├── .clang-format ├── .codespell-ignore-words ├── .codespellrc ├── .github ├── actions │ └── free-space-ubuntu │ │ └── action.yml └── workflows │ ├── c-linter.yml │ ├── ci.yml │ ├── cleanup-cache-postpr.yml │ ├── cleanup-cache.yml │ ├── codespell.yml │ ├── cuda-ci.yml │ ├── dependencies │ └── documentation.sh │ ├── docs.yml │ ├── draft-pdf.yml │ ├── gcc.yml │ ├── hip.yml │ ├── macos.yml │ ├── post-pr.yml │ ├── style.yml │ ├── style │ ├── check_tabs.sh │ └── check_trailing_whitespaces.sh │ ├── sycl.yml │ └── windows.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yml ├── Build ├── clone_copy_build.sh ├── cmake.sh ├── cmake_with_netcdf.sh ├── cmake_with_particles.sh ├── compare_flat_tweak_inputs.patch ├── cori-env.sh ├── differences_list.txt ├── in2inputs.sh └── saul-env.sh ├── CMake ├── BuildREMORAExe.cmake ├── FindPNetCDF.cmake ├── FindSphinx.cmake ├── REMORAConfig.cmake.in ├── SetAmrexOptions.cmake ├── SetREMORACompileFlags.cmake └── SetRpath.cmake ├── CMakeLists.txt ├── CONTRIBUTING.md ├── CTestConfig.cmake ├── Docs ├── .gitignore ├── BuildDocs.sh ├── CMakeLists.txt ├── Doxyfile.breathe.in ├── Doxyfile.in ├── main.dox ├── requirements.txt └── sphinx_doc │ ├── AMReX.rst │ ├── ArakawaCGrid.rst │ ├── BoundaryConditions.rst │ ├── Checkpoint.rst │ ├── Climatology.rst │ ├── Discretizations.rst │ ├── Doxygen.rst │ ├── GettingStarted.rst │ ├── InputFiles.rst │ ├── Inputs.rst │ ├── Makefile │ ├── MeshRefinement.rst │ ├── Numerical_Solution_Technique.rst │ ├── Particles.rst │ ├── Performance.rst │ ├── Plotfiles.rst │ ├── ProblemSetup.rst │ ├── RegressionTests.rst │ ├── Time_Stepping.rst │ ├── Verification.rst │ ├── VerticalSCoord.rst │ ├── Visualization.rst │ ├── building.rst │ ├── coc.rst │ ├── conf.py │ ├── figures │ ├── Barostep.png │ ├── Horns_Rev_annotated.png │ ├── ParaView.png │ ├── ParaView_filegroup.png │ ├── ParaView_particles.png │ ├── Shortstep.png │ ├── Timestep_1.png │ ├── VisIt_2D.png │ ├── VisIt_3D.png │ ├── grid_cell.png │ ├── grid_discretization │ │ ├── Arakawa_1.png │ │ ├── Arakawa_2.png │ │ ├── Arakawa_3.png │ │ ├── Arakawa_4.png │ │ ├── Arakawa_5.png │ │ ├── EddyViscosity.PNG │ │ ├── StrainRate.PNG │ │ ├── TKE_x.PNG │ │ ├── TKE_y.PNG │ │ ├── TKE_z.PNG │ │ ├── continuity_x.PNG │ │ ├── continuity_y.PNG │ │ ├── continuity_z.PNG │ │ ├── scalar_advec_x.PNG │ │ ├── scalar_advec_y.PNG │ │ ├── scalar_advec_z.PNG │ │ ├── stagger_XY.PNG │ │ ├── stagger_YZ.PNG │ │ ├── temp_advec_x.PNG │ │ ├── temp_advec_y.PNG │ │ ├── temp_advec_z.PNG │ │ ├── x_mom_advec_x.PNG │ │ ├── x_mom_advec_y.PNG │ │ ├── x_mom_advec_z.PNG │ │ ├── x_mom_diff_a.PNG │ │ ├── x_mom_diff_b.PNG │ │ ├── y_mom_advec_x.PNG │ │ ├── y_mom_advec_y.PNG │ │ ├── y_mom_advec_z.PNG │ │ ├── y_mom_diff_a.PNG │ │ ├── y_mom_diff_b.PNG │ │ ├── z_mom_advec_x.PNG │ │ ├── z_mom_advec_y.PNG │ │ ├── z_mom_advec_z.PNG │ │ ├── z_mom_diff_a.PNG │ │ └── z_mom_diff_b.PNG │ ├── multiscale_atmospheric_sim.png │ ├── rt_2048_paraview_000500.png │ ├── rt_2048_visit_000500.png │ ├── scalar_whitebg_circle_hr_00010.png │ ├── staggered_grid_rho_cells.png │ ├── strong.png │ ├── tests │ │ ├── TGV_end.png │ │ ├── TGV_start.png │ │ ├── scalar_advec_diff_end.png │ │ ├── scalar_advec_diff_start.png │ │ ├── scalar_advec_rigid_rot_end.png │ │ ├── scalar_advec_rigid_rot_start.png │ │ ├── scalar_advec_sheared_u_end.png │ │ ├── scalar_advec_sheared_u_start.png │ │ ├── scalar_advec_uniform_u_end.png │ │ ├── scalar_advec_uniform_u_start.png │ │ ├── scalar_diff_end.png │ │ ├── scalar_diff_sine_end.png │ │ ├── scalar_diff_sine_start.png │ │ └── scalar_diff_start.png │ ├── vertical_grid.png │ ├── vieste-dubrovnik.png │ ├── weak.png │ ├── weak_scale.png │ ├── yt_Nyx_density_slice.png │ └── yt_Nyx_density_vol_rend.png │ ├── index.rst │ ├── make.bat │ ├── perlmutter.rst │ ├── static │ ├── Horns_Rev_annotated.jpg │ └── multiscale_atmospheric_sim.jpg │ ├── submodule.rst │ ├── testing.rst │ └── theory │ ├── Equations.rst │ ├── Variables.rst │ └── VerticalMixing.rst ├── Exec ├── Advection │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── Palette │ ├── README │ ├── inputs │ ├── inputs_ml │ ├── prob.H │ └── prob.cpp ├── BlankProblem │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── amrvis.defaults │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── BoundaryLayer │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── CMakeLists.txt ├── Channel_Test │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README │ ├── inputs │ ├── inputs_orlanski │ ├── prob.H │ └── prob.cpp ├── Dogbone │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── DogboneAnalytic │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── inputs │ ├── inputs_ml │ ├── inputs_ml_mid │ ├── inputs_ml_quad │ ├── prob.H │ └── prob.cpp ├── DoubleGyre │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── DoublyPeriodic │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── Palette │ ├── README │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── IdealMiniGrid │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── inputs │ ├── inputs_cf_orlanski │ ├── inputs_chapman_flather │ ├── inputs_clim_nudg │ ├── inputs_frc │ ├── prob.H │ └── prob.cpp ├── IdealRivGrid │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── Make.REMORA ├── ParticlesOverSeaMount │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── Seamount │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── amrvis.defaults │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── Upwelling │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── README.rst │ ├── inputs │ ├── inputs_gls │ ├── prob.H │ └── prob.cpp └── Upwelling_ML │ ├── CMakeLists.txt │ ├── GNUmakefile │ ├── Make.package │ ├── inputs │ ├── prob.H │ └── prob.cpp ├── LICENSE.md ├── README.rst ├── Source ├── BoundaryConditions │ ├── Make.package │ ├── REMORA_BoundaryConditions_cons.cpp │ ├── REMORA_BoundaryConditions_netcdf.cpp │ ├── REMORA_BoundaryConditions_xvel.cpp │ ├── REMORA_BoundaryConditions_yvel.cpp │ ├── REMORA_BoundaryConditions_zvel.cpp │ ├── REMORA_FillPatch.cpp │ ├── REMORA_FillPatcher.H │ ├── REMORA_FillPatcher.cpp │ ├── REMORA_PhysBCFunct.H │ ├── REMORA_PhysBCFunct.cpp │ └── REMORA_TimeInterpolatedData.H ├── IO │ ├── Make.package │ ├── REMORA_Checkpoint.cpp │ ├── REMORA_NCFile.H │ ├── REMORA_NCFile.cpp │ ├── REMORA_NCInterface.H │ ├── REMORA_NCInterface.cpp │ ├── REMORA_NCPlotFile.H │ ├── REMORA_NCPlotFile.cpp │ ├── REMORA_NCTimeSeries.H │ ├── REMORA_NCTimeSeries.cpp │ ├── REMORA_NCTimeSeriesBoundary.H │ ├── REMORA_NCTimeSeriesBoundary.cpp │ ├── REMORA_NCTimeSeriesRiver.H │ ├── REMORA_NCTimeSeriesRiver.cpp │ ├── REMORA_Plotfile.cpp │ ├── REMORA_ReadFromInitNetcdf.cpp │ ├── REMORA_SetPlotVars.cpp │ ├── REMORA_console_io.cpp │ └── REMORA_writeJobInfo.cpp ├── Initialization │ ├── Make.package │ ├── REMORA_init.cpp │ ├── REMORA_init1d.cpp │ ├── REMORA_init_bcs.cpp │ ├── REMORA_init_from_netcdf.cpp │ ├── REMORA_make_new_level.cpp │ └── REMORA_prob_common.H ├── Make.package ├── Particles │ ├── Make.package │ ├── REMORA_PC.H │ ├── REMORA_PC_Evolve.cpp │ ├── REMORA_PC_Init.cpp │ ├── REMORA_PC_Utils.cpp │ ├── REMORA_ParticleData.H │ └── REMORA_Tracers.cpp ├── REMORA.H ├── REMORA.cpp ├── REMORA_Constants.H ├── REMORA_DataStruct.H ├── REMORA_Derive.H ├── REMORA_Derive.cpp ├── REMORA_IndexDefines.H ├── REMORA_MOAB.H ├── REMORA_MOAB.cpp ├── REMORA_SumIQ.cpp ├── REMORA_Tagging.cpp ├── TimeIntegration │ ├── FUNWAVE │ │ ├── Make.package │ │ ├── REMORA_funwave_Fortran_Interface.H │ │ ├── REMORA_funwave_advance.F90 │ │ └── REMORA_funwave_isohelper.F90 │ ├── Make.package │ ├── REMORA_Advance.cpp │ ├── REMORA_ComputeTimestep.cpp │ ├── REMORA_TimeStep.cpp │ ├── REMORA_TimeStepML.cpp │ ├── REMORA_advance_2d.cpp │ ├── REMORA_advance_2d_onestep.cpp │ ├── REMORA_advance_3d.cpp │ ├── REMORA_advance_3d_ml.cpp │ ├── REMORA_apply_clim_nudg.cpp │ ├── REMORA_bulk_flux.cpp │ ├── REMORA_coriolis.cpp │ ├── REMORA_gls.cpp │ ├── REMORA_prestep.cpp │ ├── REMORA_prestep_diffusion.cpp │ ├── REMORA_prestep_t_advection.cpp │ ├── REMORA_prsgrd.cpp │ ├── REMORA_rho_eos.cpp │ ├── REMORA_rhs_t_3d.cpp │ ├── REMORA_rhs_uv_2d.cpp │ ├── REMORA_rhs_uv_3d.cpp │ ├── REMORA_scale_rhs_vars.cpp │ ├── REMORA_set_weights.cpp │ ├── REMORA_setup_step.cpp │ ├── REMORA_t3dmix.cpp │ ├── REMORA_update_massflux_3d.cpp │ ├── REMORA_uv3dmix.cpp │ ├── REMORA_vert_mean_3d.cpp │ └── REMORA_vert_visc_3d.cpp ├── Utils │ ├── Make.package │ ├── REMORA_DepthStretchTransform.H │ └── REMORA_Math.H └── main.cpp ├── Tests ├── CMakeLists.txt ├── CTestList.cmake ├── REMORA_Gold_Files │ ├── Advection │ │ ├── Header │ │ └── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_D_00001 │ │ │ ├── Cell_D_00002 │ │ │ ├── Cell_D_00003 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ ├── Nu_nd_D_00001 │ │ │ ├── Nu_nd_D_00002 │ │ │ ├── Nu_nd_D_00003 │ │ │ └── Nu_nd_H │ ├── Advection_ML │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ └── Cell_H │ │ ├── Level_1 │ │ │ ├── Cell_D_00000 │ │ │ └── Cell_H │ │ └── job_info │ ├── BoundaryLayer │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── Channel_Test │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── DogboneAnalytic │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── DogboneAnalytic_MLquad │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ ├── Level_1 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── DogboneAnalytic_MLvel │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ └── Cell_H │ │ ├── Level_1 │ │ │ ├── Cell_D_00000 │ │ │ └── Cell_H │ │ └── job_info │ ├── DoubleGyre │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── DoublyPeriodic │ │ ├── Header │ │ └── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_D_00001 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ ├── Nu_nd_D_00001 │ │ │ └── Nu_nd_H │ ├── DoublyPeriodic_bathy │ │ ├── Header │ │ └── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_D_00001 │ │ │ ├── Cell_D_00002 │ │ │ ├── Cell_D_00003 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ ├── Nu_nd_D_00001 │ │ │ ├── Nu_nd_D_00002 │ │ │ ├── Nu_nd_D_00003 │ │ │ └── Nu_nd_H │ ├── Seamount │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── Upwelling │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── Upwelling_GLS │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── Upwelling_NLEOS │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ ├── Upwelling_logdrag │ │ ├── Header │ │ ├── Level_0 │ │ │ ├── Cell_D_00000 │ │ │ ├── Cell_H │ │ │ ├── Nu_nd_D_00000 │ │ │ └── Nu_nd_H │ │ └── job_info │ └── Upwelling_qdrag │ │ ├── Header │ │ ├── Level_0 │ │ ├── Cell_D_00000 │ │ ├── Cell_H │ │ ├── Nu_nd_D_00000 │ │ └── Nu_nd_H │ │ └── job_info └── test_files │ ├── Advection │ └── Advection.i │ ├── Advection_ML │ └── Advection_ML.i │ ├── BoundaryLayer │ └── BoundaryLayer.i │ ├── Channel_Test │ └── Channel_Test.i │ ├── DogboneAnalytic │ └── DogboneAnalytic.i │ ├── 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