024 -0700 Merge pull request #226 from hklion/fix_restart checkpoint bathymetry commit cabdd0ddd6c0cfbe18dea1f2d55dc56bb7a198f4 Author: Hannah Klion Date: Fri Jul 12 18:31:10 2024 -0700 checkpoint bathymetry Source/IO/Checkpoint.cpp commit 1a59b261cb5034a69e75354891a61e5c630a830e Merge: cb7f9c28 be31f7ba Author: Hannah Klion Date: Fri Jul 12 17:26:32 2024 -0700 Merge pull request #225 from hklion/fix_restart checkpoint ru2d and rv2d commit be31f7ba9b866249137a6a53ec495882ab5b6618 Author: Hannah Klion Date: Fri Jul 12 17:05:14 2024 -0700 checkpoint ru2d and rv2d Source/IO/Checkpoint.cpp commit cb7f9c28d8f4cfd6c2420676d37fca8115072c06 Merge: 9082e8cc 31120bb1 Author: Hannah Klion Date: Fri Jul 12 16:43:32 2024 -0700 Merge pull request #224 from hklion/fix_restart Fix restart for Advection commit 31120bb15d97e3a5de13f5005109a56ad6c856e7 Author: Hannah Klion Date: Fri Jul 12 15:38:32 2024 -0700 checkpoint old cons, xvel, yvel, zvel Source/IO/Checkpoint.cpp Source/REMORA.cpp commit 9082e8ccdc2faf6facfa1b0a0029b1ee0846b608 Merge: 319f2b4b 368cf436 Author: Hannah Klion Date: Fri Jul 12 14:48:51 2024 -0700 Merge pull request #223 from hklion/idealminigrid_zeta set zeta to Ztavg when reading from netcdf commit 368cf436075462624b9d138f2b885e7c10774d37 Author: Hannah Klion Date: Fri Jul 12 13:42:02 2024 -0700 set zeta to Ztavg when reading from netcdf Source/REMORA.cpp commit 319f2b4bcbe409d156ddc66c69ed297fca73a1be Merge: 7f141de8 55ff7447 Author: Hannah Klion Date: Fri Jul 12 12:59:54 2024 -0700 Merge branch 'development' of github.com:seahorce-scidac/REMORA into development commit 7f141de8869563f61ee15be1f92f4282f528e08b Author: Hannah Klion Date: Fri Jul 12 12:59:22 2024 -0700 inputs_ml tracer horizontal advection rename Exec/Advection/inputs_ml commit 55ff744707c025abc951a439e86f63a2b45b4722 Merge: cb86e74a b756d53f Author: Ann Almgren Date: Mon Jul 8 18:32:35 2024 -0700 Merge pull request #222 from seahorce-scidac/fix_spelling fix some spelling commit b756d53f680aae8b1829ab687f5a3e81e60b9b92 Author: Ann Almgren Date: Mon Jul 8 18:31:49 2024 -0700 fix spelling README.rst commit 01678e851760cf695c62c5d41dcf8d3b9daaf95f Author: Ann Almgren Date: Mon Jul 8 18:30:24 2024 -0700 more spelling fixes Docs/sphinx_doc/Discretizations.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/Time_Stepping.rst Docs/sphinx_doc/Visualization.rst Docs/sphinx_doc/coc.rst Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/DataStruct.H Source/IO/NCFile.H Source/Particles/ParticleData.H Source/REMORA_Tagging.cpp Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i commit b9bfa1489d64b0449227e5f0aad9ce8f958f1956 Author: Ann Almgren Date: Mon Jul 8 18:26:42 2024 -0700 fix more spellings .codespell-ignore-words Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/ProblemSetup.rst Docs/sphinx_doc/Visualization.rst Exec/Advection/inputs Exec/Advection/inputs_ml Exec/DoublyPeriodic/inputs Exec/IdealMiniGrid/inputs Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/inputs_ml Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_gls Exec/Upwelling_ML/inputs Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_gls.cpp paper/paper.md commit ddc70c11ec0ac2cb86379d9f7bdeec768791c267 Author: Ann Almgren Date: Mon Jul 8 18:22:10 2024 -0700 fix some spelling Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/TimeIntegration/REMORA_gls.cpp commit cb86e74a981a8f426f8cc3fcf62a68b13c89cf28 Merge: 8295d93e a0cfca74 Author: Ann Almgren Date: Mon Jul 8 18:20:32 2024 -0700 Merge pull request #221 from WeiqunZhang/codespell CI: Add codespell commit a0cfca74a08525e7f399a9299168ecd64fe83f26 Author: Weiqun Zhang Date: Mon Jul 8 17:25:26 2024 -0700 CI: Add codespell .codespell-ignore-words .codespellrc .github/workflows/codespell.yml commit b72be5df4ab966b3bb6218734eb0715ecbd82995 Author: Hannah Klion Date: Sat Jul 6 13:12:32 2024 -0700 do stretch transform after reading in checkpointed data Source/IO/Checkpoint.cpp commit 8295d93e47f4f04f2e067137eec482e752fbdbb8 Merge: f7c76ec1 9c4f6b4b Author: Hannah Klion Date: Fri Jul 5 18:10:47 2024 -0700 Merge pull request #220 from hklion/add_amr_restart add option for amr namespace for restart params commit 9c4f6b4b0974653d3f9a9de18bb70d2663f27c66 Author: Hannah Klion Date: Fri Jul 5 17:58:29 2024 -0700 add option for amr namespace for restart params Source/REMORA.cpp commit f7c76ec19b3a3c79dd41f67cd0d06ec3d6b6a50d Merge: e7e328f1 afb6e1a4 Author: Hannah Klion Date: Wed Jul 3 18:14:27 2024 -0400 Merge pull request #219 from hklion/uv_advection_c2 add centered2 to 2d horizontal advection commit afb6e1a4df49a525b2b22fe6a0c53fedae241730 Author: Hannah Klion Date: Wed Jul 3 15:13:31 2024 -0700 add centered2 to 2d horizontal advection Source/TimeIntegration/REMORA_rhs_uv_2d.cpp commit e7e328f10b242de3a04f21eaa6ba32513742e9d9 Merge: b50c8437 3adcf6a2 Author: Hannah Klion Date: Wed Jul 3 17:45:19 2024 -0400 Merge pull request #218 from hklion/uv_advection_c2 adjust input files and add c2 horiz derivatives for vertical advection component commit 3adcf6a25ae8e5eccfdc2ad8a2e661210ae22d16 Author: Hannah Klion Date: Wed Jul 3 14:43:57 2024 -0700 2nd order horizontal for vertical advection Source/TimeIntegration/REMORA_rhs_uv_3d.cpp commit 504ead791e446c451ba2d97f17d9d2270ebc0e6b Author: Hannah Klion Date: Wed Jul 3 14:43:34 2024 -0700 update input file names Exec/Advection/inputs Exec/DoublyPeriodic/inputs Exec/IdealMiniGrid/inputs Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/inputs Exec/Seamount/inputs Exec/Upwelling/inputs Tests/test_files/Advection/Advection.i Tests/test_files/Advection_ML/Advection_ML.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Upwelling/Upwelling.i Tests/test_files/Upwelling_GLS/Upwelling_GLS.i commit b50c8437f1866a45e9c1cac09f47e47f49015455 Merge: 4c512eb9 3582c7bd Author: Hannah Klion Date: Wed Jul 3 16:55:40 2024 -0400 Merge pull request #217 from hklion/uv_advection_c2 add centered 2nd order advection scheme for momenta commit 3582c7bd438ca5b55418bb0a1216604af0e01c9c Author: Hannah Klion Date: Wed Jul 3 13:54:24 2024 -0700 update docs and rename tracer horizontal advection Docs/sphinx_doc/Inputs.rst Source/DataStruct.H Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp commit 849667c6a8ec1cc58574df996d8edf7998bdce2a Author: Hannah Klion Date: Wed Jul 3 13:28:41 2024 -0700 udpate docs Docs/sphinx_doc/Inputs.rst commit dfa5273bafe75ecad39f9bc9cd945c74683baf46 Author: Hannah Klion Date: Wed Jul 3 12:48:43 2024 -0700 add centered 2nd order advection scheme for momenta Source/DataStruct.H Source/TimeIntegration/REMORA_rhs_uv_3d.cpp commit 4c512eb9399bb601d7da7ec0822352cdd24c9f22 Author: Hannah Klion Date: Tue Jul 2 13:55:17 2024 -0700 add gnumakefile for Upwelling_ML Exec/Upwelling_ML/GNUmakefile commit 686f3c203df99ce5ee12d5871bee998b921ddcf8 Merge: 86dd4391 0d3a0de4 Author: Hannah Klion Date: Thu Jun 27 16:19:20 2024 -0400 Merge pull request #216 from hklion/fillpatcher_issues FillPatchers for ubar/vbar, and also add init options for ML commit 0d3a0de4a0a67b95e097263cd49d75b21a1e0979 Merge: 9741dd6d 86dd4391 Author: Hannah Klion Date: Thu Jun 27 11:48:05 2024 -0700 Merge branch 'development' into fillpatcher_issues commit 9741dd6df1fcf3972e516d6b148891ee1dfdcb6f Author: Hannah Klion Date: Thu Jun 27 11:46:33 2024 -0700 adjust set_bathymetry arguments to take refinement ratio and remove print statements Exec/Advection/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/OCCAMS/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Exec/Upwelling_ML/inputs Exec/Upwelling_ML/prob.cpp Source/BoundaryConditions/REMORA_FillPatcher.H Source/Initialization/prob_common.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit 86dd43911dcf5e18217a9aa3eddd87cafb59e640 Merge: 2d63604c f627933e Author: Hannah Klion Date: Thu Jun 27 14:01:57 2024 -0400 Merge pull request #211 from hklion/scale_upwelling_resolution scale tanh profile in upwelling by resolution commit f627933e608f9489f4e7c971913556cc9dda2b92 Author: Hannah Klion Date: Thu Jun 27 10:11:40 2024 -0700 update tests Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling/job_info Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/job_info commit a9197bbbe476d57e7f3d335ffbe769d059ea490c Author: Hannah Klion Date: Wed Jun 26 16:13:28 2024 -0700 remove prints and fix FillPatcher Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit bf2c29a22d231fcb2b110b08cd29c48dbec84d7c Author: Hannah Klion Date: Mon Jun 24 09:40:02 2024 -0700 first pass at fillpatchers for ubar/vbar Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.H Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp commit 2d63604c278d78b9cc6390a74c59fa4fc0392cda Merge: d7549a7e da47552b Author: Hannah Klion Date: Fri Jun 21 18:49:47 2024 -0400 Merge pull request #215 from hklion/fix_bug_fillpatcher_logic remove a conditional on fill_all from FillPatcher logic in FillPatch commit da47552b4d791a928cb734dcc863d0a572b6e032 Author: Hannah Klion Date: Fri Jun 21 14:17:26 2024 -0700 remove a conditional on fill_all from FillPatcher logic in FillPatch Source/BoundaryConditions/REMORA_FillPatch.cpp commit d7549a7e10ef1d97daa06227ddcfbf2876f8710d Merge: f66ff4ea 105064bb Author: Hannah Klion Date: Thu Jun 20 14:05:11 2024 -0400 Merge pull request #214 from hklion/bc_docs BC documentation commit 105064bb7347670b5d5c7c383e8e5c64cd4d7ce6 Author: Hannah Klion Date: Thu Jun 20 11:04:39 2024 -0700 BC documentation Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/index.rst commit f66ff4eae14727e4f0bc7fe84333c9b4d296e1d3 Merge: 9481bea8 9e93bf84 Author: Ann Almgren Date: Wed Jun 19 06:57:42 2024 -0700 Merge pull request #213 from WeiqunZhang/ccache Update CI commit 9e93bf8428f5b5417f104a62a38555386de99da4 Author: Weiqun Zhang Date: Tue Jun 18 21:55:52 2024 -0700 Update CI * Bump up actions' version * Use ccache and github cache .github/workflows/c-linter.yml .github/workflows/ci.yml .github/workflows/cleanup-cache-postpr.yml .github/workflows/cleanup-cache.yml .github/workflows/cuda-ci.yml .github/workflows/docs.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/post-pr.yml .github/workflows/style.yml .github/workflows/sycl.yml .github/workflows/windows.yml commit 70e26b2e672ace66049c4af65804873a7d8e8484 Author: Hannah Klion Date: Mon Jun 17 12:25:37 2024 -0700 add runtime option for intialization Exec/Upwelling_ML/CMakeLists.txt Exec/Upwelling_ML/Make.package Exec/Upwelling_ML/inputs Exec/Upwelling_ML/prob.H Exec/Upwelling_ML/prob.cpp Source/DataStruct.H Source/Initialization/prob_common.H Source/REMORA.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp commit 091ac753dc5793007e2d5c11709b441e6d3c49d4 Author: Hannah Klion Date: Mon Jun 17 10:03:31 2024 -0700 scale tanh profile in upwelling by resolution Exec/Upwelling/prob.cpp commit 9481bea86bd2ef9610d6e2ad61289fa02c826459 Merge: 9773ef71 dc2952cd Author: Hannah Klion Date: Thu Jun 13 14:15:59 2024 -0400 Merge pull request #210 from hklion/average_down_zeta average down zeta commit dc2952cde251d07a3866ea71511708ce0e659539 Author: Hannah Klion Date: Thu Jun 13 10:54:11 2024 -0700 average down zeta Source/REMORA.cpp commit 9773ef714638651187e0bd0dcec54e8c7d7aa92a Merge: 1c0aeb2f 00c73dce Author: Hannah Klion Date: Wed Jun 12 19:58:39 2024 -0400 Merge pull request #209 from hklion/whitespace update whitespace commit 00c73dce5fb9cca115f7a6e9bf01c505c2e3f559 Author: Hannah Klion Date: Wed Jun 12 16:57:10 2024 -0700 update whitespace Source/REMORA.H Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp commit 1c0aeb2f7ed64ca263c3adbb122202de34c46def Merge: 0fa1641f 3916e7b9 Author: Hannah Klion Date: Wed Jun 12 19:56:49 2024 -0400 Merge pull request #208 from hklion/rhs_2d_ownvar scale ru/rv and ru2d/rv2d before FillPatch commit 3916e7b969f49da9a6cbbfe7e26e90b0873659e8 Author: Hannah Klion Date: Wed Jun 12 16:29:04 2024 -0700 add scale rhs vars function Source/TimeIntegration/REMORA_scale_rhs_vars.cpp commit 9b209bf8025049d8d714c7a3a9d82d8e1d0c5a3f Author: Hannah Klion Date: Wed Jun 12 16:28:14 2024 -0700 scale ru/rv and ru2d/rv2d before FillPatch CMake/BuildREMORAExe.cmake Source/REMORA.H Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_TimeStepML.cpp commit 0fa1641f5943fa77369404ac4ac699c9efbc3ad2 Merge: 1b43fa73 cd74df6e Author: Hannah Klion Date: Tue Jun 11 20:03:08 2024 -0400 Merge pull request #207 from hklion/netcdf_gpu make netcdf work with gpu commit cd74df6ec892eb19008fde5b48f2e9099efb44ab Author: Hannah Klion Date: Tue Jun 11 16:38:46 2024 -0700 make netcdf work with gpu Source/IO/NCPlotFile.cpp commit 1b43fa734fda85ba13f5e233d48d3e54b04b8904 Merge: 80c7bcfb a005a595 Author: Hannah Klion Date: Mon Jun 10 17:14:34 2024 -0400 Merge pull request #206 from hklion/rhs_2d_ownvar make ru2d/rv2d their own variable commit a005a595a41df6056d059bd6c021f7b44e298e08 Author: Hannah Klion Date: Mon Jun 10 13:50:00 2024 -0700 make ru2d/rv2d their own variable Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp commit 80c7bcfba10cb3bc2f271a7ee89800d478a941a9 Merge: 27d3a2c4 eb0fe3aa Author: Hannah Klion Date: Fri Jun 7 18:01:26 2024 -0400 Merge pull request #205 from hklion/gls_ML GLS vars fillpatched correctly commit eb0fe3aaff0d981a254b6a17797b0a6cdf227ffc Author: Hannah Klion Date: Fri Jun 7 14:33:58 2024 -0700 update GLS test Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/job_info commit aa6310d9682ab983271b219ae5e6ad8725361da5 Author: Hannah Klion Date: Fri Jun 7 10:24:49 2024 -0700 GLS vars fillpatched correctly Source/TimeIntegration/REMORA_gls.cpp commit 27d3a2c45f0f5315479facfa8dcd26c47a2f5f4d Merge: 1bab9100 b73b798d Author: Hannah Klion Date: Fri Jun 7 12:51:02 2024 -0400 Merge pull request #204 from hklion/ML_bathymetry first stab at multilevel with bathymetry commit b73b798ddb03a1e70334e8603f5d8e2fc9e7735e Merge: a26e521d 1bab9100 Author: Hannah Klion Date: Fri Jun 7 09:26:23 2024 -0700 Merge remote-tracking branch 'upstream' into ML_bathymetry commit 1bab9100dc5d3e3dcd69de5a9f49f14055303a3b Merge: b4bbe22e e9670055 Author: Hannah Klion Date: Thu Jun 6 18:09:48 2024 -0400 Merge pull request #203 from seahorce-scidac/vort_for_tagging Vorticity and other fields allowed for tagging commit e9670055a6ce1e3db63c22313d2b4ace6fe7f53d Author: Hannah Klion Date: Thu Jun 6 14:48:10 2024 -0700 add docs for more mesh refinement options Docs/sphinx_doc/MeshRefinement.rst commit bdbfc8987e394658e630abb311193750363f18d7 Author: Hannah Klion Date: Thu Jun 6 14:42:17 2024 -0700 add temp, salt, and velocities to tagging Source/REMORA_Tagging.cpp commit e91270c554b4f046044105b29006e3799c337125 Author: Hannah Klion Date: Thu Jun 6 14:19:51 2024 -0700 tagging vorticity should work Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.H Source/REMORA_Tagging.cpp commit 093b4fd2bed0849b1fb0c2c20c60cf1c7ecdf026 Merge: c0c85997 67976613 Author: Hannah Klion Date: Thu Jun 6 11:11:12 2024 -0700 Merge branch 'development' into vort_for_tagging commit b4bbe22edcf844da500e449ef9a139f5c93d09f4 Merge: 67976613 6ada345c Author: Hannah Klion Date: Thu Jun 6 14:03:53 2024 -0400 Merge pull request #202 from hklion/gls_documentation add GLS flags documentation commit 6ada345cf12c1ee5e6481cf695be10d29d28f660 Author: Hannah Klion Date: Thu Jun 6 10:59:32 2024 -0700 add GLS flags documentation Docs/sphinx_doc/Inputs.rst commit a26e521dd3c91b4fb18bba905dfea072177bf248 Author: Hannah Klion Date: Thu Jun 6 10:21:58 2024 -0700 switch order of level and 2d advance lop Source/TimeIntegration/REMORA_TimeStepML.cpp commit 53655dd188fd0d91535c6c67faae86c3e1292f66 Author: Hannah Klion Date: Thu Jun 6 10:13:06 2024 -0700 fillpatch tweaks Source/TimeIntegration/REMORA_advance_2d.cpp commit ac5201baa551d4e4994fbf6a2fd491f93b007d6f Author: Hannah Klion Date: Thu Jun 6 10:11:04 2024 -0700 update level initialization routines to accomodate lev=1 Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 7e4ace636ec38a5c0b28741b1f06c8989eb7f869 Author: Hannah Klion Date: Thu Jun 6 10:09:08 2024 -0700 start component for fillpatchtwolevels Source/BoundaryConditions/REMORA_FillPatch.cpp commit 679766130719657f2ac35c904d2a40edcc035a3d Merge: 38e43df5 ac81e1fe Author: Hannah Klion Date: Tue May 21 21:41:51 2024 -0700 Merge pull request #201 from hklion/gls Add support for GLS mixing scheme commit ac81e1fee2ea5bdddcdb90bf6c054061e8d1fb69 Merge: 7fc8ae5c 0ba6b725 Author: Hannah Klion Date: Tue May 21 17:31:01 2024 -0700 Merge branch 'gls' of github.com:hklion/REMORA into gls commit 7fc8ae5c655d7fa5fe7a3f4034632c063571e46a Author: Hannah Klion Date: Tue May 21 17:30:46 2024 -0700 add inputs file for GLS to Upwelling Exec Exec/Upwelling/inputs_gls commit 0ba6b7251965ec9fe6645febf1f2f2f684e94402 Author: Hannah Klion Date: Tue May 21 17:26:50 2024 -0700 copy varialbes out of of solverChoice namespace Source/TimeIntegration/REMORA_gls.cpp commit c098e4549dc0fbea68fdb9b5eded2335232d7dec Author: Hannah Klion Date: Tue May 21 17:00:15 2024 -0700 add GLS test Tests/CTestList.cmake Tests/REMORA_Gold_Files/Upwelling_GLS/Header Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling_GLS/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling_GLS/job_info Tests/test_files/Upwelling_GLS/Upwelling_GLS.i commit 3ea98f2e8e82237eb5329fb12b5d99b0aecdd0c0 Author: Hannah Klion Date: Tue May 21 16:49:15 2024 -0700 allow Canuto B and Galperin stability types Source/DataStruct.H Source/TimeIntegration/REMORA_gls.cpp commit 34c6cc768380f911f96d5fa4258fec13a708c525 Author: Hannah Klion Date: Tue May 21 14:37:38 2024 -0700 fix tiling Source/TimeIntegration/REMORA_gls.cpp commit b328b2442d22800833d5cd6c5f7eb82bcc544110 Author: Hannah Klion Date: Mon May 20 18:01:32 2024 -0700 update ML Gold file Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/job_info commit bcf6924427310cf5d6cebc02aa1f7b7c08796d31 Author: Hannah Klion Date: Mon May 20 17:42:07 2024 -0700 GLS working Source/DataStruct.H Source/Initialization/REMORA_init.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 38e43df5e2bca759c80400c57b8bd6ba70457d5f Merge: 475b7fc2 5ad23d2f Author: Ann Almgren Date: Mon May 20 12:56:50 2024 -0700 Merge pull request #200 from seahorce-scidac/fix_zphys_nd fix computation of z_phys_nd from z_w commit 5ad23d2f0d2a2f7191cdb050089c0c438303e900 Author: Ann Almgren Date: Mon May 20 12:34:15 2024 -0700 fix computation of z_phys_nd from z_w Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA_SumIQ.cpp Source/Utils/DepthStretchTransform.H commit 0c130fe74051d64d6028c3e9b7ac71f1cd8bd892 Author: Hannah Klion Date: Fri May 17 11:00:08 2024 -0700 runs with gls Source/TimeIntegration/REMORA_gls.cpp commit e9c7db9c9d25bb6698cd76373aa8892cde06524b Author: Hannah Klion Date: Thu May 16 17:21:31 2024 -0700 normal analytical mixing works Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 51c84bf9670712894744585db11e31844c7fe95c Author: Hannah Klion Date: Mon May 6 16:30:41 2024 -0700 debug bounds of GLS corrector Source/TimeIntegration/REMORA_gls.cpp commit 8e705df4605891535d94906e60315bd8005d807a Author: Hannah Klion Date: Mon May 6 16:30:04 2024 -0700 initialize Akv and Akt to background values Source/Initialization/REMORA_init.cpp commit 912a17bcbd6dbaac7a7c7978b5502b9adf270851 Author: Hannah Klion Date: Thu May 2 15:26:20 2024 -0700 add gls corrector step; k indexing is maybe off Source/DataStruct.H Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_gls.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit f9f990c29f1e29da3f62beaea85a3c83cd98c06c Author: Hannah Klion Date: Sat Apr 27 12:31:06 2024 -0700 actually add gls file Source/TimeIntegration/REMORA_gls.cpp commit cae36bd1b5055f2fa502e2bbbfa36117b352e55e Author: Hannah Klion Date: Thu Apr 25 17:19:33 2024 -0700 first pass at adding GLS prestep CMake/BuildREMORAExe.cmake Source/DataStruct.H Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_setup_step.cpp commit 475b7fc2f7b258dd81567a1142ee29df4d013b21 Merge: 27096110 f208c87f Author: Hannah Klion Date: Thu May 16 16:13:37 2024 -0700 Merge pull request #199 from hklion/fix_W fix race condition in W commit f208c87fa6ea896177133639313280f3b843c4da Author: Hannah Klion Date: Thu May 16 15:55:29 2024 -0700 fix race condition in W Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp commit 2709611097a769890182925fbdcdba1fbfb96630 Merge: 58a72679 e6ee39c6 Author: Hannah Klion Date: Wed May 15 18:49:36 2024 -0700 Merge pull request #198 from hklion/z_nodal Make z vars nodal and adjust indexing commit e6ee39c61187b03589cea64902d7418c4e2e1210 Author: Hannah Klion Date: Wed May 15 17:10:00 2024 -0700 fix compile bug Source/TimeIntegration/REMORA_prestep_t_advection.cpp commit f65313fdd81bbc239b6a6bc8199a13706b0dd110 Author: Hannah Klion Date: Wed May 15 16:58:51 2024 -0700 adjust nodality of z_w and W Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H commit 1f5e89f30aef006682c2a2c0113c340764374772 Author: Hannah Klion Date: Wed May 15 16:49:22 2024 -0700 add z velocity boundary conditions Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp commit 58a72679cc790d0e123327a14e92852f25d8e271 Merge: a79a2ce1 12665c91 Author: Ann Almgren Date: Sun May 12 21:40:52 2024 -0700 Merge pull request #197 from seahorce-scidac/update_hip_ci update amrex submodule to fix HIP CI commit 12665c91e4e04600b739f9a5250c7ee082f7a88d Author: Ann Almgren Date: Sun May 12 21:06:32 2024 -0700 update amrex submodule to fix HIP CI Submodules/AMReX commit a79a2ce1e325c2067d3da6ba89f0be1195b3683d Merge: ca88e227 53a2a4dd Author: Hannah Klion Date: Thu May 2 17:55:22 2024 -0700 Merge pull request #196 from hklion/z_nodality Make Akv and Akt be on w-points commit 53a2a4dd038d894ced92dfc5621577fb1425b8c0 Author: Hannah Klion Date: Thu May 2 17:34:38 2024 -0700 update advection test Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/job_info commit d46abe9f8a0556cd5d6c44f18fd0590a561972c0 Author: Hannah Klion Date: Thu May 2 17:12:17 2024 -0700 make Akv and Akt be on w-faces Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.cpp commit 92194b202ca815116b2890638dcd8e3fb1432c39 Author: Hannah Klion Date: Thu May 2 15:28:42 2024 -0700 remove visc3d Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit c0c85997b6d994bfea4c9a562e48c4b8eff7d921 Author: Ann Almgren Date: Tue Apr 30 15:06:58 2024 -0700 these don't actually compile Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/Plotfile.cpp Source/REMORA.H Source/REMORA_Tagging.cpp commit ca88e2277956b1bde260a98411cef281a0611e5e Merge: 6a0c10e3 f3ca9217 Author: Hannah Klion Date: Mon Apr 29 13:05:19 2024 -0700 Merge pull request #195 from hklion/doc_typo fix typo: coawst->remora commit f3ca92171af0ee5b665fcc671b4d80e76ae58c59 Author: Hannah Klion Date: Mon Apr 29 13:04:47 2024 -0700 fix typo: coawst->remora Docs/sphinx_doc/building.rst commit 6a0c10e3b578d4fb2445b3f980baa3879a021866 Merge: 6a36935d a6e674a4 Author: Hannah Klion Date: Tue Apr 23 15:17:47 2024 -0700 Merge pull request #194 from hklion/patch_fillbdry_periodic add EnforcePeriodicity on bathymetry and add FillBoundary on zeta commit a6e674a4ba3821eade696a27d62bf9ddb182715a Author: Hannah Klion Date: Tue Apr 23 14:59:51 2024 -0700 add EnforcePeriodicity on bathymetry and add FillBoundary on zeta Source/REMORA.cpp commit 6a36935d89a6383bd9303df625d448c6220b96bf Merge: 3b84d60b 5ff07025 Author: Hannah Klion Date: Thu Apr 18 15:57:45 2024 -0700 Merge pull request #193 from hklion/patch_checkpoint remove unneeded checkpoint variables and adjust multifab nodality and ghost cells to match commit 3b84d60b4fc757c93b5a42a1e46eaad15e2d9afa Merge: fdae6c0a 40467f50 Author: Hannah Klion Date: Thu Apr 18 15:39:08 2024 -0700 Merge pull request #192 from hklion/zero_velbar zero out ubar and vbar before setting commit 5ff070253e1880284f567320123ba6e16070ae4e Author: Hannah Klion Date: Thu Apr 18 15:38:53 2024 -0700 remove unneeded checkpoint variables and adjust multifab nodality and ghost cells to match Source/IO/Checkpoint.cpp commit 40467f5063fa8cbc84fb3ebcca05cf40b69b035b Author: Hannah Klion Date: Thu Apr 18 14:55:50 2024 -0700 zero out ubar and vbar before setting Source/Initialization/REMORA_init.cpp commit fdae6c0a0282d625a3d8e93682da61d6705e6682 Merge: f1d98d3b 5af72521 Author: Hannah Klion Date: Wed Apr 17 17:04:25 2024 -0700 Merge pull request #191 from hklion/vorticity_walls fill mf with 0s before averaging velocities to cell centers commit 5af7252120818f628900341a646d63cf17d8aa38 Author: Hannah Klion Date: Wed Apr 17 16:42:49 2024 -0700 fill mf with 0s before averaging velocities to cell centers Source/Derive.cpp Source/IO/Plotfile.cpp commit f1d98d3b34e91d3d874fa6ab3dcdc20751629337 Merge: dd5c02bd b2412d95 Author: Hannah Klion Date: Tue Apr 16 16:55:11 2024 -0700 Merge pull request #190 from hklion/refine_netcdf_output Refine netcdf output commit b2412d9510dfd01ab239cb4688e09f9748c37fd8 Author: Hannah Klion Date: Tue Apr 16 16:32:21 2024 -0700 update docs Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/index.rst commit 9eed949c8a4ed9d4212f1dc175c204b5500c22f6 Author: Hannah Klion Date: Tue Apr 16 15:09:41 2024 -0700 netcdf files now include time, zeta, bathymetry, ubar/vbar Source/IO/NCPlotFile.cpp Source/REMORA.H Source/REMORA.cpp commit dd5c02bdf218efc3d4a53fc2309fabdb67501952 Merge: dec57672 ba4928da Author: Hannah Klion Date: Mon Apr 15 10:12:06 2024 -0700 Merge pull request #189 from hklion/integrated_quantities Integrated quantities commit ba4928daf679abec7d5033ca70dcb88be48f5ffe Author: Hannah Klion Date: Fri Apr 12 15:13:59 2024 -0700 update docs on verbosity Docs/sphinx_doc/Inputs.rst commit e7fe25f874310a5acbc655085b17f18a7296390f Author: Hannah Klion Date: Fri Apr 12 14:54:38 2024 -0700 update input file comments about verbosity and integrated quantities Exec/Advection/inputs Exec/Advection/inputs_ml Exec/DoublyPeriodic/inputs Exec/IdealMiniGrid/inputs Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/inputs Exec/Seamount/inputs Exec/Upwelling/inputs commit 97f6c3c0780297d80897f78af56ade79da660be0 Author: Hannah Klion Date: Fri Apr 12 14:27:06 2024 -0700 Update integrated quantities - Modify kinetic energy to match ROMS and use actual volume element size - Add a max velocity value Source/REMORA_SumIQ.cpp commit dec5767230466905586a7bf802cd65b8d775218d Merge: a32ed228 7be2cbb5 Author: Hannah Klion Date: Tue Apr 9 16:47:47 2024 -0700 Merge pull request #188 from hklion/delete_pcinterp actually get rid of pcinterp_interp commit 7be2cbb5e11de5324b6753e6cf587f5e5ac0c9c6 Author: Hannah Klion Date: Tue Apr 9 16:37:58 2024 -0700 actually get rid of pcinterp_interp Source/IO/Plotfile.cpp commit a32ed2287f0d93288dc8a3150c067c1794cb86bb Merge: 587cfb44 acdb4a72 Author: Hannah Klion Date: Tue Apr 9 16:17:57 2024 -0700 Merge pull request #187 from hklion/interp_from_coarse_in_plotfile do InterpFromCoarseLevel instead of pcinterp_interp commit acdb4a729dd7644d6cf5424fdcf47db2625fdd22 Author: Hannah Klion Date: Tue Apr 9 15:44:30 2024 -0700 do InterpFromCoarseLevel instead of pcinterp_interp when interpolating to a grid that's refined in the z direction Source/IO/Plotfile.cpp commit 587cfb4493267a542346b81143fb2a7be56c88f9 Merge: 28bbbb2a 25057dd6 Author: Hannah Klion Date: Tue Apr 9 09:14:20 2024 -0700 Merge pull request #186 from hklion/boundary_zeta_netcdf apply physical boundaries to zeta after reading in from netcdf commit 25057dd6d6c1f0789c89a3b7e7923c7841c8846e Author: Hannah Klion Date: Tue Apr 9 09:13:26 2024 -0700 apply physical boundaries to zeta after reading in from netcdf Source/Initialization/REMORA_init_from_netcdf.cpp commit 28bbbb2ad6787e2c3f3f0d5141a454982790fa63 Merge: c4756ef9 652dc535 Author: Hannah Klion Date: Mon Apr 8 16:13:25 2024 -0700 Merge pull request #184 from hklion/update_ml_ctest update multilevel ctest to include RemakeLevel and making new level from coarse commit c4756ef94c53fbaee1717cc884343c6581564a65 Merge: 65f511c2 d650d883 Author: Hannah Klion Date: Mon Apr 8 16:13:13 2024 -0700 Merge pull request #185 from hklion/add_ml_inputs add an inputs file for ML commit 652dc5355a560843c476d73da6ce8decada0f28b Author: Hannah Klion Date: Mon Apr 8 15:52:50 2024 -0700 update multilevel ctest to include RemakeLevel and making new level from coarse Source/BoundaryConditions/REMORA_FillPatch.cpp Tests/REMORA_Gold_Files/Advection_ML/Header Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/job_info Tests/test_files/Advection_ML/Advection_ML.i commit d650d8833af566e403f3ec153024551ae371a4f7 Author: Hannah Klion Date: Mon Apr 8 14:02:09 2024 -0700 add an inputs file for ML Exec/Advection/inputs_ml commit 65f511c27972b88918b5b761551818508ea7bb50 Merge: 30044f2b 0a89ee0b Author: Hannah Klion Date: Mon Apr 8 13:44:47 2024 -0700 Merge pull request #183 from hklion/make_level_from_coarse make new level from coarse works commit 0a89ee0b8360c07ef361345631c5c0d004a1817d Author: Hannah Klion Date: Mon Apr 8 13:26:04 2024 -0700 make new level from coarse works Source/BoundaryConditions/REMORA_FillPatch.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_TimeStepML.cpp commit 30044f2b51e05f014a57b61dc45c96aaed14504d Merge: be3b2bb1 faaa3733 Author: Hannah Klion Date: Mon Apr 8 10:47:43 2024 -0700 Merge pull request #182 from hklion/vorticity_curvilinear calculate vorticity using curvilinear grid commit be3b2bb1d94a8023bbe1382815924e17aafb1b60 Merge: c0121119 310952db Author: Hannah Klion Date: Mon Apr 8 10:29:39 2024 -0700 Merge pull request #181 from seahorce-scidac/debug_ml Remake level works commit faaa37331c7e21a4732b01dd45c1ad6e1e72b673 Author: Hannah Klion Date: Mon Apr 8 10:06:15 2024 -0700 calculate vorticity using curvilinear grid Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp commit 310952db3c6eb1bb47cf05ed747f665537b02b0d Author: Hannah Klion Date: Mon Apr 8 09:49:14 2024 -0700 update to get ML to work Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit c0121119a44e160610471f9d63beb99225fe2195 Merge: b62fd3e8 06df44ba Author: Hannah Klion Date: Wed Apr 3 11:19:44 2024 -0700 Merge pull request #180 from seahorce-scidac/init_time_to_docs add start_time parameter to docs commit 06df44ba19f15ecc6675793e1b03330a6f05965a Author: Hannah Klion Date: Wed Apr 3 11:19:06 2024 -0700 add start_time parameter to docs Docs/sphinx_doc/Inputs.rst commit b62fd3e8ba57f88e5f923ac974ee07154983effe Merge: 37f11949 9aa8f327 Author: Hannah Klion Date: Tue Apr 2 15:28:04 2024 -0700 Merge pull request #179 from hklion/init_time read in start_time from params commit 9aa8f32756523b968c406a67572675655217370d Author: Hannah Klion Date: Tue Apr 2 13:46:35 2024 -0700 read in start_time from params Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp commit bb7f1c6363bf12a0949f059ba7b6db28766c6a64 Author: Hannah Klion Date: Tue Apr 2 11:46:17 2024 -0700 work on RemakeLevel Source/Initialization/REMORA_make_new_level.cpp commit d1d3dd545b9950a749a78574888d4e10a650eac2 Author: Hannah Klion Date: Fri Mar 29 11:09:26 2024 -0700 fillset to false in RemakeLevel Source/Initialization/REMORA_make_new_level.cpp commit 37f1194918535a3e5d48b8a1bccec8b5ef997a9b Merge: 2a3b3da1 f3aa924c Author: Hannah Klion Date: Thu Mar 28 15:52:45 2024 -0700 Merge pull request #178 from hklion/docs_updates update perlmutter build docs commit f3aa924c17487e0bec88ae87a04f30b66c99dbb5 Author: Hannah Klion Date: Thu Mar 28 15:22:26 2024 -0700 update perlmutter build docs Docs/sphinx_doc/building.rst commit 2a3b3da1ed8506e0fb1b5e5666709235aad85ef6 Merge: 089f65db 7546a07b Author: Hannah Klion Date: Thu Mar 28 14:58:04 2024 -0700 Merge pull request #177 from hklion/netcdf_mask masks in netcdf files don't have a time axis commit 7546a07ba17d08daf7efbef3d1338247439728d7 Author: Hannah Klion Date: Thu Mar 28 11:36:19 2024 -0700 masks in netcdf files don't have a time axis Source/IO/ReadFromInitNetcdf.cpp commit 089f65db700d9dbb20f9530fa791f1ece3b3af22 Merge: cef11c2f 4dd20a1c Author: Ann Almgren Date: Wed Mar 27 16:43:41 2024 -0700 Merge pull request #176 from seahorce-scidac/fix_remake_level fix remake_level commit 4dd20a1cbc5398a303fa0286d28af10d758316d1 Author: Ann Almgren Date: Wed Mar 27 16:35:51 2024 -0700 fix remake_level Source/IO/Plotfile.