Rebase with development

wiersema1 · Nov 6, 2024 · ff442b2 · ff442b2
2 parents adf406a + 4bc4950
commit ff442b2
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Showing 372 changed files with 3,060 additions and 2,958 deletions.
diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,18 @@
+# 24.11
+    -- AMReX submodule set to 24.11 release hash (4a6e7c8)
+
+    -- AMR functionality (#1916-1920)
+
+    -- GAD functionality (#1912, #1875)
+
+    -- Remove QKE (#1905)
+
+    -- NOAH-MP interface (#1835)
+
+    -- Line and plane sampling (#1897)
+
+    -- AMReX & KOKKOS docs (#1889)
+
 # 24.10
     -- Add WENO7 advection operators (#1858)
 

diff --git a/CMake/BuildERFExe.cmake b/CMake/BuildERFExe.cmake
@@ -187,6 +187,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/TimeIntegration/ERF_fast_rhs_N.cpp
        ${SRC_DIR}/TimeIntegration/ERF_fast_rhs_T.cpp
        ${SRC_DIR}/TimeIntegration/ERF_fast_rhs_MT.cpp
+       ${SRC_DIR}/Utils/ERF_AverageDown.cpp
        ${SRC_DIR}/Utils/ERF_ChopGrids.cpp
        ${SRC_DIR}/Utils/ERF_MomentumToVelocity.cpp
        ${SRC_DIR}/Utils/ERF_TerrainMetrics.cpp
@@ -202,10 +203,10 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Microphysics/Kessler/ERF_Init_Kessler.cpp
        ${SRC_DIR}/Microphysics/Kessler/ERF_Kessler.cpp
        ${SRC_DIR}/Microphysics/Kessler/ERF_Update_Kessler.cpp
-	   ${SRC_DIR}/WindFarmParametrization/Fitch/ERF_AdvanceFitch.cpp
-	   ${SRC_DIR}/WindFarmParametrization/EWP/ERF_AdvanceEWP.cpp
-	   ${SRC_DIR}/WindFarmParametrization/SimpleActuatorDisk/ERF_AdvanceSimpleAD.cpp
-	   ${SRC_DIR}/WindFarmParametrization/GeneralActuatorDisk/ERF_AdvanceGeneralAD.cpp
+       ${SRC_DIR}/WindFarmParametrization/Fitch/ERF_AdvanceFitch.cpp
+       ${SRC_DIR}/WindFarmParametrization/EWP/ERF_AdvanceEWP.cpp
+       ${SRC_DIR}/WindFarmParametrization/SimpleActuatorDisk/ERF_AdvanceSimpleAD.cpp
+       ${SRC_DIR}/WindFarmParametrization/GeneralActuatorDisk/ERF_AdvanceGeneralAD.cpp
        ${SRC_DIR}/LandSurfaceModel/SLM/ERF_SLM.cpp
        ${SRC_DIR}/LandSurfaceModel/MM5/ERF_MM5.cpp
   )

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -247,7 +247,7 @@ target_link_libraries(erf_api PUBLIC erf_srclib)
 add_library(${PROJECT_NAME}::erf_api ALIAS erf_srclib)
 
