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Use ERF_ prefix (#1799)
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WeiqunZhang authored Sep 11, 2024
1 parent 8813259 commit 9933258
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Showing 384 changed files with 1,104 additions and 1,105 deletions.
144 changes: 72 additions & 72 deletions CMake/BuildERFExe.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ function(build_erf_lib erf_lib_name)

if(ERF_ENABLE_MULTIBLOCK)
target_sources(${erf_lib_name} PRIVATE
${SRC_DIR}/MultiBlock/MultiBlockContainer.cpp)
${SRC_DIR}/MultiBlock/ERF_MultiBlockContainer.cpp)
target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_MULTIBLOCK)
target_include_directories(${erf_lib_name} PUBLIC ${SRC_DIR}/MultiBlock)
endif()
Expand Down Expand Up @@ -49,40 +49,40 @@ function(build_erf_lib erf_lib_name)
if(ERF_ENABLE_EB)
target_sources(${erf_lib_name} PRIVATE
${SRC_DIR}/EB/Init_EB.cpp
${SRC_DIR}/EB/eb_box.cpp
${SRC_DIR}/EB/eb_cylinder.cpp
${SRC_DIR}/EB/eb_regular.cpp
${SRC_DIR}/EB/initEB.cpp
${SRC_DIR}/EB/writeEBsurface.cpp)
${SRC_DIR}/EB/ERF_eb_box.cpp
${SRC_DIR}/EB/ERF_eb_cylinder.cpp
${SRC_DIR}/EB/ERF_eb_regular.cpp
${SRC_DIR}/EB/ERF_initEB.cpp
${SRC_DIR}/EB/ERF_writeEBsurface.cpp)
target_include_directories(${erf_lib_name} PUBLIC ${SRC_DIR}/EB)
target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_EB)
endif()

if(ERF_ENABLE_NETCDF)
target_sources(${erf_lib_name} PRIVATE
${SRC_DIR}/IO/NCInterface.cpp
${SRC_DIR}/IO/NCPlotFile.cpp
${SRC_DIR}/IO/NCCheckpoint.cpp
${SRC_DIR}/IO/NCMultiFabFile.cpp
${SRC_DIR}/IO/ReadFromMetgrid.cpp
${SRC_DIR}/IO/ReadFromWRFBdy.cpp
${SRC_DIR}/IO/ReadFromWRFInput.cpp
${SRC_DIR}/IO/NCColumnFile.cpp)
${SRC_DIR}/IO/ERF_NCInterface.cpp
${SRC_DIR}/IO/ERF_NCPlotFile.cpp
${SRC_DIR}/IO/ERF_NCCheckpoint.cpp
${SRC_DIR}/IO/ERF_NCMultiFabFile.cpp
${SRC_DIR}/IO/ERF_ReadFromMetgrid.cpp
${SRC_DIR}/IO/ERF_ReadFromWRFBdy.cpp
${SRC_DIR}/IO/ERF_ReadFromWRFInput.cpp
${SRC_DIR}/IO/ERF_NCColumnFile.cpp)
target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_NETCDF)
endif()