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit cef11c2fd2ba14ab644d8923252f070de098fe4c Merge: 5832c563 3db18b49 Author: Hannah Klion Date: Wed Mar 27 13:26:49 2024 -0700 Merge pull request #175 from hklion/update_time_docs update documentaiton on time step controls commit 3db18b49acd1209e2a800dc62bbbfc26f5eea16a Author: Hannah Klion Date: Wed Mar 27 13:25:40 2024 -0700 update documentaiton on time step controls Docs/sphinx_doc/Inputs.rst commit 5832c5631c89b94035a6a797bcf2b0f3bead3135 Merge: 7ae95368 8af868dc Author: Hannah Klion Date: Wed Mar 27 13:15:50 2024 -0700 Merge pull request #174 from hklion/init_zeta initialize zeta and Zt_avg1 from file commit 7ae953684c7271ed2ff34714e48150b233aa8a75 Merge: 848c3c96 d8289058 Author: Hannah Klion Date: Wed Mar 27 13:14:31 2024 -0700 Merge pull request #173 from hklion/activate_ml_ctest activate ML ctest commit d8289058e1a4573d565eb76b540d1259e112669c Author: Hannah Klion Date: Wed Mar 27 12:40:22 2024 -0700 activate ML ctest Tests/CTestList.cmake commit 8af868dc9bed90ca4f5b672d3b6d24329a04529a Author: Hannah Klion Date: Wed Mar 27 12:36:51 2024 -0700 initialize zeta and Zt_avg1 from file Exec/Advection/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/IdealMiniGrid/prob.cpp Exec/OCCAMS/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Initialization/prob_common.H Source/REMORA.H Source/REMORA.cpp commit 848c3c96afcca86e2b9a9c5157a9686f10923732 Merge: a00262ac 093a1f77 Author: Ann Almgren Date: Tue Mar 26 13:21:47 2024 -0700 Merge pull request #172 from seahorce-scidac/add_vorticity add vorticity as a plotfile option commit 093a1f774330c28805b078408758d7c8a6684199 Author: Ann Almgren Date: Tue Mar 26 12:11:30 2024 -0700 fix oops Source/IO/Plotfile.cpp commit 76ac78fc53be19af514494c41f94b1fc91ba26b7 Author: Ann Almgren Date: Tue Mar 26 11:41:08 2024 -0700 add vorticity as a plotfile option Exec/Advection/prob.cpp Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp Source/REMORA.H commit a00262ac98df5454ede936316e03fa0a3ba80141 Merge: d384b44f 6c7af189 Author: Hannah Klion Date: Mon Mar 25 16:16:27 2024 -0700 Merge pull request #171 from hklion/add_ml_ctest add Advection multilevel test commit 6c7af189c9b31f41a1a2949413fc6b20b764df56 Author: Hannah Klion Date: Mon Mar 25 13:32:43 2024 -0700 add Advection multilevel test Tests/REMORA_Gold_Files/Advection_ML/Header Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_D_00000 Tests/REMORA_Gold_Files/Advection_ML/Level_1/Cell_H Tests/REMORA_Gold_Files/Advection_ML/job_info Tests/test_files/Advection_ML/Advection_ML.i commit d384b44f3d9a2a3c502498be6071b675c31f2e23 Merge: 974a9d75 5accdd67 Author: Ann Almgren Date: Mon Mar 25 11:20:32 2024 -0700 Merge pull request #170 from seahorce-scidac/fix_tagging fix tagging commit 5accdd67e03f553de2d005f27665cbb3730a7434 Author: Ann Almgren Date: Mon Mar 25 11:19:42 2024 -0700 fix tagging Source/REMORA_Tagging.cpp commit 974a9d758227937b274ff2318d226a6972b3b806 Merge: bad7d11d 6a27f154 Author: Ann Almgren Date: Sun Mar 24 18:27:52 2024 -0700 Merge pull request #169 from seahorce-scidac/fix_regridding fix tagging on particles commit 6a27f154d0ff329bd86b7d28094c105c84fb3fb0 Author: Ann Almgren Date: Sun Mar 24 18:25:04 2024 -0700 fix tagging on particles CMake/BuildREMORAExe.cmake Source/REMORA_Tagging.cpp commit bad7d11dc0c06e06eaae83e6bddc4498de4d7c72 Merge: 590d98c1 bec7aa2a Author: Ann Almgren Date: Sun Mar 24 17:05:20 2024 -0700 Merge pull request #168 from seahorce-scidac/update_particles update particles to new SoA format commit bec7aa2a71e5584c2c7ba08d16659eb59d7716a4 Author: Ann Almgren Date: Sun Mar 24 14:34:54 2024 -0700 update particles to new SoA format Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/prob.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Particles/Make.package Source/Particles/ParticleData.H Source/Particles/REMORA_PC.H Source/Particles/REMORA_PC_Evolve.cpp Source/Particles/REMORA_PC_Init.cpp Source/Particles/REMORA_PC_Utils.cpp Source/Particles/REMORA_Tracers.cpp Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Tagging.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/Utils/DepthStretchTransform.H commit 590d98c14a206b7f69f7f29bdc93262555ec40f6 Merge: 55822e72 8cdc9857 Author: Hannah Klion Date: Fri Mar 22 16:01:08 2024 -0700 Merge pull request #167 from hklion/fix_upwelling add back FillBoundary in advance3d_ml to fix Upwelling commit 8cdc9857cce14e896be801bbae1c2bdeddc4e47f Author: Hannah Klion Date: Fri Mar 22 15:45:47 2024 -0700 add back FillBoundary in advance3d_ml Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit 55822e72583b0f382ee30ee7da01feca22a8fbe3 Merge: 7c24c871 113ea2a1 Author: Hannah Klion Date: Fri Mar 22 12:17:23 2024 -0700 Merge pull request #166 from hklion/fill_patcher Multi-level works for advection problem commit 113ea2a15a3df00718cd7d12f021de535b932f96 Author: Hannah Klion Date: Fri Mar 22 11:58:07 2024 -0700 multilevel works for advection problem Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit ad6ac1955e5e1c120a25a5b37f4aa4ec9b365664 Merge: 80586268 7c24c871 Author: Hannah Klion Date: Thu Mar 21 10:20:46 2024 -0700 Merge branch 'development' into fill_patcher commit 7c24c87189df2a7c97d8e91e46c7811a9574ef53 Merge: aa6d7530 3d193d78 Author: Hannah Klion Date: Wed Mar 20 19:33:42 2024 -0700 Merge pull request #165 from hklion/IdealGrid_uvel Uvel initial data works commit 3d193d78ce3cf8f46164aef1dac3751fc82fa0fb Author: Hannah Klion Date: Wed Mar 20 18:00:30 2024 -0700 try to compile on GPU Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit dae4b1ba357a0edef231107a94505e21d075baad Author: Hannah Klion Date: Wed Mar 20 16:59:13 2024 -0700 Uvel initial data works Exec/IdealMiniGrid/prob.cpp Source/IO/NCFile.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp commit aa6d7530873ca359f78c7ce96c33436481901cd6 Merge: 4ef8dcf1 49e72594 Author: Hannah Klion Date: Mon Mar 18 15:07:11 2024 -0700 Merge pull request #164 from hklion/fix_scalar_bry scalar boundary data matches commit 49e72594de797777414af0cdf9e1f6ba460c1fc8 Author: Hannah Klion Date: Mon Mar 18 14:27:59 2024 -0700 scalar boundary data matches Source/IO/ReadFromBdryNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/TimeIntegration/REMORA_t3dmix.cpp commit 80586268f4cb19911a00a900eb826feed7287546 Author: Hannah Klion Date: Fri Mar 15 15:44:50 2024 -0700 initial pass at debugging FillPatcher Exec/Advection/prob.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit 4ef8dcf18c4e32c06ef3f5bc0d863fc318ac08e7 Merge: f735d89f 86c01c4a Author: Hannah Klion Date: Thu Mar 14 12:55:12 2024 -0700 Merge pull request #160 from seahorce-scidac/add_fillpatcher Add REMORA_FillPatcher functionality commit f735d89f20291230179d56e668976096e9bcbeaf Merge: 76951f68 317b15a6 Author: Hannah Klion Date: Thu Mar 14 10:42:52 2024 -0700 Merge pull request #162 from hklion/seamount_no_debug Seamount makefile turn off debug commit 76951f68dea99c0799c4f60776881dc73d539bcf Merge: 7e7b370b 8144581d Author: Hannah Klion Date: Thu Mar 14 10:42:25 2024 -0700 Merge pull request #161 from hklion/fix_vel_bdry_data Read in and evolve velocity boundary data commit 317b15a61eeb0aad30e8e8c83b20be720519f736 Author: Hannah Klion Date: Thu Mar 14 10:42:07 2024 -0700 Seamount makefile turn off debug Exec/Seamount/GNUmakefile commit 8144581d3bcf5867b6e6e1c1fd5a0d96af69a619 Author: Hannah Klion Date: Thu Mar 14 10:25:41 2024 -0700 update Seamount test file Tests/REMORA_Gold_Files/Seamount/Header Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_H Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00002 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00003 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount/job_info commit 8715229dbf8f59603e728643bf82ce23b645a78d Author: Hannah Klion Date: Wed Mar 13 17:39:40 2024 -0700 correctly use face-centered pm and pn Source/TimeIntegration/REMORA_vert_mean_3d.cpp commit 9acb860230ddf21a9e26ae52fcbaa2796c676f3c Author: Hannah Klion Date: Wed Mar 13 17:25:56 2024 -0700 Fix reading velocity boundary data - FillPatch at the correct time in advance_2d - Filling boundary from file can now take a component to fill - Fix filling corner data for velocities Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp commit 86c01c4a79d6ceace2a387d14188cf07497fa3dc Author: Ann Almgren Date: Tue Mar 12 16:16:31 2024 -0700 Add REMORA_FillPatcher functionality CMake/BuildREMORAExe.cmake Source/BoundaryConditions/Make.package Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_FillPatcher.H Source/BoundaryConditions/REMORA_FillPatcher.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Particles/ParticleData.H Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_Advance.cpp Submodules/AMReX commit 7e7b370bd592bd5d4a6b1f1a5e7d310521c8c057 Merge: 1b618b0e 241167e1 Author: Hannah Klion Date: Mon Mar 11 14:42:19 2024 -0700 Merge pull request #159 from hklion/bdry_in_arena read boundary data into the pinned arena commit 241167e19e84e3649142a17d037ab6afad0fe878 Author: Hannah Klion Date: Mon Mar 11 14:25:33 2024 -0700 fix tabs Source/IO/ReadFromBdryNetcdf.cpp commit 6446589f5f3f1e85f9ea0e844a36ef257d98e18c Author: Hannah Klion Date: Mon Mar 11 14:18:34 2024 -0700 read boundary data into the pinned arena Source/IO/ReadFromBdryNetcdf.cpp commit 1b618b0e1bdf3a5a19760a7a02ce573edd059e91 Merge: b3a5ec9a f3a6348f Author: Hannah Klion Date: Mon Mar 11 11:33:56 2024 -0700 Merge pull request #158 from hklion/fix_device_lambda make device methods public commit f3a6348f1160dc15e3fba38c56377bc89d336720 Author: Hannah Klion Date: Mon Mar 11 11:13:18 2024 -0700 make device methods public Source/REMORA.H commit b3a5ec9acebd602b70035333cf6b8279d0b2afff Merge: 42ab246f 958ead2d Author: Hannah Klion Date: Fri Mar 8 15:08:11 2024 -0800 Merge pull request #157 from hklion/salt_default_file change default boundary to be Salt not Temp commit 958ead2da1c9af416ce90523dc54d48254144f27 Author: Hannah Klion Date: Fri Mar 8 14:55:58 2024 -0800 change default boundary to be Salt not Temp Exec/IdealMiniGrid/inputs commit 42ab246ffea2e973cb7470cb5018490b3dd8b3d3 Merge: 268afac2 111d2db4 Author: Hannah Klion Date: Fri Mar 8 14:14:22 2024 -0800 Merge pull request #156 from hklion/addIdealMiniGrid add IdealMiniGrid test commit 111d2db42662259f5e45d135868ead452d913069 Author: Hannah Klion Date: Fri Mar 8 14:09:44 2024 -0800 add IdealMiniGrid test Exec/IdealMiniGrid/GNUmakefile Exec/IdealMiniGrid/Make.package Exec/IdealMiniGrid/inputs Exec/IdealMiniGrid/prob.H Exec/IdealMiniGrid/prob.cpp commit 268afac28920a96d58749073eb821262ad8cc03a Merge: 32d6cbcf c916cd8b Author: Hannah Klion Date: Thu Mar 7 17:13:26 2024 -0800 Merge pull request #154 from hklion/tracer_real_bc Adjust more to get tracer BCs working commit c916cd8bb3ed85d639f0fb5946902d1c3b12caea Author: Hannah Klion Date: Thu Mar 7 16:53:13 2024 -0800 fix boundary application Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp commit 32d6cbcfa279b17e8df62145c1144fa09c9d7841 Author: Hannah Klion Date: Thu Mar 7 16:35:01 2024 -0800 fix cmake build with netcdf CMake/BuildREMORAExe.cmake commit 6184dfc8a02e9f4284346613fae8c259c5ab6dc5 Author: Hannah Klion Date: Thu Mar 7 09:49:27 2024 -0800 put whether BC is real on device memory Source/BoundaryConditions/BoundaryConditions_cons.cpp commit f5f77925f0c0200d4f58131357d8ba8a4df47190 Merge: 3486281b f7b85a1b Author: Hannah Klion Date: Wed Mar 6 14:38:34 2024 -0800 Merge pull request #153 from hklion/tracer_real_bc Fix where real BCs are applied for tracers commit f7b85a1b67992bf00dda479520588a8932b13c35 Author: Hannah Klion Date: Wed Mar 6 14:15:06 2024 -0800 change bc info to a pointer Source/BoundaryConditions/BoundaryConditions_cons.cpp commit 3f58eb6c8dddb572f427bad2f66138a3c3d25c59 Author: Hannah Klion Date: Wed Mar 6 13:51:08 2024 -0800 correct real_bcs Source/BoundaryConditions/BoundaryConditions_cons.cpp commit 76de0a379677636aae1e19b199c3915c78aeea0f Author: Hannah Klion Date: Wed Mar 6 11:53:20 2024 -0800 Fix where real BCs are applied for tracers - Apply real BCs for salt/temp outside of domain - Handle corners in the same was as ROMS for real BCs Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/Initialization/REMORA_make_new_level.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp commit 3486281b87253fab6e87acf43985add8cacf09ab Author: Hannah Klion Date: Mon Mar 4 11:36:40 2024 -0800 Update README.rst Update URLs README.rst commit c112f2719d1b592d0fc9a106b7e7fce7a951706d Merge: f7615727 3b2c86e8 Author: Hannah Klion Date: Thu Feb 29 15:41:19 2024 -0800 Merge pull request #151 from hklion/fix_read_from_file Fixes for initialization from file commit 3b2c86e836f0c79c20a767f0709d743fd13da6cc Author: Hannah Klion Date: Wed Feb 28 17:17:08 2024 -0800 remove setval on pn or pm to 1e34 Source/Initialization/REMORA_make_new_level.cpp commit a4f83c831663761a12f48400db808fd6f4831aee Author: Hannah Klion Date: Wed Feb 28 17:15:42 2024 -0800 fill patch on bathymetry after init Source/Initialization/REMORA_init_from_netcdf.cpp commit cbaf752f4397e9b73b77f1c9cfd7f5f8e7dbc7f2 Author: Hannah Klion Date: Wed Feb 28 17:13:11 2024 -0800 make Drhs 2D Source/TimeIntegration/REMORA_advance_2d.cpp commit b011e0f3ce2d7e4a60e0588dcb077a6050ddbc03 Author: Hannah Klion Date: Wed Feb 28 17:12:19 2024 -0800 adjust bounds on initialization of velocity buffers Source/IO/NCFile.H commit f7615727e7f1644e0712dc13260f003bf1244c84 Merge: f84a77aa 6ea6cca9 Author: Hannah Klion Date: Wed Feb 7 14:21:38 2024 -0800 Merge pull request #150 from hklion/add_upwelling_ctest make upwelling ctest commit 6ea6cca97dd6890691656666cfbf745f7532159b Author: Hannah Klion Date: Wed Feb 7 14:00:35 2024 -0800 device copiable Exec/Upwelling/prob.cpp commit 69c6d11bed12928e07322634b9223cb2d44c9642 Author: Hannah Klion Date: Wed Feb 7 13:37:44 2024 -0800 update parms in prob.cpp Exec/Upwelling/prob.cpp commit f84a77aa2add29025ff4a1db21612e59805ffd5d Author: Hannah Klion Date: Wed Feb 7 10:26:45 2024 -0800 turn off netcdf for upwelling by default Exec/Upwelling/GNUmakefile commit 5589df73ec9b995f2b2ce2bc9e2609af24b5f62e Author: Hannah Klion Date: Tue Feb 6 18:32:27 2024 -0800 make upwelling ctest Exec/CMakeLists.txt Tests/CTestList.cmake Tests/REMORA_Gold_Files/Upwelling/Header Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Cell_H Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Upwelling/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Upwelling/job_info Tests/test_files/Upwelling/Upwelling.i commit 0851aff05fc1cbab3abdfaa85ff19984fdef0df3 Merge: 15069ddf 95e5dbc9 Author: Hannah Klion Date: Tue Feb 6 17:47:56 2024 -0800 Merge pull request #149 from hklion/fix_bccomp slip walls implemented commit 95e5dbc93857f4800a9a23f66792dfb950295c56 Author: Hannah Klion Date: Tue Feb 6 17:31:38 2024 -0800 fix bcrec access in gpu Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit 9d2f59ad0bfe93ece9f8215a0151f038b9f0c13a Author: Hannah Klion Date: Tue Feb 6 12:26:22 2024 -0800 correctly handle boundary corrections and turn on walls in upwelling problem Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp commit 94b44e608a23132664169b966ba7b84cf6160611 Author: Hannah Klion Date: Tue Feb 6 11:05:17 2024 -0800 add a NoBC version of FillPatch Source/BoundaryConditions/REMORA_FillPatch.cpp Source/REMORA.H commit 938a094dfadf04eb669202ffbc1682b68786ca64 Author: Hannah Klion Date: Tue Feb 6 10:57:48 2024 -0800 can have multiple components for rho-point variables Source/BoundaryConditions/REMORA_PhysBCFunct.cpp commit d6367efed1c48a3c465e4cc48d0fd0b1679cacf5 Author: Hannah Klion Date: Fri Jan 26 17:29:19 2024 -0800 use BCVars instead of BdyVars Source/TimeIntegration/REMORA_advance_3d.cpp commit 15069ddff55606661cc230c44a56cd5137c846d9 Merge: ad610049 33c51d87 Author: Ann Almgren Date: Fri Jan 26 15:36:02 2024 -0800 Merge pull request #148 from jmsexton03/sanity_check_command Add usage statement and banner commit 33c51d8753e2fdd890efc479647b708246cbe383 Author: Jean M. Sexton Date: Fri Jan 26 12:24:51 2024 -0800 Forgot mpi finalize Source/main.cpp commit 79ec110c9274988e927e939e4a3f24f8313f9bca Author: Jean M. Sexton Date: Fri Jan 26 12:02:49 2024 -0800 Forgot CMake CMake/BuildREMORAExe.cmake commit 0c4bc48606edfd690afd58c33f76911e3d61952e Author: Jean M. Sexton Date: Fri Jan 26 11:48:07 2024 -0800 Fix tab Source/main.cpp commit ad6100495b8a21b8ba17292667bff6e8607eeb24 Merge: 4fef5ab6 5567ed43 Author: Ann Almgren Date: Fri Jan 26 11:46:14 2024 -0800 Merge pull request #147 from hklion/patch_filling Fixes for boundaries with walls commit 2fc51f913b9a757abce365ceb4c23364a3e4a902 Author: Jean M. Sexton Date: Fri Jan 26 11:43:23 2024 -0800 Add banner and updates Source/IO/Make.package Source/IO/NCInterface.H Source/IO/console_io.cpp Source/REMORA.H Source/main.cpp commit 5567ed4352e8a2487830758d32f40313f09477f3 Author: Hannah Klion Date: Fri Jan 26 11:29:40 2024 -0800 apply physical boundary conditions after u/v updates in advance_3d Source/TimeIntegration/REMORA_advance_3d.cpp commit fc53f139c3a835384fb5cef387be91700647e987 Author: Jean M. Sexton Date: Mon Jan 22 13:38:50 2024 -0800 Add usage message Source/main.cpp commit 7df6e72f5d99aed2005939c6b36e2d58c40bae33 Author: Hannah Klion Date: Fri Jan 26 11:19:17 2024 -0800 FillPatch on the most-recently updated component of ubar and vbar at the end of advance_2d Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/REMORA.H Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp commit eb559175e49c1a8822b33a9cf51bea202c4570cd Author: Hannah Klion Date: Wed Jan 24 14:35:58 2024 -0800 switch FillPatch to FillBoundary for z grid variables Source/Utils/DepthStretchTransform.H commit 4fef5ab61b380a021df7dd16fade83a830628f1d Merge: 479f322b 20c55988 Author: Ann Almgren Date: Wed Jan 24 13:04:20 2024 -0800 Merge pull request #146 from seahorce-scidac/more_particle_fix need to update idata in first pass as well commit 20c559889b8f9265b80039d985a20fb1f87d2104 Author: Ann Almgren Date: Wed Jan 24 11:59:02 2024 -0800 need to update idata in first pass as well Source/Particles/ParticleData.H Source/Particles/TracerPC.cpp commit 479f322b33c5f30122b0a804a24b97b3a3c03059 Merge: db2f0c9a 59db60fc Author: Ann Almgren Date: Wed Jan 24 08:57:27 2024 -0800 Merge pull request #145 from seahorce-scidac/update_particles_and_amrex Update particle functionality and amrex submodule commit 59db60fc1224733de9ba46db936bec6172d4daf0 Author: Ann Almgren Date: Tue Jan 23 15:53:53 2024 -0800 Update particle functionality and amrex submodule Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Submodules/AMReX commit db2f0c9aadcc85155a36487d0beadf238176d6b4 Merge: 8ac91c31 0f7e3799 Author: Ann Almgren Date: Sat Jan 20 13:18:49 2024 -0800 Merge pull request #144 from jmsexton03/more_sp Single Precision Validation and Paper Updates commit 0f7e37992d650f551e01d4a94bb73eb3bff5154b Author: Jean M. Sexton Date: Fri Jan 19 10:16:33 2024 -0800 Update paper for sp changes and name paper/paper.md commit ab55401792b3150813670ca81ef910db1199736a Author: Jean M. Sexton Date: Fri Jan 19 10:16:02 2024 -0800 Update prob for sp Exec/DoublyPeriodic/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp commit f6466d1f6836dfce974e88d8bc1eef88a72864f6 Author: Jean M. Sexton Date: Fri Jan 19 07:55:16 2024 -0800 Remove spurious rt on int and minor fix Source/REMORA.H Source/REMORA.cpp commit b6e03de7a427c8626643e68915f9afeb8151816c Author: Jean M. Sexton Date: Fri Jan 19 07:44:34 2024 -0800 Fixes for exponents and some headers Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/Checkpoint.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/Utils/DepthStretchTransform.H commit 82c929fdcb010342a5f0cfe433e122a3619a4a5b Author: Jean M. Sexton Date: Fri Jan 19 07:22:54 2024 -0800 Regex and sed pass at updates Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/IO/Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_make_new_level.cpp Source/Particles/TracerPC.cpp Source/REMORA.cpp Source/REMORA_SumIQ.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp commit 2c9ed4dd6c1fbd8a61e075df81c0cd1575390687 Author: Jean M. Sexton Date: Thu Jan 18 15:30:48 2024 -0800 Minor float fixes Source/BoundaryConditions/REMORA_FillPatch.cpp Source/IO/NCPlotFile.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp Source/REMORA_Constants.H Source/REMORA_SumIQ.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/main.cpp commit 65a9db8d9b2faeb1e61bc560ea47fc0d8400f75a Author: Jean M. Sexton Date: Thu Jan 18 09:16:22 2024 -0800 Change Real pi Source/REMORA_Constants.H commit 8208b5969fd3b113afc19b7c8091e4f557cda901 Merge: d75911e5 8ac91c31 Author: Jean M. Sexton Date: Thu Jan 18 08:56:47 2024 -0800 Merge branch 'development' into more_sp commit 8ac91c314a3f0ef21d244e7281fe6aa55f4e3b6b Merge: 41b2ddaf ed00ef5d Author: Ann Almgren Date: Tue Jan 16 11:09:20 2024 -0800 Merge pull request #143 from seahorce-scidac/update_paper_and_particles update paper and particles commit ed00ef5dcb72d3ca07f2df8b1dbd263cc7f25263 Author: Ann Almgren Date: Tue Jan 16 10:43:31 2024 -0800 update paper and particles Source/Particles/TracerPC.cpp paper/paper.md commit 41b2ddaf6490c2512ddb4994a4ad48cdfa0ad280 Merge: 4af278ab 353464e3 Author: Hannah Klion Date: Tue Jan 16 09:45:55 2024 -0800 Merge pull request #139 from hklion/patch_to_boundary_bathymetry fillboundary rather than fillpatch for bathymetry init commit 4af278ab457817777bd001657acce17b8f8f0b1c Merge: e0bd9709 750319ad Author: Ann Almgren Date: Mon Jan 15 19:47:16 2024 -0800 Merge pull request #142 from seahorce-scidac/fix_particles fix how we tell which cell a particle is in commit 750319ad404b606b307276ff7d1dd6bd6c882ba1 Author: Ann Almgren Date: Mon Jan 15 18:47:46 2024 -0800 fix how we tell which cell a particle is in Source/Particles/TracerPC.cpp commit e0bd97095193e02d52382170a08464bde015c39f Merge: b1194e8b 003f9fab Author: Ann Almgren Date: Sat Jan 13 15:02:33 2024 -0800 Merge pull request #141 from seahorce-scidac/fix_pm_pm fix pm,pn when init_type=real commit 003f9fab7df6b009700fc05d3f1908d1967e6608 Author: Ann Almgren Date: Sat Jan 13 14:42:54 2024 -0800 fix pm,pn when init_type=real Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromBdryNetcdf.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H Source/REMORA.cpp commit b1194e8b2947ac6fb2306c1cf374a797a9bac316 Merge: 70e01252 be8814b0 Author: Ann Almgren Date: Sat Jan 13 09:23:47 2024 -0800 Merge pull request #140 from seahorce-scidac/fix_mask_read fix mask read from netcdf commit be8814b01fd8bd164a47e7c4b0f1c4df2298e372 Author: Ann Almgren Date: Sat Jan 13 09:08:02 2024 -0800 fix mask read from netcdf Source/IO/NCFile.H commit 70e012524e6465c4f1b676288b4698c6cbaa4afb Merge: 069bc35c 07cfc2af Author: Ann Almgren Date: Sat Jan 13 08:53:04 2024 -0800 Merge pull request #138 from seahorce-scidac/add_masks add mask_rho, mask_u, mask_v commit 353464e3b922ecf20787369d99ce683577f19b7b Author: Hannah Klion Date: Fri Jan 12 18:11:27 2024 -0800 fillboundary rather than fillpatch for bathymetry init Source/REMORA.cpp commit 07cfc2af94ea1cc9435225ca5871152f289d7c84 Author: Ann Almgren Date: Fri Jan 12 18:11:16 2024 -0800 add mask_rho, mask_u, mask_v Source/IO/Checkpoint.cpp Source/IO/NCPlotFile.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Initialization/REMORA_make_new_level.cpp Source/REMORA.H commit 069bc35cd7ea0f1ba3dbf0e74c60a8712154a202 Merge: 95ad6e3f 37c7bc10 Author: Ann Almgren Date: Fri Jan 12 18:08:29 2024 -0800 Merge pull request #137 from hklion/slab_boxes_2d made some boxes slabs in advance_2d commit 95ad6e3f16698a547eeb005d80b6f39284157ba5 Merge: 9b7f78de e8b3ed5f Author: Ann Almgren Date: Fri Jan 12 17:01:41 2024 -0800 Merge pull request #136 from seahorce-scidac/fix_plt use plot_int not plot_int_1, and allow netcdf to use inputs-specified… commit 37c7bc10cd1ba2783ae331509fce1f0a7003a83a Author: Hannah Klion Date: Fri Jan 12 16:58:41 2024 -0800 made some boxes slabs in advance_2d Source/TimeIntegration/REMORA_advance_2d.cpp commit e8b3ed5f6be2edbad44852f3a9e95fc899759b69 Author: Ann Almgren Date: Fri Jan 12 16:36:24 2024 -0800 use plot_int not plot_int_1, and allow netcdf to use inputs-specified string for filename Exec/Advection/inputs Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/inputs_ml Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/inputs Exec/Seamount/inputs Exec/Upwelling/inputs Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/REMORA.H Source/REMORA.cpp Tests/test_files/Advection/Advection.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i commit 9b7f78def7abb7e32459b7c97782ff03af7d7a0a Merge: c15f273e 86c6b093 Author: Ann Almgren Date: Thu Jan 11 18:54:41 2024 -0800 Merge pull request #135 from seahorce-scidac/rename_files_to_old fix writing netcdf files commit 86c6b093a1d662175ce3969669fbe631f49abbeb Author: Ann Almgren Date: Thu Jan 11 18:22:14 2024 -0800 only do rename on IOProcessor Source/IO/NCPlotFile.cpp commit f0a9d39bfdf84dc54c7fae72a8569845aa4e6f5e Author: Ann Almgren Date: Thu Jan 11 18:13:48 2024 -0800 fix writing netcdf files Source/IO/NCPlotFile.cpp Source/REMORA.H Source/REMORA.cpp commit c15f273eec8b4625e81a4d5190611468358093b9 Merge: 2b9c2e90 b3e3c145 Author: Ann Almgren Date: Thu Jan 11 17:57:00 2024 -0800 Merge pull request #134 from seahorce-scidac/update_workflows only do CI on pull request, not on push commit b3e3c145a21f58e5f90fd873bc820e9bc7133fa5 Author: Ann Almgren Date: Thu Jan 11 17:08:20 2024 -0800 only do CI on pull request, not on push .github/workflows/c-linter.yml .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/docs.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/style.yml .github/workflows/sycl.yml .github/workflows/windows.yml commit 2b9c2e9064d434679bbfc29a19ef7642219e58bb Merge: 8c3c54b9 8682c20d Author: Hannah Klion Date: Thu Jan 11 16:36:03 2024 -0800 Merge pull request #133 from hklion/check_bc_type Check BC type is outflow when init from netcdf commit 8c3c54b93465bd189e7c324050f5a7c671f1883b Merge: 7ee28423 7be4306c Author: Hannah Klion Date: Thu Jan 11 16:35:53 2024 -0800 Merge pull request #130 from WeiqunZhang/cmake_sycl ERF_ENABLE_SYCL -> REMORA_ENABLE_SYCL commit 8682c20d8c8b91bcbae8a9dc6b728a9bc6426757 Author: Hannah Klion Date: Thu Jan 11 15:56:35 2024 -0800 set OCCAMS to use outflow bcs Exec/OCCAMS/inputs commit 7ee2842395d1029625fc0c65f47d6f0f0c23fdd6 Merge: 09ef7fb7 31c11c25 Author: Ann Almgren Date: Thu Jan 11 15:24:20 2024 -0800 Merge pull request #132 from seahorce-scidac/fix_oops fix oops with icomp commit 31c11c256ebc98093855a6a6083899e6e27a6e4e Author: Ann Almgren Date: Thu Jan 11 15:23:48 2024 -0800 fix oops with icomp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 07061b3380295b1d19f6419e9a68e23a4ad6f976 Author: Hannah Klion Date: Thu Jan 11 13:49:10 2024 -0800 ensure BC type is outflow when reading from file Source/Initialization/REMORA_init_bcs.cpp commit 09ef7fb70d464429a0571dc0a6e5ef75b439cbcc Merge: 01d5b710 11f119e2 Author: Ann Almgren Date: Thu Jan 11 11:04:29 2024 -0800 Merge pull request #131 from seahorce-scidac/generalize_netcdf_write generalize the netcdf plotfile write so we can write MultiFab data wi… commit 11f119e2d79c45d27cac3eaf117a7cb307bb90ef Author: Ann Almgren Date: Thu Jan 11 10:46:43 2024 -0800 fix tab Source/IO/NCPlotFile.cpp commit 280395de6921f507d95b433e58c797ddbce33dab Author: Ann Almgren Date: Thu Jan 11 10:44:37 2024 -0800 generalize the netcdf plotfile write so we can write MultiFab data with more than one grid Source/IO/NCPlotFile.cpp commit 7be4306c4ade32c4911611a611241c734cb3e606 Author: Weiqun Zhang Date: Wed Jan 10 23:32:40 2024 +0000 Fix some device copyable issues Exec/Advection/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/Seamount/prob.cpp commit e3c3b32a751575d2e8ada7087119b034f6b77623 Author: Weiqun Zhang Date: Wed Jan 10 14:21:31 2024 -0800 ERF_ENABLE_SYCL -> REMORA_ENABLE_SYCL CMake/SetAmrexOptions.cmake commit 01d5b7107822f0bc5cbf71613c83f04103060c24 Merge: d7957863 06bfc95c Author: Ann Almgren Date: Wed Jan 10 14:13:26 2024 -0800 Merge pull request #129 from WeiqunZhang/sycl_ci Add SYCL CI commit 06bfc95ce6d346a40efe241ee0bf4ee63a2fa0cc Author: Weiqun Zhang Date: Wed Jan 10 13:17:15 2024 -0800 Add SYCL CI .github/workflows/sycl.yml commit d7957863bc93da1c951231daf30966fd4760729a Merge: eb0fc7cb 701f8d2c Author: Hannah Klion Date: Wed Jan 10 11:59:44 2024 -0800 Merge pull request #128 from hklion/fix_ocean_time_units Fix ocean time units commit 701f8d2cf08a934cd368a05e86b8c7365110723a Author: Hannah Klion Date: Wed Jan 10 10:15:07 2024 -0800 add assert so we don't read past the end of the boundary array in time Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 82721c14e04dfd195431cee3909f155906d5700b Author: Hannah Klion Date: Tue Jan 9 15:36:56 2024 -0800 convert ocean_time from days and check that it is in days when reading in Source/IO/Make.package Source/IO/NCFile.H Source/IO/NCFile.cpp Source/IO/ReadFromBdryNetcdf.cpp commit eb0fc7cb8276479721c13c25d9fe71e1de46dc3d Merge: bbcad3fd f37ed882 Author: Hannah Klion Date: Tue Jan 9 20:57:13 2024 -0800 Merge pull request #127 from hklion/fix_netcdf fix netcdf writing commit f37ed882f12405ed083da029488242e1e2d0fc09 Author: Hannah Klion Date: Tue Jan 9 18:28:52 2024 -0800 fix netcdf writing Source/IO/NCPlotFile.cpp Source/REMORA.cpp commit bbcad3fdf3a7f9498833c51a2871f8bc69262099 Merge: 2bd48594 34a0a7b2 Author: Ann Almgren Date: Tue Jan 9 18:09:28 2024 -0800 Merge pull request #126 from seahorce-scidac/generalize_netcdf Generalize netcdf commit 34a0a7b20b2391a6b5ec73173dd2f005ae5274cc Merge: 2d98cc47 2bd48594 Author: Ann Almgren Date: Tue Jan 9 18:07:52 2024 -0800 Merge branch 'development' into generalize_netcdf commit 2bd485945ac1e273ddac371ff76d1a253cff7960 Merge: 10caa6b8 8f89d5fa Author: Ann Almgren Date: Tue Jan 9 18:07:29 2024 -0800 Merge pull request #125 from WeiqunZhang/ci_amrex Use amrex's scripts to install cuda, hip, gcc, and mac dependencies commit 2d98cc47868146f467cca9c490cfe463c8a3d3c5 Author: Ann Almgren Date: Tue Jan 9 18:07:05 2024 -0800 back to doing multi-d arrays Source/IO/NCInterface.cpp Source/IO/NCPlotFile.cpp commit 8f89d5fa0cd0753197a7c27c6692992da1cd84ca Author: Weiqun Zhang Date: Tue Jan 9 16:44:13 2024 -0800 Use amrex's scripts to install cuda, hip, gcc, and mac dependencies .github/workflows/cuda-ci.yml .