 # Collect all headers and make them installable with the target
-set(ERF_INCLUDES "Source/ERF.H;Source/ERF_Constants.H;Source/WindFarmParametrization/SimpleActuatorDisk/ERF_SimpleAD.H;Source/WindFarmParametrization/EWP/ERF_EWP.H;Source/WindFarmParametrization/Null/ERF_NullWindFarm.H;Source/WindFarmParametrization/ERF_WindFarm.H;Source/WindFarmParametrization/Fitch/ERF_Fitch.H;Source/BoundaryConditions/ERF_PhysBCFunct.H;Source/BoundaryConditions/ERF_MOSTAverage.H;Source/BoundaryConditions/ERF_MOSTRoughness.H;Source/BoundaryConditions/ERF_ABLMost.H;Source/BoundaryConditions/ERF_FillPatcher.H;Source/BoundaryConditions/ERF_MOSTStress.H;Source/BoundaryConditions/ERF_TimeInterpolatedData.H;Source/Utils/ERF_Interpolation.H;Source/Utils/ERF_TileNoZ.H;Source/Utils/ERF_PlaneAverage.H;Source/Utils/ERF_Interpolation_WENO.H;Source/Utils/ERF_DirectionSelector.H;Source/Utils/ERF_ParFunctions.H;Source/Utils/ERF_Wstar.H;Source/Utils/ERF_Microphysics_Utils.H;Source/Utils/ERF_Sat_methods.H;Source/Utils/ERF_Interpolation_1D.H;Source/Utils/ERF_Interpolation_UPW.H;Source/Utils/ERF_TerrainMetrics.H;Source/Utils/ERF_Interpolation_WENO_Z.H;Source/Utils/ERF_Thetav.H;Source/Utils/ERF_Water_vapor_saturation.H;Source/Utils/ERF_Utils.H;Source/Utils/ERF_Orbit.H;Source/Utils/ERF_EOS.H;Source/Utils/ERF_HSE_utils.H;Source/EB/ERF_TerrainIF.H;Source/EB/ERF_FlowerIF.H;Source/EB/ERF_eb_if.H;Source/Particles/ERFPC.H;Source/Particles/ERF_ParticleData.H;Source/Prob/ERF_init_density_hse_dry.H;Source/Prob/ERF_init_rayleigh_damping.H;Source/Prob/ERF_init_constant_density_hse.H;Source/ERF_prob_common.H;Source/ERF_Derive.H;Source/Radiation/ERF_Mam4_constituents.H;Source/Radiation/ERF_Mam4_aero.H;Source/Radiation/ERF_Optics.H;Source/Radiation/ERF_Modal_aero_wateruptake.H;Source/Radiation/ERF_Cloud_rad_props.H;Source/Radiation/ERF_Phys_prop.H;Source/Radiation/ERF_Radiation.H;Source/Radiation/ERF_Albedo.H;Source/Radiation/ERF_Parameterizations.H;Source/Radiation/ERF_Rad_constants.H;Source/Radiation/ERF_Aero_rad_props.H;Source/Radiation/ERF_m2005_effradius.H;Source/Radiation/ERF_Linear_interpolate.H;Source/Radiation/ERF_Slingo.H;Source/Radiation/ERF_Rrtmgp.H;Source/Radiation/ERF_Ebert_curry.H;Source/SourceTerms/ERF_NumericalDiffusion.H;Source/SourceTerms/ERF_Src_headers.H;Source/IO/ERF_NCInterface.H;Source/IO/ERF_NCWpsFile.H;Source/IO/ERF_NCPlotFile.H;Source/IO/ERF_ReadBndryPlanes.H;Source/IO/ERF_WriteBndryPlanes.H;Source/PBL/ERF_MYNNStruct.H;Source/PBL/ERF_PBLModels.H;Source/PBL/ERF_PBLHeight.H;Source/TimeIntegration/ERF_TI_fast_rhs_fun.H;Source/TimeIntegration/ERF_TI_slow_headers.H;Source/TimeIntegration/ERF_TI_slow_rhs_fun.H;Source/TimeIntegration/ERF_TI_fast_headers.H;Source/TimeIntegration/ERF_TI_utils.H;Source/TimeIntegration/ERF_MRI.H;Source/TimeIntegration/ERF_TI_no_substep_fun.H;Source/LandSurfaceModel/Null/ERF_NullSurf.H;Source/LandSurfaceModel/ERF_LandSurface.H;Source/LandSurfaceModel/MM5/ERF_MM5.H;Source/LandSurfaceModel/SLM/ERF_SLM.H;Source/ERF_IndexDefines.H;Source/Advection/ERF_AdvectionSrcForMom_N.H;Source/Advection/ERF_AdvectionSrcForScalars.H;Source/Advection/ERF_AdvectionSrcForMom_T.H;Source/Advection/ERF_Advection.H;Source/MultiBlock/ERF_MultiBlockContainer.H;Source/Initialization/ERF_Metgrid_utils.H;Source/Diffusion/ERF_EddyViscosity.H;Source/Diffusion/ERF_Diffusion.H;Source/Microphysics/Null/ERF_NullMoistLagrangian.H;Source/Microphysics/Null/ERF_NullMoist.H;Source/Microphysics/ERF_Microphysics.H;Source/Microphysics/ERF_LagrangianMicrophysics.H;Source/Microphysics/ERF_EulerianMicrophysics.H;Source/Microphysics/Kessler/ERF_Kessler.H;Source/Microphysics/SAM/ERF_SAM.H;Source/DataStructs/ERF_InputSpongeData.H;Source/DataStructs/ERF_TurbPertStruct.H;Source/DataStructs/ERF_SpongeStruct.H;Source/DataStructs/ERF_AdvStruct.H;Source/DataStructs/ERF_DataStruct.H;Source/DataStructs/ERF_InputSoundingData.H;Source/DataStructs/ERF_DiffStruct.H;Source/DataStructs/ERF_TurbStruct.H")