if(ERF_ENABLE_RRTMGP)
target_sources(${erf_lib_name} PRIVATE
${SRC_DIR}/Utils/Orbit.cpp
${SRC_DIR}/Radiation/Init_rrtmgp.cpp
${SRC_DIR}/Radiation/Finalize_rrtmgp.cpp
${SRC_DIR}/Radiation/Run_longwave_rrtmgp.cpp
${SRC_DIR}/Radiation/Run_shortwave_rrtmgp.cpp
${SRC_DIR}/Radiation/Cloud_rad_props.cpp
${SRC_DIR}/Radiation/Aero_rad_props.cpp
${SRC_DIR}/Radiation/Optics.cpp
${SRC_DIR}/Radiation/Radiation.cpp
${SRC_DIR}/Radiation/Albedo.cpp
${SRC_DIR}/Utils/ERF_Orbit.cpp
${SRC_DIR}/Radiation/ERF_Init_rrtmgp.cpp
${SRC_DIR}/Radiation/ERF_Finalize_rrtmgp.cpp
${SRC_DIR}/Radiation/ERF_Run_longwave_rrtmgp.cpp
${SRC_DIR}/Radiation/ERF_Run_shortwave_rrtmgp.cpp
${SRC_DIR}/Radiation/ERF_Cloud_rad_props.cpp
${SRC_DIR}/Radiation/ERF_Aero_rad_props.cpp
${SRC_DIR}/Radiation/ERF_Optics.cpp
${SRC_DIR}/Radiation/ERF_Radiation.cpp
${SRC_DIR}/Radiation/ERF_Albedo.cpp
${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/examples/mo_load_coefficients.cpp
${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/extensions/fluxes_byband/mo_fluxes_byband_kernels.cpp
)
Expand All @@ -103,35 +103,35 @@ function(build_erf_lib erf_lib_name)