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml commit 10caa6b889da3b70fb459f214e8faf6ce23b2f9c Merge: c5aa9ae4 15abf53c Author: Ann Almgren Date: Tue Jan 9 16:18:41 2024 -0800 Merge pull request #124 from seahorce-scidac/generalize_netcdf generalize to write history file commit 15abf53c90dfd5ce5172bc9603b1139b048f05f2 Author: Ann Almgren Date: Tue Jan 9 16:17:49 2024 -0800 generalize to write history file Source/IO/NCPlotFile.cpp Source/REMORA.H commit c5aa9ae4e12cd83ff8c2e8585d222de75d5bfd1a Merge: 3542814d 11476838 Author: Ann Almgren Date: Tue Jan 9 15:30:23 2024 -0800 Merge pull request #123 from seahorce-scidac/fix_up_netcdf_write Fix up netcdf write commit 1147683836c9a9ce740dc21aaadc7bcc6bd6edbe Author: Ann Almgren Date: Tue Jan 9 15:23:51 2024 -0800 fix compile without netcdf Exec/Seamount/prob.cpp Source/REMORA.cpp commit 91b6231eeaa1dac97747deb6f6b26fd7028c2100 Author: Ann Almgren Date: Tue Jan 9 15:20:37 2024 -0800 this version seems to correctly write plotfiles in netcdf format for single level, single grid, in serial CMake/BuildREMORAExe.cmake Docs/sphinx_doc/Plotfiles.rst Source/IO/Make.package Source/IO/NCMultiFabFile.cpp Source/IO/NCPlotFile.cpp Source/Initialization/Make.package Source/Initialization/REMORA_make_new_level.cpp Source/Make.package Source/REMORA.H Source/REMORA.cpp commit 90f8818b7c1240b04873052c6d82ee900b66b0ba Merge: c9d5c5b1 3542814d Author: Ann Almgren Date: Tue Jan 9 14:52:48 2024 -0800 Merge branch 'development' into fix_up_netcdf_write commit c9d5c5b14892aa1eca30e58d5b7f1d201c622f93 Author: Ann Almgren Date: Tue Jan 9 14:52:33 2024 -0800 fixing up netcdf write Exec/Advection/GNUmakefile Exec/DoublyPeriodic/GNUmakefile Exec/OCCAMS/GNUmakefile Exec/ParticlesOverSeaMount/GNUmakefile Exec/Seamount/GNUmakefile Exec/Upwelling/GNUmakefile Source/IO/NCPlotFile.cpp Source/REMORA.H commit 3542814db2d5471fd141b64883cf105209f08b04 Merge: 398679d2 1d9e8a23 Author: Ann Almgren Date: Tue Jan 9 14:51:44 2024 -0800 Merge pull request #122 from hklion/plotfile_type add enum for plotfile type and add checks when writing plotfiles commit 1d9e8a235d672dbdc7dc4fd75f97f1b727c470a9 Author: Hannah Klion Date: Tue Jan 9 12:10:00 2024 -0800 add enum for plotfile type and add checks when writing plotfiles Source/DataStruct.H Source/IO/Plotfile.cpp Source/REMORA.H Source/REMORA.cpp commit 398679d22d66e9dd4b85cf437f36c16c6c761245 Merge: 258c739c 042b001d Author: Hannah Klion Date: Mon Jan 8 20:55:39 2024 -0800 Merge pull request #121 from hklion/docs_updates Docs updates commit 042b001d2813b5989970d8f7df61473ab331a9ed Author: Hannah Klion Date: Mon Jan 8 20:46:08 2024 -0800 fix documentation build warnings Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/Time_Stepping.rst Docs/sphinx_doc/index.rst commit f3c4ea99c4908bff98d93cf72ebbb50c5c9a85c8 Author: Hannah Klion Date: Mon Jan 8 20:33:12 2024 -0800 add pointer to testing in cmake section Docs/sphinx_doc/building.rst commit 258c739c5ee0774d39142a0b5a86d46b5c852167 Merge: 1b7dff0f 93568529 Author: Ann Almgren Date: Mon Jan 8 20:26:13 2024 -0800 Merge pull request #120 from seahorce-scidac/netcdf_write working on writing in netcdf format commit 9356852936a7579e39ac75bd0d4e11b48a264d4b Author: Ann Almgren Date: Mon Jan 8 20:24:39 2024 -0800 fix white space Source/IO/NCPlotFile.cpp commit b5686d0e3f2ac34d41b9ce06e7f3fcb373d69074 Author: Ann Almgren Date: Mon Jan 8 20:23:41 2024 -0800 working on writing in netcdf format Exec/OCCAMS/GNUmakefile Exec/OCCAMS/inputs Exec/OCCAMS/prob.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/Initialization/REMORA_init.cpp Source/REMORA.H Source/REMORA.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_setup_step.cpp commit 1b7dff0f39ed38623c2cd993c82541597faf99cf Merge: 966fe972 0051f3a0 Author: Ann Almgren Date: Mon Jan 8 16:41:56 2024 -0800 Merge pull request #119 from seahorce-scidac/another_netcdf_fix fix oops from previous commit commit 0051f3a09c374b9d3ad2c5ef9f137433c5188a3f Author: Ann Almgren Date: Mon Jan 8 16:41:18 2024 -0800 fix oops from previous commit Source/IO/ReadFromInitNetcdf.cpp commit 966fe972d4aa8d96fe337636d4de5ea2f72253bc Author: Hannah Klion Date: Mon Jan 8 16:29:45 2024 -0800 fix netcdf compile Source/IO/ReadFromInitNetcdf.cpp commit bb01df68f552d46b684626a841939e33a367258c Author: Hannah Klion Date: Mon Jan 8 16:11:13 2024 -0800 make C4 default advection scheme again Exec/Advection/inputs commit 80c6f1160e929f577218626aabaaa4f15545c88d Merge: f449159a 63147f4a Author: Ann Almgren Date: Mon Jan 8 14:53:17 2024 -0800 Merge pull request #118 from seahorce-scidac/fix_for_remora forgot to commit this file commit 63147f4aa70eaf332bad1ccfc83dcf5fc6943bd3 Author: Ann Almgren Date: Mon Jan 8 14:15:50 2024 -0800 forgot to commit this file Source/Initialization/REMORA_init_from_netcdf.cpp commit f449159a47e34832496bf8a924add90df4f741c5 Merge: b553961f c6a5fe91 Author: Ann Almgren Date: Mon Jan 8 13:31:44 2024 -0800 Merge pull request #117 from seahorce-scidac/roms_to_remora ROMS-X/ROMSX --> REMORA commit c6a5fe912e2844f96f298f9a1a6007b875b63bf0 Merge: 70f54415 b553961f Author: Ann Almgren Date: Mon Jan 8 13:14:05 2024 -0800 sync up with latest commit to development commit 70f54415e80bfa5241ecbf2ba7658f4f55e85b0d Author: Ann Almgren Date: Mon Jan 8 12:55:38 2024 -0800 ROMS-X/ROMSX --> REMORA .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/docs.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/windows.yml Build/clone_copy_build.sh Build/cmake.sh Build/cmake_with_netcdf.sh Build/cmake_with_particles.sh Build/differences_list.txt CMake/BuildREMORAExe.cmake CMake/BuildROMSXExe.cmake CMake/SetAmrexOptions.cmake CMake/SetREMORACompileFlags.cmake CMakeLists.txt CONTRIBUTING.md CTestConfig.cmake Docs/Doxyfile.breathe.in Docs/Doxyfile.in Docs/main.dox Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Discretizations.rst Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/InputFiles.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/Makefile Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst Docs/sphinx_doc/Particles.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/ProblemSetup.rst Docs/sphinx_doc/TimeAdvance.rst Docs/sphinx_doc/Time_Stepping.rst Docs/sphinx_doc/VerticalSCoord.rst Docs/sphinx_doc/Visualization.rst Docs/sphinx_doc/building.rst Docs/sphinx_doc/conf.py Docs/sphinx_doc/index.rst Docs/sphinx_doc/make.bat Docs/sphinx_doc/testing.rst Docs/sphinx_doc/theory/Equations.rst Exec/Advection/CMakeLists.txt Exec/Advection/GNUmakefile Exec/Advection/inputs Exec/CMakeLists.txt Exec/DoublyPeriodic/CMakeLists.txt Exec/DoublyPeriodic/GNUmakefile Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/inputs_ml Exec/Make.REMORA Exec/OCCAMS/GNUmakefile Exec/OCCAMS/inputs Exec/ParticlesOverSeaMount/CMakeLists.txt Exec/ParticlesOverSeaMount/GNUmakefile Exec/ParticlesOverSeaMount/inputs Exec/Seamount/CMakeLists.txt Exec/Seamount/GNUmakefile Exec/Seamount/inputs Exec/Upwelling/CMakeLists.txt Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs LICENSE.md README.rst Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/Make.package Source/BoundaryConditions/REMORA_FillPatch.cpp Source/BoundaryConditions/REMORA_PhysBCFunct.H Source/BoundaryConditions/REMORA_PhysBCFunct.cpp Source/BoundaryConditions/TimeInterpolatedData.H Source/DataStruct.H Source/Derive.H Source/Derive.cpp Source/EOS.H Source/IO/Checkpoint.cpp Source/IO/NCInterface.H Source/IO/NCMultiFabFile.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromBdryNetcdf.cpp Source/IO/ReadFromInitNetcdf.cpp Source/IO/writeJobInfo.cpp Source/IndexDefines.H Source/Initialization/Make.package Source/Initialization/REMORA_init.cpp Source/Initialization/REMORA_init1d.cpp Source/Initialization/REMORA_init_bcs.cpp Source/Initialization/REMORA_init_from_netcdf.cpp Source/Make.package Source/Particles/ParticleData.H Source/REMORA.H Source/REMORA.cpp Source/REMORA_Constants.H Source/REMORA_SumIQ.cpp Source/REMORA_Tagging.cpp Source/REMORA_make_new_level.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/REMORA_Advance.cpp Source/TimeIntegration/REMORA_ComputeTimestep.cpp Source/TimeIntegration/REMORA_TimeStep.cpp Source/TimeIntegration/REMORA_TimeStepML.cpp Source/TimeIntegration/REMORA_advance_2d.cpp Source/TimeIntegration/REMORA_advance_2d_onestep.cpp Source/TimeIntegration/REMORA_advance_3d.cpp Source/TimeIntegration/REMORA_advance_3d_ml.cpp Source/TimeIntegration/REMORA_coriolis.cpp Source/TimeIntegration/REMORA_prestep.cpp Source/TimeIntegration/REMORA_prestep_diffusion.cpp Source/TimeIntegration/REMORA_prestep_t_advection.cpp Source/TimeIntegration/REMORA_prsgrd.cpp Source/TimeIntegration/REMORA_rho_eos.cpp Source/TimeIntegration/REMORA_rhs_t_3d.cpp Source/TimeIntegration/REMORA_rhs_uv_2d.cpp Source/TimeIntegration/REMORA_rhs_uv_3d.cpp Source/TimeIntegration/REMORA_set_weights.cpp Source/TimeIntegration/REMORA_setup_step.cpp Source/TimeIntegration/REMORA_t3dmix.cpp Source/TimeIntegration/REMORA_update_massflux_3d.cpp Source/TimeIntegration/REMORA_uv3dmix.cpp Source/TimeIntegration/REMORA_vert_mean_3d.cpp Source/TimeIntegration/REMORA_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H Source/Utils/Make.package Source/Utils/REMORA_Math.H Source/main.cpp Submodules/AMReX Tests/CTestList.cmake Tests/REMORA_Gold_Files/Advection/Header Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/Advection/Level_0/Cell_H Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00002 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_D_00003 Tests/REMORA_Gold_Files/Advection/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoublyPeriodic/Header Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Cell_H Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Header Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_H Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00002 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00003 Tests/REMORA_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_H Tests/REMORA_Gold_Files/Seamount/Header Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00002 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_D_00003 Tests/REMORA_Gold_Files/Seamount/Level_0/Cell_H Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00000 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00001 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00002 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_D_00003 Tests/REMORA_Gold_Files/Seamount/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/Advection/job_info Tests/ROMSX_Gold_Files/DoublyPeriodic/job_info Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/job_info Tests/ROMSX_Gold_Files/Seamount/job_info Tests/test_files/Advection/Advection.i Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i commit b553961fff1475da8f0d7bfed08e83a7d53cf393 Author: Hannah Klion Date: Fri Jan 5 16:41:44 2024 -0800 add coriolis stub to ParticlesOverSeaMount Exec/ParticlesOverSeaMount/prob.cpp commit 7532e63aaecd81d205cd64f2a9b15ba67c9db42f Merge: 2ffa82e5 1f98b86b Author: Hannah Klion Date: Fri Jan 5 16:13:22 2024 -0800 Merge pull request #116 from hklion/coriolis Adds option for custom coriolis forcing or reading it from grid file commit 2ffa82e574ac011d0cd2eee70b267064c5e687f6 Author: Hannah Klion Date: Fri Jan 5 16:03:23 2024 -0800 add Hannah ORCID paper/paper.md commit 1f98b86b78e6f010fe69b85ddcae3a116b1445bd Merge: 9533e6f7 a3c5017a Author: Hannah Klion Date: Fri Jan 5 15:54:37 2024 -0800 Merge branch 'development' into coriolis commit 9533e6f7623a5df87379c384d088fb84523fc1ab Author: Hannah Klion Date: Fri Jan 5 15:49:43 2024 -0800 make function public Source/ROMSX.H commit ee31571ce25186b85129831328a2321aa2fa0159 Author: Hannah Klion Date: Fri Jan 5 15:23:16 2024 -0800 try to fix gpu errors Source/Initialization/ROMSX_init.cpp commit d4e89b11bdb1e4e36975c9562a6b2771da6d769f Author: Hannah Klion Date: Fri Jan 5 15:19:30 2024 -0800 prevent invalid arithmetic when coriolis turned off Source/Initialization/ROMSX_init.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 2faa1ac9142fac019b6f7d7674ff3be0ae732e4a Author: Hannah Klion Date: Fri Jan 5 14:56:54 2024 -0800 update docs Docs/sphinx_doc/Inputs.rst commit 98dd422bde86d2be076b92578748932a4e0b8ba4 Author: Hannah Klion Date: Fri Jan 5 14:46:20 2024 -0800 add custom coriolis stubs to prob.cpp Exec/Advection/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/Seamount/prob.cpp commit 4cbe1861b9ff08c565d9d1c52de635c94fc2f4d7 Author: Hannah Klion Date: Fri Jan 5 14:36:10 2024 -0800 move beta plane coriolis outside of netcdf Source/ROMSX.H commit 5f250bef7f0bdfc8eb5e811846c4dd026db6d699 Author: Hannah Klion Date: Fri Jan 5 14:32:23 2024 -0800 coriolis forcing from file, custom, or as a beta plane approximation Exec/OCCAMS/inputs Exec/OCCAMS/prob.cpp Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/DataStruct.H Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/ROMSX_init.cpp Source/Initialization/ROMSX_init_from_netcdf.cpp Source/Initialization/prob_common.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit a3c5017a2688f9998bffb154d8b7218e9c280b6e Merge: 8a63dbf1 c665822d Author: Ann Almgren Date: Fri Jan 5 09:50:33 2024 -0800 Merge pull request #115 from seahorce-scidac/update_paper add Vijay commit c665822dd5a757076adfbc5c328b8931d2cca14f Author: Ann Almgren Date: Fri Jan 5 09:50:06 2024 -0800 add Vijay paper/paper.md commit 8a63dbf1733a70e8cabe92e261df4d16ab91b234 Merge: 432329ed 6fcb95c3 Author: Ann Almgren Date: Fri Jan 5 09:33:34 2024 -0800 Merge pull request #114 from iulian787/development Iulian's orcid commit 432329ed39091c680ad90b468c9af8643f04ff0b Merge: 7402612d 99d0a213 Author: Ann Almgren Date: Fri Jan 5 09:33:18 2024 -0800 Merge pull request #113 from kyle-hinson/development Kyle Hinson ORCID commit 6fcb95c3f4ac569eaf46158c94177532e97f017f Author: Iulian Grindeanu Date: Fri Jan 5 11:29:28 2024 -0600 Iulian's orcid paper/paper.md commit 99d0a213f8c49ec866b90ddf4a0646aa6ca9c218 Merge: 7402612d 84adab7f Author: kyle-hinson <101892482+kyle-hinson@users.noreply.github.com> Date: Fri Jan 5 10:28:00 2024 -0600 Merge pull request #1 from kyle-hinson/kyle-hinson-patch-1 Hinson ORCID added to paper.md commit d75911e59f84568777d89942967fbad312e08cdb Author: Jean M. Sexton Date: Fri Jan 5 06:41:56 2024 -0800 Real without namespace Data Source/DataStruct.H commit 094675c81b04b9e2301a57c0efd19531bdcbd725 Author: Jean M. Sexton Date: Fri Jan 5 06:02:20 2024 -0800 Upwelling prob sp Exec/Upwelling/prob.cpp commit 0a6245031c263b02c06d37bbc3456e3ce76bc96f Author: Jean M. Sexton Date: Thu Jan 4 07:52:54 2024 -0800 First pass at updating prob for float Exec/Upwelling/prob.cpp commit 84adab7ff03d428a12cf265ef0fae239ce135839 Author: kyle-hinson <101892482+kyle-hinson@users.noreply.github.com> Date: Thu Jan 4 09:06:37 2024 -0600 Hinson ORCID added to paper.md paper/paper.md commit 69e041e4740bf6b8ed7e888689a0e6af58eede27 Author: Jean M. Sexton Date: Wed Jan 3 17:47:11 2024 -0800 Add ORCID paper/paper.md commit 7402612d1658f4ded8a080056f9c637a8af1162d Merge: 5a17e803 b9e7be3c Author: Ann Almgren Date: Wed Jan 3 17:35:23 2024 -0800 Merge pull request #112 from seahorce-scidac/some_sp start for moving to single precision option commit b9e7be3c2f3d79a7cc2b2ae81eb9f422524087d8 Author: Ann Almgren Date: Wed Jan 3 17:33:22 2024 -0800 update paper authors paper/paper.md commit 7c83c3319a6c3d4cb4a439387d2eb70d8307dad8 Author: Ann Almgren Date: Wed Jan 3 17:31:39 2024 -0800 start for moving to single precision option Source/IO/Plotfile.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_advection.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_set_weights.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 5a17e8035fbca3d5202b4c333f38c3159599a463 Merge: 0ae0e57b ffc054bc Author: Ann Almgren Date: Wed Jan 3 16:40:00 2024 -0800 Merge pull request #111 from seahorce-scidac/fix_netcdf_bdy fix netcdf bdy stuff commit ffc054bc626a22cffef691b7182df614a892f407 Author: Ann Almgren Date: Wed Jan 3 15:59:16 2024 -0800 fix netcdf bdy stuff Source/BoundaryConditions/BoundaryConditions_netcdf.cpp commit 0ae0e57b54d75819f74e532afc896bb0467ce953 Merge: c7c50b50 d8f1d419 Author: Ann Almgren Date: Wed Jan 3 15:31:30 2024 -0800 Merge pull request #110 from seahorce-scidac/average_vels_in_plotfile Modify amrex-format plotfiles to use cell-centered average velocity commit d8f1d41943b5dee531734a0b0c81d5a58e7da18e Author: Ann Almgren Date: Wed Jan 3 15:13:34 2024 -0800 Modify amrex-format plotfiles to use cell-centered average velocity Docs/sphinx_doc/Plotfiles.rst Exec/OCCAMS/prob.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/ROMSX_init_from_netcdf.cpp Source/ROMSX.H Source/ROMSX.cpp Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Header Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_H Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00002 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00003 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/job_info Tests/ROMSX_Gold_Files/Seamount/Header Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_H Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00002 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00003 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/Seamount/job_info commit c7c50b501a6dd15a467290be912d0bdb668c1371 Merge: 43035cfa 11b40139 Author: Ann Almgren Date: Tue Jan 2 18:55:06 2024 -0800 Merge pull request #109 from seahorce-scidac/read_bdy_files Add ability to use time-dependent bcs from netcdf bdry file commit 11b40139081184d2ab48f939dc16fff9a8852fd4 Author: Ann Almgren Date: Tue Jan 2 18:31:52 2024 -0800 Add ability to use time-dependent bcs from netcdf bdry file Exec/OCCAMS/inputs Source/BoundaryConditions/BoundaryConditions_netcdf.cpp Source/BoundaryConditions/Make.package Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Checkpoint.cpp Source/IO/Make.package Source/IO/Plotfile.cpp Source/IO/ReadFromBdryNetcdf.cpp Source/IO/ReadFromInitNetcdf.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init.cpp Source/Initialization/ROMSX_init_from_netcdf.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_set_weights.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 43035cfa6d03a6a8c703c683ba5bfbc6f52c30dd Merge: 7fe876e0 f13ddea4 Author: Ann Almgren Date: Sat Dec 23 20:29:08 2023 -0800 Merge pull request #108 from seahorce-scidac/fix_upwind fix upwind advection commit f13ddea4df89f1eea9bbbdc755a04fb4f557dd75 Author: Ann Almgren Date: Sat Dec 23 20:10:53 2023 -0800 update ctest for Advection Tests/ROMSX_Gold_Files/Advection/Header Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_H Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_D_00002 Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_D_00003 Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/Advection/job_info commit 1a124f61e6f1d0a2c6056770c8960d7ed97125af Author: Ann Almgren Date: Sat Dec 23 16:50:15 2023 -0800 fix upwind advection Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_advection.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 7fe876e082ccee2d05eec8eec54c7398a8f3b5c1 Merge: a3e301ea 071516e5 Author: Ann Almgren Date: Sat Dec 23 09:27:48 2023 -0800 Merge pull request #107 from seahorce-scidac/use_real_pm_pn we define pm,pn at initialization and use those values commit 071516e54e8692302cd06c7c1b83f223ed154f71 Author: Ann Almgren Date: Sat Dec 23 09:09:42 2023 -0800 Removed all uses of dx and dxi from TimeIntegration except for hard-wired coriolis CMake/BuildROMSXExe.cmake Source/Initialization/ROMSX_init.cpp Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 1c4115f390f87564a0013bc9410a2ef67380c2f1 Author: Ann Almgren Date: Fri Dec 22 17:50:18 2023 -0800 we define pm,pn at initialization and use those values Source/IO/Make.package Source/IO/NCCheckpoint.cpp Source/Initialization/ROMSX_init.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_diffusion.cpp Source/TimeIntegration/ROMSX_prestep_t_advection.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit a3e301eae57d36e31ae45175018ada060c5f1909 Merge: 1ca8d69d a53011bc Author: Ann Almgren Date: Fri Dec 22 12:48:20 2023 -0800 Merge pull request #106 from seahorce-scidac/read_from_grid_file Read from grid file as well as init file when ic_bc_type = real commit a53011bcd8386105e07111edbc6c110ee3d8570a Author: Ann Almgren Date: Fri Dec 22 10:39:30 2023 -0800 Read from grid file as well as init file when ic_bc_type = real Exec/Advection/prob.cpp Exec/DoublyPeriodic/prob.cpp Exec/OCCAMS/inputs Exec/OCCAMS/prob.cpp Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/IO/NCFile.H Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/ROMSX_init.cpp Source/Initialization/ROMSX_init_from_netcdf.cpp Source/Initialization/prob_common.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/Utils/DepthStretchTransform.H commit 1ca8d69dd2d9c33c76151609816a69b47b004e12 Merge: 8c2d3679 2f6e00aa Author: Ann Almgren Date: Fri Dec 22 07:47:16 2023 -0800 Merge pull request #105 from seahorce-scidac/fix_oops fix mistaken commit commit 2f6e00aaaf0a60f60098ca72b4d8c8d32073d6b2 Author: Ann Almgren Date: Fri Dec 22 07:46:45 2023 -0800 fix mistaken commit Source/IO/NCFile.H commit 8c2d367938a0f831b4e6a6db6ece2e264805a5fb Merge: 4ec76047 01896d99 Author: Ann Almgren Date: Thu Dec 21 13:59:00 2023 -0800 Merge pull request #104 from seahorce-scidac/init_from_netcdf We can now initialize from a netcdf file commit 01896d9978258547719087f220b4504b08b62dcd Author: Ann Almgren Date: Thu Dec 21 13:21:55 2023 -0800 We can now initialize from a netcdf file Exec/OCCAMS/GNUmakefile Exec/OCCAMS/Make.package Exec/OCCAMS/inputs Exec/OCCAMS/prob.H Exec/OCCAMS/prob.cpp Source/IO/Make.package Source/IO/NCFile.H Source/IO/NCPlotFile.cpp Source/IO/ReadFromInitNetcdf.cpp Source/Initialization/Make.package Source/Initialization/ROMSX_init_from_netcdf.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_advection.cpp commit 4ec760472567e07a33ab49819664a645c09ecc0b Merge: 7a0492c8 ec34e882 Author: Hannah Klion Date: Thu Dec 21 11:50:02 2023 -0800 Merge pull request #103 from hklion/scalar_advection make C4 the default scheme for advection test and set bottom drag to 0 commit ec34e8827bd6c9014cc6526523825caccb658664 Author: Hannah Klion Date: Thu Dec 21 11:26:27 2023 -0800 make C4 the default scheme for advection test and set bottom drag to 0 Exec/Advection/inputs commit 7a0492c803c5aa4dfbc902e66bcf4393ad82154c Merge: 9311d604 bd6500f2 Author: Hannah Klion Date: Tue Dec 19 15:29:33 2023 -0800 Merge pull request #102 from hklion/scalar_advection Scalar advection commit bd6500f25c67fac0159c80157c4469f9c163501a Author: Hannah Klion Date: Tue Dec 19 15:02:06 2023 -0800 maybe actually change them for real now? Tests/CMakeLists.txt Tests/CTestList.cmake commit 6a8358c3439bba612305cfe21d75278288a83dc5 Author: Hannah Klion Date: Tue Dec 19 14:46:20 2023 -0800 actually change tolerances Tests/CMakeLists.txt commit f4b727fa292687111064d5ae794d4e5ed09a4866 Author: Hannah Klion Date: Tue Dec 19 14:25:25 2023 -0800 loosen tolerances on ctest Tests/CMakeLists.txt commit 9927344327e3465b29c40f240d5eeea657f8619a Author: Hannah Klion Date: Tue Dec 19 13:56:05 2023 -0800 fix errors not filling mixing coeffs Exec/Advection/inputs Exec/DoublyPeriodic/prob.cpp Exec/Seamount/prob.cpp Tests/test_files/Advection/Advection.i commit 9311d604b69a292ca36d82793e9f7e20b4dca07b Merge: d42e76c1 2991482a Author: Ann Almgren Date: Tue Dec 19 13:41:46 2023 -0800 Merge pull request #101 from seahorce-scidac/add_paper start first draft of JOSS paper commit 2991482a784d7d91b646aa947e8cf4a57b2393af Author: Ann Almgren Date: Tue Dec 19 13:41:18 2023 -0800 start first draft of JOSS paper paper/paper.bib paper/paper.md commit 50a5e13dc6a63aa0c1b2f3df9a090880431a8540 Author: Hannah Klion Date: Tue Dec 19 12:38:22 2023 -0800 remove last vec_t3 and vec_s3 Source/TimeIntegration/ROMSX_advance_3d_ml.cpp commit 0b0ac6a5d4562ca19936f1efd11658232fc8a810 Merge: 82c3cd85 d42e76c1 Author: Hannah Klion Date: Tue Dec 19 12:30:15 2023 -0800 Merge branch 'development' into scalar_advection commit 82c3cd852f8aad9d02e1c80d975720d03713911f Author: Hannah Klion Date: Tue Dec 19 12:21:22 2023 -0800 fix prob.cpp Exec/Upwelling/prob.cpp commit d42e76c10c134e17369c04be9780c45a19f3a367 Merge: cbe6b220 b22ec9c7 Author: Ann Almgren Date: Tue Dec 19 11:39:33 2023 -0800 Merge pull request #100 from seahorce-scidac/fix_init_type Fix init type commit b22ec9c7bc8866140bd3ec5f3dc46c127548ec6d Author: Ann Almgren Date: Tue Dec 19 11:13:02 2023 -0800 fcompare --> amrex_fcompare Tests/CMakeLists.txt commit 25acdb359fa64fe533f905fe854a804282ad28ab Author: Ann Almgren Date: Tue Dec 19 11:01:34 2023 -0800 update ic_bc_type Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/DataStruct.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_Tagging.cpp commit 4f4c68d5df743c636dc062e463dd5d5281fbee38 Author: Hannah Klion Date: Tue Dec 19 10:57:39 2023 -0800 add advection/diffusion of a passive scalar CMake/BuildROMSXExe.cmake Exec/Advection/CMakeLists.txt Exec/Advection/GNUmakefile Exec/Advection/Make.package Exec/Advection/Palette Exec/Advection/inputs Exec/Advection/prob.H Exec/Advection/prob.cpp Exec/CMakeLists.txt Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_diffusion.cpp Source/TimeIntegration/ROMSX_prestep_t_advection.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Tests/CTestList.cmake Tests/ROMSX_Gold_Files/Advection/Header Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Advection/Level_0/Cell_H Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/Advection/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/Advection/job_info Tests/test_files/Advection/Advection.i commit bc83cb670b3c1b0ee1c8395a8417ffdcacd82dfd Author: Ann Almgren Date: Tue Dec 19 09:30:47 2023 -0800 updated amrex version Submodules/AMReX commit cbe6b2203cd2e70dd9fa4d7537daef517ae7e0b3 Merge: c798eccb e67cfe5c Author: Ann Almgren Date: Mon Dec 18 19:23:01 2023 -0800 Merge pull request #99 from WeiqunZhang/rocm_60 Fix CI for ROCm 6.0 commit e67cfe5cd1e2296c81fbf447269606ba6cb20d4d Author: Weiqun Zhang Date: Mon Dec 18 19:04:08 2023 -0800 Fix CI for ROCm 6.0 Need to explicitly install hiprand package in CI because it's now a standalone project, not a submodule for rocRand according to the release notes. .github/workflows/dependencies/dependencies_hip.sh commit c798eccb6fd8dd9988ce2bb2b95a64c1724e80ca Merge: 41c80098 3af355bb Author: Ann Almgren Date: Mon Dec 18 17:51:40 2023 -0800 Merge pull request #98 from seahorce-scidac/phys_bc_steps We can run Upwelling with walls now commit 3af355bb7d1f30f3205da78ce94310809ec60ed9 Author: Ann Almgren Date: Mon Dec 18 17:38:31 2023 -0800 We can run Upwelling with walls now Exec/Upwelling/GNUmakefile Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp commit 41c8009836cd128712658dd5f7b586c8859aaeec Merge: 3f2a1f89 7ca11b15 Author: Ann Almgren Date: Sat Dec 16 08:42:16 2023 -0800 Merge pull request #97 from seahorce-scidac/phys_bc_steps Add bcs for walls and add new Upwelling test that has periodic / wall… commit 7ca11b15c8cd9460a6e0a6d3a2b700324437efe0 Author: Ann Almgren Date: Sat Dec 16 08:32:29 2023 -0800 Add bcs for walls and add new Upwelling test that has periodic / wall lateral bcs Exec/Upwelling/CMakeLists.txt Exec/Upwelling/GNUmakefile Exec/Upwelling/Make.package Exec/Upwelling/inputs Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init_bcs.