+set(ERF_INCLUDES "Source/ERF.H;Source/ERF_Constants.H;Source/WindFarmParametrization/SimpleActuatorDisk/ERF_SimpleAD.H;Source/WindFarmParametrization/EWP/ERF_EWP.H;Source/WindFarmParametrization/Null/ERF_NullWindFarm.H;Source/WindFarmParametrization/ERF_WindFarm.H;Source/WindFarmParametrization/Fitch/ERF_Fitch.H;Source/BoundaryConditions/ERF_PhysBCFunct.H;Source/BoundaryConditions/ERF_MOSTAverage.H;Source/BoundaryConditions/ERF_MOSTRoughness.H;Source/BoundaryConditions/ERF_ABLMost.H;Source/BoundaryConditions/ERF_FillPatcher.H;Source/BoundaryConditions/ERF_MOSTStress.H;Source/BoundaryConditions/ERF_TimeInterpolatedData.H;Source/Utils/ERF_Interpolation.H;Source/Utils/ERF_TileNoZ.H;Source/Utils/ERF_PlaneAverage.H;Source/Utils/ERF_Interpolation_WENO.H;Source/Utils/ERF_DirectionSelector.H;Source/Utils/ERF_ParFunctions.H;Source/Utils/ERF_Wstar.H;Source/Utils/ERF_Microphysics_Utils.H;Source/Utils/ERF_Sat_methods.H;Source/Utils/ERF_Interpolation_1D.H;Source/Utils/ERF_Interpolation_UPW.H;Source/Utils/ERF_TerrainMetrics.H;Source/Utils/ERF_Interpolation_WENO_Z.H;Source/Utils/ERF_Thetav.H;Source/Utils/ERF_Water_vapor_saturation.H;Source/Utils/ERF_Utils.H;Source/Utils/ERF_Orbit.H;Source/Utils/ERF_EOS.H;Source/Utils/ERF_HSE_utils.H;Source/EB/ERF_TerrainIF.H;Source/EB/ERF_FlowerIF.H;Source/EB/ERF_eb_if.H;Source/Particles/ERFPC.H;Source/Particles/ERF_ParticleData.H;Source/Prob/ERF_init_density_hse_dry.H;Source/Prob/ERF_init_rayleigh_damping.H;Source/Prob/ERF_init_constant_density_hse.H;Source/ERF_prob_common.H;Source/ERF_Derive.H;Source/Radiation/ERF_Mam4_constituents.H;Source/Radiation/ERF_Mam4_aero.H;Source/Radiation/ERF_Optics.H;Source/Radiation/ERF_Modal_aero_wateruptake.H;Source/Radiation/ERF_Cloud_rad_props.H;Source/Radiation/ERF_Phys_prop.H;Source/Radiation/ERF_Radiation.H;Source/Radiation/ERF_Albedo.H;Source/Radiation/ERF_Parameterizations.H;Source/Radiation/ERF_Rad_constants.H;Source/Radiation/ERF_Aero_rad_props.H;Source/Radiation/ERF_m2005_effradius.H;Source/Radiation/ERF_Linear_interpolate.H;Source/Radiation/ERF_Slingo.H;Source/Radiation/ERF_Rrtmgp.H;Source/Radiation/ERF_Ebert_curry.H;Source/SourceTerms/ERF_NumericalDiffusion.H;Source/SourceTerms/ERF_Src_headers.H;Source/IO/ERF_NCInterface.H;Source/IO/ERF_NCWpsFile.H;Source/IO/ERF_NCPlotFile.H;Source/IO/ERF_ReadBndryPlanes.H;Source/IO/ERF_WriteBndryPlanes.H;Source/PBL/ERF_MYNNStruct.H;Source/PBL/ERF_PBLModels.H;Source/PBL/ERF_PBLHeight.H;Source/TimeIntegration/ERF_TI_substep_fun.H;Source/TimeIntegration/ERF_TI_slow_headers.H;Source/TimeIntegration/ERF_TI_slow_rhs_fun.H;Source/TimeIntegration/ERF_TI_fast_headers.H;Source/TimeIntegration/ERF_TI_utils.H;Source/TimeIntegration/ERF_MRI.H;Source/TimeIntegration/ERF_TI_no_substep_fun.H;Source/LandSurfaceModel/Null/ERF_NullSurf.H;Source/LandSurfaceModel/ERF_LandSurface.H;Source/LandSurfaceModel/MM5/ERF_MM5.H;Source/LandSurfaceModel/SLM/ERF_SLM.H;Source/ERF_IndexDefines.H;Source/Advection/ERF_AdvectionSrcForMom_N.H;Source/Advection/ERF_AdvectionSrcForScalars.H;Source/Advection/ERF_AdvectionSrcForMom_T.H;Source/Advection/ERF_Advection.H;Source/MultiBlock/ERF_MultiBlockContainer.H;Source/Initialization/ERF_Metgrid_utils.H;Source/Diffusion/ERF_EddyViscosity.H;Source/Diffusion/ERF_Diffusion.H;Source/Microphysics/Null/ERF_NullMoistLagrangian.H;Source/Microphysics/Null/ERF_NullMoist.H;Source/Microphysics/ERF_Microphysics.H;Source/Microphysics/ERF_LagrangianMicrophysics.H;Source/Microphysics/ERF_EulerianMicrophysics.H;Source/Microphysics/Kessler/ERF_Kessler.H;Source/Microphysics/SAM/ERF_SAM.H;Source/DataStructs/ERF_InputSpongeData.H;Source/DataStructs/ERF_TurbPertStruct.H;Source/DataStructs/ERF_SpongeStruct.H;Source/DataStructs/ERF_AdvStruct.H;Source/DataStructs/ERF_DataStruct.H;Source/DataStructs/ERF_InputSoundingData.H;Source/DataStructs/ERF_DiffStruct.H;Source/DataStructs/ERF_TurbStruct.H")
 set_target_properties(
   erf_srclib PROPERTIES PUBLIC_HEADER "${ERF_INCLUDES}")
 