target_sources(${erf_lib_name}
PRIVATE
${SRC_DIR}/Derive.cpp
${SRC_DIR}/ERF_Derive.cpp
${SRC_DIR}/ERF.cpp
${SRC_DIR}/ERF_make_new_arrays.cpp
${SRC_DIR}/ERF_make_new_level.cpp
${SRC_DIR}/ERF_read_waves.cpp
${SRC_DIR}/ERF_Tagging.cpp
${SRC_DIR}/Advection/AdvectionSrcForMom.cpp
${SRC_DIR}/Advection/AdvectionSrcForState.cpp
${SRC_DIR}/Advection/AdvectionSrcForOpenBC.cpp
${SRC_DIR}/BoundaryConditions/ABLMost.cpp
${SRC_DIR}/BoundaryConditions/MOSTAverage.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_cons.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_xvel.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_yvel.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_zvel.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_bndryreg.cpp
${SRC_DIR}/BoundaryConditions/BoundaryConditions_realbdy.cpp
${SRC_DIR}/Advection/ERF_AdvectionSrcForMom.cpp
${SRC_DIR}/Advection/ERF_AdvectionSrcForState.cpp
${SRC_DIR}/Advection/ERF_AdvectionSrcForOpenBC.cpp
${SRC_DIR}/BoundaryConditions/ERF_ABLMost.cpp
${SRC_DIR}/BoundaryConditions/ERF_MOSTAverage.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_cons.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_xvel.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_yvel.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_zvel.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_bndryreg.cpp
${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_realbdy.cpp
${SRC_DIR}/BoundaryConditions/ERF_FillPatch.cpp
${SRC_DIR}/BoundaryConditions/ERF_FillPatcher.cpp
${SRC_DIR}/BoundaryConditions/ERF_PhysBCFunct.cpp
${SRC_DIR}/Diffusion/DiffusionSrcForMom_N.cpp
${SRC_DIR}/Diffusion/DiffusionSrcForMom_T.cpp
${SRC_DIR}/Diffusion/DiffusionSrcForState_N.cpp
${SRC_DIR}/Diffusion/DiffusionSrcForState_T.cpp
${SRC_DIR}/Diffusion/ComputeStress_N.cpp
${SRC_DIR}/Diffusion/ComputeStress_T.cpp
${SRC_DIR}/Diffusion/ComputeStrain_N.cpp
${SRC_DIR}/Diffusion/ComputeStrain_T.cpp
${SRC_DIR}/Diffusion/ComputeTurbulentViscosity.cpp
${SRC_DIR}/Diffusion/ERF_DiffusionSrcForMom_N.cpp
${SRC_DIR}/Diffusion/ERF_DiffusionSrcForMom_T.cpp
${SRC_DIR}/Diffusion/ERF_DiffusionSrcForState_N.cpp
${SRC_DIR}/Diffusion/ERF_DiffusionSrcForState_T.cpp
${SRC_DIR}/Diffusion/ERF_ComputeStress_N.cpp
${SRC_DIR}/Diffusion/ERF_ComputeStress_T.cpp
${SRC_DIR}/Diffusion/ERF_ComputeStrain_N.cpp
${SRC_DIR}/Diffusion/ERF_ComputeStrain_T.cpp
${SRC_DIR}/Diffusion/ERF_ComputeTurbulentViscosity.cpp
${SRC_DIR}/Initialization/ERF_init_custom.cpp
${SRC_DIR}/Initialization/ERF_init_from_hse.cpp
${SRC_DIR}/Initialization/ERF_init_from_input_sounding.cpp
Expand All @@ -141,25 +141,25 @@ function(build_erf_lib erf_lib_name)
${SRC_DIR}/Initialization/ERF_init1d.cpp
${SRC_DIR}/Initialization/ERF_init_TurbPert.cpp
${SRC_DIR}/Initialization/ERF_input_sponge.cpp
${SRC_DIR}/IO/Checkpoint.cpp
${SRC_DIR}/IO/ERF_Checkpoint.cpp
${SRC_DIR}/IO/ERF_ReadBndryPlanes.cpp
${SRC_DIR}/IO/ERF_WriteBndryPlanes.cpp
${SRC_DIR}/IO/ERF_Write1DProfiles.cpp
${SRC_DIR}/IO/ERF_Write1DProfiles_stag.cpp
${SRC_DIR}/IO/ERF_WriteScalarProfiles.cpp
${SRC_DIR}/IO/Plotfile.cpp
${SRC_DIR}/IO/writeJobInfo.cpp
${SRC_DIR}/IO/console_io.cpp
${SRC_DIR}/PBL/ComputeDiffusivityMYNN25.cpp
${SRC_DIR}/PBL/ComputeDiffusivityYSU.cpp
${SRC_DIR}/IO/ERF_Plotfile.cpp
${SRC_DIR}/IO/ERF_writeJobInfo.cpp
${SRC_DIR}/IO/ERF_console_io.cpp
${SRC_DIR}/PBL/ERF_ComputeDiffusivityMYNN25.cpp
${SRC_DIR}/PBL/ERF_ComputeDiffusivityYSU.cpp
${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs.cpp
${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs_ReadFromFile.cpp
${SRC_DIR}/SourceTerms/ERF_make_buoyancy.cpp
${SRC_DIR}/SourceTerms/ERF_add_thin_body_sources.cpp
${SRC_DIR}/SourceTerms/ERF_make_mom_sources.cpp
${SRC_DIR}/SourceTerms/ERF_make_sources.cpp
${SRC_DIR}/SourceTerms/ERF_moist_set_rhs.cpp
${SRC_DIR}/SourceTerms/NumericalDiffusion.cpp
${SRC_DIR}/SourceTerms/ERF_NumericalDiffusion.cpp
${SRC_DIR}/TimeIntegration/ERF_ComputeTimestep.cpp
${SRC_DIR}/TimeIntegration/ERF_Advance.cpp
${SRC_DIR}/TimeIntegration/ERF_TimeStep.cpp
Expand All @@ -174,26 +174,26 @@ 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/ChopGrids.cpp
${SRC_DIR}/Utils/MomentumToVelocity.cpp
${SRC_DIR}/Utils/TerrainMetrics.cpp
${SRC_DIR}/Utils/VelocityToMomentum.cpp
${SRC_DIR}/Utils/InteriorGhostCells.cpp
${SRC_DIR}/Utils/Time_Avg_Vel.cpp
${SRC_DIR}/Microphysics/SAM/Init_SAM.cpp
${SRC_DIR}/Microphysics/SAM/Cloud_SAM.cpp
${SRC_DIR}/Microphysics/SAM/IceFall.cpp
${SRC_DIR}/Microphysics/SAM/Precip.cpp
${SRC_DIR}/Microphysics/SAM/PrecipFall.cpp
${SRC_DIR}/Microphysics/SAM/Update_SAM.cpp
${SRC_DIR}/Microphysics/Kessler/Init_Kessler.cpp
${SRC_DIR}/Microphysics/Kessler/Kessler.cpp
${SRC_DIR}/Microphysics/Kessler/Update_Kessler.cpp
${SRC_DIR}/WindFarmParametrization/Fitch/AdvanceFitch.cpp
${SRC_DIR}/WindFarmParametrization/EWP/AdvanceEWP.cpp
${SRC_DIR}/WindFarmParametrization/SimpleActuatorDisk/AdvanceSimpleAD.cpp
${SRC_DIR}/LandSurfaceModel/SLM/SLM.cpp
${SRC_DIR}/LandSurfaceModel/MM5/MM5.cpp
${SRC_DIR}/Utils/ERF_ChopGrids.cpp
${SRC_DIR}/Utils/ERF_MomentumToVelocity.cpp
${SRC_DIR}/Utils/ERF_TerrainMetrics.cpp
${SRC_DIR}/Utils/ERF_VelocityToMomentum.cpp
${SRC_DIR}/Utils/ERF_InteriorGhostCells.cpp
${SRC_DIR}/Utils/ERF_Time_Avg_Vel.cpp
${SRC_DIR}/Microphysics/SAM/ERF_Init_SAM.cpp
${SRC_DIR}/Microphysics/SAM/ERF_Cloud_SAM.cpp
${SRC_DIR}/Microphysics/SAM/ERF_IceFall.cpp
${SRC_DIR}/Microphysics/SAM/ERF_Precip.cpp
${SRC_DIR}/Microphysics/SAM/ERF_PrecipFall.cpp
${SRC_DIR}/Microphysics/SAM/ERF_Update_SAM.cpp
${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}/LandSurfaceModel/SLM/ERF_SLM.cpp
${SRC_DIR}/LandSurfaceModel/MM5/ERF_MM5.cpp
)