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 3f2a1f89fa089db68827cbb9046f80580fb13d77 Merge: 7557e725 229c48f7 Author: Ann Almgren Date: Fri Dec 15 14:11:46 2023 -0800 Merge pull request #96 from seahorce-scidac/rename_Upwelling moved Upwelling --> DoublyPeriodic commit 229c48f7e1ab17950d0c910a267eebb905fc0d73 Author: Ann Almgren Date: Fri Dec 15 13:23:27 2023 -0800 moved Upwelling --> DoublyPeriodic Exec/CMakeLists.txt Exec/DoublyPeriodic/CMakeLists.txt Exec/DoublyPeriodic/GNUmakefile Exec/DoublyPeriodic/Make.package Exec/DoublyPeriodic/Palette Exec/DoublyPeriodic/inputs Exec/DoublyPeriodic/inputs_ml Exec/DoublyPeriodic/prob.H Exec/DoublyPeriodic/prob.cpp Source/Initialization/ROMSX_init.cpp Tests/CTestList.cmake Tests/ROMSX_Gold_Files/DoublyPeriodic/Header Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Cell_H Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/DoublyPeriodic/job_info Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Header Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Cell_H Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/DoublyPeriodic_bathy/job_info Tests/ROMSX_Gold_Files/Seamount/Header Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_H Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Nu_nd_H Tests/ROMSX_Gold_Files/Seamount/job_info Tests/ROMSX_Gold_Files/Upwelling/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Upwelling/Level_0/Cell_H Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_H Tests/test_files/DoublyPeriodic/DoublyPeriodic.i Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i Tests/test_files/Seamount/Seamount.i commit 7557e72500602dd35f17bed961cb0605783fbfdf Author: Hannah Klion Date: Fri Dec 15 13:09:05 2023 -0800 add note about plotfile prefixes containing directory Docs/sphinx_doc/Plotfiles.rst commit 787293cadc39597679b545f78157ceee95ebddbb Merge: f1f18933 77d60b4c Author: Ann Almgren Date: Fri Dec 15 12:15:52 2023 -0800 Merge pull request #95 from seahorce-scidac/add_redist_again we do need Redistribute in plotfile writing commit 77d60b4cb63ac3484def8c993ec996856408ae67 Author: Ann Almgren Date: Fri Dec 15 12:15:30 2023 -0800 we do need Redistribute in plotfile writing Source/IO/Plotfile.cpp commit f1f18933ac01018758fce02718010d4fc0f4e3ce Merge: f27bdf24 696fbb3f Author: Ann Almgren Date: Fri Dec 15 11:52:50 2023 -0800 Merge pull request #94 from seahorce-scidac/friday_am_2 always use bathymetry when defining z_phys_nd and particles commit 696fbb3fd856f4ec16c3d8415f0318ad01c87b14 Author: Ann Almgren Date: Fri Dec 15 11:52:24 2023 -0800 always use bathymetry when defining z_phys_nd and particles Source/IO/Plotfile.cpp Source/Particles/ParticleData.H Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Source/Utils/DepthStretchTransform.H commit f27bdf249ee04c07f3e837d2eb43c527d02e816a Merge: a3dbcf0d e9ce2e81 Author: Ann Almgren Date: Fri Dec 15 11:15:04 2023 -0800 Merge pull request #93 from seahorce-scidac/friday_am cleanup and hopefully fix commit e9ce2e811e6a5b9cc244ccbaa6e7f32dcbfa1426 Merge: 21eb3619 a3dbcf0d Author: Ann Almgren Date: Fri Dec 15 11:06:19 2023 -0800 merge with development commit 21eb3619b602a71d9b73ee940e5a67c3345222f6 Author: Ann Almgren Date: Fri Dec 15 11:04:52 2023 -0800 cleanup and hopefully fix Source/IO/Plotfile.cpp Source/Particles/TracerPC.cpp Source/ROMSX.H Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit a3dbcf0d5a88e16157251878f795cbe3bbb10ad8 Merge: cad15334 8f3461d0 Author: Ann Almgren Date: Fri Dec 15 09:51:56 2023 -0800 Merge pull request #92 from seahorce-scidac/output_loc optionally output cell-centered location commit 8f3461d0da9b039908033dccc4a3d1c28dfc1b0d Author: Ann Almgren Date: Fri Dec 15 09:38:15 2023 -0800 optionally output cell-centered location Source/IO/Plotfile.cpp Source/ROMSX.H Source/Utils/DepthStretchTransform.H commit cad153346c5c479b362fc8164839bd10e128e5cb Merge: 6c8a66c5 f7825ed7 Author: Ann Almgren Date: Fri Dec 15 08:35:35 2023 -0800 Merge pull request #91 from seahorce-scidac/add_z_phys_in_plot add z_phys_nd to the plotfile commit f7825ed7162c3fd3fb0f71762ec0b31f42d7a321 Author: Ann Almgren Date: Fri Dec 15 08:34:34 2023 -0800 add z_phys_nd to the plotfile Source/IO/Plotfile.cpp Source/ROMSX.H commit 6c8a66c52fc06ffbd74c02075301971edd801bd6 Merge: 0a954149 075e247b Author: Ann Almgren Date: Thu Dec 14 18:01:11 2023 -0800 Merge pull request #90 from seahorce-scidac/fix fix FillBoundary and add a ctest Upwelling_bathy commit 075e247b0687e3443eae9f6625152ef5ac00d48a Author: Ann Almgren Date: Thu Dec 14 16:25:21 2023 -0800 fix FillBoundary and add a ctest Upwelling_bathy Exec/ParticlesOverSeaMount/inputs Exec/Seamount/inputs Exec/Upwelling/inputs Exec/Upwelling/inputs_ml Source/TimeIntegration/ROMSX_advance_2d.cpp Tests/CTestList.cmake Tests/ROMSX_Gold_Files/Upwelling_bathy/Header Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Upwelling_bathy/Level_0/Cell_H Tests/ROMSX_Gold_Files/Upwelling_bathy/job_info Tests/test_files/Upwelling_bathy/Upwelling_bathy.i commit 0a95414963311069af17181660b477fe5f8cdb80 Merge: a779c97b e29688b5 Author: Ann Almgren Date: Thu Dec 14 15:44:50 2023 -0800 Merge pull request #89 from seahorce-scidac/thurs remove more FillBoundary calls commit e29688b5eba7d86493c9f27b87e00a81ff0b357f Author: Ann Almgren Date: Thu Dec 14 15:44:19 2023 -0800 remove more FillBoundary calls Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp commit a779c97b1bc1368ca2b8ffed985f8654e70d55d1 Merge: 3cde8015 b432f699 Author: Hannah Klion Date: Thu Dec 14 15:20:44 2023 -0800 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 3cde8015e818035656601c7d9faae304b8b1a19f Author: Hannah Klion Date: Thu Dec 14 15:20:32 2023 -0800 update readthedocs requirements .readthedocs.yml Docs/requirements.txt commit b432f6992a23a1b35e4b66812e0a506abaa732a8 Merge: aa534a3f 9f987bd2 Author: Ann Almgren Date: Thu Dec 14 14:43:58 2023 -0800 Merge pull request #88 from seahorce-scidac/more_fb_changes more FillBoundary->FillPatch commit 9f987bd2ed78e03f8d7e6b6ccef015921c51e8bf Author: Ann Almgren Date: Thu Dec 14 14:29:01 2023 -0800 more FillBoundary->FillPatch Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit aa534a3f3d65e79b0543fa29cb5d06a143f23c17 Merge: d30be9b4 765e3eee Author: Ann Almgren Date: Thu Dec 14 14:08:22 2023 -0800 Merge pull request #87 from seahorce-scidac/tweak Remove some FillBoundary commit 765e3eee51a58cbb31bbc9f2bded73773e05c17d Author: Ann Almgren Date: Thu Dec 14 14:07:28 2023 -0800 Remove some FillBoundary Source/Initialization/ROMSX_init.cpp Source/ROMSX.cpp commit d30be9b4aebee2aa211dbd6826c57d1bbaf90ffb Merge: cf382eb4 2a3c19a0 Author: Ann Almgren Date: Thu Dec 14 13:21:23 2023 -0800 Merge pull request #86 from seahorce-scidac/add_scalar_to_upwelling add non-zero scalar initialization commit 2a3c19a0dce0a5da34fcc6331bf3650cad5a8fd7 Author: Ann Almgren Date: Thu Dec 14 13:20:42 2023 -0800 add non-zero scalar initialization Exec/Upwelling/prob.cpp commit cf382eb44fddd8b78dbc73f6436aa1fd6b705fbd Author: Hannah Klion Date: Thu Dec 14 13:04:09 2023 -0800 try to get ProblemSetup to appear Docs/sphinx_doc/index.rst commit cd023ac940a26ec6fa4ce7ab8fbfdaab9250da84 Merge: 0de4e2e2 3885d64e Author: Ann Almgren Date: Thu Dec 14 13:01:46 2023 -0800 Merge pull request #85 from seahorce-scidac/cleanup_io remove FillBoundary calls from Checkpoint and Plotfile commit 3885d64ec93f4bee58669d18a076f38fabd097b1 Author: Ann Almgren Date: Thu Dec 14 13:01:18 2023 -0800 remove FillBoundary calls from Checkpoint and Plotfile Source/IO/Checkpoint.cpp Source/IO/Plotfile.cpp commit 0de4e2e24b87e780cd4e1fc014dd7ede8cc97d7c Merge: b2ea063d 979f72bb Author: Ann Almgren Date: Thu Dec 14 11:51:36 2023 -0800 Merge pull request #84 from seahorce-scidac/update_fillpatch update fillpatch commit 979f72bb7e69f590cd03eb2511d310e12d14197f Author: Ann Almgren Date: Thu Dec 14 11:31:40 2023 -0800 remove unwanted file Exec/Upwelling/amrvis.defaults Exec/Upwelling/inputs_ml Source/:w commit 640c6901fad8ee9fa12c4abb91abfc5a11f9d13b Author: Ann Almgren Date: Thu Dec 14 11:28:10 2023 -0800 update fillpatch Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/Utils/DepthStretchTransform.H commit b2ea063da8961dfba505b9f2692ffd756af2c637 Merge: 4392090e 3b5807ed Author: Ann Almgren Date: Thu Dec 14 11:22:22 2023 -0800 Merge pull request #83 from seahorce-scidac/update_particles update particle component names commit 3b5807eda758c370f2023a157f17c0ee5d40bcba Author: Ann Almgren Date: Thu Dec 14 11:21:59 2023 -0800 update particle component names Source/Particles/ParticleData.H Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp commit 4392090e0a483d800156a3c2db515e63366fc077 Merge: 33071c69 349e7d72 Author: Ann Almgren Date: Thu Dec 14 11:14:22 2023 -0800 Merge pull request #82 from seahorce-scidac/fix_particles fix particle advection commit 349e7d72bdd60a8fa6ded413952a1e3027a6a53a Author: Ann Almgren Date: Thu Dec 14 11:13:51 2023 -0800 fix particle advection Source/Particles/TracerPC.cpp commit 33071c6903a3b2f1230db22ba5c40abaf7a6e224 Merge: e27cf502 615f9294 Author: Hannah Klion Date: Thu Dec 14 09:51:08 2023 -0800 Merge pull request #81 from seahorce-scidac/more_tweaks more tweaks commit e27cf502819f9d93268d8e059564447d9299b3e4 Author: Hannah Klion Date: Wed Dec 13 17:03:01 2023 -0800 add coriolis back into ParticlesOverSeamount Exec/ParticlesOverSeaMount/inputs commit 615f9294419a64bee4aa5c1a7d0f06f242b4050e Author: Ann Almgren Date: Wed Dec 13 16:15:08 2023 -0800 more tweaks Source/:w Source/Particles/TracerPC.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 170563b1a4204ba2e31029ed48d13aa956404cf2 Author: Hannah Klion Date: Wed Dec 13 15:39:08 2023 -0800 particles test updates with inputs Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp commit 61f3b8a87bf058645a5f192b67c0a1b605b66dc7 Author: Hannah Klion Date: Wed Dec 13 14:27:43 2023 -0800 try to get Problem Setup to show Docs/sphinx_doc/ProblemSetup.rst commit 7a011a63e23bd08542bca0f397da0e9b25e6eb70 Author: Hannah Klion Date: Wed Dec 13 14:23:37 2023 -0800 Params in inputs (#80) * make EOS and coriolis parameters runtime options * tweak inputs file * update test input file for Upwelling test * host vs device variables * set local vars that can go on device * missing brace * update seamount test * move var to outside kernel Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/InputsPhysics.rst Exec/Seamount/inputs Exec/Seamount/prob.H Exec/Seamount/prob.cpp Exec/Upwelling/inputs Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Source/DataStruct.H Source/ROMSX_Constants.H Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Tests/ROMSX_Gold_Files/Seamount/Header Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_H Tests/ROMSX_Gold_Files/Seamount/job_info Tests/test_files/Seamount/Seamount.i Tests/test_files/Upwelling/Upwelling.i commit e2ec1402f23a2db5dad44acd3f6118cbb05ebf44 Merge: c7283fb0 3e2d7901 Author: Ann Almgren Date: Wed Dec 13 13:58:07 2023 -0800 Merge pull request #79 from seahorce-scidac/change_component_order change order of Salt_comp and Scalar_comp so Salt_comp directly follo… commit 3e2d79019ac5889a5a4a4746298804cad40ea11d Author: Ann Almgren Date: Wed Dec 13 13:40:45 2023 -0800 change order of Salt_comp and Scalar_comp so Salt_comp directly follows Temp_comp Source/IndexDefines.H Source/ROMSX.H commit c7283fb0a40d922ce3a55be282263240ee0d2372 Author: Ann Almgren Date: Wed Dec 13 13:18:49 2023 -0800 remove Omega_comp Source/IndexDefines.H Source/ROMSX.H Source/TimeIntegration/ROMSX_setup_step.cpp commit 44b0b53d5b574b12e2387f0311a3e66c506523ae Merge: 1d4106c1 603da00a Author: Ann Almgren Date: Wed Dec 13 08:48:39 2023 -0800 Merge pull request #78 from seahorce-scidac/remove_SALINITY more cleanup, remove SALINITY and add use_salt, change NVAR --> NCONS commit 603da00ac0f9d3f7964344fdf6edfdb0283b531e Author: Ann Almgren Date: Wed Dec 13 08:02:22 2023 -0800 more cleanup, remove SALINITY and add use_salt, change NVAR --> NCONS Build/cmake.sh CMake/BuildROMSXExe.cmake CMakeLists.txt Exec/Make.ROMSX Exec/ParticlesOverSeaMount/GNUmakefile Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/GNUmakefile Exec/Seamount/prob.cpp Exec/Upwelling/GNUmakefile Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/DataStruct.H Source/IO/Checkpoint.cpp Source/IO/NCCheckpoint.cpp Source/IO/Plotfile.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init_bcs.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 1d4106c11a9555647bd8b6f2d4b2bb2ce8c9181a Merge: 600f3be2 de00e078 Author: Ann Almgren Date: Tue Dec 12 20:42:09 2023 -0800 Merge pull request #77 from seahorce-scidac/fix_compilation fix compilation commit de00e078ca3c6e4fda0cf2b689b302eb7e47ba76 Author: Ann Almgren Date: Tue Dec 12 20:41:37 2023 -0800 fix compilation Exec/ParticlesOverSeaMount/prob.cpp commit 600f3be29d2c2fb33119848c64f3b812135ec4e9 Merge: 0bac68ea d864b5c6 Author: Ann Almgren Date: Tue Dec 12 18:35:39 2023 -0800 Merge pull request #76 from seahorce-scidac/cleanup more cleanup commit d864b5c627c1c2ec0e2c865469540c59fde723fc Author: Ann Almgren Date: Tue Dec 12 18:06:27 2023 -0800 more cleanup Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/Initialization/prob_common.H Source/Particles/TracerPC.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_SumIQ.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_ComputeTimestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 0bac68ea288ed7f6e46a918a4efe4a0eddc0c38c Merge: fe8d9019 9b07df20 Author: Ann Almgren Date: Tue Dec 12 14:20:53 2023 -0800 Merge pull request #75 from seahorce-scidac/update_ctest add seamount to ctests commit 9b07df20692a9ccac8c38d844bd5cf73a86da67d Author: Ann Almgren Date: Tue Dec 12 13:58:51 2023 -0800 add seamount to ctests Exec/CMakeLists.txt Exec/Seamount/inputs Tests/CTestList.cmake Tests/ROMSX_Gold_Files/Seamount/Header Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/Seamount/Level_0/Cell_H Tests/ROMSX_Gold_Files/Seamount/job_info Tests/test_files/Seamount/Seamount.i commit fe8d90198157227651755c1339626440468b0bb7 Merge: 743302a1 480d83bc Author: Ann Almgren Date: Mon Dec 11 15:18:07 2023 -0800 Merge pull request #74 from seahorce-scidac/modify_exec_name add .NC to exec name when building with NetCDF commit 480d83bcbed5c88d4a31b981c412dc10a5653eec Author: Ann Almgren Date: Mon Dec 11 15:17:39 2023 -0800 add .NC to exec name when building with NetCDF Exec/Make.ROMSX commit 743302a1d3fa5ae39d1a082756928ee65f915993 Merge: 8a7578bc 651c157f Author: Hannah Klion Date: Mon Dec 11 12:09:54 2023 -0800 Merge pull request #73 from seahorce-scidac/fix_for_netcdf remove WRF-related I/O stuff and get this compiling again with netcdf commit 651c157f70f1c114f9dff2bad869f8b395680ed6 Author: Ann Almgren Date: Mon Dec 11 11:33:56 2023 -0800 remove WRF-related I/O stuff and get this compiling again with netcdf Source/BoundaryConditions/BoundaryConditions_wrfbdy.cpp Source/BoundaryConditions/Make.package Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/IO/Make.package Source/IO/NCBuildFABs.cpp Source/IO/NCCheckpoint.cpp Source/IO/NCWpsFile.H Source/IO/ReadFromWRFBdy.cpp Source/IO/ReadFromWRFInput.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init.cpp Source/ROMSX.H Source/ROMSX.cpp commit 8a7578bc3067df77c3fe366169e2afa809302357 Author: Hannah Klion Date: Mon Dec 11 10:39:36 2023 -0800 turn off NETCDF in Seamount for now Exec/Seamount/GNUmakefile commit f6460ab5b6df08b03d8f1cb1e958062e95c2d664 Author: Hannah Klion Date: Mon Dec 11 08:37:42 2023 -0800 Revert "Cleanup" This reverts commit f9d9f5450e09950e1f7d8357e721762de91459b4. Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit f9d9f5450e09950e1f7d8357e721762de91459b4 Author: Hannah Klion Date: Sat Dec 9 23:17:15 2023 -0800 Cleanup Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 5cefe813acbe89a42968322306ab88e4b2bbbcef Merge: c281b3e5 7fbe3730 Author: Ann Almgren Date: Sat Dec 9 16:49:01 2023 -0800 Merge pull request #72 from seahorce-scidac/more_to_ml more cleanup towards multilevel commit 7fbe3730ba3a5e533b3f5f3cb66bf2002c8be95c Author: Ann Almgren Date: Sat Dec 9 16:31:17 2023 -0800 more cleanup towards multilevel Source/ROMSX.H Source/ROMSX_SumIQ.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_set_weights.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit c281b3e59e3051f2dc3b3c19c0c73f79afd58d8c Merge: a0853a81 76d56332 Author: Ann Almgren Date: Sat Dec 9 12:40:15 2023 -0800 Merge pull request #71 from seahorce-scidac/remove_rho_comp Remove Rho_comp and Theta_comp and associated ... commit 76d56332ae54a465eaf52a6714a2ededa7b61a93 Author: Ann Almgren Date: Sat Dec 9 12:18:59 2023 -0800 Remove Rho_comp and Theta_comp and associated ... Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/prob.cpp Source/DataStruct.H Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromWRFBdy.cpp Source/IO/ReadFromWRFInput.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init.cpp Source/Initialization/ROMSX_init_bcs.cpp Source/ROMSX.H Source/ROMSX_SumIQ.cpp Source/ROMSX_Tagging.cpp commit a0853a813c692c7956587e46ca4ca461e4c3fda7 Merge: ec7eac5d 82e43bc7 Author: Ann Almgren Date: Sat Dec 9 11:32:54 2023 -0800 Merge pull request #70 from seahorce-scidac/add_free_slip_at_top add free slip condition at top -- this fixes the particle advection commit 82e43bc7bbfd4ebe69fcb11901c869ac595453f1 Author: Ann Almgren Date: Sat Dec 9 11:32:30 2023 -0800 move FillPatch from private to public Source/ROMSX.H commit 55f3c6cbb21ee03cf311cb095ac6c436737fd4a4 Author: Ann Almgren Date: Sat Dec 9 10:52:49 2023 -0800 fix for CUDA plus some cleanup Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 81b50966c1e28a4cdb21b3c6e84c8df952c2a3e3 Author: Ann Almgren Date: Sat Dec 9 09:25:42 2023 -0800 add free slip condition at top -- this fixes the particle advection Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/IO/Make.package Source/IO/NCColumnFile.cpp Source/ROMSX.H commit ec7eac5df2298c9ed2f9534e305714f9790e3612 Merge: d513472e d80e0c2b Author: Ann Almgren Date: Sat Dec 9 08:01:30 2023 -0800 Merge pull request #69 from seahorce-scidac/fix_particles fix particle functionality commit d80e0c2b4d6cc52a6f633e1ed3d6b9bd48d626bc Author: Ann Almgren Date: Sat Dec 9 08:00:34 2023 -0800 fix particle functionality Source/Particles/ParticleData.H Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp commit d513472ed000a8cb4d009417503fc37a722ca74d Merge: 9a6287eb 41e1c60c Author: Hannah Klion Date: Fri Dec 8 23:46:29 2023 -0800 Merge pull request #68 from hklion/fix_ubar_nodal Fix ubar nodal commit 41e1c60c78ab323a1abb36838d2e5a0faa9b53b9 Merge: 2d6e390d 9a6287eb Author: Hannah Klion Date: Fri Dec 8 23:45:42 2023 -0800 Merge branch 'development' into fix_ubar_nodal commit 2d6e390d235c79aa7355f86696df580c5eebd19c Author: Hannah Klion Date: Fri Dec 8 23:44:33 2023 -0800 fix errors introduced by making ubar nodal Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 9a6287eb8330ce66932b6cee445d00201838cd02 Merge: 71a22959 795059ac Author: Ann Almgren Date: Fri Dec 8 19:13:36 2023 -0800 Merge pull request #67 from seahorce-scidac/add_fillpatch split out vars_new and vars_old into separate arrays and modify FillP… commit 795059acdcfbbf484e9d3aa201ca580943b117bc Author: Ann Almgren Date: Fri Dec 8 18:36:56 2023 -0800 split out vars_new and vars_old into separate arrays and modify FillPatch Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Checkpoint.cpp Source/IO/NCCheckpoint.cpp Source/IO/NCColumnFile.cpp Source/IO/Plotfile.cpp Source/IndexDefines.H Source/Initialization/ROMSX_init.cpp Source/Particles/ParticleData.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_SumIQ.cpp Source/ROMSX_Tagging.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_ComputeTimestep.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/Utils/DepthStretchTransform.H commit 71a22959b56150dab80c1f36afe99e03e42e3187 Author: Hannah Klion Date: Thu Dec 7 12:40:59 2023 -0800 remove unused box from rhs_uv_3d Source/ROMSX.H Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 61273a8bcb8ddbd13129a6a91c0dc29ce9e9eff0 Author: Hannah Klion Date: Thu Dec 7 11:24:32 2023 -0800 rename variables in rhs_2d to match 2d case Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 54ea2dc61e3d0ee1acdfe805f0edd371c018fe20 Merge: e09b2913 b94091a5 Author: Hannah Klion Date: Wed Dec 6 21:43:08 2023 -0800 Merge pull request #66 from hklion/fix_rhoS Fix rhoS commit b94091a5b3074cfc72758f29d23614594bc660d0 Merge: 6cb4b03b e09b2913 Author: Hannah Klion Date: Wed Dec 6 21:41:47 2023 -0800 Merge branch 'development' into fix_rhoS commit 6cb4b03be5811015eb01efb495f9e9f0e3d360a0 Author: Hannah Klion Date: Wed Dec 6 21:06:35 2023 -0800 change wrong rhoA to rhoS Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp commit e09b29135e7a4851e2c3c8a7c52e80b2634ca707 Merge: c080eaf3 b2a5e6bf Author: Ann Almgren Date: Wed Dec 6 19:21:43 2023 -0800 Merge pull request #65 from seahorce-scidac/fix_previous_commit fix previous commit commit b2a5e6bf6e8bbc8f8fad14c83ff56e187da9018b Author: Ann Almgren Date: Wed Dec 6 19:18:46 2023 -0800 fix previous commit Source/TimeIntegration/ROMSX_advance_3d.cpp commit c080eaf35ef7ceee65c2034afb8c620a0cb44da8 Merge: 9fdacdc8 260528a8 Author: Ann Almgren Date: Wed Dec 6 12:39:22 2023 -0800 Merge pull request #64 from seahorce-scidac/tweaks2 some cleanup but no change to answers commit 260528a80fb4290b0b060eab23e5b208facffced Author: Ann Almgren Date: Wed Dec 6 12:36:38 2023 -0800 some cleanup but no change to answers Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 9fdacdc871f2fb939a3617fb6ba408ca367f05ce Merge: 6f3c1ceb 1f64a816 Author: Hannah Klion Date: Tue Dec 5 15:24:45 2023 -0800 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 6f3c1ceb5dac2f974a536aa4795ab9ae9fd4690a Author: Hannah Klion Date: Tue Dec 5 15:24:32 2023 -0800 indentation and annotate boxes Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 1f64a816495886ccaf6bda6bc6aa44dbd2035e84 Merge: e1ec820e e289e947 Author: Hannah Klion Date: Tue Dec 5 14:55:32 2023 -0800 Merge pull request #63 from hklion/cleanup simplify loops in vertical viscosity, and call loops in vert_visc/vert_mean only on valid commit e289e9477e6c0d83293181d524e1954809a83be9 Author: Hannah Klion Date: Tue Dec 5 14:53:50 2023 -0800 simplify loops in vertical viscosity, and call loops in vert_visc/vert_mean/advance3d only on valid cells Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit e1ec820eb99fc912283a99a9c17b9195ad964f25 Merge: b155dc46 69f237aa Author: Hannah Klion Date: Tue Dec 5 09:47:12 2023 -0800 Merge pull request #62 from seahorce-scidac/cleanup Cleanup and add annotations to prestep commit 69f237aadaa5656e34ad0de345a764ae3aef0fab Merge: 86e3cb22 b155dc46 Author: Hannah Klion Date: Tue Dec 5 09:45:53 2023 -0800 Merge branch 'development' into cleanup commit 86e3cb225068639b09486ef8ef0ba1d1196b642c Author: Hannah Klion Date: Tue Dec 5 09:45:14 2023 -0800 add annotation and clean up some calls Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit b155dc4648efb9a2fd84bcbcb119ad5d8270e402 Merge: e61bda58 b5f75449 Author: Ann Almgren Date: Tue Dec 5 09:41:45 2023 -0800 Merge pull request #61 from seahorce-scidac/more_tweaks cleanup but no change to answers commit b5f754499d9e12f9a9586c93c73e92bc3b2cdde2 Author: Ann Almgren Date: Tue Dec 5 09:30:57 2023 -0800 cleanup but no change to answers Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_TimeStepML.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit e61bda58daa1f0fdd7f44ce8e599533de1e98e64 Author: Hannah Klion Date: Mon Dec 4 16:01:34 2023 -0800 clean up unneded var in rho_eos and add in/out for params Source/ROMSX.H Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 1ca52cd9c1adb14033aa82e03dd826695a36e9f3 Merge: 427a4867 5ba8b188 Author: Ann Almgren Date: Fri Dec 1 20:13:27 2023 -0800 Merge pull request #60 from seahorce-scidac/fix_indices fixing loop indices for face-centered arrays commit 5ba8b1888b8aace1f5dbb8fa22295bbf34c49149 Author: Ann Almgren Date: Fri Dec 1 18:54:12 2023 -0800 fixing loop indices for face-centered arrays Exec/Upwelling/prob.cpp Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_setup_step.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 427a486716230fe07739f6768700f50941b52446 Merge: 925d2c02 843fa59e Author: Hannah Klion Date: Fri Dec 1 18:38:12 2023 -0800 Merge pull request #59 from seahorce-scidac/timestepML Multilevel timestepping commit 843fa59e00347f5cd69a47a6115e58684e9330ba Merge: 6ab00801 925d2c02 Author: Hannah Klion Date: Fri Dec 1 18:33:03 2023 -0800 Merge branch 'development' into timestepML commit 6ab008017180395039afedffa5d1b79af7f7eaea Author: Hannah Klion Date: Fri Dec 1 18:17:06 2023 -0800 remove extraneous prints Source/TimeIntegration/ROMSX_TimeStepML.cpp commit 925d2c02e1de0920ab636ebc0131315bb9de47ac Author: Hannah Klion Date: Thu Nov 30 16:04:36 2023 -0800 make boxes in advance_2d align Source/TimeIntegration/ROMSX_advance_2d.cpp commit c499fbba64487b3dc5d6fccbfe485d2c45b19dc8 Author: Hannah Klion Date: Thu Nov 30 15:41:35 2023 -0800 make create velocity-related arrays on faces Source/ROMSX_make_new_level.cpp commit 30b886e86a46f27182a7c0948d01fb51440a2688 Author: Hannah Klion Date: Thu Nov 30 14:54:38 2023 -0800 create timestep multilevel version CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_TimeStepML.cpp commit 2dd84d68da4d70f6f3f6da0d71a39426bdf7e030 Merge: 81a2ee44 b1221129 Author: Ann Almgren Date: Wed Nov 29 18:49:02 2023 -0800 Merge pull request #57 from seahorce-scidac/cleanup clean up commit b1221129d866d6f257248622c7c95323d38ad005 Author: Ann Almgren Date: Wed Nov 29 18:01:50 2023 -0800 clean up Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/TimeIntegration/save_me commit 81a2ee440075644397bafe1bb6918e54bc4ebe7e Author: Hannah Klion Date: Wed Nov 29 16:07:05 2023 -0800 add new files to cmake list CMake/BuildROMSXExe.cmake commit df8da899d0b03798269a5f22d88bf0c3a62d6403 Author: Hannah Klion Date: Wed Nov 29 15:48:11 2023 -0800 add back FillBoundary Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 2260ecc4034b4a4d6900be51a7bb010b1619cebf Merge: c73da888 0dbf5f9a Author: Hannah Klion Date: Wed Nov 29 15:34:34 2023 -0800 Merge remote-tracking branch 'upstream/development' into split_advance commit c73da888fcb35fc7eda04a6c7b74d2a2ffb7ccf3 Author: Hannah Klion Date: Wed Nov 29 15:29:43 2023 -0800 first pass at splitting advance Source/ROMSX.H Source/ROMSX_make_new_level.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_2d_onestep.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_advance_3d_ml.cpp Source/TimeIntegration/ROMSX_setup_step.cpp commit 0dbf5f9a3531b2ce3a4794750420a9f2c8ee952c Author: Hannah Klion Date: Wed Nov 29 10:20:06 2023 -0800 add flag to turn off substepping on fine grids Source/ROMSX.H Source/ROMSX.cpp commit 8eaed634ff27f7f41daf012204188de6e75b49d7 Merge: dbd754e7 a5758912 Author: Ann Almgren Date: Tue Nov 28 17:33:35 2023 -0800 Merge pull request #55 from seahorce-scidac/fix2 fix2 commit a5758912a266cced751f8402608e8706d2635f1b Author: Ann Almgren Date: Tue Nov 28 16:46:24 2023 -0800 fix2 Exec/ParticlesOverSeaMount/prob.cpp Exec/Seamount/prob.cpp Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/Initialization/ROMSX_init.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/save_me Source/Utils/DepthStretchTransform.H Source/main.cpp commit dbd754e7efe945a65f38f3cf304434a01e24b4cc Merge: 29a013cc 38cbf17e Author: Ann Almgren Date: Tue Nov 28 12:59:13 2023 -0800 Merge pull request #54 from seahorce-scidac/fix1 tweaks commit 38cbf17e3ff1e2dae74f676fd08a100301a71f1b Author: Ann Almgren Date: Tue Nov 28 12:58:41 2023 -0800 tweaks Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 29a013cced8c02d41e5f4681b08c65107153003e Author: Hannah Klion Date: Tue Nov 28 12:16:22 2023 -0800 initialize Hz, z_w, etc with three ghost zones Source/ROMSX_make_new_level.cpp Source/Utils/DepthStretchTransform.H commit 41e399baa8f61fb8c345369e124bf4d641fba42f Merge: 12077cb8 6525c00d Author: Ann Almgren Date: Fri Nov 24 10:24:50 2023 -0800 Merge pull request #53 from seahorce-scidac/docs_fix update docs commit 6525c00d7a53adbf61380ef93a06c86281fff0dd Author: Ann Almgren Date: Fri Nov 24 10:23:12 2023 -0800 update docs Docs/sphinx_doc/index.rst Docs/sphinx_doc/theory/Equations.rst commit 12077cb8c40368b21a92e80f819a2bcd84004d27 Merge: d815108d 1897198e Author: Ann Almgren Date: Fri Nov 24 09:53:03 2023 -0800 Merge pull request #52 from seahorce-scidac/reorg more cleanup and get ready for multilevel commit 1897198e901ed662b3dea94d7cbd24be2ff95a68 Author: Ann Almgren Date: Fri Nov 24 09:25:30 2023 -0800 more cleanup and get ready for multilevel CMake/BuildROMSXExe.cmake Docs/sphinx_doc/Discretizations.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/MeshRefinement.rst Exec/Make.ROMSX Source/DataStruct.H Source/Initialization/Make.package Source/Initialization/ROMSX_init.cpp Source/Initialization/ROMSX_init1d.cpp Source/Initialization/ROMSX_init_bcs.cpp Source/Initialization/prob_common.H Source/Make.package Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_make_new_level.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp commit d815108d4d5bc7c614d04bc75c2876246e59218b Merge: eb275ae1 720e02f3 Author: Ann Almgren Date: Wed Nov 22 12:57:04 2023 -0800 Merge pull request #51 from seahorce-scidac/fix_particle_output fix particle output commit 720e02f3d56df39f30ae4866ae011ec2c6e4bdbf Author: Ann Almgren Date: Wed Nov 22 12:54:46 2023 -0800 fix particle output Source/IO/Plotfile.cpp commit eb275ae19b0846c65e07dfc0b49dd1399951ead9 Merge: dad68e6a 8d17d99e Author: Ann Almgren Date: Wed Nov 22 10:17:37 2023 -0800 Merge pull request #50 from seahorce-scidac/fix_another_particle_oops fix typo commit 8d17d99ea915d93b589fcbbb303d388872a72ea3 Author: Ann Almgren Date: Wed Nov 22 10:17:08 2023 -0800 fix typo Source/Particles/ParticleData.H commit dad68e6a7e20a72f0da7b58b436f1c0f0e6d9d4d Merge: 62a4687d c6eb4c49 Author: Ann Almgren Date: Wed Nov 22 09:59:24 2023 -0800 Merge pull request #49 from seahorce-scidac/fix_oops fix oops commit c6eb4c495b4bf2d23a176d98f9130d30c6e213a9 Author: Ann Almgren Date: Wed Nov 22 09:58:52 2023 -0800 fix oops Source/IO/Plotfile.cpp commit 62a4687d033b9447fc16a5955568af195cbc38af Merge: 6e04b0c3 9264b68e Author: Ann Almgren Date: Wed Nov 22 09:28:17 2023 -0800 Merge pull request #48 from seahorce-scidac/update_inputs update inputs commit 9264b68e7a5ab85743c8c604309419dfde108647 Author: Ann Almgren Date: Wed Nov 22 09:27:41 2023 -0800 update inputs Exec/ParticlesOverSeaMount/inputs commit 6e04b0c3c44af0e2e70cc8a24c7b102300dcecf5 Merge: 1f9c352d 56ce2250 Author: Ann Almgren Date: Wed Nov 22 09:19:22 2023 -0800 Merge pull request #47 from seahorce-scidac/update_particles update particles plus more cleanup commit 56ce22501b91768b02ce449e4b158d05a1c47b0b Author: Ann Almgren Date: Wed Nov 22 08:58:06 2023 -0800 update input Docs/sphinx_doc/Particles.rst commit 3c8cbc4f8b809702a9598d8f0d7aa2698aa75fa1 Author: Ann Almgren Date: Wed Nov 22 08:55:34 2023 -0800 trailing white space Exec/ParticlesOverSeaMount/prob.cpp commit cc68153d6e1ef9e9657ba07ed171eb0da48d28e4 Author: Ann Almgren Date: Wed Nov 22 08:54:06 2023 -0800 update particles plus more cleanup CMake/BuildROMSXExe.cmake Exec/ParticlesOverSeaMount/prob.cpp Source/IO/Checkpoint.cpp Source/IO/Plotfile.cpp Source/Particles/Make.package Source/Particles/ParticleData.H Source/Particles/TracerPC.H Source/Particles/TracerPC.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 1f9c352db4b8470ce23c6e80fab82653d71ebc76 Merge: 31dba2ee b2474da0 Author: Ann Almgren Date: Tue Nov 21 19:34:01 2023 -0800 Merge pull request #46 from seahorce-scidac/fix_for_gpu fix for CUDA commit b2474da0165c5785ae7614c989eba01a60729c39 Author: Ann Almgren Date: Tue Nov 21 19:32:40 2023 -0800 fix for CUDA Source/TimeIntegration/ROMSX_advance_3d.cpp commit 31dba2ee3abf23c2ecef5af9dd6cd7d66486ebf5 Merge: d166bb20 a822e8e6 Author: Ann Almgren Date: Tue Nov 21 19:00:30 2023 -0800 Merge pull request #45 from seahorce-scidac/fix_particles fix commit a822e8e643639771e0b4d564883bc6f692270328 Author: Ann Almgren Date: Tue Nov 21 18:59:41 2023 -0800 fix Source/IO/Plotfile.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit d166bb206cde551534d5f7174ab1edd8c97ecab8 Merge: ec500dfa 8441bd28 Author: Ann Almgren Date: Tue Nov 21 17:05:57 2023 -0800 Merge pull request #44 from seahorce-scidac/multilevel some changes for multilevel and cleanup of unused variables commit 8441bd28d4c904f9d6c5d7318b4ea6fb083967e7 Author: Ann Almgren Date: Tue Nov 21 16:56:19 2023 -0800 fix white space Exec/Upwelling/prob.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit f12e85cf7df92d5e6cd6614a939807d72f83bdf6 Author: Ann Almgren Date: Tue Nov 21 16:54:40 2023 -0800 some changes for multilevel and cleanup of unused variables Exec/Upwelling/Palette Exec/Upwelling/amrvis.defaults Exec/Upwelling/inputs_ml Exec/Upwelling/prob.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Plotfile.cpp Source/ROMSX.cpp Source/ROMSX_Tagging.cpp Source/ROMSX_init.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_set_weights.