diff --git a/Docs/sphinx_doc/Inputs.rst b/Docs/sphinx_doc/Inputs.rst
@@ -23,11 +23,21 @@ Governing Equations
 |                          | equations (instead of       |               |             |
 |                          | the compressible equations) |               |             |
 +--------------------------+-----------------------------+---------------+-------------+
+| **erf.use_fft**          | use FFT rather than         | true / false  | false       |
+|                          | multigrid to solve the      |               |             |
+|                          | the Poisson equations       |               |             |
++--------------------------+-----------------------------+---------------+-------------+
+| **erf.mg_v**             | verbosity of the multigrid  | Integer >= 0  | 0           |
+|                          | solver if used              |               |             |
+|                          | the Poisson equations       |               |             |
++--------------------------+-----------------------------+---------------+-------------+
 
 .. note::
 
-   To solve the anelastic equations, you must set ERF_USE_POISSON_SOLVE = TRUE if using
-   gmake or ERF_ENABLE_POISSON_SOLVE if using cmake.
+   To solve the anelastic equations, you must set USE_POISSON_SOLVE = TRUE if using
+   gmake or ERF_ENABLE_POISSON_SOLVE if using cmake.  This will enable use of the
+   AMReX-based Poisson solver.   To optionally use the FFT solver, you must additionally
+   set USE_FFT = TRUE if using gmake.
 
 Problem Geometry
 ================
@@ -1331,7 +1341,8 @@ integrating the hydrostatic equation from the surface.
 
 If **erf.init_type = custom** or **erf.init_type = input_sounding**, ``erf.nc_init_file`` and ``erf.nc_bdy_file`` do not need to be set.
 
-Setting **erf.project_initial_velocity = 1** will have no effect if the code is not built with **ERF_USE_POISSON_SOLVE** defined.
+Setting **erf.project_initial_velocity = 1** will have no effect if the code is not built with **ERF_USE_POISSON_SOLVE** defined
+if using cmake or with **USE_POISSON_SOLVE = TRUE** if using gmake.
 
 Map Scale Factors
 =================