if(NOT "${erf_exe_name}" STREQUAL "erf_unit_tests")
Expand Down
2 changes: 1 addition & 1 deletion Exec/ABL/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ set(erf_exe_name erf_abl)
add_executable(${erf_exe_name} "")
target_sources(${erf_exe_name}
PRIVATE
prob.cpp
ERF_prob.cpp
)

target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
Expand Down
10 changes: 5 additions & 5 deletions Exec/ABL/prob.H → Exec/ABL/ERF_prob.H
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#ifndef _PROB_H_
#define _PROB_H_
#ifndef ERF_PROB_H_
#define ERF_PROB_H_

#include <string>

#include "AMReX_REAL.H"

#include "prob_common.H"
#include "ERF_prob_common.H"

struct ProbParm : ProbParmDefaults {
amrex::Real rho_0 = 0.0;
Expand Down Expand Up @@ -51,8 +51,8 @@ class Problem : public ProblemBase
public:
Problem(const amrex::Real* problo, const amrex::Real* probhi);

#include "Prob/init_constant_density_hse.H"
#include "Prob/init_rayleigh_damping.H"
#include "Prob/ERF_init_constant_density_hse.H"
#include "Prob/ERF_init_rayleigh_damping.H"

void init_custom_pert (
const amrex::Box& bx,
Expand Down
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#include "prob.H"
#include "ERF_prob.H"
#include "AMReX_Random.H"

using namespace amrex;
Expand Down
4 changes: 2 additions & 2 deletions Exec/ABL/Make.package
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
CEXE_headers += prob.H
CEXE_sources += prob.cpp
CEXE_headers += ERF_prob.H
CEXE_sources += ERF_prob.cpp
2 changes: 1 addition & 1 deletion Exec/ABL_input_sounding/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ set(erf_exe_name erf_abl_input_sounding)
add_executable(${erf_exe_name} "")
target_sources(${erf_exe_name}
PRIVATE
prob.cpp
ERF_prob.cpp
)

target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#ifndef _PROB_H_
#define _PROB_H_
#ifndef ERF_PROB_H_
#define ERF_PROB_H_