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/Utils/DepthStretchTransform.H commit ec500dfae5ce49962d878fb8ab0f1e2e9414b974 Author: Hannah Klion Date: Fri Nov 17 14:45:42 2023 -0800 Make sure Problem Setup docs show up in sidebar and adjust tables Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/ProblemSetup.rst commit fd5277ea262319c012e4ddc2556f52c0e1a8a018 Author: Hannah Klion Date: Fri Nov 17 09:33:56 2023 -0800 remove verbose Source/Utils/DepthStretchTransform.H commit fb5f749f212989d76aabcfd141edd2623100cb53 Author: Hannah Klion Date: Fri Nov 17 09:18:44 2023 -0800 remove another verbose from GPU region Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit b060e2cad9b8cc141b3c2ae6c2e90dee6c8f89de Author: Hannah Klion Date: Fri Nov 17 09:03:09 2023 -0800 remove verbose from GPU region Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit f6539bd7accef72ebbb1405c258767ec61ca1491 Author: Hannah Klion Date: Thu Nov 16 17:04:42 2023 -0800 remove another stray verbose Source/TimeIntegration/ROMSX_prsgrd.cpp commit f36463973d6c45e9227c82cb772259a3c4a56630 Author: Hannah Klion Date: Thu Nov 16 16:52:37 2023 -0800 move stray verbose Source/TimeIntegration/ROMSX_advance_2d.cpp commit 5099f1af38af4434d24ec1b252f9fe59dc5c1c0c Author: Hannah Klion Date: Thu Nov 16 16:04:48 2023 -0800 fix compile errors Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 9dcb493ec0ceee5efba1620fc374643dd8631d41 Author: Hannah Klion Date: Thu Nov 16 15:57:11 2023 -0800 move verbose logic out of gpu loops Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit e4415ba1951c524d133ea97138f100a76713b547 Author: Hannah Klion Date: Thu Nov 16 15:21:57 2023 -0800 update boxes in pressure gradient to be nodal and add prints Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 96abb09b8e6b5a4fdb6820aaa7a772d7617b7193 Author: Hannah Klion Date: Mon Nov 13 15:00:21 2023 -0800 fix boxes and put print statements in verbose if statements Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H commit a500f4c85390fdbc14d50914971cb24f9393faa1 Merge: 1f1b5789 d1733eab Author: Ann Almgren Date: Thu Nov 9 08:58:51 2023 -0800 Merge pull request #43 from seahorce-scidac/add_kineng Add kinetic energy as part of sum_integrated_quantities commit d1733eab6e2694f03e544e7304cc54be48a74b37 Author: Ann Almgren Date: Wed Nov 8 13:40:35 2023 -0800 Add kinetic energy as part of sum_integrated_quantities Exec/Upwelling/inputs Source/ROMSX_SumIQ.cpp commit 1f1b57895865be83dc6a35e6ef44667f7242e0f4 Author: Hannah Klion Date: Mon Oct 23 16:32:23 2023 -0700 don't update uv3dmix on overlapping cells Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 1bedf41f748006198c5b45164b1103ca1d280885 Author: Hannah Klion Date: Mon Oct 23 13:30:59 2023 -0700 adjust ProblemSetup.rst header Docs/sphinx_doc/ProblemSetup.rst commit a0aace0c1cb8c8b36bf9f9d2866546a2c2256532 Author: Hannah Klion Date: Mon Oct 23 13:22:11 2023 -0700 get ProblemSetup to show up Docs/sphinx_doc/ProblemSetup.rst commit 0b1320053a6ca0a76a748cb2e4cd48a7c01ff6f2 Author: Hannah Klion Date: Mon Oct 23 11:10:02 2023 -0700 add documentation for how to set up problems Docs/sphinx_doc/ProblemSetup.rst Docs/sphinx_doc/index.rst commit cb29a06fa67bbea3fbbcb94ffc966211f4687b14 Author: Hannah Klion Date: Tue Oct 17 10:03:57 2023 -0700 fix boxes in rhs_t_3d for centered4 Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 731237fc0fe286459ff093c76e68b40fcfb9a0db Author: Hannah Klion Date: Mon Oct 16 13:50:00 2023 -0700 fill boundary on mass fluxes in advance3d Source/TimeIntegration/ROMSX_advance_3d.cpp commit 737a8e9f787779717f1be1d1d9ecde24bab84e53 Author: Hannah Klion Date: Fri Oct 13 17:02:46 2023 -0700 fill boundary on ru and rv after each call to advance_2d Source/TimeIntegration/ROMSX_advance_2d.cpp commit 06d328bd30599f2e8fd26e7833ca9a68226e60c7 Author: Hannah Klion Date: Fri Oct 13 14:39:39 2023 -0700 Fix k indexing in rhs3d Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit cbf1411f8ea07b8f16358f0c012bceb47a4da562 Merge: a01f1184 d57d474c Author: Ann Almgren Date: Fri Oct 13 09:29:09 2023 -0700 Merge pull request #42 from jmsexton03/update_license Update license commit d57d474cc54a9865b6f964c6e72743a4ba425db4 Author: Jean M. Sexton Date: Fri Oct 13 09:28:55 2023 -0700 Fix style README.rst commit 450553eeb20e2149956e49a50d899387f5fe86d5 Author: Jean M. Sexton Date: Fri Oct 13 09:25:25 2023 -0700 Tweak links README.rst commit 0bff26bb9a77ff167150f8e950093e05a87eb698 Author: Jean M. Sexton Date: Fri Oct 13 09:23:56 2023 -0700 Change file type README.rst commit edc67861618d8c45ce254f96e43321d98c677fe3 Author: Jean M. Sexton Date: Fri Oct 13 09:20:26 2023 -0700 README and LICENSE updates LICENSE.md README.md commit a01f11849ef344034ef421c2a26fcfb5e7b8d2f0 Author: Hannah Klion Date: Thu Oct 12 14:30:53 2023 -0700 calculate EOS with [tracer]old, and fix braces on first step copy conditional Source/TimeIntegration/ROMSX_Advance.cpp commit 7c2c2f56d24d9ba3372bb80b8caa0077d0526f8e Author: Hannah Klion Date: Wed Oct 11 16:44:54 2023 -0700 only copy old state into new at first step Source/TimeIntegration/ROMSX_Advance.cpp commit e75bbf43956d872e1954665eb4df2f2ac3925580 Author: Hannah Klion Date: Mon Oct 9 16:28:21 2023 -0700 update vmix with new z_w Source/TimeIntegration/ROMSX_Advance.cpp commit 68d8c43b6d53fd4edb71912a1c456f7d6f8ebb19 Author: Hannah Klion Date: Mon Oct 9 13:55:20 2023 -0700 update zeta with a 2d box, not 3d Source/TimeIntegration/ROMSX_Advance.cpp commit a4516cca6a7c7a7a9fe8fa39c3bffa6c5d1701cb Author: Hannah Klion Date: Sun Oct 8 16:51:22 2023 -0700 update free surface to average value before barotropic step Source/TimeIntegration/ROMSX_Advance.cpp commit 9d8cd2d6a9bb8dae41a861b163405e4ee2c1ec2e Merge: 656fa79b c26f817e Author: Jean M. Sexton Date: Mon Oct 2 10:24:54 2023 -0700 Merge pull request #39 from WeiqunZhang/paren_macro Add parentheses around macro expressions commit 656fa79be497e69586430df96aca42a507e39bfc Merge: a49b1c6d 81a545b7 Author: Jean M. Sexton Date: Mon Oct 2 10:24:09 2023 -0700 Merge pull request #41 from jmsexton03/ctest_fix_dev Remove spurious test, uncomment test action commit 81a545b75865913e4144b7773f6e7979fec314e2 Author: Jean M. Sexton Date: Fri Sep 29 17:26:19 2023 -0700 Use wildcard in ctest fcompare name Tests/CMakeLists.txt commit e9164ad83870460990394c0e196c497b937e716f Author: Jean M. Sexton Date: Fri Sep 29 17:12:37 2023 -0700 Try wildcard Tests/CTestList.cmake commit dec975f2a0d0b56b1889cdecbe622d6d9d4519f7 Author: Jean M. Sexton Date: Fri Sep 29 17:02:03 2023 -0700 Change exe name if on windows Tests/CTestList.cmake commit 2aa25541b3f9f11e446d38ccce0d06770813c6d2 Author: Hannah Klion Date: Thu Sep 28 22:22:46 2023 -0700 reduce processors in ctest Tests/CTestList.cmake commit 20410dfc14e0a5fd6fc8e14a1f31c9370b51af44 Author: Jean M. Sexton Date: Fri Sep 29 15:52:44 2023 -0700 Specify tests and make ctest verbose .github/workflows/gcc.yml .github/workflows/macos.yml .github/workflows/windows.yml commit 2c15855f8a26b07279eac4f78a4d0110854dc752 Author: Jean M. Sexton Date: Mon Sep 25 10:26:02 2023 -0700 Remove spurious test, uncomment test action .github/workflows/gcc.yml .github/workflows/macos.yml .github/workflows/windows.yml Tests/CTestList.cmake commit a49b1c6dea19839d828b032b815f0fb62a91253c Author: Hannah Klion Date: Tue Sep 26 20:27:59 2023 -0700 update prob.cpp for ParticlesOverSeaMount to include problem-specific functions Exec/ParticlesOverSeaMount/prob.cpp commit 921538355c52842f9ea1917405b3b0e8a7f18428 Author: Hannah Klion Date: Tue Sep 26 20:12:07 2023 -0700 fixed bug where Akv was being used instead of Akt Source/TimeIntegration/ROMSX_advance_3d.cpp commit c26f817e5f44cd272bf273858d7eb2e082290c7d Author: Weiqun Zhang Date: Tue Sep 26 09:55:16 2023 -0700 Add parentheses around macro expressions Things like #define NUM_PRIM NVAR-1 is error prone. For example, `N - NUM__PRIM` will become `N - NVAR - 1` instead of `N - (NVAR - 1)`. Source/IndexDefines.H Source/ROMSX_Constants.H commit 70cd484115d6e3771d3dec0352f6eabbb7143174 Merge: 1ab3618a 73d963b1 Author: Jean M. Sexton Date: Mon Sep 25 09:53:04 2023 -0700 Merge pull request #37 from hklion/seamount_exec Create Exec directory for seamount and move custom functions to prob.cpp commit 1ab3618a5caa67df00b13b0353d58ec86be67ac7 Merge: 89b1b30e 9ec95e8a Author: Jean M. Sexton Date: Mon Sep 25 09:50:50 2023 -0700 Merge pull request #38 from JessCG/beta test log filepath commit 9ec95e8afa527e426d28c10802709943b9a65d58 Author: JessCG Date: Mon Sep 25 09:33:51 2023 -0700 test log filepath The log files for tests show up in Testing/Temporary/LastTest.log Docs/sphinx_doc/testing.rst commit 73d963b1664e31e55057b965311d57d9afd8bbde Author: Hannah Klion Date: Fri Sep 22 18:11:48 2023 -0700 finish setting up seamount problem -- still undebugged Exec/Seamount/inputs Exec/Seamount/prob.cpp commit c60667a36f9b04b4aebec4f2f71ca59b6c89a263 Author: Hannah Klion Date: Fri Sep 22 15:52:02 2023 -0700 move set_2darrays to Init, and adjust prob for seamount Exec/Seamount/prob.cpp Source/ROMSX_init.cpp Source/Utils/DepthStretchTransform.H commit 40876f77fa003514d63b20934794752634531e5e Author: Hannah Klion Date: Fri Sep 22 12:11:50 2023 -0700 add set_weights to CMake lists CMake/BuildROMSXExe.cmake commit 71eae701ac44dbf8c66b96dc8d25fc395c43d98c Author: Hannah Klion Date: Fri Sep 22 11:14:53 2023 -0700 add file for calculating 2D step weights Source/TimeIntegration/ROMSX_set_weights.cpp commit 89b1b30ed32c05ac9924f790a0d0a4d8613b0acb Author: Jean M. Sexton Date: Fri Sep 22 08:29:47 2023 -0700 Fix style Docs/sphinx_doc/submodule.rst commit 2e72290a68c03dcf59d92d9e167919ffe866adc4 Author: Jean M. Sexton Date: Fri Sep 22 08:27:24 2023 -0700 Add submodule docs section to use config example Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/submodule.rst commit 97dcf2a6f6c2e746b26a151bf1f1328bd01b16d3 Author: Hannah Klion Date: Wed Sep 20 17:49:11 2023 -0700 set up pseudo-seamount problem. Many things are still set like upwelling Exec/Seamount/CMakeLists.txt Exec/Seamount/GNUmakefile Exec/Seamount/Make.package Exec/Seamount/amrvis.defaults Exec/Seamount/inputs Exec/Seamount/prob.H Exec/Seamount/prob.cpp commit 6d27dc0d2b915d8eaf178d4fab05bd7634d8395b Author: Hannah Klion Date: Wed Sep 20 17:44:05 2023 -0700 move problem-specific values such as Akv, Akt, sustr, svstr to prob.cpp from DepthStretchTransform Exec/Upwelling/prob.cpp Source/DataStruct.H Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/Utils/DepthStretchTransform.H Source/prob_common.H commit 36d32b3f0dcf1146341e77c684e3053b8ff8aacd Author: Hannah Klion Date: Mon Sep 11 10:10:48 2023 -0700 add ParserExecutors to prob_common Source/prob_common.H commit 9f4180e46eb4e3b3356d6713624cca4fe8f5d859 Merge: 6880f89f 571ee6c2 Author: Ann Almgren Date: Tue Sep 19 17:56:08 2023 -0700 Merge pull request #30 from jmsexton03/bathymetry_2d_boxes Bathymetry 2d boxes commit 571ee6c263c3b6d42cd3dca76870ac4ff013bab0 Merge: 345996f7 6880f89f Author: Ann Almgren Date: Tue Sep 19 17:17:08 2023 -0700 Merge branch 'development' into bathymetry_2d_boxes commit 6880f89f1ab971d8f2a017c5e594a53d9e95d7e3 Merge: 94ec5491 4a0abf34 Author: Ann Almgren Date: Tue Sep 19 17:06:53 2023 -0700 Merge pull request #35 from WeiqunZhang/atomic_add Refactor a kernel in rhs_3d commit 4a0abf348d890d945dc7253ad8c45a4442ae2ce9 Author: Weiqun Zhang Date: Tue Sep 19 14:41:09 2023 -0700 Refactor a kernel in rhs_3d By avoiding atomicAdd, we can make the GPU and CPU results agree with each other much better. Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 94ec5491fb5b7b681f953c4e6bc68ab8b1771944 Merge: 9bb5fbe5 da3b4501 Author: Ann Almgren Date: Tue Sep 19 15:39:44 2023 -0700 Merge pull request #34 from seahorce-scidac/fixes cleanup only commit da3b4501b2d6c36043da022e2011114f2dc375e7 Author: Ann Almgren Date: Tue Sep 19 14:08:59 2023 -0700 fix white space Source/ROMSX_SumIQ.cpp commit d2cab3c8179459ef5f76f47f88c73c2c303bb0e6 Author: Ann Almgren Date: Tue Sep 19 14:02:14 2023 -0700 fix cmake CMake/BuildROMSXExe.cmake commit c912803cf0070d562404c4ec9ce644016fc6352a Author: Ann Almgren Date: Tue Sep 19 13:59:39 2023 -0700 cleanup only Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_SumIQ.cpp Source/ROMSX_init.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/Utils/Interpolation.H Source/Utils/Make.package Source/Utils/MomentumToVelocity.cpp Source/Utils/Utils.H Source/Utils/VelocityToMomentum.cpp commit 9bb5fbe5e3b9c8ba13c57079cf9ded6099f95d0c Merge: 1156c402 13bb291e Author: Ann Almgren Date: Tue Sep 19 12:56:18 2023 -0700 Merge pull request #33 from WeiqunZhang/more_race_conditions Fix more race conditions and clean up commit 13bb291e4c1bcb26a34523528b5d9d0404df9ad5 Author: Weiqun Zhang Date: Tue Sep 19 07:47:43 2023 -0700 Fix more race conditions and clean up Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/Utils/DepthStretchTransform.H commit 345996f742013c9f7d8326cb6ffdbff28160bc54 Author: Jean M. Sexton Date: Tue Sep 19 10:04:15 2023 -0700 Make submodule match development fix Submodules/AMReX commit fe793a3e4aaa83d98927c77ef980c27bbfabf800 Author: Jean M. Sexton Date: Tue Sep 19 10:00:39 2023 -0700 Make submodule match development Submodules/AMReX commit 0d2ebc8f765ea740ac51d73e13d5553f8312582c Author: Jean M. Sexton Date: Tue Sep 19 09:56:05 2023 -0700 Apply suggestions from code review Co-authored-by: Weiqun Zhang Source/TimeIntegration/ROMSX_advance_2d.cpp commit 1156c402942ee9b51a051158e0e2c36c588b4dcd Merge: aabb8e41 506565fb Author: Ann Almgren Date: Mon Sep 18 18:10:34 2023 -0700 Merge pull request #32 from seahorce-scidac/particles_fixed fix for particles; update amrex submodule commit 506565fbff2709ddbb746125209cacbba9ca94cb Author: Ann Almgren Date: Mon Sep 18 17:58:30 2023 -0700 fix for particles; update amrex submodule Exec/ParticlesOverSeaMount/GNUmakefile Submodules/AMReX commit aabb8e41f8caca1468c9a967c9bff49a88f41a81 Merge: b0ea9a77 d8607a4d Author: Ann Almgren Date: Mon Sep 18 16:04:23 2023 -0700 Merge pull request #31 from atmyers/fix_increment_call Call redistribute before calling increment. commit d8607a4db09d583ee1061a066681d853d3441bca Author: Andrew Myers Date: Mon Sep 18 15:06:07 2023 -0700 remove unused increment function Source/Particles/TerrainFittedPC.H Source/Particles/TerrainFittedPC.cpp commit 12e376cb350b91409d9cbb20b98541357afcdc76 Author: Andrew Myers Date: Mon Sep 18 14:52:48 2023 -0700 Call redistribute before calling increment. Source/IO/Plotfile.cpp Source/Particles/TerrainFittedPC.H Source/Particles/TerrainFittedPC.cpp commit c6cee59095ca95a2991029aaecdf7dde749e544a Author: Ann Almgren Date: Fri Sep 15 08:22:30 2023 -0700 remove unusued variables and update amrex submodule Source/DataStruct.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Submodules/AMReX commit 69414f55278fc29558056865460ccc02c50e8ea5 Author: Jean M. Sexton Date: Mon Sep 18 10:28:13 2023 -0700 Fix boxes by using contains Source/TimeIntegration/ROMSX_advance_2d.cpp commit 266f06decceda2aecc9ca5964791c9c7f9210fb0 Author: Jean M. Sexton Date: Thu Sep 14 17:44:12 2023 -0700 Add FillBoundary on DUon and DVom for -2 index Source/TimeIntegration/ROMSX_advance_2d.cpp commit 53edca18ec5d7aa8ddb1d02bbcd2d3b6167a4561 Author: Hannah Klion Date: Thu Sep 14 16:19:40 2023 -0700 add fill boundary for W and fix calculation of z_w at surface Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit b0ea9a77c0dbd89a4d185d1089c9fb8e0c479781 Merge: ac2091b6 f9480d71 Author: Ann Almgren Date: Sun Sep 17 20:45:24 2023 -0700 Merge pull request #29 from seahorce-scidac/update_increment add to particle functionality commit f9480d7145e2846fcc99dd05c09dff34c7759df7 Author: Ann Almgren Date: Sun Sep 17 19:51:54 2023 -0700 add to particle functionality Docs/sphinx_doc/Particles.rst Source/Particles/TerrainFittedPC.H Source/Particles/TerrainFittedPC.cpp commit ac2091b6679634eb548c0a6f4b8fa488501166e3 Merge: 6ce096e1 8fe5237b Author: Ann Almgren Date: Sun Sep 17 18:54:36 2023 -0700 Merge pull request #28 from seahorce-scidac/update_docs_for_particles get particle example working, clean out a lot of unused stuff from ER… commit 8fe5237b1bd5762f47d78e3deac74477e9052cc2 Author: Ann Almgren Date: Sun Sep 17 17:28:14 2023 -0700 get particle example working, clean out a lot of unused stuff from ERF, add docs for particles Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Particles.rst Docs/sphinx_doc/building.rst Docs/sphinx_doc/index.rst Exec/ParticlesOverSeaMount/CMakeLists.txt Exec/ParticlesOverSeaMount/GNUmakefile Exec/ParticlesOverSeaMount/Make.package Exec/ParticlesOverSeaMount/inputs Exec/ParticlesOverSeaMount/prob.H Exec/ParticlesOverSeaMount/prob.cpp Exec/Upwelling/GNUmakefile Exec/Upwelling/prob.cpp Source/DataStruct.H Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp Source/IndexDefines.H Source/Particles/TerrainFittedPC.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp Source/ROMSX_init_bcs.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/Utils/DepthStretchTransform.H Source/prob_common.H commit 6ce096e1e3dbe52aa7ba87a386bc6c4775b44c25 Author: Hannah Klion Date: Fri Sep 15 15:41:50 2023 -0700 Update documentation about NetCDF files and checkpointing Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/Plotfiles.rst Docs/sphinx_doc/building.rst Docs/sphinx_doc/index.rst Source/ROMSX.cpp commit e46f22e7a009cbb9224a09ad7b0c5cdd7b404a55 Author: Hannah Klion Date: Fri Sep 15 14:20:23 2023 -0700 remove old ERF pages from documentation table of contents Docs/sphinx_doc/index.rst commit 3bd557abc9e04c6d9aacdc48c9c03c2af8900a9b Author: Hannah Klion Date: Fri Sep 15 10:41:31 2023 -0700 Revert "add fill boundary for W and fix calculation of z_w at surface" This reverts commit 978b11e0779391160ca720708dd994528095302f. Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit 37ff856b810a846a517e9a5db24438d01a0cc4ae Author: Hannah Klion Date: Fri Sep 15 10:40:59 2023 -0700 Revert "Add FillBoundary on DUon and DVom for -2 index" This reverts commit 0625dcc98eb15cd1881ebce4dd6da77a4b5b798e. Source/TimeIntegration/ROMSX_advance_2d.cpp commit 3f2d01da64a466d8b2ac8c88a0693984d85ac34b Author: Hannah Klion Date: Fri Sep 15 10:40:47 2023 -0700 Revert "remove unusued variables and update amrex submodule" This reverts commit 8ec974ee33492cac000c93da298fc4698d19a9b3. Source/DataStruct.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Submodules/AMReX commit bf84bef83777782e80e4d0bc9c5ad31aeb46a146 Author: Hannah Klion Date: Fri Sep 15 10:26:22 2023 -0700 Revert "adjust boxes for fluxes in advance_2d" This reverts commit 85c710114e3572b710ae5ef845c33b29ca0db08f. Source/TimeIntegration/ROMSX_advance_2d.cpp commit 85c710114e3572b710ae5ef845c33b29ca0db08f Author: Hannah Klion Date: Fri Sep 15 09:45:21 2023 -0700 adjust boxes for fluxes in advance_2d Source/TimeIntegration/ROMSX_advance_2d.cpp commit 8ec974ee33492cac000c93da298fc4698d19a9b3 Author: Ann Almgren Date: Fri Sep 15 08:22:30 2023 -0700 remove unusued variables and update amrex submodule Source/DataStruct.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Submodules/AMReX commit 1fbb848b33cc22114d57e42d34127bd3154bc436 Merge: 0625dcc9 5d6bb654 Author: Jean M. Sexton Date: Fri Sep 15 06:45:16 2023 -0700 Merge pull request #27 from WeiqunZhang/weiqun/development Fix race conditions commit 5d6bb6541d026e36cd22e99c70564a8f1f22cc26 Author: Weiqun Zhang Date: Thu Sep 14 14:41:22 2023 -0700 Fix race conditions Source/IO/NCColumnFile.cpp Source/ROMSX_SumIQ.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 0625dcc98eb15cd1881ebce4dd6da77a4b5b798e Author: Jean M. Sexton Date: Thu Sep 14 17:44:12 2023 -0700 Add FillBoundary on DUon and DVom for -2 index Source/TimeIntegration/ROMSX_advance_2d.cpp commit 978b11e0779391160ca720708dd994528095302f Author: Hannah Klion Date: Thu Sep 14 16:19:40 2023 -0700 add fill boundary for W and fix calculation of z_w at surface Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit 59a74dfe4e591123834ce3c4d10b007695dede94 Author: Hannah Klion Date: Tue Sep 12 17:33:34 2023 -0700 call update_vel on tempold in prestep_t Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit dd03bfd08b5e76a8089adb139588473268acd8cc Author: Hannah Klion Date: Tue Sep 12 13:45:58 2023 -0700 calculate harmonic viscosity on a larger box Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 88799a1bb2445b9e46d7366c98b875409db44575 Author: Hannah Klion Date: Mon Sep 11 11:16:14 2023 -0700 use uold and vold in 3d calls to uv3dmix, and also correct flux terms Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit c30e6f0bedde2f1e6e8e392ec8964bf10c65a2dc Author: Hannah Klion Date: Tue Sep 5 18:02:50 2023 -0700 fix compilation error and call 2D uv3dmix with Drhs not Drhs_p Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_2d.cpp commit a8de3fc69dc409d812b62f38fbfce9ef43ee3a01 Author: Hannah Klion Date: Tue Sep 5 13:24:52 2023 -0700 remove print statement Source/TimeIntegration/ROMSX_rho_eos.cpp commit b9fb6bcb71001847077f76bb0a7a7385c3ae5324 Author: Hannah Klion Date: Tue Sep 5 12:46:34 2023 -0700 bugfixes and debugging Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 7e2c067fb4afa98e376b959cbe9d6a1591a905f3 Author: Hannah Klion Date: Mon Aug 28 16:01:41 2023 -0700 update h(i,j,0,1) Exec/Upwelling/prob.cpp commit bf26d645a290f4feaf2fe79d913e6bd3fcfa9b9b Author: Hannah Klion Date: Mon Aug 28 11:07:58 2023 -0700 patch for merge Source/Utils/DepthStretchTransform.H commit 45ade0344fc72ede290a170d22b68780f63041a0 Author: Hannah Klion Date: Fri Aug 25 15:35:21 2023 -0700 re-remove set_detph from depth stretch transform Source/Utils/DepthStretchTransform.H commit 197e70a2baffe2d79de3671124106f79b9ef4da7 Author: Hannah Klion Date: Fri Aug 25 15:20:11 2023 -0700 remove extraneous comments Exec/Upwelling/prob.cpp commit c5ecc1e93c965a517f703ecfc618f5e938fb53eb Author: Hannah Klion Date: Fri Aug 25 12:07:55 2023 -0700 bathymetry is now set in prob Exec/Upwelling/prob.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/prob_common.H commit c75b2d1fa002f5c60145b4105d63448505feac18 Author: Hannah Klion Date: Thu Aug 24 09:40:39 2023 -0700 first pass at moving depth to prob Exec/Upwelling/prob.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H Source/prob_common.H commit 27f26921530aeda60c36a7ab5d46feb33ec68e3c Author: Hannah Klion Date: Tue Aug 22 17:23:42 2023 -0700 split function for setting depth out from stretch and transform Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit a1e9db04932d5be290649a1c3304d792bc355712 Merge: 9a6c241c 870ec83d Author: Ann Almgren Date: Sat Sep 2 14:33:46 2023 -0700 Merge pull request #26 from melbarkerlbl/variable-table-and-time-stepping Variable table and time stepping docs commit 870ec83d40aa642dd4a97e229003d885a59cd0b6 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Sep 1 09:13:59 2023 -0700 add time stepping page Docs/sphinx_doc/Time_Stepping.rst commit a517505b5f4565a1ab144f6f5bdc614372d58b2a Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Sep 1 09:12:32 2023 -0700 add figure for time stepping page Docs/sphinx_doc/figures/Timestep_1.png commit 55e86488ba1d565130a2437a329d9e11f943ba05 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Sep 1 09:10:28 2023 -0700 Update index.rst Docs/sphinx_doc/index.rst commit eb54f62d1429861a26f9b98018663ead2eecb3e9 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Sep 1 09:09:49 2023 -0700 add variable table Docs/sphinx_doc/Numerical_Solution_Technique.rst commit 9a6c241c46a3b5e108304740eebff08495e5d9e9 Author: Hannah Klion Date: Mon Aug 28 09:39:30 2023 -0700 made z_w nodal, fixing bounds issue Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit a5412051b48db34879e8b8a31b9895866906d87e Author: Ann Almgren Date: Fri Aug 25 19:25:57 2023 -0700 mixed up arrays Source/ROMSX.cpp commit 19377b251b0dcde3083279a8daee1728da4aa728 Merge: 3ef89ca3 9177446a Author: Jean M. Sexton Date: Fri Aug 25 16:44:34 2023 -0700 Merge pull request #23 from jmsexton03/bathymetry_advection_fluxes Bathymetry advection flux changes and prsgrd term commit 9177446a71a147bcc45cf70b522e153b54c641a7 Merge: 42e95e36 3ef89ca3 Author: Ann Almgren Date: Fri Aug 25 14:39:25 2023 -0700 Merge branch 'development' into bathymetry_advection_fluxes commit 3ef89ca30e75b79590d4e3c35d97b7138ea743b4 Author: Ann Almgren Date: Fri Aug 25 14:28:06 2023 -0700 fix whitespace Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 62440635996d23d3f8dd2c71d40b63cc98ea03f0 Author: Ann Almgren Date: Fri Aug 25 14:24:58 2023 -0700 update z_phys_nd Source/Particles/TerrainFittedPC.H Source/Particles/TerrainFittedPC.cpp Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit 42e95e36387d3362e21bc19dc0b963554d30ec9b Merge: cc5ee468 aca8e191 Author: Jean M. Sexton Date: Fri Aug 25 13:05:56 2023 -0700 Merge branch 'development' into bathymetry_advection_fluxes commit cc5ee46866fdc2d7bf31f7a6ac12473dbbf3e89e Author: Jean M. Sexton Date: Fri Aug 25 07:24:11 2023 -0700 Duplicate code and shift indices for rv in prsgrd Source/TimeIntegration/ROMSX_prsgrd.cpp commit f55c554fbcf7c220ab13bd998c14d0be7d3de8d1 Author: Jean M. Sexton Date: Fri Aug 25 07:15:10 2023 -0700 fix index conditional, swap cff and 1 typo Source/TimeIntegration/ROMSX_prsgrd.cpp commit aca8e19148ed1c64ed9dc5c63bb2ca1c80db2574 Author: Jean M. Sexton Date: Thu Aug 24 16:50:43 2023 -0700 Fix hip ci similarly to ERF PR 1125 (#22) CMake/SetAmrexCompileFlags.cmake CMakeLists.txt commit 899e2cad15ca62583f33e20bf66beae18940b6d7 Author: Hannah Klion Date: Thu Aug 24 10:41:41 2023 -0700 removed extraneous variables Source/TimeIntegration/ROMSX_set_massflux_3d.cpp commit 2bdae62d5720a1d95bee7438a5b87d7c307eed7f Merge: 92f09c68 85dc3663 Author: Ann Almgren Date: Thu Aug 24 10:04:31 2023 -0700 Merge pull request #20 from seahorce-scidac/update_hip_yml update hip.yml commit 85dc3663aa4767eb3f18ae9248ffd71b5cfb8b8f Author: Ann Almgren Date: Thu Aug 24 08:54:02 2023 -0700 update hip.yml .github/workflows/hip.yml commit 92f09c68f37ed9bf5bd1200ca13623be73057b87 Merge: 7e1b6498 d19648be Author: Ann Almgren Date: Thu Aug 24 08:50:13 2023 -0700 Merge pull request #18 from jmsexton03/add_z_phys_nd Add nodal z variable for particles commit 7e1b6498d925920980547580704dd1ef83557704 Merge: 39142729 e3c4d20a Author: Ann Almgren Date: Thu Aug 24 08:46:28 2023 -0700 Merge pull request #19 from melbarkerlbl/doc_adding Doc adding commit d19648be695abe7dc0063ea945a97bbaa8504e0c Author: Jean M. Sexton Date: Wed Aug 23 16:13:38 2023 -0700 Make nodal use 4 neighbors instead of 2 Source/Utils/DepthStretchTransform.H commit 39142729b3ddf0913c43d2163484cb3b122b2a38 Author: Hannah Klion Date: Wed Aug 23 15:47:03 2023 -0700 disable docs deployment on pull requests .github/workflows/docs.yml commit e3c4d20acf19c03b4beea83e53116f5bdd9ac10a Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 23 15:21:16 2023 -0700 Update Numerical_Solution_Technique.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst commit 4967e457ec291aac9ddfaace9ee2905e5ba6dd1a Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 23 15:13:24 2023 -0700 Update Numerical_Solution_Technique.rst Docs/sphinx_doc/Numerical_Solution_Technique.rst commit 98c18280c3c7c1dfc35f9eb60a8a859c4a415518 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 23 15:09:11 2023 -0700 Update Numerical_Solution_Technique.rst added several sections Docs/sphinx_doc/Numerical_Solution_Technique.rst commit dc6dcfc3d1d08fbb968e37eb29ff620aae846240 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 23 15:01:59 2023 -0700 add to numerical solution doc page Docs/sphinx_doc/figures/Barostep.png Docs/sphinx_doc/figures/Shortstep.png commit 03a498774fcf55561bdc8db2b5fc4e4aa4b44376 Author: Jean M. Sexton Date: Wed Aug 23 14:22:42 2023 -0700 Fix style Source/Utils/DepthStretchTransform.H commit 0b0d92a2a0a7273e191c8a68be0110e2f2009806 Author: Jean M. Sexton Date: Wed Aug 23 14:15:05 2023 -0700 Move z_phys_nd loop, fix variable names Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 428d96855a1d7afd17412f931514cca5fb3d3c22 Author: Jean M. Sexton Date: Wed Aug 23 11:47:40 2023 -0700 Add z_phys_nd Source/ROMSX.H Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 57752375ad4b068ce776b00f72025d4cd23f9333 Author: Jean M. Sexton Date: Tue Aug 22 19:52:42 2023 -0700 Next pass fix typos Source/TimeIntegration/ROMSX_prsgrd.cpp commit 33a286e5d376807cfab4c01ca129cdf99d6cdef7 Merge: 4f65a30b 647ebe6b Author: Ann Almgren Date: Tue Aug 22 19:42:53 2023 -0700 Merge pull request #17 from seahorce-scidac/add_particle_dir add Source/Particles commit 647ebe6bd13a744386bb67b0f89230bc3fc09ede Author: Ann Almgren Date: Tue Aug 22 19:17:16 2023 -0700 add Source/Particles Source/Particles/Make.package Source/Particles/TerrainFittedPC.H Source/Particles/TerrainFittedPC.cpp Source/ROMSX.H commit 4f65a30bb23fad1e63d64505bd19e59d120f6fe5 Merge: 96027a42 e1b1bf4a Author: Ann Almgren Date: Tue Aug 22 19:06:33 2023 -0700 Merge pull request #16 from seahorce-scidac/fix_for_particles rest of particle functionality -- but still need to replace z_phys_nd commit e1b1bf4a66aa9fe6ae11ca6078749e70adf972e6 Author: Ann Almgren Date: Tue Aug 22 19:00:56 2023 -0700 rest of particle functionality -- but still need to replace z_phys_nd Source/BoundaryConditions/BoundaryConditions_bndryreg.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/IO/Checkpoint.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp commit 96027a42709f51da42647a5f66d8a69158accd93 Merge: 51d95fdb 47ef39dd Author: Ann Almgren Date: Tue Aug 22 18:49:52 2023 -0700 Merge pull request #15 from seahorce-scidac/add_particles_to_erfh changes to ROMSX.H for particles commit 581a824376210bfccdafbbfbd602d8c39f925879 Author: Jean M. Sexton Date: Tue Aug 22 18:38:22 2023 -0700 Second pass at prsgrd Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prsgrd.cpp commit 47ef39dde8947fa52c38c0dd3196c413680b594b Author: Ann Almgren Date: Tue Aug 22 17:52:12 2023 -0700 changes to ROMSX.H for particles Source/ROMSX.H commit 51d95fdbfda7210583d73bc7091091e90bac5eab Author: Ann Almgren Date: Tue Aug 22 17:48:52 2023 -0700 Start to add particles, update CUDA CI testing and remove some MOISTURE stuff .github/workflows/cuda-ci.yml Build/cmake_with_particles.sh CMake/BuildROMSXExe.cmake CMake/SetAmrexOptions.cmake Exec/Make.ROMSX Source/IndexDefines.H Source/ROMSX.H Source/ROMSX.cpp commit be39cebf8b8b1cdfd474d7f370f511a3a8bd47b4 Author: Jean M. Sexton Date: Tue Aug 22 17:41:06 2023 -0700 Add structure for 3d pressure gradient CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_prsgrd.cpp commit 06b8b341fe4a3e7c8111c005d450adb49250d083 Author: Hannah Klion Date: Wed Aug 16 11:16:17 2023 -0700 Remove init_terrain_from_wrfinput Source/ROMSX.H Source/ROMSX_init.cpp commit 939fcd2a7e7ae522abc6e86aa46e37382975e329 Author: Hannah Klion Date: Sat Aug 19 10:10:11 2023 -0700 change boxes in prestep flux calculations to be nodal Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 436da0c7d339e107a9b8e2dc15273109904b06ca Author: Jean M. Sexton Date: Fri Aug 18 20:11:08 2023 -0700 Fix style Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/Utils/DepthStretchTransform.H commit 028f5b4c35c41e14205e808d9b4d3ddf9e2bcadd Author: Jean M. Sexton Date: Fri Aug 18 20:04:48 2023 -0700 Remove prints Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/Utils/DepthStretchTransform.H commit 0bbc2c61e3d589e06ba6524c06977f58d70c54c7 Author: Jean M. Sexton Date: Fri Aug 18 19:58:05 2023 -0700 swap boxes back to smaller Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit a66a0bc1d1e20a786e901b4acb7f76c04ae3afc0 Author: Jean M. Sexton Date: Fri Aug 18 19:55:03 2023 -0700 Update advance_3d W Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 970224ec23bad3cc1c09f3d64c35e8c4bee6183c Author: Jean M. Sexton Date: Fri Aug 18 19:45:54 2023 -0700 Adjust free surface correction index Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/Utils/DepthStretchTransform.H commit 394f6bd7dbf4f7dd951dbaa450a0d30f34eb6fed Author: Jean M. Sexton Date: Fri Aug 18 18:45:20 2023 -0700 Pass z_w through and use it in t Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/Utils/DepthStretchTransform.H commit f19ecf601f420e51cb01d4e8d1fbdd54d7c93b44 Author: Hannah Klion Date: Fri Aug 18 11:22:20 2023 -0700 add note to docs about C indexing Docs/sphinx_doc/Numerical_Solution_Technique.rst commit e0e79c6af26654c5be83d2a420bf046b6282edc2 Author: Jean M. Sexton Date: Thu Aug 17 18:57:00 2023 -0700 Tweak boxes, original temp used, minus sign Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 600fed5618ec07c5c84f3136838b793dfe71458e Author: Hannah Klion Date: Wed Aug 16 11:16:17 2023 -0700 Remove init_terrain_from_wrfinput Source/ROMSX.H Source/ROMSX_init.cpp commit 607f9c3e2f01b2cf1c8740dbb3ffe06c90f0d6fb Author: Hannah Klion Date: Tue Aug 15 15:00:29 2023 -0700 fix compile bugs Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit bee605bea3f8d899c3bbeb26116a8e04cc79ff79 Author: Hannah Klion Date: Tue Aug 15 14:54:19 2023 -0700 first pass at putting back in the corrected fluxes Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit c2a871181367086da475883ddb523d3a9333c18a Author: Jean M. Sexton Date: Wed Jun 7 10:51:55 2023 -0700 roll back change to rhs_t for flat Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit c4fb1258bd428b2fc35fea1c4c6543c56290a824 Author: Jean M. Sexton Date: Mon Aug 14 10:10:30 2023 -0700 Update compare script undoing changes and ndtfast (#14) Build/clone_copy_build.sh commit 6987d075cdc3bdf853b07877c62fb1f96715f540 Author: Jean M. Sexton Date: Tue Aug 1 13:56:22 2023 -0700 Add additional patch to be consistent with plotfile call Source/TimeIntegration/ROMSX_Advance.cpp commit c17f1fbc815f2c887d8944c90e624be91ec4bf73 Merge: 5121abfb 927b9ef6 Author: Jean M. Sexton Date: Fri Aug 11 08:22:13 2023 -0700 Remove intermediate copies of u and v and fix bugs * Replace intermediate multifab copies with alias mf * Remove setval(0) and tweak Advance mfiter * Use gbx1 with vert_mean so that boundaries are consistent commit 927b9ef67443c0c2f923bd1eb09e11ff7fb00dac Merge: 1b1749ab 868a4b63 Author: Hannah Klion Date: Thu Aug 10 17:46:23 2023 -0700 Merge pull request #11 from jmsexton03/swap_fill_copy Swap order of copy and FillBoundary commit 868a4b635f2b5bb29e3714ba766a6ee38b1c46af Author: Jean M. Sexton Date: Thu Aug 10 17:36:12 2023 -0700 Swap order of copy and FillBoundary Source/TimeIntegration/ROMSX_Advance.cpp commit 5121abfb84c402cdf0278cbb86f49b67c4372435 Author: Jean M. Sexton Date: Thu Aug 10 17:22:56 2023 -0700 Use gbx1 with vert_mean so that boundaries are consistent Source/TimeIntegration/ROMSX_advance_3d.cpp commit 4fb7e93a43dd7e09b20f3ceb5ece7c2f84d28440 Author: Jean M. Sexton Date: Wed Aug 9 14:49:02 2023 -0700 Remove setval(0) and tweak Advance mfiter Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit dddd16d165d4e9b69a316da85bf226061fc09213 Author: Jean M. Sexton Date: Mon Aug 7 16:31:56 2023 -0700 Replace intermediate multifab copies with alias mf Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_prestep.cpp commit 1b1749ab24d38214f2d69365de8c26c6aaa75310 Merge: 4addc675 13394e52 Author: Hannah Klion Date: Fri Aug 4 12:09:09 2023 -0700 Merge pull request #10 from melbarkerlbl/doc_adding Adding discretization doc commit 13394e5235bc19765f06ecdf2a32ceecdde1ded4 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Aug 4 09:21:49 2023 -0700 adding new discretization page Docs/sphinx_doc/index.rst commit 7b3f21815912d48905caeeae9d81a49e3c28851e Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Aug 4 09:20:24 2023 -0700 adding new discretization page Docs/sphinx_doc/Numerical_Solution_Technique.rst commit 1962c05fafd8aaf474c020b40807a6fe51c539ce Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Fri Aug 4 09:18:20 2023 -0700 Image files for new discretization pages Docs/sphinx_doc/figures/grid_cell.png Docs/sphinx_doc/figures/staggered_grid_rho_cells.png Docs/sphinx_doc/figures/vertical_grid.png Docs/sphinx_doc/figures/vieste-dubrovnik.png commit 4addc67520659deb7ee522cb6d4adb478a4037cd Author: Hannah Klion Date: Thu Aug 3 16:39:40 2023 -0700 fix variable tables and add more detail Docs/sphinx_doc/theory/Variables.rst commit 0fa26ef51a1ca48ab91f9bfa09daa48ca1eddec0 Merge: c5a95737 8a0706cb Author: Hannah Klion Date: Thu Aug 3 11:37:29 2023 -0700 Merge pull request #8 from jmsexton03/nans_vertical Split up ParallelFor loops for race conditions commit 8a0706cbe49c635559effa2bc6033be4be057e33 Author: Jean M. Sexton Date: Thu Aug 3 11:33:35 2023 -0700 Split up ParallelFor loops for race conditions Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit c5a9573740296fc66257d5955e7fe312fa8fe08a Merge: 0012bc4c e4109bb0 Author: Jean M. Sexton Date: Wed Aug 2 14:09:09 2023 -0700 Merge pull request #7 from melbarkerlbl/doc_adding Fixed the display issues for the Vertical S Coordinates doc. commit e4109bb0f14cfcfd7abbed738a0cc0abbf29bff1 Merge: 508ab68b 0012bc4c Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 2 11:57:46 2023 -0700 Merge branch 'seahorce-scidac:development' into doc_adding commit 508ab68b5fe5bcf006cf5f7caa3d6ae2ef8ab50b Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 2 11:57:06 2023 -0700 Update VerticalSCoord.rst remove trailing whitespaces Docs/sphinx_doc/VerticalSCoord.rst commit ac28ba10f83986fca2e06da6ffafc9c89d465bd5 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 2 11:35:20 2023 -0700 Update VerticalSCoord.rst more display fixes Docs/sphinx_doc/VerticalSCoord.rst commit 9555f879a75cc48b3dbeb80da70859ec6820f067 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Wed Aug 2 11:33:29 2023 -0700 Update VerticalSCoord.rst fixed display issues Docs/sphinx_doc/VerticalSCoord.rst commit 0012bc4cdc0e2000621799e5b1949dbd456918dd Merge: 189b7047 0bf85238 Author: Jean M. Sexton Date: Tue Aug 1 16:33:10 2023 -0700 Merge pull request #6 from melbarkerlbl/doc_adding adding vertical docs commit 0bf85238fa6644fc82bfb227224ec30d09317845 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 16:21:15 2023 -0700 Update VerticalSCoord.rst removed sediment comment due to not currently relevant Docs/sphinx_doc/VerticalSCoord.rst commit 008ee363fe026c623c0796f8f8b3cef9406b45eb Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 16:17:10 2023 -0700 Update VerticalSCoord.rst Docs/sphinx_doc/VerticalSCoord.rst commit 6a6b55c3ceb7ae99f07dc75432018d745dbe7b6e Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 15:55:48 2023 -0700 Update VerticalSCoord.rst some changes Jean suggested Docs/sphinx_doc/VerticalSCoord.rst commit f205b44e3f4c909347cf2f4696e28750e7f4c693 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 15:21:44 2023 -0700 Update index.rst to add VerticalSCoord.rst Docs/sphinx_doc/index.rst commit 89b54afa00ba8e1f7e44f30237e2ca20faa9c727 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 15:17:42 2023 -0700 moved new doc into position and referred to it Docs/sphinx_doc/VerticalSCoord.rst Docs/sphinx_doc/index.rst commit 598711dfdef99770503be163a619f227fb3591b6 Author: melbarkerlbl <140650204+melbarkerlbl@users.noreply.github.com> Date: Tue Aug 1 14:58:10 2023 -0700 adding vertical docs VerticalSCoord.rst commit 189b7047ff4d6adf705575096d921cdfe76e9049 Merge: 1ca81305 4032473d Author: Ann Almgren Date: Tue Aug 1 09:01:47 2023 -0700 Merge pull request #5 from asalmgren/update_cmake fix make and update DPCPP-->SYCL commit 4032473db5fb9f32111b3abcfb0f620f4468d78c Author: Ann Almgren Date: Tue Aug 1 08:53:21 2023 -0700 fix make and update DPCPP-->SYCL CMake/SetAmrexOptions.cmake CMakeLists.txt Exec/Make.ROMSX Exec/Upwelling/GNUmakefile Submodules/AMReX commit 1ca813056b0e79469ea6a823e64478fb6013f9a6 Merge: 23f20e32 ca06e25f Author: Ann Almgren Date: Mon Jul 31 18:06:27 2023 -0700 Merge pull request #4 from asalmgren/cleanup2 remove z_nd commit ca06e25fee7578f6ff32c10183fbc078d1da5ffc Author: Ann Almgren Date: Mon Jul 31 18:05:53 2023 -0700 remove z_nd Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp commit 23f20e328f8e4c654638f57d0ce98f3292cea5e2 Merge: 553a3795 aa16495e Author: Ann Almgren Date: Mon Jul 31 17:43:37 2023 -0700 Merge pull request #3 from asalmgren/fix_cmake fix cmake/ctest so the Upwelling test passes commit aa16495e6295d4cbdf215fb2a23dfab48f643fe6 Author: Ann Almgren Date: Mon Jul 31 17:35:27 2023 -0700 fix cmake/ctest so the Upwelling test passes Build/cmake.sh CMake/BuildROMSXExe.cmake CMakeLists.txt Exec/Upwelling/inputs Tests/ROMSX_Gold_Files/DoubleGyre/Header Tests/ROMSX_Gold_Files/DoubleGyre/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/DoubleGyre/Level_0/Cell_D_00001 Tests/ROMSX_Gold_Files/DoubleGyre/Level_0/Cell_D_00002 Tests/ROMSX_Gold_Files/DoubleGyre/Level_0/Cell_D_00003 Tests/ROMSX_Gold_Files/DoubleGyre/Level_0/Cell_H Tests/ROMSX_Gold_Files/Upwelling/Header Tests/ROMSX_Gold_Files/Upwelling/Level_0/Cell_D_00000 Tests/ROMSX_Gold_Files/Upwelling/Level_0/Cell_H Tests/ROMSX_Gold_Files/Upwelling/job_info Tests/test_files/Upwelling/Upwelling.i commit 553a3795af989fd8539cbd37d03dd753fd7c8af9 Merge: 1c8b7efc 1f16ee00 Author: Ann Almgren Date: Mon Jul 31 17:03:32 2023 -0700 Merge pull request #2 from asalmgren/cleanup more cleanup commit 1f16ee000e8a989e7633d047c9c348a979cb8f4f Author: Ann Almgren Date: Mon Jul 31 17:03:11 2023 -0700 more cleanup CMake/BuildROMSXExe.cmake Exec/Make.ROMSX Exec/Upwelling/GNUmakefile Source/BoundaryConditions/DirectionSelector.H Source/BoundaryConditions/Make.package Source/BoundaryConditions/PlaneAverage.H Source/BoundaryConditions/VelPlaneAverage.H Source/DataStruct.H Source/IO/Plotfile.cpp commit 1c8b7efc0de1324c81efe6abd1777b252a450983 Merge: f95f48e4 4dcb2a88 Author: Ann Almgren Date: Mon Jul 31 16:37:43 2023 -0700 Merge pull request #1 from asalmgren/remove_zphys remove all mention of z_phys_nd commit 4dcb2a88a9e2ccf9677daea0320f5d5658bd6c03 Author: Ann Almgren Date: Mon Jul 31 16:37:16 2023 -0700 remove all mention of z_phys_nd Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_cons.cpp Source/BoundaryConditions/BoundaryConditions_xvel.cpp Source/BoundaryConditions/BoundaryConditions_yvel.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Checkpoint.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_SumIQ.cpp Source/ROMSX_init.cpp Source/Utils/Make.package Source/Utils/TerrainMetrics.H Source/Utils/TerrainMetrics.cpp Source/Utils/Utils.H Source/prob_common.H commit f95f48e49432b59d5d449c6ef857eeb725e025ca Author: Jean M. Sexton Date: Fri Jul 21 11:23:52 2023 -0700 Fix style Source/DataStruct.H Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 31df6da7237199258d68d69b22a88718fea18538 Author: Jean M. Sexton Date: Fri Jul 21 11:16:55 2023 -0700 Include grown for check write for ru,rv,ubar,vbar Source/IO/Checkpoint.cpp commit ac8ad4d76f36ce7feda50b4044ef3ef89f827da5 Author: Jean M. Sexton Date: Wed Jul 19 14:28:36 2023 -0700 Add debugging input flags to isolate code Source/DataStruct.H Source/TimeIntegration/ROMSX_Advance.cpp commit 1ae4c02f8c57d4263d14d0aaabbc0752d94a9b23 Author: Jean M. Sexton Date: Wed Jul 19 14:09:50 2023 -0700 Shift verbosity levels Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit dbecf8ff8756fae18d40652d32251b29adc9ed48 Author: Hannah Date: Wed Jul 19 10:49:57 2023 -0400 remove printinloop and improve documentation entry for verbosity Docs/sphinx_doc/Inputs.rst Exec/Upwelling/inputs Source/ROMSX.H Source/ROMSX.cpp commit d284270b83b3ccf718900cae54f2c37796ba30d2 Author: Jean M. Sexton Date: Tue Jul 18 15:39:23 2023 -0700 Tweak test_vertical flag Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 17a0f3709bf81888399eaab4012b6e01a7f550d2 Author: Hannah Klion Date: Thu Jul 13 10:37:22 2023 -0700 reduce default verbosity and plot interval Exec/Upwelling/inputs commit 06cda5c6ddc01e02e961cb9b0003161512cd350e Author: Jean M. Sexton Date: Tue Jul 11 15:28:44 2023 -0700 Change inputs to default to ndtfast=30 Exec/Upwelling/inputs commit b753f19d6c347c7acb21335ccf362ad4b6463764 Merge: 7be42277 0257cce1 Author: Jean M. Sexton Date: Tue Jul 11 14:29:44 2023 -0700 Merge branch 'gpu_arena_syncs' into tiling Co-authored by: Hannah Klion commit 7be42277db66bb17d8d0d6d2775ee9cc2b17c25b Author: Hannah Klion Date: Tue Jul 11 11:18:16 2023 -0700 fix cmake CMake/BuildROMSXExe.cmake commit ae6c4708307bfecccebe2792c9ce1a55f7ee0649 Author: Hannah Klion Date: Mon Jul 10 18:37:03 2023 -0700 Tiling is now correct and added verbosity flags Exec/Upwelling/inputs Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 9f714c208c6f8af343cff418e281a5558a167157 Merge: 3ee1c473 054e1815 Author: Hannah Klion Date: Mon Jul 10 15:28:41 2023 -0700 Merge remote-tracking branch 'origin/development' into tiling commit 054e1815f539cd3800eb3e3990064b8e44657640 Author: Hannah Klion Date: Mon Jul 10 15:26:46 2023 -0700 fix bug in timestep indices in call to update_vel_3d in tracer calls Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 0257cce14efac73d0903bb92f2f8e2eb7b0a5a12 Author: Jean M. Sexton Date: Fri Jul 7 06:09:13 2023 -0700 Add flag for testing without vertical Source/DataStruct.H Source/TimeIntegration/ROMSX_advance_3d.cpp commit ff7cd9be0152370528cf60f46b8c272f1ef85560 Author: Jean M. Sexton Date: Thu Jul 6 19:44:42 2023 -0700 sed delete extra Print Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 3ee1c47391672c5a357406f18382eb6291e45cca Author: Hannah Klion Date: Thu Jul 6 11:00:26 2023 -0700 tiling almost works and also addded a bunch of prints Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 28e73a1253f1a2b758289655dd2b9c058f5921ec Author: Jean M. Sexton Date: Wed Jul 5 14:53:09 2023 -0700 Fix spacing Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/Utils/DepthStretchTransform.H commit bb6d2950928d00aacae50b60a793c86e8b91c3de Author: Jean M. Sexton Date: Wed Jul 5 14:50:57 2023 -0700 remove print_state so device arena works Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 6ad31be3b0f1dc14d28a6dbd66e0dc42e1f3fa9b Author: Jean M. Sexton Date: Wed Jul 5 13:54:48 2023 -0700 Use The_Async_Arena Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/Utils/DepthStretchTransform.H commit 412c780f6d94329aa966d91132179a3b99c71c1a Author: Jean M. Sexton Date: Wed Jul 5 13:36:59 2023 -0700 Rewrite cpu-only loops Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/Utils/DepthStretchTransform.H commit fbc7b7c3f6a6f45b1858f5eb40eb5906e8f9d931 Author: Hannah Klion Date: Wed Jun 28 18:29:52 2023 -0700 first attempt at getting tiling to work Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 47b3cf3eb342a6a2068bdcd8dd087103b0072d05 Author: Jean M. Sexton Date: Tue Jun 27 06:41:28 2023 -0700 fix style Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit b6ee9fa099c226378bf4b5bc5c2fe883a3e67fc4 Author: Hannah Klion Date: Mon Jun 26 17:01:03 2023 -0700 updated boxes in ROMSX_prestep Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit b082efaab5f9faf701e7e5742802d8f53c9fa33d Author: Jean M. Sexton Date: Mon Jun 26 11:36:44 2023 -0700 Uncomment some temp and salt terms Source/TimeIntegration/ROMSX_advance_3d.cpp commit 45a9efa12a3987797bf1add44eb256340d243dbd Author: Jean M. Sexton Date: Mon Jun 26 11:33:52 2023 -0700 Move from Async_Arena to Arena and tweak sync Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/Utils/DepthStretchTransform.H commit a767d3bb3dba01b55aaa4229e08379f4b584c7a2 Author: Jean M. Sexton Date: Mon Jun 26 10:27:02 2023 -0700 matches with commented out Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 701db8f16d8a519f882e07ec4cfb8b42d9eeba2e Author: Jean M. Sexton Date: Fri Jun 23 15:36:37 2023 -0700 matches with commented out Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit f2b0201340202e150e7d3f572dc3b7c87fab4e2c Author: Jean M. Sexton Date: Fri Jun 23 13:52:10 2023 -0700 matches with commented out Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit e8de47ebd83fcf7602361717d17872473f906065 Author: Jean M. Sexton Date: Fri Jun 23 12:01:05 2023 -0700 Clean up and add a few syncs Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 068062ba8a970aad9852a535c0a36f2ef4cdc94a Author: Jean M. Sexton Date: Fri Jun 23 11:20:22 2023 -0700 fix up removed gpu options Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 8a41bee48512068ff833794f2734a83421f6f2c2 Author: Jean M. Sexton Date: Fri Jun 23 08:38:59 2023 -0700 Revert "Revert "Remove PrintToFile"" This reverts commit 797e13b36690c60e5d3c854fd2f7b8a59af626e7. Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 2e416a10d521183bd87cbdd744afd720acb4ff54 Author: Hannah Klion Date: Thu Jun 22 19:27:34 2023 -0700 fix tabs Source/TimeIntegration/ROMSX_advance_3d.cpp commit e05cacf7fad25269c99596a64793d87957b9d59b Merge: f44db92f 797e13b3 Author: Hannah Klion Date: Thu Jun 22 19:23:19 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit f44db92f3c1803b522c88b6cf58165e65d7b3bac Author: Hannah Klion Date: Thu Jun 22 19:23:02 2023 -0700 Make horizontal advection scheme a runtime option Docs/sphinx_doc/Inputs.rst Exec/Upwelling/inputs Source/DataStruct.H Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 797e13b36690c60e5d3c854fd2f7b8a59af626e7 Author: Jean M. Sexton Date: Tue Jun 13 12:44:41 2023 -0700 Revert "Remove PrintToFile" This reverts commit 68429c50cc9e76cdfe569781a6494fa2f28a895b. Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 412d98f5882ded7df2047a6799aa4c5f618ba9fd Author: Jean M. Sexton Date: Tue Jun 13 11:16:22 2023 -0700 Extra writes and reads in check Source/IO/Checkpoint.cpp commit 9b2c7d933f727d138f967887df2550d11b123c59 Author: Hannah Klion Date: Fri Jun 16 17:57:00 2023 -0700 Whether to use Coriolis set by input parameter - Removed UV_COR (always compile Coriolis terms) - The use_coriolis input option now controls whether the Coriolis functions are called in the advance. Residual ERF Coriolis setup has been removed from DataStruct.H - Updated documentation and makefile accordingly Docs/sphinx_doc/InputsPhysics.rst Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs Source/DataStruct.H Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp commit 63dc0eb86296a235938ae8e94407def383d68044 Author: Hannah Klion Date: Fri Jun 16 15:58:15 2023 -0700 remove option to evolve free surface -- always do it Exec/Upwelling/inputs Source/DataStruct.H Source/TimeIntegration/ROMSX_advance_2d.cpp commit 84c22f30d487f7707d0a1ff1b5b6468132dc6b2c Author: Hannah Klion Date: Tue Jun 13 17:13:35 2023 -0700 Adjust indices in calls to advance_2d so that fast substepping works Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/Utils/DepthStretchTransform.H commit dc1b5751948e7a55562fafdb0d88152c0d67a510 Author: Jean M. Sexton Date: Tue Jun 13 08:12:56 2023 -0700 Tweak spacing Source/IO/Checkpoint.cpp Source/TimeIntegration/ROMSX_Advance.cpp commit ab627bb4a1f245466816e51f0b99b122434483c1 Author: Jean M. Sexton Date: Tue Jun 13 06:54:36 2023 -0700 Restart temp and salt match, vels off by a constant Source/IO/Checkpoint.cpp Source/TimeIntegration/ROMSX_Advance.cpp commit 8664d753db4858019d760b025d3143a913bdfdc7 Author: Jean M. Sexton Date: Mon Jun 12 18:23:30 2023 -0700 Entirely revert changes to advection scheme in tracers Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 4f7ec1a95a8994a9a18e2de2936c7ff543a51ccf Author: Jean M. Sexton Date: Thu Jun 8 10:25:52 2023 -0700 change NETCDF build default Exec/Upwelling/GNUmakefile commit 72552d8e115abdd354316576d37e366cfd38687a Author: Jean M. Sexton Date: Thu Jun 8 10:25:03 2023 -0700 Fix cuda compile Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 4d64088e1ac86b80824d6a6bd8bde56ead3b9130 Author: Jean M. Sexton Date: Wed Jun 7 10:51:55 2023 -0700 roll back change to rhs_t for flat Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit bcc9af988dd456524e76b855861fc87a9b769af9 Author: Jean M. Sexton Date: Wed Jun 7 10:41:55 2023 -0700 Use centered2 values for prestep_t with flat Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 757609e805826f4002dd92ef69f3f6e7c6743668 Merge: 63bfeea0 61aec292 Author: Hannah Klion Date: Wed Jun 7 10:21:38 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 63bfeea0bd0aebc18644b8c0750306d5edf34cfd Author: Hannah Klion Date: Wed Jun 7 10:21:31 2023 -0700 change boxes in the free surface update so there are no NaNs, and add pressure balance terms Source/TimeIntegration/ROMSX_advance_2d.cpp commit 61aec2929670c9ea95ef8d9c243c40f877bd8760 Author: Jean M. Sexton Date: Tue Jun 6 05:07:40 2023 -0700 Fix u3 and centered4 for hadv in rhs_t Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit b391258e5a33534c1914403f36db5a00f766d473 Author: Jean M. Sexton Date: Tue Jun 6 05:02:38 2023 -0700 Fix u3 and centered4 for hadv in prestep_t Source/DataStruct.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/Utils/DepthStretchTransform.H commit e384b7df03d5035569aa7118a35c9089b43ed335 Author: Jean M. Sexton Date: Mon Jun 5 14:01:14 2023 -0700 Add commenting out free surface and pgrad to diff Build/compare_flat_tweak_inputs.patch commit 0d89bf36e63d77c1e1105e3b9dfae8e1d9550bfa Author: Jean M. Sexton Date: Mon Jun 5 13:56:29 2023 -0700 Change valid index check to be general to box rather than domain, this will need a cleaner fix with bathymetry on Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 820f15a692db2a5bcba5142cadc42082da29a5d0 Author: Hannah Klion Date: Mon Jun 5 12:08:31 2023 -0700 comment out a lot of print statements Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 89649af70b0b19f5f32869ed1ebadd10c8107772 Author: Jean M. Sexton Date: Mon Jun 5 07:42:11 2023 -0700 Fix swapping order Source/TimeIntegration/ROMSX_advance_2d.cpp commit d5e8822e28192d3c05b0157c248db00188651478 Author: Jean M. Sexton Date: Sat Jun 3 08:13:52 2023 -0700 bstr to sstr in prestep, add swap for -1 ru rv Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit cff70de55ab477edf6a879f53c473f21d87375a7 Author: Jean M. Sexton Date: Fri Jun 2 19:06:52 2023 -0700 Hard-code indices in ru rv update for 2d Source/TimeIntegration/ROMSX_advance_2d.cpp commit c1fcd568542f69c3b808b5ebd77f2da2c3397bfc Author: Hannah Klion Date: Fri Jun 2 11:33:46 2023 -0700 corrected time index logic in advance_2d Source/TimeIntegration/ROMSX_advance_2d.cpp commit f6134c15db4ad6200e5b146532b6851ade421603 Author: Jean M. Sexton Date: Fri Jun 2 11:15:40 2023 -0700 revert box changes for uv3dmix Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 68429c50cc9e76cdfe569781a6494fa2f28a895b Author: Jean M. Sexton Date: Thu Jun 1 13:04:48 2023 -0700 Remove PrintToFile Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit f56ec06814e2283eb06ae6ef6756285cf9317f0c Author: Jean M. Sexton Date: Thu Jun 1 12:59:36 2023 -0700 Change some boxes and make additional place to store old mf Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 5f37dc8877317c214b0da55306fc2c39deee7370 Author: Hannah Klion Date: Wed May 31 18:14:24 2023 -0700 Calculate bottom stress with prior step velocity, and no longer re-calculate drag Source/TimeIntegration/ROMSX_Advance.cpp commit 5eda07530373a861ba458060cb2e5ec0462bfe21 Author: Hannah Klion Date: Wed May 31 16:09:15 2023 -0700 adjusted expression for cff2 to match fortran Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit c98ce3f60b295d6b12cc45f9d6051a912ab16968 Author: Hannah Klion Date: Tue May 30 15:24:41 2023 -0700 change boxes sostep 1 works! Source/IndexDefines.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit d4315decc59e307025801e1f1878733abe690f91 Author: Hannah Klion Date: Tue May 30 11:38:06 2023 -0700 add a fillboundary in plotfile output Source/IO/Plotfile.cpp commit fceb8a2be9f557cf0c53da42b91c89208c19b0fa Author: Jean M. Sexton Date: Fri May 26 14:34:57 2023 -0700 Fix netcdf index space Source/IO/NCPlotFile.cpp commit abcc80e2b372d255eff1f1098bf8a0a0bffd394a Author: Hannah Klion Date: Fri May 26 14:36:40 2023 -0700 zero out temp arrays going into vertical viscosity and set test_functionality true Source/TimeIntegration/ROMSX_advance_3d.cpp commit 4203774fe413e6aff6cefbf2118b5216b66f3c5e Author: Hannah Klion Date: Fri May 26 14:17:40 2023 -0700 change an update in vertical viscosity to be on the grown box rather than valid Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 5322f838cd5daede4f683e43a4bf32196c834c16 Author: Jean M. Sexton Date: Fri May 26 10:55:52 2023 -0700 Fix style Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 5734b016bb90a3b4c450e42c0fac14bbda427eb6 Author: Jean M. Sexton Date: Fri May 26 10:50:32 2023 -0700 Set first_2d_step properly and use it Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 84dd2570998730251058ecfce0f7d7aac7aaa916 Author: Hannah Klion Date: Fri May 26 10:50:43 2023 -0700 Fix some vertical viscosity - In advance_2d, use ru(k=-1) instead of ru(k=0) (and similar for rv) - Do viscosity calculations on larger box and pass in valid box - NGROW = 3 Source/IndexDefines.H Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit cd810df0a7794d073c5142d4118c569d0f6eca77 Author: Hannah Klion Date: Thu May 25 10:20:53 2023 -0700 Flow updates to ROMSX_Advance.cpp - Skip corrector on last fast step - Call set_depth between 2D and 3D advance, like in ROMS Source/TimeIntegration/ROMSX_Advance.cpp commit ac261e3026bccae2ccf45fedcf981fac3d1370bc Author: Hannah Klion Date: Thu May 25 10:16:31 2023 -0700 continue instead of return if skipping part of advance2d loop Source/TimeIntegration/ROMSX_advance_2d.cpp commit 24706b7ed096d322c5e1f0fd226557100fcf8db3 Author: Hannah Klion Date: Wed May 24 16:55:13 2023 -0700 update box dimensions for coriolis Source/TimeIntegration/ROMSX_coriolis.cpp commit fb1fa1ba9a54bd70a262d205ab19dc02ccdd2a02 Author: Hannah Klion Date: Wed May 24 16:52:05 2023 -0700 update FillBoundary calls in advance_2d, advance_3d, and Advance to take periodicity as an argument; fixes many issues with advance2d Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 58bac7db203c3d386526775b1129724bb69f543d Author: Jean M. Sexton Date: Wed May 24 13:56:39 2023 -0700 Inputs tweaks to change plotfile type and not test free surface Exec/Upwelling/inputs commit 0e23e64ad72eb021e25eaa879dedf1daf1647e77 Author: Jean M. Sexton Date: Wed May 24 12:09:20 2023 -0700 Fix style Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp commit 403e7e3ffbb252dd4fdd35942d71481c19cc8669 Author: Jean M. Sexton Date: Wed May 24 11:00:20 2023 -0700 Added NGROW macro and propogated it through the code .gitignore Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/IO/Checkpoint.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/IndexDefines.H Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/Utils/DepthStretchTransform.H Source/main.cpp commit ddb3bb10cbc6d75d737865dc7c2c19754f00ee12 Merge: a5864f6c e4b33a2b Author: Jean M. Sexton Date: Tue May 23 11:17:11 2023 -0700 Merge branch 'rhoeos' into development commit e4b33a2bb2097675294ad8f500c442e2f7c346e4 Author: Jean M. Sexton Date: Tue May 23 08:38:16 2023 -0700 Update indexing and add additional needed variables to pass Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp commit a5864f6c0a2b65f9e45bb7e28615f97868dab0f3 Author: Hannah Klion Date: Mon May 22 17:04:06 2023 -0700 fix indexing in uv3dmix so that fluxes are updated for all k, not just index 0 Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 7aa2791cab9bd90b6989ed57249aec7b5879cfe0 Author: Hannah Klion Date: Mon May 22 15:47:43 2023 -0700 more slabifying, including an option for the bottom and surface stress update in rhs3d Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 51be31919eff0b96258db7124359385522970b8a Author: Hannah Klion Date: Mon May 22 14:45:12 2023 -0700 runs through with slabbed boxes for 2D variables Source/TimeIntegration/ROMSX_advance_2d.cpp commit 55c0a2ef75ac3add68661277c5b20f65e33a384d Author: Hannah Klion Date: Mon May 22 14:30:06 2023 -0700 initial conversion to 2D multifabs Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp commit f488970e1328115e313797d4405ac829715f7b8e Author: Hannah Klion Date: Mon May 22 11:23:12 2023 -0700 indentation in advance 2d Source/TimeIntegration/ROMSX_advance_2d.cpp commit 422d349d0696011d629afa661c285a966c8714c3 Author: Hannah Klion Date: Mon May 22 10:45:08 2023 -0700 get advance_2d to work with no free surface update Source/TimeIntegration/ROMSX_advance_2d.cpp commit b9102db116ee911c3959c6688a0f8f2224cad4e2 Author: Hannah Klion Date: Fri May 19 14:45:50 2023 -0700 first fast step in advance2d is my_iif==0 Source/TimeIntegration/ROMSX_advance_2d.cpp commit c04c2a0570008d777b9652342697da7f03fced73 Author: Hannah Klion Date: Fri May 19 10:53:43 2023 -0700 update box size in 2D advection Source/TimeIntegration/ROMSX_advance_2d.cpp commit edf1b4681e8949e3e8fe6fa0023b0973138c0755 Author: Hannah Klion Date: Fri May 19 10:38:25 2023 -0700 add vec_visc3d_r back in to the header so the code compiles, to remove completely later Source/ROMSX.H commit 9ddef7a83da78fb3327d064804aa5c0cc8051e04 Author: Hannah Klion Date: Fri May 19 10:37:55 2023 -0700 add a fill boundary on ubar vbar when they get set Source/Utils/DepthStretchTransform.H commit 9245e36eb193aed5673ea9206b41e36dfff5c2b0 Author: Hannah Klion Date: Fri May 19 10:37:32 2023 -0700 change box of some 2D averages to have one grow cell to handle edges correctly Source/TimeIntegration/ROMSX_advance_2d.cpp commit 53b901c1e11a77b20fb1ed37044f773892ca590b Author: Hannah Klion Date: Thu May 18 16:30:42 2023 -0700 doxygenization of some members of the ROMSX class and description of state variables Source/ROMSX.H commit f9a381e8e1e005bdcdc8f3cc179f5e14718ddc81 Author: Jean M. Sexton Date: Thu May 18 10:50:39 2023 -0700 Start building with rho_eos CMake/BuildROMSXExe.cmake Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp commit 8352826ec1b26084e7afa300b5faf50d16ffbb82 Author: Jean M. Sexton Date: Thu May 18 10:50:04 2023 -0700 Start adding functions and memory for rho_eos Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rho_eos.cpp commit 4dccfeb631148deaa7732d6d08bb9381bbf5a341 Author: Hannah Klion Date: Tue May 16 16:26:02 2023 -0700 change bvstr to bustr Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp commit 47b54840c5e0b9946966446fb84915c103d9f430 Author: Hannah Klion Date: Tue May 16 15:56:56 2023 -0700 remove checkpoint and visualization pages, and make an ERF->ROMSX change Docs/sphinx_doc/index.rst commit 2d417e97fdfcc610c16e7856dbbad944f07b51a6 Author: Hannah Klion Date: Tue May 16 15:15:00 2023 -0700 Some fixes to match with ROMS - Added comments to explain variables and whether things should be 2D or 3D - Updated indices for storing ubar and vbar - Only calculate rdrag on step 2; before just use constant value - Use u not ubar for calculating bottom stress Exec/Upwelling/inputs Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/Utils/DepthStretchTransform.H commit 26837db532b15485fe2ab4f18f692f5a4d34dd8f Author: Hannah Klion Date: Tue May 16 13:36:10 2023 -0700 flipped order of and store in call to update_3d_vel Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 8d4db84afb552debb79dd40dfb3210db853e606c Author: Jean M. Sexton Date: Tue May 16 12:26:58 2023 -0700 Update comparison setup Build/clone_copy_build.sh Build/compare_example/Linux-ftn-gnu.mk Build/compare_example/Linux-ftn.mk Build/compare_example/Linux-gfortran.mk Build/compare_example/ana_grid.h Build/compare_example/ana_initial.h Build/compare_example/coawst.bash Build/compare_example/main3d.F Build/compare_example/pre_step3d.F Build/compare_example/pre_step3d.F.onlyfixedt Build/compare_example/pre_step3d.F.onlyfixedt.prints Build/compare_example/rhs3d.F Build/compare_example/roms_upwelling.in Build/compare_example/set_depth.F Build/compare_example/step3d_t.F Build/compare_example/step3d_uv.F Build/compare_example/upwelling.h Build/compare_example/uv3dmix2_s.h Build/compare_flat_tweak_inputs.patch Build/differences_list.txt commit 0ca23ad0dfac7fdc92e7228a132568917c23c21d Author: Jean M. Sexton Date: Tue May 16 10:34:58 2023 -0700 First pass at rho_eos Source/ROMSX.H commit 5b9432761548b09720f6ccc8c59cb54138a4bf1d Author: Hannah Klion Date: Mon May 15 17:48:55 2023 -0700 made images larger for discretization diagrams Docs/sphinx_doc/ArakawaCGrid.rst Docs/sphinx_doc/Discretizations.rst commit cdb7243510f9d976b3dd246ced79c27f23be9f5c Author: Hannah Klion Date: Mon May 15 11:10:15 2023 -0700 add t3dmix to cmake CMake/BuildROMSXExe.cmake Source/TimeIntegration/Make.package commit bb7146a1b0fdaa2e7b163c6b34bcaae9ba8baf77 Merge: 3a83335e 117fd92d Author: Hannah Klion Date: Mon May 15 10:58:47 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 3a83335eb2af1308c61c73892e6fff86eb7ffd55 Author: Hannah Klion Date: Mon May 15 10:58:40 2023 -0700 update t3dmix so it compiles and runs Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/Utils/DepthStretchTransform.H commit 117fd92d73abd8a8d8eab5fac399bda8f528fc5c Author: Ann Almgren Date: Fri May 12 17:40:41 2023 -0700 fix indent Docs/sphinx_doc/theory/Equations.rst commit af76c6950b73fd2ff1002672eeef4e3eec4f7465 Author: Ann Almgren Date: Fri May 12 17:37:37 2023 -0700 another tweak Docs/sphinx_doc/theory/Equations.rst commit f2e5de9eb055808d6cd74afce50f8987e3e4ff81 Author: Ann Almgren Date: Fri May 12 17:17:16 2023 -0700 fix overbar Docs/sphinx_doc/theory/Equations.rst Docs/sphinx_doc/theory/Variables.rst commit abbbe3fc1683ec327d42cb637ae2918e273fc61b Author: Ann Almgren Date: Fri May 12 17:11:56 2023 -0700 table fix Docs/sphinx_doc/theory/Variables.rst commit 9457fe395b54ef4723df8bad7e316764acf7a5e9 Author: Ann Almgren Date: Fri May 12 17:04:19 2023 -0700 more docs fix Docs/sphinx_doc/DerivedQuantities.rst Docs/sphinx_doc/index.rst Docs/sphinx_doc/theory/Forcings.rst Docs/sphinx_doc/theory/UnitsAndConstants.rst Docs/sphinx_doc/theory/VerticalMixing.rst commit 937e25d388d0efe5d32b289790a57b67e9919f8c Author: Ann Almgren Date: Fri May 12 16:57:13 2023 -0700 fix equations Docs/sphinx_doc/theory/Equations.rst Docs/sphinx_doc/theory/Variables.rst commit 2b2328cd8427a4840ff4f2d93c0eb0d30f9c479c Author: Ann Almgren Date: Fri May 12 13:57:33 2023 -0700 add variables page Docs/sphinx_doc/index.rst Docs/sphinx_doc/theory/Equations.rst Docs/sphinx_doc/theory/Variables.rst Docs/sphinx_doc/theory/VerticalMixing.rst commit 99f5850c238d390542c1a0f46361c83c9b2f8b14 Merge: d45b30af e3e5239c Author: Hannah Klion Date: Fri May 12 12:09:36 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit d45b30af798425506758d2f4064ae0e9ee2260f1 Author: Hannah Klion Date: Fri May 12 12:09:31 2023 -0700 initial commit of t3dmix Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_t3dmix.