#include <string>

#include "AMReX_REAL.H"

#include "prob_common.H"
#include "ERF_prob_common.H"

struct ProbParm : ProbParmDefaults {
amrex::Real rho_0 = 0.0;
Expand Down Expand Up @@ -45,8 +45,8 @@ class Problem : public ProblemBase
public:
Problem(const amrex::Real* problo, const amrex::Real* probhi);

#include "Prob/init_constant_density_hse.H"
#include "Prob/init_rayleigh_damping.H"
#include "Prob/ERF_init_constant_density_hse.H"
#include "Prob/ERF_init_rayleigh_damping.H"

void init_custom_pert (
const amrex::Box& bx,
Expand Down
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#include "prob.H"
#include "ERF_prob.H"
#include "AMReX_Random.H"

using namespace amrex;
Expand Down
4 changes: 2 additions & 2 deletions Exec/ABL_input_sounding/Make.package
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
CEXE_headers += prob.H
CEXE_sources += prob.cpp
CEXE_headers += ERF_prob.H
CEXE_sources += ERF_prob.cpp
2 changes: 1 addition & 1 deletion Exec/DevTests/ABL_with_WW3/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ set(erf_exe_name erf_abl)
add_executable(${erf_exe_name} "")
target_sources(${erf_exe_name}
PRIVATE
prob.cpp
ERF_prob.cpp
)

target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#ifndef _PROB_H_
#define _PROB_H_
#ifndef ERF_PROB_H_
#define ERF_PROB_H_

#include <string>

#include "AMReX_REAL.H"

#include "prob_common.H"
#include "ERF_prob_common.H"

struct ProbParm : ProbParmDefaults {
amrex::Real rho_0 = 0.0;
Expand Down Expand Up @@ -51,8 +51,8 @@ class Problem : public ProblemBase
public:
Problem(const amrex::Real* problo, const amrex::Real* probhi);

#include "Prob/init_constant_density_hse.H"
#include "Prob/init_rayleigh_damping.H"
#include "Prob/ERF_init_constant_density_hse.H"
#include "Prob/ERF_init_rayleigh_damping.H"

void init_custom_pert (
const amrex::Box& bx,
Expand Down
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#include "prob.H"
#include "ERF_prob.H"
#include "AMReX_Random.H"

using namespace amrex;
Expand Down
4 changes: 2 additions & 2 deletions Exec/DevTests/ABL_with_WW3/Make.package
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
CEXE_headers += prob.H
CEXE_sources += prob.cpp
CEXE_headers += ERF_prob.H
CEXE_sources += ERF_prob.cpp
2 changes: 1 addition & 1 deletion Exec/DevTests/EB_Test/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ if(ERF_ENABLE_PARTICLES)
add_executable(${erf_exe_name} "")
target_sources(${erf_exe_name}
PRIVATE
prob.cpp
ERF_prob.cpp
)

target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#ifndef _PROB_H_
#define _PROB_H_
#ifndef ERF_PROB_H_
#define ERF_PROB_H_

#include <string>

#include "AMReX_REAL.H"

#include "prob_common.H"
#include "ERF_prob_common.H"

struct ProbParm : ProbParmDefaults {
amrex::Real rho_0 = 0.0;
Expand All @@ -31,7 +31,7 @@ class Problem : public ProblemBase
public:
Problem();

#include "Prob/init_constant_density_hse.H"
#include "Prob/ERF_init_constant_density_hse.H"

void init_custom_pert (
const amrex::Box& bx,
Expand Down
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#include "prob.H"
#include "TerrainMetrics.H"
#include "ERF_prob.H"
#include "ERF_TerrainMetrics.H"

using namespace amrex;

Expand Down
4 changes: 2 additions & 2 deletions Exec/DevTests/EB_Test/Make.package
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
CEXE_headers += prob.H
CEXE_sources += prob.cpp
CEXE_headers += ERF_prob.H
CEXE_sources += ERF_prob.cpp
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