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp commit e3e5239cf3018b2a47d7c8f60f3546b19fb5cf01 Author: Ann Almgren Date: Fri May 12 12:07:25 2023 -0700 fix spacing Docs/sphinx_doc/index.rst commit 2670d50f86492958d0c4bcd708394c3884bdcf9c Author: Ann Almgren Date: Fri May 12 10:12:36 2023 -0700 remove file with broken links Docs/sphinx_doc/RegressionTests.rst commit c30503b04066b83744843439ae913922846bb331 Author: Ann Almgren Date: Fri May 12 10:09:43 2023 -0700 remove broken links Docs/sphinx_doc/index.rst commit bd1a1bc30d171a5039aefdacdae212a14be3328b Author: Ann Almgren Date: Fri May 12 10:03:17 2023 -0700 update docs.yml .github/workflows/docs.yml Docs/sphinx_doc/boxlib_bits.rst commit 022cb3e55e55d64833b0fd045334b9d64269d26f Author: Ann Almgren Date: Fri May 12 09:41:30 2023 -0700 add theory Docs/sphinx_doc/index.rst commit f9f0ad3d57c4dc9b53e7ae8511a8d0cc1f10e291 Author: Ann Almgren Date: Fri May 12 09:38:39 2023 -0700 unhide equations Docs/sphinx_doc/index.rst commit 6f9c9b3d3ed127af20cd38304f77645759bd72ae Merge: caa6bd64 0d28fab4 Author: Ann Almgren Date: Fri May 12 09:35:15 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit caa6bd648e6332eaade8bd696d020f90a68dd62f Author: Ann Almgren Date: Fri May 12 09:35:10 2023 -0700 update 3d equations Docs/sphinx_doc/theory/Equations.rst commit 0d28fab43e4e95664260f28f44b6d8010cdeb9e0 Author: Jean M. Sexton Date: Thu May 11 14:57:35 2023 -0700 Tweak weight vector offsets, use weight in 2d Source/TimeIntegration/ROMSX_advance_2d.cpp Source/Utils/DepthStretchTransform.H commit 41c2726e1c10e710385f89214499d1477158adc8 Author: Jean M. Sexton Date: Thu May 11 14:46:40 2023 -0700 Appears to match weights Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/Utils/DepthStretchTransform.H commit 7e7c3242c94c7524f1f6a09a41b2630e591ae197 Author: Jean M. Sexton Date: Thu May 11 14:20:25 2023 -0700 Add weight function Source/ROMSX.H Source/Utils/DepthStretchTransform.H commit 4e4836fd43079fab039c194c91f7ff6ec694ed0e Merge: 92b0cf90 caded762 Author: Hannah Klion Date: Wed May 10 12:11:44 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 92b0cf90685b677b978a05ea9f5a43c17e7c81f8 Author: Hannah Klion Date: Wed May 10 12:11:38 2023 -0700 added bottom stress terms Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/Utils/DepthStretchTransform.H commit caded76270f97f756d92f962475d15889c866898 Merge: a395d431 f848e6e8 Author: Ann Almgren Date: Tue May 9 17:40:24 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit a395d43110e9078d5ea65fdeebb50594d027baba Author: Ann Almgren Date: Tue May 9 17:40:19 2023 -0700 update git location Docs/sphinx_doc/GettingStarted.rst commit f848e6e871110be3d9b66e16821c1b38ec1aeb7c Merge: 3309e38e 1fb224f4 Author: Andrew Myers Date: Tue May 9 17:37:49 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 3309e38e123bd237fc202c29a46499df1bc9f9f0 Author: Andrew Myers Date: Tue May 9 17:37:28 2023 -0700 Add Doxygen link Docs/sphinx_doc/index.rst commit 1fb224f4ab152aaf76ecd69722df23fe0b75ffb8 Author: Ann Almgren Date: Tue May 9 17:36:33 2023 -0700 more docs cleanup Docs/sphinx_doc/ArakawaCGrid.rst Docs/sphinx_doc/CouplingToAMRWind.rst Docs/sphinx_doc/MeshRefinement.rst Docs/sphinx_doc/TimeAdvance.rst Docs/sphinx_doc/Visualization.rst Exec/Make.ROMSX commit 17a11c2662fa259e87ef313d9c91aadf4d3b0fd1 Merge: 162894ab bd51ade1 Author: Ann Almgren Date: Tue May 9 17:33:30 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 162894abfab55c657907e6aba26ec7c6d009d2a2 Author: Ann Almgren Date: Tue May 9 17:33:24 2023 -0700 clean up docs Docs/sphinx_doc/Applications_Requirements.rst Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/E3D_mol_ppm.png Docs/sphinx_doc/ERFvsWRF.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/KE_mol_ppm.png Docs/sphinx_doc/RegressionTests.rst Docs/sphinx_doc/dissipation_mol_ppm.png Docs/sphinx_doc/figures/density_current_600.png Docs/sphinx_doc/figures/density_current_900.png Docs/sphinx_doc/figures/ekman_spiral_errors.png Docs/sphinx_doc/figures/ekman_spiral_profiles.png Docs/sphinx_doc/index.rst Docs/sphinx_doc/theory/DNSvsLES.rst Docs/sphinx_doc/theory/Equations.rst Docs/sphinx_doc/theory/PBLschemes.rst commit bd51ade154762247becfe684e628c79b03cfcdc9 Author: Andrew Myers Date: Tue May 9 17:20:31 2023 -0700 Add .readthedocs.yml .readthedocs.yml commit 5a718cecc417642549f985ed9cd3040a4ee9dc64 Author: Ann Almgren Date: Tue May 9 14:37:19 2023 -0700 update amrex hash Submodules/AMReX commit b57e150cdde05decd126e6cb78409a2514be6f7d Merge: 41f84f5e 6c9b0ffc Author: Ann Almgren Date: Tue May 9 14:27:15 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 41f84f5e882c3d6b2113a018646eb929d377e951 Author: Ann Almgren Date: Tue May 9 14:27:06 2023 -0700 add license LICENSE.md commit 6c9b0ffc3e5e5b86d39d79cc296968e8dae07025 Author: Jean M. Sexton Date: Mon May 8 16:31:28 2023 -0700 add comments to Advance and remove if 1 Source/TimeIntegration/ROMSX_Advance.cpp commit a62f97c8597e4d1663dca9befef5bfbb5907a25c Author: Jean M. Sexton Date: Mon May 8 13:34:21 2023 -0700 Store rhs_ubar rhs_vbar Source/TimeIntegration/ROMSX_advance_2d.cpp commit 43de7a43365a5c3a15f38e688082fb9c59b9c1ec Author: Jean M. Sexton Date: Mon May 8 13:30:33 2023 -0700 Use rhs_ubar rhs_vbar update Source/TimeIntegration/ROMSX_advance_2d.cpp commit 230410d375425bf799c61a210bc816a6920081ec Author: Jean M. Sexton Date: Mon May 8 13:17:59 2023 -0700 Move test bool Source/TimeIntegration/ROMSX_advance_2d.cpp commit 9590f91fb63acea48d5dc2ae096b6ceebea3a5a1 Author: Jean M. Sexton Date: Mon May 8 13:06:14 2023 -0700 call harmonic viscosity for ubar vbar Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit c3b64043815c5554ec9a28cbe974f1f7631fa7f2 Author: Jean M. Sexton Date: Mon May 8 08:46:23 2023 -0700 Change if guards Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit b2325fa3c4c873626ed0e6459cd30dc624942052 Author: Jean M. Sexton Date: Mon May 8 08:21:20 2023 -0700 First pass at apply rufrc and rvfrc to 2d Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 96495cde167708cc34f4dd4c8925ff6b3abad4bb Author: Jean M. Sexton Date: Sat May 6 17:09:04 2023 -0700 Change boxes, comment out temp 3d adv Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 59343da5672f5a0dd2d901b9486d860f405c763f Author: Jean M. Sexton Date: Sat May 6 16:31:27 2023 -0700 Gets rid of nans but seems unstable Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit c85e76d280b570bff5034e240d70e4e6c3d0201c Author: Jean M. Sexton Date: Sat May 6 14:12:05 2023 -0700 Add input flag for free surface testing Source/DataStruct.H Source/TimeIntegration/ROMSX_advance_2d.cpp commit 9f1db863f124bf48bc3981ccde6d615dfa22f0ff Author: Jean M. Sexton Date: Sat May 6 12:24:23 2023 -0700 First pass at adding free surface update Source/TimeIntegration/ROMSX_advance_2d.cpp commit c25f63172ecc8ad738d4f275670da92033fe5bcc Author: Jean M. Sexton Date: Sat May 6 11:19:34 2023 -0700 Pass in dtfast to advance_2d Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 0bb8e608c90ac815bf62667c24af377dedb4c879 Author: Jean M. Sexton Date: Sat May 6 08:53:26 2023 -0700 Use fast input flags Exec/Upwelling/inputs Source/DataStruct.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp commit 1d1844b7d5ab316eb3ae811b4d5415d53e4974e5 Author: Jean M. Sexton Date: Sat May 6 08:34:46 2023 -0700 Add input flags being read for fast Source/DataStruct.H Source/ROMSX.H Source/ROMSX.cpp commit 92b0117276692ce5a38a17686d0999ddeede91de Author: Jean M. Sexton Date: Sat May 6 07:50:22 2023 -0700 Fix ubar vbar mean swap and ini index Source/TimeIntegration/ROMSX_advance_3d.cpp Source/Utils/DepthStretchTransform.H commit 0d91e326548b921327a07f06a4ec2f672806e800 Author: Jean M. Sexton Date: Sat May 6 07:10:41 2023 -0700 Make default depth consistent, initialize some variables Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp Source/Utils/DepthStretchTransform.H commit 7ab4398782b85752ca066705cc98af9ea07f2686 Merge: 4fddc6d6 4d4c0bb5 Author: Hannah Klion Date: Fri May 5 18:37:03 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 4fddc6d6f1be9d080eff2a8d52fc2464f5694a8e Author: Hannah Klion Date: Fri May 5 18:33:55 2023 -0700 Call uv3dmix in Advance - Added the variables needed by uv3dmix - Added a function in DepthStretchTransform to set horizontal mixing coefficients (currently just hard-coded values) - Allocated scratch variables only used in uv3dmix and removed them from the function signature Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_uv3dmix.cpp Source/Utils/DepthStretchTransform.H commit 4d4c0bb5b8b00519215267b7a28a59dd44fcc4d4 Author: Jean M. Sexton Date: Fri May 5 16:26:26 2023 -0700 Fix typos Source/IO/NCWpsFile.H Source/ROMSX.cpp Source/ROMSX_Tagging.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/Utils/ROMSX_Math.H commit f9797f74dc1428721095bed300d3b61c0ca282b1 Author: Jean M. Sexton Date: Fri May 5 14:31:08 2023 -0700 Fix tabs Source/ROMSX.H Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 3b9d3809952b0454a533a3c8119e0c06f1361c81 Author: Jean M. Sexton Date: Fri May 5 14:13:18 2023 -0700 Update rhs_ubar rhs_vbar indexing and coriolis index Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 770e8f42f7f54d33096d90a9b2b272151240a4b7 Author: Jean M. Sexton Date: Fri May 5 14:05:50 2023 -0700 First pass at horizontal advection of 2d ubar vbar CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_rhs_uv_2d.cpp commit 691ecc5d0d8d37e389ea33b9e413fefdd969f2d8 Author: Jean M. Sexton Date: Thu May 4 16:31:48 2023 -0700 Add comments for ubar vbar mean nudging and swap Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 940c92cceaa254fd2cb9e63922267ca64ea8d81b Author: Jean M. Sexton Date: Thu May 4 16:07:33 2023 -0700 Fix some if 0 * Replace if 0 in depth with parameter that is always false * Replace if 0 in update_massflux with test on periodicity Source/DataStruct.H Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/Utils/DepthStretchTransform.H commit 03ae5658e9d0074a83892f08cb07124de3c7c51c Author: Hannah Klion Date: Thu May 4 15:45:42 2023 -0700 fixed and re-added vert_mean_3d, and removed 'if 0's in advance_3d Build/compare_example/step3d_uv.F Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 486532f725072eb7cb65862f882000ec16fd3823 Author: Jean M. Sexton Date: Thu May 4 11:01:25 2023 -0700 fix tabs Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit f7636a64260045b2f8c1f11f628bea930b45073d Author: Jean M. Sexton Date: Thu May 4 10:53:37 2023 -0700 Add comments of other terms and functions inplace Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit b98395664516a3c4db4ff8f29e8bfdf30f41b2c1 Author: Jean M. Sexton Date: Tue May 2 16:52:14 2023 -0700 Second pass on forcing 2d Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 9339d8ade4f496ec88872fe2d197738e2e01fbfc Author: Jean M. Sexton Date: Tue May 2 13:43:51 2023 -0700 Start adding forcing to rhs coupling Build/compare_example/rhs3d.F Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/Utils/DepthStretchTransform.H commit c1730908dafde1cf031ad56703f2d0532f8d81f6 Author: Hannah Klion Date: Wed May 3 12:07:46 2023 -0700 fix tabs Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 5324fadb7e3dd2483fac9936131c0648d7e7bbb9 Merge: 2bbc16b4 f475b648 Author: Hannah Klion Date: Wed May 3 11:23:09 2023 -0700 Merge branch 'development' of github.com:seahorce-scidac/ROMSX into development commit 2bbc16b485fca8fc3071b814296e1e00ffe65b01 Author: Hannah Klion Date: Wed May 3 11:23:01 2023 -0700 Fix tabs and trailing whitespace Build/compare_example/main3d.F Build/compare_example/step3d_t.F Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit f475b648454c833ffd5b7b60da818ce0c52bf5b1 Author: Hannah Klion Date: Wed May 3 11:18:04 2023 -0700 Set c-linter to run ever .github/workflows/c-linter.yml commit 43c4c59e06426f244caa4119ef6663a19e3d3cca Author: Hannah Klion Date: Wed May 3 11:05:20 2023 -0700 trigger re-enabled Github actions commit 6a82b0e6442713b013ffbb2551092e0fee13b958 Author: Hannah Klion Date: Tue May 2 13:20:49 2023 -0700 Fix bounds issues in update_massflux Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 15cf7f235a621eb9b541281067f7236d6412d87a Author: Jean M. Sexton Date: Tue May 2 11:23:17 2023 -0700 Update indexes for corrector Build/compare_example/main3d.F Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 6606f02d75b6c455f315b61f1a200b6619b9886c Author: Jean M. Sexton Date: Tue May 2 10:53:00 2023 -0700 Set first step bool Source/TimeIntegration/ROMSX_Advance.cpp commit 7d8b8defb7f96cefb888058eed0482d0f532e5cf Author: Jean M. Sexton Date: Tue May 2 10:50:02 2023 -0700 Add bool to advance_2d proto, fix loop structure Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 7d6ea2cd7271794953328c73c2485cfe39161efa Author: Jean M. Sexton Date: Fri Apr 28 14:51:00 2023 -0700 Add argument to advance_2d to help with indexing Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp commit 261f1f4332b96c5932335004baf222808791b15c Author: Jean M. Sexton Date: Fri Apr 28 13:36:02 2023 -0700 Change time to t_old and recalibrate dstart for wind Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit 068c49f29977c46dca595b654442fae8498ce9bf Author: Jean M. Sexton Date: Thu Apr 27 15:04:25 2023 -0700 Remove unneeded file Build/compare_example/set_massflux.F commit 0889796eb6f9879944f2f892a20562342dd51f20 Author: Jean M. Sexton Date: Thu Apr 27 14:46:24 2023 -0700 Remove t adv Build/compare_example/main3d.F Build/compare_example/set_massflux.F Build/compare_example/step3d_t.F Source/TimeIntegration/ROMSX_advance_3d.cpp commit 3437356b27388b52ed53dcb8b194c47ad3318f06 Author: Jean M. Sexton Date: Thu Apr 27 14:42:05 2023 -0700 Matches t adv vertical Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit 2b939ea6d90bc6f00b9655c7beb7596b7a40f54d Author: Hannah Klion Date: Mon Apr 24 18:31:44 2023 -0700 initial commit of uv3dmix implementation Source/ROMSX.H Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 4424fc13d9e9fa8ccd967456eb31bdff27587afb Author: Jean M. Sexton Date: Mon Apr 24 14:31:36 2023 -0700 Remove most _arr prefixes Source/IO/NCPlotFile.cpp Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H commit 557feba18b71ca358fa97c449512f10ac52dfc25 Author: Jean M. Sexton Date: Mon Apr 24 14:22:47 2023 -0700 Prefix MultiFab vectors with vec_ Source/IO/NCPlotFile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/Utils/DepthStretchTransform.H commit 097be764a7221abef169d89708ca2ec542e7c834 Author: Jean M. Sexton Date: Mon Apr 24 13:53:06 2023 -0700 Add viscosity function stubs CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_uv3dmix.cpp commit 4e5c683f73c943c082ad81b403a883a106e5877e Author: Jean M. Sexton Date: Mon Apr 24 12:41:54 2023 -0700 Add comment about massflux box Source/TimeIntegration/ROMSX_advance_3d.cpp commit 9d70c8eb214c54b8b78ca8255ad5732e562e83d1 Author: Jean M. Sexton Date: Thu Apr 20 17:41:59 2023 -0700 Fix step 1 of uv Source/TimeIntegration/ROMSX_Advance.cpp commit 8dbc9b783f712b042e1912480e06c5e300c848e6 Author: Jean M. Sexton Date: Thu Apr 20 17:05:47 2023 -0700 Temp matches, remove t adv for now Build/compare_example/step3d_t.F Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 0932b42ff27148ccfe63195aa3b02e254e903a59 Author: Jean M. Sexton Date: Thu Apr 20 11:38:43 2023 -0700 Remove nans Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit adf980b5d871124202afb3dc096ee28a988b7883 Author: Jean M. Sexton Date: Thu Apr 20 10:38:31 2023 -0700 Remove nans from prestep_t except ghost cells out 2 Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 95fa6fe8351383367386130a3e8d31f4366545c7 Author: Jean M. Sexton Date: Mon Apr 17 13:36:05 2023 -0700 Third pass at prestep_t Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp commit ec350bc7bcc8448554e619f9ba93f161f2dfe6c4 Author: Jean M. Sexton Date: Mon Apr 17 13:04:06 2023 -0700 prints match for two steps Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp commit 0eeb08320a204a9b62edff023b0fc01c1eb28a58 Author: Jean M. Sexton Date: Mon Apr 17 12:41:44 2023 -0700 current prints Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp commit 23b19822232f4fc38b74ed21ec719cba0264b066 Author: Jean M. Sexton Date: Mon Apr 17 11:42:33 2023 -0700 Remove vertical mean interior update Build/compare_example/pre_step3d.F Build/compare_example/step3d_uv.F commit 27e95e95cc9ee4fb09c935e8521533a8da3c03ce Author: Jean M. Sexton Date: Mon Apr 17 11:41:28 2023 -0700 second pass prestep _t Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp commit 36832925a8d88431a24b5caf5b3954050c904401 Author: Jean M. Sexton Date: Mon Apr 17 10:52:29 2023 -0700 pass at Matching for prestep and horizontal Build/compare_example/main3d.F Build/compare_example/pre_step3d.F Build/compare_example/step3d_t.F commit 1dd0b174a38080b7dad358bede60c53942a36d2e Author: Jean M. Sexton Date: Mon Apr 17 10:51:09 2023 -0700 Match most of pre_step_t_3d setup, need to tweak uv CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp Source/TimeIntegration/ROMSX_set_massflux_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit 783f6ca8ce0401ea3058735a61182b0da409ce76 Author: Jean M. Sexton Date: Fri Apr 14 09:01:12 2023 -0700 Matches first step tracers Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit dd97a044cd2278f8f5338185e6eda47c10162164 Author: Jean M. Sexton Date: Thu Apr 13 15:32:46 2023 -0700 Default to upstream 3 for horizontal advection of tracers Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 22f38cb57b53d57113d6bd44f50f739a8c70f2fb Author: Jean M. Sexton Date: Thu Apr 13 15:19:10 2023 -0700 Second pass at update_massflux Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit e389aac607fdc4d65b55f68b9285e3faa11513f2 Author: Jean M. Sexton Date: Thu Apr 13 11:13:35 2023 -0700 Update CI names and variables .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/docs.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/windows.yml commit 1691eee963a11a20e3f72c1b8e959a5272fcd1c7 Author: Jean M. Sexton Date: Thu Apr 13 11:04:54 2023 -0700 Fix Huon Hvom bounds Source/ROMSX.cpp commit 68d033afceb70e68115c36ebbf28285dea71be8a Author: Jean M. Sexton Date: Thu Apr 13 10:44:31 2023 -0700 Pass in Hz and DU_avg1 to massflux update Source/ROMSX.H Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 7288630d7ce528023be6b7cf0770045ce4185899 Author: Jean M. Sexton Date: Thu Apr 13 10:26:33 2023 -0700 Fix typo and tabs Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit 36eda1a0d930c989b82a2646d923ebc0d6cf70cd Author: Jean M. Sexton Date: Thu Apr 13 10:13:23 2023 -0700 Make massflux stored in header file CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_update_massflux_3d.cpp commit 27e93bba8d87b9c22700978f54a60566b5b5dcb8 Author: Jean M. Sexton Date: Thu Apr 13 09:23:29 2023 -0700 Forgot file Source/TimeIntegration/ROMSX_rhs_t_3d.cpp commit beac211de25601def3d66654b51740f1f5c2f67e Author: Jean M. Sexton Date: Wed Apr 12 17:42:11 2023 -0700 Pass at horizontal advection tracers CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_uv_3d.cpp commit c6e0b5d3029623fb6754c6ca59ca8e8bf543f9e2 Author: Jean M. Sexton Date: Mon Apr 10 16:06:41 2023 -0700 Tweak cuda compilation Exec/Upwelling/prob.cpp Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H commit 61d97591c5ce8ba18d7efbd218160de294076964 Author: Jean M. Sexton Date: Mon Apr 10 15:45:13 2023 -0700 Add inline and move some setval and private funs Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_rhs_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 92b8f2ef90fb2a763f2cfd5cf4561d148810e4c3 Author: Jean M. Sexton Date: Mon Apr 10 11:48:39 2023 -0700 Add coriolis ubar vbar source Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp commit e3bde1502d9c20ecaf0791e6a690bffe5582c378 Author: Jean M. Sexton Date: Thu Apr 6 18:02:15 2023 -0700 Leave out prestep testing until step3d set up Build/compare_example/pre_step3d.F Build/compare_example/roms_upwelling.in Source/TimeIntegration/ROMSX_Advance.cpp commit fdfa5299750778afa170938ea7a213a89d834b63 Author: Jean M. Sexton Date: Thu Apr 6 18:00:59 2023 -0700 Third pass at prestep tracers Build/compare_example/pre_step3d.F Build/compare_example/roms_upwelling.in Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit 4abc5794eb03b2e21293233585aeec7ed3c944fd Author: Jean M. Sexton Date: Thu Apr 6 17:12:31 2023 -0700 Second pass at prestep temp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 71c67d744e581bccd01b899fe0c79085d420ff20 Author: Jean M. Sexton Date: Thu Apr 6 08:51:01 2023 -0700 Fix style Build/compare_example/step3d_t.F Source/ROMSX_init.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 132d9edcf4b3444c331975f588773e5899654e48 Author: Jean M. Sexton Date: Thu Apr 6 08:21:10 2023 -0700 First pass at prestep temp and salt CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_prestep_t_3d.cpp commit 86e335bc9ab72f02f2e6ba411066794647143f3e Author: Jean M. Sexton Date: Wed Apr 5 14:23:56 2023 -0700 Add tracer vert visc Build/compare_example/step3d_t.F Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit 2d9c86904c58dfdacd62dc0d2b13db9f5bef0a95 Author: Jean M. Sexton Date: Wed Apr 5 12:06:10 2023 -0700 Revert changes to let ubar vbar update u v Build/compare_example/main3d.F Build/compare_example/step2d_LF_AM3.h Build/compare_example/step3d_uv.F commit 9c034a734efc5bbf576ba9fd94415c11debce08b Author: Jean M. Sexton Date: Wed Apr 5 11:58:55 2023 -0700 Add ifdef for avg1 updates in 3d advance Source/TimeIntegration/ROMSX_advance_3d.cpp commit 4bcb692cdd415056e69e074a3e49ad624d792801 Author: Jean M. Sexton Date: Wed Apr 5 12:04:17 2023 -0700 Second pass at vertical mean Build/compare_example/main3d.F Build/compare_example/roms_upwelling.in Build/compare_example/step2d_LF_AM3.h Build/compare_example/step3d_uv.F commit b9474c6f10b5c65a291147eed2f0b6fe8595402a Author: Jean M. Sexton Date: Mon Apr 3 12:42:33 2023 -0700 Second pass at vertical mean, fix vertical index Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 8c1f3f2495b42fdeec351c933ccb670c31feb836 Author: Jean M. Sexton Date: Mon Apr 3 10:16:48 2023 -0700 Add vertical mean correction CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_vert_mean_3d.cpp commit 3765a9ed4c4cfdda05b2edceb0ecd14146007480 Author: Jean M. Sexton Date: Mon Apr 3 10:04:14 2023 -0700 Remove broken function Source/ROMSX_init.cpp commit a9c24d2ce994c66d0facee2cb6f7dd7ae006a4f3 Author: asalmgren Date: Mon Apr 3 12:15:43 2023 -0700 Create README.md README.md commit fb9765b0b7241e1abbaec1561a43ae55bdca2feb Author: Ann Almgren Date: Sat Apr 1 14:55:22 2023 -0700 clang-tidy cleanup Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit d6ae68e9951556be0848c39945e9718b95952d99 Author: Ann Almgren Date: Sat Apr 1 14:22:25 2023 -0700 remove unused variables Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_zvel.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/DataStruct.H Source/EOS.H Source/IO/NCColumnFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_3d.cpp Source/Utils/DepthStretchTransform.H Source/Utils/TerrainMetrics.cpp commit 9bcee6fb7594c9accb86755af006b70543b26f05 Author: Ann Almgren Date: Sat Apr 1 13:12:45 2023 -0700 split out rhs_3d CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_rhs_3d.cpp commit 93fbe6700981a614e274ee6902051f81cbdca5c9 Author: Ann Almgren Date: Sat Apr 1 12:42:19 2023 -0700 more cleanup Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp commit 8151acfe2dfa9d414db6ef2e8fad39c47a2fd624 Author: Ann Almgren Date: Sat Apr 1 12:16:30 2023 -0700 more clean-up Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_update_vel_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp commit fea318bd33856156aa270d10c20f4395918a4c02 Author: Ann Almgren Date: Sat Apr 1 11:37:36 2023 -0700 separate out update_vel_3d for more code-resuse CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_update_vel_3d.cpp commit e0759a1cd4bd10fcd16dcd265951d19ea5224656 Author: Ann Almgren Date: Sat Apr 1 11:15:09 2023 -0700 Separate out vertical visc routine for code re-use. Passes the plt00100 test CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp Source/TimeIntegration/ROMSX_vert_visc_3d.cpp Source/Utils/DepthStretchTransform.H commit 3b309a78b65384599ebd2df0cf96b95903048496 Author: Jean M. Sexton Date: Fri Mar 31 17:29:33 2023 -0700 Fix tabs Source/TimeIntegration/ROMSX_advance_3d.cpp commit 851522a22021a930a2ede52fc03907639dfe535a Author: Jean M. Sexton Date: Fri Mar 31 16:50:22 2023 -0700 Fix up Hz to tweak ubar vbar Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/Utils/DepthStretchTransform.H commit c978b3bd39289c430040a9b210a2f3d5ed69f0f2 Author: Jean M. Sexton Date: Fri Mar 31 13:45:34 2023 -0700 Add k indices Source/TimeIntegration/ROMSX_advance_2d.cpp commit 2b25ad12867bb0732ac1951e4ba070c0ae392cc8 Author: Jean M. Sexton Date: Fri Mar 31 12:14:02 2023 -0700 First pass add DU_avg1 etc Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit a6fdc533099979ae53bfc66516f0327c9774fc28 Author: Jean M. Sexton Date: Thu Mar 30 16:43:29 2023 -0700 Fix AK averaging in j direction Source/TimeIntegration/ROMSX_advance_3d.cpp commit f56cf8ea41ab05807cd7b3c47708819d0cd6546e Author: Jean M. Sexton Date: Thu Mar 30 13:29:19 2023 -0700 Use 2d variables Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 3555f174a7cc9985f36ab07e350c03deae5d3b71 Author: Ann Almgren Date: Fri Mar 31 16:51:28 2023 -0700 more separation of subroutines CMake/BuildROMSXExe.cmake Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/TimeIntegration/ROMSX_coriolis.cpp Source/TimeIntegration/ROMSX_prestep_uv_3d.cpp commit 31eaa09c32e9c38d0f6b01d685d7f17fc34233ff Author: Jean M. Sexton Date: Thu Mar 30 10:21:29 2023 -0700 Remove unused header file and fix ifdef Source/Derive.H Source/Derive.cpp Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit 13f1d4022b6a281e0b3d6fd09dd6c2d5cfd19658 Author: Jean M. Sexton Date: Wed Mar 29 19:27:10 2023 -0700 Fix style Build/compare_example/ana_initial.h Exec/Upwelling/prob.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp Source/Utils/DepthStretchTransform.H commit 01c37a30dc181c405ccfb90e2587c4a57bea9709 Author: Ann Almgren Date: Wed Mar 29 19:06:26 2023 -0700 start to make different boxes Source/TimeIntegration/ROMSX_advance_3d.cpp commit ca730669ca59db9a9061e3c549a8872ac36523dc Author: Ann Almgren Date: Wed Mar 29 18:44:28 2023 -0700 more splitting of files .github/workflows/draft-pdf.yml CMake/BuildROMSXExe.cmake Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_advance_2d.cpp Source/TimeIntegration/ROMSX_advance_3d.cpp commit b7fddf025bf51d45823328443bc02919407d9a78 Author: Ann Almgren Date: Wed Mar 29 18:41:06 2023 -0700 matches at plt00100 Source/ROMSX.H Source/TimeIntegration/ROMSX_Advance.cpp commit 6744eb0969aed35d220ec2c91fa8145f3f1bb3ef Author: Ann Almgren Date: Wed Mar 29 17:26:27 2023 -0700 fix oops -- shouldn't have included TimeIntegration2 Source/TimeIntegration2/Make.package Source/TimeIntegration2/ROMSX_Advance.cpp Source/TimeIntegration2/ROMSX_ComputeTimestep.cpp Source/TimeIntegration2/ROMSX_TimeStep.cpp commit b6f93a138d8f22a35d92008b0a7026fff67c2e56 Author: Ann Almgren Date: Wed Mar 29 17:25:56 2023 -0700 fix trailing white space and more re-factor .github/workflows/c-linter.yml .github/workflows/ci.yml .github/workflows/cuda-ci.yml .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/documentation.sh .github/workflows/docs.yml .github/workflows/draft-pdf.yml .github/workflows/gcc.yml .github/workflows/hip.yml .github/workflows/macos.yml .github/workflows/style.yml .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh .github/workflows/windows.yml Build/compare_example/main3d.F Build/compare_example/rhs3d.F Build/compare_example/set_depth.F Build/compare_example/step3d_t.F CMake/BuildROMSXExe.cmake Exec/Upwelling/prob.H Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_Advance.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration2/Make.package Source/TimeIntegration2/ROMSX_Advance.cpp Source/TimeIntegration2/ROMSX_ComputeTimestep.cpp Source/TimeIntegration2/ROMSX_TimeStep.cpp Source/Utils/DepthStretchTransform.H commit 730fb6f0a6eb8f3dc94b2ab1c520d151a0784d55 Author: Ann Almgren Date: Wed Mar 29 16:47:33 2023 -0700 start to break files apart Source/TimeIntegration/Make.package Source/TimeIntegration/ROMSX_ComputeTimestep.cpp Source/TimeIntegration/ROMSX_TimeStep.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 672a78c6e958bccf851756e7af2507b8acf61dfd Author: Jean M. Sexton Date: Wed Mar 29 14:12:47 2023 -0700 Change bounds omega and z_r and z_w Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 028f2ce293464b214859b6a027b92fb060ce896e Author: Jean M. Sexton Date: Mon Mar 27 10:55:08 2023 -0700 Tweak spacing Source/Utils/DepthStretchTransform.H commit 5b02ac943392ca944dcd08bac6a485d3e15ec5ac Author: Jean M. Sexton Date: Mon Mar 27 09:53:27 2023 -0700 Revert "Second pass at fixing nonflat" This reverts commit d15486a0c7b883fa21abb91800fcdfd38f252da1. Revert "Revert "Revert "Fix up Hz to use periodic fill""" This reverts commit 0819fed49b30bb9ba90b3585fb8c454404016406. Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 3067b6e7591df76db0fdf6c52ef87c04e9d05b4b Author: Jean M. Sexton Date: Mon Mar 27 09:52:34 2023 -0700 Second pass at fixing nonflat Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit fab4da8d0b1ec2eb2bf83d0ae3edda86e6b933b3 Author: Jean M. Sexton Date: Mon Mar 27 09:43:16 2023 -0700 Revert "Revert "Fix up Hz to use periodic fill"" This reverts commit 0d0a12d2d54f81f9a15211f46a7b14c6f5a43955. Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 8a9e393a4890f03666033ca901ac9248a294e51e Author: Jean M. Sexton Date: Mon Mar 27 09:42:43 2023 -0700 Use seperate index for summation Source/Utils/DepthStretchTransform.H commit 633be0801a30738577290c5b836b89e61c9ab0b7 Author: Jean M. Sexton Date: Sat Mar 25 20:18:22 2023 -0700 Fix indexing ubar vbar Source/ROMSX.cpp Source/ROMSX_init.cpp Source/Utils/DepthStretchTransform.H commit 9c0a9488472b84e18be2a964547d4ead46c8b38e Author: Jean M. Sexton Date: Sat Mar 25 19:56:23 2023 -0700 ubar and vbar to be inited in set_2darrays Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit e4e434e9e129faf58c78f044a9c803d5632e7f8b Author: Jean M. Sexton Date: Sat Mar 25 19:44:52 2023 -0700 Add example setup Source/TimeIntegration/ROMSX_TimeStepping.cpp commit e9cba5ec3c9dc10becbbad49f73dec15aff305cd Author: Jean M. Sexton Date: Sat Mar 25 15:53:14 2023 -0700 First pass at setting initial ubar vbar Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit f315b150e606d48ab4fab583cc700f381a55e2c6 Author: Jean M. Sexton Date: Sat Mar 25 15:05:13 2023 -0700 Split mfiter loop for rhs and prestep Source/TimeIntegration/ROMSX_TimeStepping.cpp commit fc4354308051ac1fbad7cf061e1a6ba8bc60e4ec Author: Jean M. Sexton Date: Sat Mar 25 13:52:19 2023 -0700 Revert "Change h to be negative" This reverts commit 4bce8b6d7671e9ce2d8a2cae1d08077da9e83cda. Revert "Fix up Hz to use periodic fill" This reverts commit 973c24c221358c80c60bedd684e49f5a4347b4a4. Revert "Revert "Change h to be negative"" This reverts commit b5734edcb0b3b7a1546fe2474f923281a62a8145. Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 31d4d44fbc6364fcf047174eb39d1406f7aed49a Author: Jean M. Sexton Date: Sat Mar 25 13:02:30 2023 -0700 Add zero initialized variables for 2d Source/ROMSX.H Source/ROMSX.cpp commit 4bce8b6d7671e9ce2d8a2cae1d08077da9e83cda Author: Jean M. Sexton Date: Thu Mar 23 10:42:58 2023 -0700 Change h to be negative Source/Utils/DepthStretchTransform.H commit 9cca6f7de5bf496fdf89940d53efe578bec6b96a Author: Jean M. Sexton Date: Mon Mar 20 13:58:23 2023 -0700 Add example run line Build/compare_example/clone_copy_build.sh commit 973c24c221358c80c60bedd684e49f5a4347b4a4 Author: Jean M. Sexton Date: Fri Mar 17 09:30:20 2023 -0700 Fix up Hz to use periodic fill Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 04a44724ee20b084aca5d61c7173fc5fc9f2a056 Author: Jean M. Sexton Date: Thu Mar 16 12:37:38 2023 -0700 update omega Build/compare_example/omega.F Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 294314f7a4296dcf4b0e6c3c3d81fc6fc495b5d6 Author: Jean M. Sexton Date: Mon Mar 13 10:23:04 2023 -0700 Spacing and comment cleanup Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 86e730dff2dd29bca1c36c5feb8e8a7934f31736 Author: Jean M. Sexton Date: Thu Mar 9 09:16:26 2023 -0800 Periodic in y matches well Build/compare_example/roms_upwelling.in Exec/Upwelling/inputs commit ab5dafc8f6c74d7f501275188defe2ff9559d4c4 Author: Jean M. Sexton Date: Thu Mar 9 09:11:30 2023 -0800 Shear u Build/compare_example/ana_initial.h Exec/Upwelling/prob.cpp commit 5da7c9cae5ad4a44722fae56f27e7dbade4785d6 Author: Jean M. Sexton Date: Thu Mar 9 09:07:41 2023 -0800 Wind on Build/compare_example/pre_step3d.F Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 3bb5c7d83c66f9debbd5ae9c5922f58f123f8292 Author: Jean M. Sexton Date: Thu Mar 9 09:04:33 2023 -0800 Compare no wind, 1 periodic dir Build/compare_example/ana_initial.h Build/compare_example/pre_step3d.F Build/compare_example/roms_upwelling.in Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 224d0466a441f63e1b22de0fed303daf84204443 Author: Jean M. Sexton Date: Wed Mar 8 16:12:44 2023 -0800 Nonflat depth matches and wind term is close Hz z_r and z_w should be used differently when not flat Using flat for testing wind terms Build/compare_example/ana_grid.h Build/compare_example/pre_step3d.F Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit e9cc0c57bb27e33cde86b5aef7daabfbd6115a3d Author: Jean M. Sexton Date: Wed Mar 8 12:19:41 2023 -0800 Make depth vary, change magnitude of nonperiodic setup Build/compare_example/ana_grid.h Build/compare_example/roms_upwelling.in Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/Utils/DepthStretchTransform.H commit 6ab8c6233ecf3a3d0f2c6647a87a304f3d38c06e Author: Jean M. Sexton Date: Wed Mar 8 08:52:16 2023 -0800 Try u and v init as reciprical of pos Build/compare_example/ana_initial.h Exec/Upwelling/prob.cpp commit 5d6d7cdf7b4d7562c17e5e3a71ada60c968e31c2 Author: Jean M. Sexton Date: Wed Mar 8 08:43:16 2023 -0800 Make svstr consistent with sustr Build/compare_example/pre_step3d.F commit 2c35ca690d6d5d47493014b4660b18a684010508 Author: Jean M. Sexton Date: Tue Mar 7 10:37:56 2023 -0800 Remove prints Build/compare_example/rhs3d.F Build/compare_example/step3d_uv.F Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 4b3b3dd4f647ce75fd0902ab16401416edd460dd Author: Jean M. Sexton Date: Tue Mar 7 10:29:28 2023 -0800 Negative sign swapped Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 2b72492d1b9ffc8e5090e28521a320dc14fc02fc Author: Jean M. Sexton Date: Wed Mar 1 07:50:02 2023 -0800 Missing negative sign and order may be swapped Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 1145b63d4e9895789a7a3b12e59e7e1601423501 Author: Jean M. Sexton Date: Wed Mar 1 07:49:08 2023 -0800 Forgot coriolis Build/compare_example/upwelling.h commit b794d82e903894f494c72e8c923405b38fc502d6 Author: Jean M. Sexton Date: Mon Feb 27 16:39:17 2023 -0800 Change whitespace Source/TimeIntegration/ROMSX_TimeStepping.cpp commit ac82078a9cc3e88c49c98ea5cf17c9ae7f6c1238 Author: Jean M. Sexton Date: Mon Feb 27 16:37:22 2023 -0800 Remove prints Build/compare_example/pre_step3d.F Build/compare_example/rhs3d.F Build/compare_example/step3d_uv.F Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 24413e223f58d5b478ebeafc05a3d995ef91f6a1 Author: Jean M. Sexton Date: Mon Feb 27 14:58:17 2023 -0800 Changes Build/compare_example/pre_step3d.F Build/compare_example/rhs3d.F Build/compare_example/roms_upwelling.in Build/compare_example/step3d_uv.F commit c349cdeec0482ced09f2a52bc00fb29149654c72 Author: Jean M. Sexton Date: Mon Feb 27 14:53:29 2023 -0800 Remove stop Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 01672117873b4caa6f087f3eb0e54f078db819b5 Author: Jean M. Sexton Date: Mon Feb 27 13:28:07 2023 -0800 Try periodic in northsouth and eastwest Exec/Upwelling/inputs Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 119a116bc2e5a947985a6e73d0baaa8d9e86fdc7 Author: Jean M. Sexton Date: Mon Feb 27 08:17:28 2023 -0800 v114 check Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 0ce065ea49202814eb47cfb2ec955f65e9c33530 Author: Jean M. Sexton Date: Sat Feb 25 05:11:13 2023 -0800 Fix ordering of ru and rv swap Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit e75312efd0821cdfaaf9b82c32ddf43c8394432b Author: Jean M. Sexton Date: Sat Feb 25 04:39:15 2023 -0800 Use v instead of vold in back Source/TimeIntegration/ROMSX_TimeStepping.cpp commit d54790dc0d94ef78a91da5fc3ca9ec9d7127338b Author: Jean M. Sexton Date: Sat Feb 25 03:52:22 2023 -0800 Fix cor v Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 867c74bf8e5b0ae64bfa6c9c5f0a33d6e8af7fea Author: Jean M. Sexton Date: Fri Feb 24 12:04:33 2023 -0800 First pass at coriolis Exec/Upwelling/GNUmakefile commit 04bfc237683c9bdfbe7d957809e864beea8ca63c Author: Jean M. Sexton Date: Fri Feb 24 11:54:05 2023 -0800 Make backsub match v Source/TimeIntegration/ROMSX_TimeStepping.cpp commit bb75d04b28c41ffffb61d4966843c3a015eb4454 Author: Jean M. Sexton Date: Fri Feb 24 08:14:17 2023 -0800 Match 003 Exec/Upwelling/prob.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 49d5bce2ce07ec6368ef86b4a69c89eeb4e4da5d Author: Jean M. Sexton Date: Fri Feb 24 07:39:08 2023 -0800 Update prestep and tweak s_r grown size back .gitignore Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit cf2faf25818c80e8b338eb8439633bae440a5c17 Author: Jean M. Sexton Date: Fri Feb 24 07:26:38 2023 -0800 FIX grown box temporary plotfile write Source/IO/Plotfile.cpp commit d57769a8611cd0305c79cd941c731725f7293185 Author: Jean M. Sexton Date: Thu Feb 23 14:36:03 2023 -0800 Fix NaNs conflict from boundary Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 93e93e08060845467052da548b64447f84831461 Author: Jean M. Sexton Date: Thu Feb 23 13:27:43 2023 -0800 Fixup prestep with stash Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 49310a64570ec86e73ea4594d4b8d37d82f60245 Author: Jean M. Sexton Date: Thu Feb 23 13:22:16 2023 -0800 Fixup prestep Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 3c36412e77dbfca372760b7f1857557d1e595c95 Author: Jean M. Sexton Date: Thu Feb 23 11:29:29 2023 -0800 Make backsub match Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 99a3e0c53e645eee69bf289325195dc08febaa19 Author: Jean M. Sexton Date: Wed Feb 22 14:58:03 2023 -0800 Try to make backsub match Exec/Upwelling/prob.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 34fd513cc2038595a8d99e23f3e20aa6e1a7b715 Author: Jean M. Sexton Date: Tue Feb 21 10:41:16 2023 -0800 Fix prints Source/TimeIntegration/ROMSX_TimeStepping.cpp commit d74149b3afa81536b236d2b362a6a63365b78389 Author: Jean M. Sexton Date: Tue Feb 21 08:37:14 2023 -0800 Tweak Huon boundary setting Source/TimeIntegration/ROMSX_TimeStepping.cpp commit d2597a5420d3ef818f82395ad2a4743dda0cc201 Author: Jean M. Sexton Date: Tue Feb 21 07:01:05 2023 -0800 Fix spacing Source/TimeIntegration/ROMSX_TimeStepping.cpp commit f1ac0d3c9a7a898ca1bd5e4edcb235716afcfcfc Author: Jean M. Sexton Date: Wed Feb 8 16:01:22 2023 -0800 Remove prints Build/compare_example/pre_step3d.F Build/compare_example/rhs3d.F Build/compare_example/set_depth.F Build/compare_example/step3d_uv.F commit 6a7c0d14c49f4f9c231dc7969d99230d7858ae1c Author: Jean M. Sexton Date: Wed Feb 8 15:56:44 2023 -0800 Matching script updated Build/compare_example/ana_initial.h Build/compare_example/clone_copy_build.sh Build/compare_example/coawst.bash Build/compare_example/main3d.F Build/compare_example/pre_step3d.F Build/compare_example/rhs3d.F Build/compare_example/set_depth.F Build/compare_example/step3d_uv.F Build/compare_example/uv3dmix2_s.h commit 6a2cba8684e6839a6e561fde8302dcb5f3c7af98 Author: Jean M. Sexton Date: Tue Feb 7 17:20:45 2023 -0800 Replace nans with garbage Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 2cb29e89ada002363890679a9f193807e7584679 Author: Jean M. Sexton Date: Tue Feb 7 14:46:00 2023 -0800 Use sheared inputs Exec/Upwelling/inputs Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp commit a9349683968003be831ca66362e4df0bbe23c009 Author: Jean M. Sexton Date: Tue Feb 7 13:39:11 2023 -0800 Default to showing x_velocity Exec/Upwelling/amrvis.defaults commit 74b5ff592fe6a46b330a83d9af71a6f1d89dfd3e Author: Jean M. Sexton Date: Tue Feb 7 13:38:56 2023 -0800 pre_step3d and fill testing Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 33496d8824ff29f2239273ac227c4821786c2488 Author: Jean M. Sexton Date: Tue Feb 7 11:53:36 2023 -0800 Remove comments Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit d12757aff00fe09937079c00315c43fae4f661e2 Author: Jean M. Sexton Date: Tue Feb 7 11:45:55 2023 -0800 Remove prints Source/IO/Plotfile.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 3bd89ab1a5cb7f17ce2fd2feff7594b66fe394ae Author: Jean M. Sexton Date: Mon Feb 6 14:20:42 2023 -0800 Set more things to 0 Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 7f76dde3348cda55887452e2e7596e074823fdb7 Author: Jean M. Sexton Date: Mon Feb 6 13:48:02 2023 -0800 Comment out ru and rv effects for now to debug multiple steps Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 63d249cb93fb94007ec0c5e3d6e2bf10c071d756 Author: Jean M. Sexton Date: Mon Feb 6 13:16:19 2023 -0800 test1 Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 10bcb482f4e4bbf33287682418f657b60def77cb Author: Jean M. Sexton Date: Mon Feb 6 11:03:01 2023 -0800 Get past step 2 nans Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 4a6d9f8b1c446d4327ed8fbeb464698bf9261e0d Author: Jean M. Sexton Date: Mon Feb 6 09:57:51 2023 -0800 First pass at adding pre_step for v Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 95c08fa8548e9a7e161c8a231a9723e7770dc736 Author: Jean M. Sexton Date: Fri Feb 3 15:32:02 2023 -0800 First pass at adding pre_step for u Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 7390d345e1343a4581d181e71ca2357f92cab2ff Author: Jean M. Sexton Date: Thu Feb 2 12:23:31 2023 -0800 Make y_velocity match Source/TimeIntegration/ROMSX_TimeStepping.cpp commit e6c15dcf6a6d044daa23e6953424061a2ac5d5f1 Author: Jean M. Sexton Date: Thu Feb 2 12:11:29 2023 -0800 Vertical viscosity term commented for debugging Source/TimeIntegration/ROMSX_TimeStepping.cpp commit aa2abbb16e12333208d6f40d3f342d2c81e02415 Author: Jean M. Sexton Date: Thu Feb 2 10:51:51 2023 -0800 Add prints, plotfile write won't avg vels for now Source/IO/Plotfile.cpp Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 03ffd3f84358e36b0687f2d875e3661a668237ba Author: Jean M. Sexton Date: Wed Feb 1 14:56:36 2023 -0800 test fillboundary for nans Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 4228483ed609d1f1d65df6e35a2419bb88b81626 Author: Jean M. Sexton Date: Wed Feb 1 14:32:03 2023 -0800 Runs through 1 step with usable bounds Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 6f33fff772c353f70af8fb2775eee5d8a5b28d05 Author: Jean M. Sexton Date: Wed Feb 1 13:47:56 2023 -0800 Add prints and check k-1 Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 7dc52f11c0672c168e6aad30bfa79045b1d6255e Author: Jean M. Sexton Date: Wed Feb 1 09:46:10 2023 -0800 Run through bounds checking Exec/Upwelling/inputs Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 3d6a53760a90ce1521fae1ea6efb07e154a0734c Author: Jean M. Sexton Date: Wed Feb 1 09:11:48 2023 -0800 fix N Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 8372529ac3982629e43c1b9eb84dc343a9381d8b Author: Jean M. Sexton Date: Tue Jan 31 13:14:26 2023 -0800 update DC small end Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 8957dfb521f89aa824d934fbb980b4253b444a90 Author: Jean M. Sexton Date: Tue Jan 31 11:02:22 2023 -0800 LU decomp for u Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit fff15e832a0b76af8abf9f2b3bac7d8ba7f8b841 Author: Jean M. Sexton Date: Tue Jan 31 10:57:56 2023 -0800 forward Source/TimeIntegration/ROMSX_TimeStepping.cpp commit d14cbfef3207e272ab125be2200e56eff1553eaf Author: Jean M. Sexton Date: Tue Jan 31 10:29:36 2023 -0800 split loops Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 369e17f9b191ef7e1b7adfad410f443c75663dad Author: Jean M. Sexton Date: Tue Jan 31 09:38:51 2023 -0800 Finish back sub u Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 8d06389583b361082e3163f8b5bc9c58e29403c3 Author: Jean M. Sexton Date: Tue Jan 31 07:34:00 2023 -0800 Match first u update neglect viscosity Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 6f58da84276b98a328341840a8da9b8d45fd6014 Author: Jean M. Sexton Date: Tue Jan 31 06:10:51 2023 -0800 Match up rv Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 8e9a6a573af5e37bbd9773b59b5c8ea829b1e456 Author: Jean M. Sexton Date: Mon Jan 30 15:25:26 2023 -0800 Fiddle with Huon for UFx Source/TimeIntegration/ROMSX_TimeStepping.cpp commit ffcb4d308ed0b38b84ac74dcd0393c1f10f2053c Author: Jean M. Sexton Date: Mon Jan 30 15:04:04 2023 -0800 Mess with Hz and Huon and Hvom Exec/Upwelling/prob.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 5778f08b9e41c8802d83ff4836a107e68e0734c6 Author: Jean M. Sexton Date: Mon Jan 30 07:13:28 2023 -0800 Comment out ijk prints and u update Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 19ab6c5c4ff34f618034d059d51532e93d1d4a27 Author: Jean M. Sexton Date: Sat Jan 28 17:59:07 2023 -0800 ru rv to first u update Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 806af926835a3c89f3c8b26950369338e4bfc55b Author: Jean M. Sexton Date: Sat Jan 28 17:44:59 2023 -0800 UFx UFe VFx VFe Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 23ad207bc654c61587c59e5a18f9f14f25e3bac0 Author: Jean M. Sexton Date: Sat Jan 28 17:36:13 2023 -0800 uxx and Huxx Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit e98738e39b06815de27d302398bcd23b5ad834a0 Author: Jean M. Sexton Date: Sat Jan 28 12:41:22 2023 -0800 Add pm and pn Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 25971da57c62ae56f356712702b39235ba9ac61c Author: Jean M. Sexton Date: Sat Jan 28 09:18:37 2023 -0800 Added psudocode for ru and rv Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 61a55cfe6d254e3249bbc03c9f5d139db957f0ce Author: Jean M. Sexton Date: Sat Jan 28 08:25:17 2023 -0800 Fix compile and start adding ru and rv Source/TimeIntegration/ROMSX_TimeStepping.cpp commit dd73039e56ccab48aefef1802b0c358e9ca33888 Author: Jean M. Sexton Date: Sat Jan 28 08:24:06 2023 -0800 Update coriolis ifdef and remove analytical wind stress from advance Build/compare_example/clone_copy_build.sh Build/compare_example/pre_step3d.F Build/compare_example/pre_step3d.F.onlyfixedt.prints Build/compare_example/upwelling.h commit 552cdea3c7833d4917d9a27cac171dfe66e400df Author: Jean M. Sexton Date: Sat Jan 28 07:07:11 2023 -0800 WIP uv updates Source/ROMSX.H Source/ROMSX.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp Source/Utils/DepthStretchTransform.H commit 77d9f463e9827005f02757ae2039771e3fa7757d Author: Jean M. Sexton Date: Fri Jan 27 16:46:04 2023 -0800 Remove if 0 and cleanup Build/compare_example/pre_step3d.F.onlyfixedt Source/ROMSX.H Source/TimeIntegration/ROMSX_TimeStepping.cpp commit f5cc8463d52fb86f2a30550f9c0678db45b8a6df Author: Jean M. Sexton Date: Fri Jan 27 13:39:45 2023 -0800 Force no updates to tracers like temp and salt Build/compare_example/pre_step3d.F Build/compare_example/step3d_t.F commit 58333b4eb10c8a934baa0169a559c86894287014 Author: Jean M. Sexton Date: Fri Jan 27 13:37:59 2023 -0800 Tweak to avoid cuda warnings Source/IO/NCPlotFile.cpp Source/ROMSX.H Source/Utils/DepthStretchTransform.H commit 714165e0082928f6d124f9c140397aed2fe6ed67 Author: Jean M. Sexton Date: Thu Jan 26 14:21:42 2023 -0800 Update new FillPatch calls Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 7daf405b1015921661da7e3f52b54c0189d36001 Author: Jean M. Sexton Date: Thu Jan 26 11:32:37 2023 -0800 Add example workflow Build/compare_example/Linux-ftn-gnu.mk Build/compare_example/Linux-ftn.mk Build/compare_example/Linux-gfortran.mk Build/compare_example/clone_copy_build.sh commit 087a723995f7f66d1b0ab7df5bfe906918185834 Author: Jean M. Sexton Date: Thu Jan 26 10:49:37 2023 -0800 Add boundary update skeleton to timestepping Source/BoundaryConditions/BoundaryConditions_bndryreg.cpp Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/ROMSX.H Source/TimeIntegration/ROMSX_TimeStepping.cpp commit 7894e556076bac1308ad4dbbf6ef7cabbb16a1a3 Author: Jean M. Sexton Date: Thu Jan 26 10:48:43 2023 -0800 Try to force no updates to omega Build/compare_example/omega.F commit 9e2ae6cf8aab1dc35f1c11dfb86555d9abbce47f Author: Jean M. Sexton Date: Wed Jan 25 14:42:15 2023 -0800 Force no updates to uv .gitignore Build/compare_example/pre_step3d.F Build/compare_example/step3d_uv.F Source/TimeIntegration/ROMSX_TimeStepping.cpp commit fc8a9d21dacccb935d43d15279fba5c0199b5b61 Author: Jean M. Sexton Date: Wed Jan 25 11:27:33 2023 -0800 Make compiling with and writing to NetCDF default Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs commit 3caadd5c9ab8fb0abe2531400f20eb1210d35f90 Author: Jean M. Sexton Date: Wed Jan 25 11:13:01 2023 -0800 Change fixed timestep sizes Build/compare_example/roms_upwelling.in Exec/Upwelling/inputs commit ea035622e4fb4085b2fe10c5b96cc70aa1ffe5c8 Author: Jean M. Sexton Date: Wed Jan 25 09:43:38 2023 -0800 Add environment example scripts Build/cori-env.sh Build/saul-env.sh commit dd1d7f0d855951009ca88d3a93329ea8da2f7b5e Author: Jean M. Sexton Date: Wed Dec 7 17:03:56 2022 -0800 Only have one Exec dir for now, update make Docs/sphinx_doc/building.rst Docs/sphinx_doc/testing.rst Exec/CMakeLists.txt Exec/Upwelling/CMakeLists.txt Exec/Upwelling/GNUmakefile Source/IO/NCPlotFile.cpp Tests/CTestList.cmake Tests/test_files/Upwelling/Upwelling.i commit 689f8392a2e45e569968db0db23be069182ffd07 Author: Jean M. Sexton Date: Wed Dec 7 17:03:10 2022 -0800 Only have one Exec dir for now Exec/DoubleGyre/CMakeLists.txt Exec/DoubleGyre/GNUmakefile Exec/DoubleGyre/Make.package Exec/DoubleGyre/inputs Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Tests/test_files/Upwelling/Upwelling.i commit c7e88cc17a05b2f8b0a92b107559ebbf37dfbb1d Author: Jean M. Sexton Date: Wed Dec 7 15:52:40 2022 -0800 Fix periodicity, prints. Make grown boxes explicit Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit c64ba7e98385718cfb96ce5774151393465d03d5 Author: Jean M. Sexton Date: Wed Dec 7 11:21:20 2022 -0800 Remove duplicate variables Source/IO/NCPlotFile.cpp commit f229321125c34454e49100fb8bfa3bc68bc137d9 Author: Jean M. Sexton Date: Wed Dec 7 09:51:30 2022 -0800 Don't double write extra dimensions Source/IO/NCPlotFile.cpp commit 47e3daee66ad421f85ff8039b33351c09f8237e4 Author: Jean M. Sexton Date: Wed Dec 7 09:46:09 2022 -0800 Fix name of z_rho as coordinate Source/IO/NCPlotFile.cpp commit ba0f38dfe5ec48f948ab13c9144d87d3fecc3958 Author: Jean M. Sexton Date: Tue Dec 6 17:10:04 2022 -0800 Fix z grow cells Exec/Upwelling/prob.cpp Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp commit f4c3d11612e34519ec2c9e78ef8f4e1b03931d33 Author: Jean M. Sexton Date: Tue Dec 6 15:20:38 2022 -0800 Change z_rho to be flatter and make problem periodic in y direction Exec/Upwelling/inputs Source/IO/NCPlotFile.cpp Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit edd821d91f767d97a38f680ad0276782026b6b12 Author: Jean M. Sexton Date: Tue Dec 6 14:59:59 2022 -0800 Add z_rho as a 3d field Source/IO/NCPlotFile.cpp Source/Utils/DepthStretchTransform.H Source/Utils/Stretch.H.bak commit b551a0becd733e0cb864faa325ee2e108fc9be48 Author: Jean M. Sexton Date: Tue Dec 6 13:07:06 2022 -0800 Attempt to fix s_r and z_r outputs Source/IO/NCPlotFile.cpp Source/Utils/DepthStretchTransform.H commit 384818d2c1434e51ac1c34d93fb68e9576ca6704 Author: Jean M. Sexton Date: Tue Dec 6 12:54:19 2022 -0800 Attempt to xi and eta bounds for netcdf Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 61321f1d1306845c1adfbb906aa450f7a9d7e657 Author: Jean M. Sexton Date: Tue Dec 6 12:20:05 2022 -0800 Test using grow cells in netcdf output Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H Source/Utils/Stretch.H.bak commit 4756e870839f9872bf1e8e325428cc97197e1143 Author: Jean M. Sexton Date: Tue Dec 6 09:40:04 2022 -0800 Track comparison tweaks, coriolis and surface flux not tested Build/compare_example/ana_grid.h Build/compare_example/roms_upwelling.in Build/compare_example/upwelling.h commit a600bf372966c26effc4150f8e9cab11fb1651fe Author: Jean M. Sexton Date: Tue Dec 6 09:36:28 2022 -0800 Comments Source/Utils/DepthStretchTransform.H commit e2b079fc515bfdfe7d8801a33bd1eddc9a59813f Author: Jean M. Sexton Date: Tue Dec 6 09:33:34 2022 -0800 Force flat bottom Source/DataStruct.H Source/Utils/DepthStretchTransform.H commit 54030a2191e1a52824a034284e5b6f4bc1225f49 Author: Jean M. Sexton Date: Mon Dec 5 19:16:05 2022 -0800 Add s_r to outputs Source/IO/NCPlotFile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit d09c1a8e9d4e58b4854296fbe91c8aaf6e901740 Author: Jean M. Sexton Date: Mon Dec 5 17:02:07 2022 -0800 Change to xi_rho and eta_rho as vars and dims Source/IO/NCPlotFile.cpp Source/ROMSX.H Source/ROMSX.cpp Source/Utils/DepthStretchTransform.H commit 8150c5bf4d64fd8470b2233cac7767912dca43f5 Author: Jean M. Sexton Date: Tue Nov 29 18:18:12 2022 -0800 Change names of vars Source/IO/NCPlotFile.cpp commit 97c8a4f9e530c95dc8b4d15f98ee0dd1cb85adb6 Author: Jean M. Sexton Date: Tue Nov 29 17:52:51 2022 -0800 Add coords with approx names Source/IO/NCPlotFile.cpp commit 35b20c919441af25108cfc1628426cd437682402 Author: Jean M. Sexton Date: Tue Nov 29 16:48:22 2022 -0800 Add coords Source/IO/NCPlotFile.cpp commit f45dc062160099fbeaf4366b3cbc37d01462e3d3 Author: Jean M. Sexton Date: Tue Nov 29 16:23:04 2022 -0800 try z_w and z_r Source/IO/NCPlotFile.cpp commit b04bf4a71d5323ba924b0debd43681972e34c3e0 Author: Jean M. Sexton Date: Tue Nov 29 16:18:35 2022 -0800 Test adding vars to netcdf Exec/Upwelling/prob.cpp Source/IO/NCPlotFile.cpp commit 479380fa38bfdadf304de3ef818fb881e7173449 Author: Jean M. Sexton Date: Tue Nov 29 14:38:51 2022 -0800 Remove prints Source/Utils/DepthStretchTransform.H commit a377d44c617a4ea1fb50ccdea624c2272c970380 Author: Jean M. Sexton Date: Tue Nov 29 14:35:45 2022 -0800 Fix up ds and hc for stretching and transform Source/IO/NCPlotFile.cpp Source/Utils/DepthStretchTransform.H commit e094ac9ea5e824eb83154121100bb89cf534b1b8 Author: Jean M. Sexton Date: Fri Nov 4 17:51:15 2022 -0700 Testing Exec/Upwelling/prob.cpp Source/ROMSX.cpp Source/ROMSX_init.cpp commit b1c162ca551868ed1f439615b70b1bc980973dea Author: Jean M. Sexton Date: Fri Nov 4 14:28:35 2022 -0700 Compiles, first pass, runs Exec/Upwelling/prob.cpp Source/DataStruct.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp Source/Utils/DepthStretchTransform.H Source/Utils/Make.package Source/prob_common.H commit 7f80df75d24719effe3c4f598ca59fadf4daf2af Author: Jean M. Sexton Date: Tue Oct 18 13:54:00 2022 -0700 Rename RhoTheta to Temp, remove pressure-related functions for now Exec/DoubleGyre/prob.cpp Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/BoundaryConditions/BoundaryConditions_wrfbdy.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.cpp Source/Derive.H Source/Derive.cpp Source/EOS.H Source/IO/NCColumnFile.cpp Source/IO/Plotfile.cpp Source/IO/ReadFromWRFBdy.cpp Source/IO/ReadFromWRFInput.cpp Source/IndexDefines.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp Source/ROMSX_init_bcs.cpp commit 37e27969fff23db0f0c13ace21b451a6542f85a1 Author: Jean M. Sexton Date: Tue Oct 18 13:11:47 2022 -0700 Rename vars from temp to tmp, remove derived vars Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp Source/ROMSX.H Source/ROMSX.cpp commit 6c4d9614aba474ce7ccb814e469461fecb8b59d4 Author: Jean M. Sexton Date: Tue Oct 18 12:09:18 2022 -0700 Update initial formula and inputs Exec/Upwelling/inputs Exec/Upwelling/prob.cpp commit 5a0f56f1a0ce8d58d251a68c2a9f96827798bbf1 Author: Jean M. Sexton Date: Wed Oct 12 20:08:17 2022 -0700 Add ifdef to guard history plotfile since it hangs with MPI Source/IO/NCPlotFile.cpp commit f16b283de7b7e2b1b036dc61bb1e493d2c656838 Author: Jean M. Sexton Date: Mon Oct 10 15:15:40 2022 -0700 Netcdf history file seems to work for internally tracked number of records Source/IO/NCPlotFile.cpp Source/IO/Plotfile.cpp Source/ROMSX.H commit c52b6f79b0d32a441ac8d9ac2a46193354f729c8 Author: Jean M. Sexton Date: Mon Oct 10 14:47:06 2022 -0700 Test netcdf multiple timesteps per history file Source/IO/NCPlotFile.cpp commit 7dfa396432713c21fa298fce6fdfd89cebf8616c Author: Jean M. Sexton Date: Mon Oct 10 12:26:58 2022 -0700 Write vars as 3d in zyx Source/IO/NCPlotFile.cpp commit a9977637eee5aa17e2f5e701fd7c2d462ad5ff57 Author: Jean M. Sexton Date: Wed Oct 5 20:36:10 2022 -0700 Try strided write Source/IO/NCPlotFile.cpp commit 88531d319468781d57295acbd596b37b2f474463 Author: Jean M. Sexton Date: Tue Oct 4 16:29:38 2022 -0700 Compiles and runs with USE_NETCDF=TRUE Source/BoundaryConditions/BoundaryConditions_wrfbdy.cpp Source/BoundaryConditions/Make.package Source/IO/ReadFromWRFBdy.cpp Source/IO/ReadFromWRFInput.cpp Source/IndexDefines.H commit f5d9935c9e1e7a76eb2df2aa2fcbe72ef8f0915c Author: Jean M. Sexton Date: Tue Oct 4 16:00:16 2022 -0700 Next pass at netcdf compile Source/BoundaryConditions/ROMSX_FillPatch.cpp Source/BoundaryConditions/ROMSX_PhysBCFunct.H Source/ROMSX.H Source/ROMSX.cpp Source/ROMSX_init.cpp commit eda0bc16afb71f9c98f46086a6d0519ba057746e Author: Jean M. Sexton Date: Tue Oct 4 15:33:33 2022 -0700 Compiles with USE_NETCDF=TRUE, fails at linking Exec/Make.ROMSX commit f25c0d67e6bf1f134425f4522fdbcb50e3598f2b Author: Jean M. Sexton Date: Tue Oct 4 13:44:57 2022 -0700 First pass at Upwelling ICs Exec/DoubleGyre/GNUmakefile Exec/Make.ROMSX Exec/Upwelling/GNUmakefile Exec/Upwelling/inputs Exec/Upwelling/prob.cpp Source/Derive.H Source/Derive.cpp Source/IO/Plotfile.cpp Source/IndexDefines.H Source/ROMSX.H commit 9e471828b19866efc8a04dbea97e6995f7671ecb Author: Jean M. Sexton Date: Tue Oct 4 13:44:09 2022 -0700 WIP Upwelling and DoubleGyre proof-of-concept .gitignore Build/in2inputs.sh Exec/DoubleGyre/prob.H Exec/DoubleGyre/prob.cpp Exec/Upwelling/CMakeLists.txt Exec/Upwelling/GNUmakefile Exec/Upwelling/Make.package Exec/Upwelling/inputs Exec/Upwelling/prob.H Exec/Upwelling/prob.cpp Tests/test_files/DoubleGyre/DoubleGyre.i commit 4451ff57773f21dbee09456583240268f1078ac3 Author: Jean M. Sexton Date: Tue Oct 4 13:39:13 2022 -0700 Initial commit: ROMSX next-gen ROMS built on AMReX .clang-format .gitignore .gitmodules Build/cmake.sh Build/cmake_with_netcdf.sh CMake/BuildROMSXExe.cmake CMake/FindNetCDF.cmake CMake/FindSphinx.cmake CMake/SetAmrexCompileFlags.cmake CMake/SetAmrexOptions.cmake CMake/SetROMSXCompileFlags.cmake CMake/SetRpath.cmake CMakeLists.txt CONTRIBUTING.md CTestConfig.cmake Docs/.gitignore Docs/BuildDocs.sh Docs/CMakeLists.txt Docs/Doxyfile.breathe.in Docs/Doxyfile.in Docs/main.dox Docs/sphinx_doc/Applications_Requirements.rst Docs/sphinx_doc/ArakawaCGrid.rst Docs/sphinx_doc/BoundaryConditions.rst Docs/sphinx_doc/Checkpoint.rst Docs/sphinx_doc/CouplingToAMRWind.rst Docs/sphinx_doc/DerivedQuantities.rst Docs/sphinx_doc/Discretizations.rst Docs/sphinx_doc/E3D_mol_ppm.png Docs/sphinx_doc/ERFvsWRF.rst Docs/sphinx_doc/GettingStarted.rst Docs/sphinx_doc/InputFiles.rst Docs/sphinx_doc/Inputs.rst Docs/sphinx_doc/InputsPhysics.rst Docs/sphinx_doc/KE_mol_ppm.png 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