prepend REMORA_ onto all files

hklion · Dec 6, 2024 · b31f712 · b31f712
1 parent b5813a5
commit b31f712
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Showing 58 changed files with 136 additions and 174 deletions.
diff --git a/CMake/BuildREMORAExe.cmake b/CMake/BuildREMORAExe.cmake
@@ -15,11 +15,6 @@ function(build_remora_lib remora_lib_name)
   include(${CMAKE_SOURCE_DIR}/CMake/SetREMORACompileFlags.cmake)
   set_remora_compile_flags(${remora_lib_name})
 
-  set(REMORA_EOS_DIR "${CMAKE_SOURCE_DIR}/Source")
-  target_sources(${remora_lib_name} PRIVATE
-                 ${REMORA_EOS_DIR}/EOS.H)
-  target_include_directories(${remora_lib_name} SYSTEM PUBLIC ${REMORA_EOS_DIR})
-
   if(REMORA_ENABLE_PARTICLES)
     target_sources(${remora_lib_name} PRIVATE
                    ${SRC_DIR}/Particles/REMORA_PC_Evolve.cpp
@@ -32,15 +27,15 @@ function(build_remora_lib remora_lib_name)
 
   if(REMORA_ENABLE_PNETCDF)
     target_sources(${remora_lib_name} PRIVATE
-                   ${SRC_DIR}/IO/NCInterface.H
-                   ${SRC_DIR}/IO/NCPlotFile.H
-                   ${SRC_DIR}/IO/NCFile.H
-                   ${SRC_DIR}/IO/NCInterface.cpp
-                   ${SRC_DIR}/IO/NCPlotFile.cpp
-                   ${SRC_DIR}/IO/NCFile.cpp
-                   ${SRC_DIR}/IO/ReadFromInitNetcdf.cpp
-                   ${SRC_DIR}/IO/ReadFromBdryNetcdf.cpp
-                   ${SRC_DIR}/BoundaryConditions/BoundaryConditions_netcdf.cpp
+                   ${SRC_DIR}/IO/REMORA_NCInterface.H
+                   ${SRC_DIR}/IO/REMORA_NCPlotFile.H
+                   ${SRC_DIR}/IO/REMORA_NCFile.H
+                   ${SRC_DIR}/IO/REMORA_NCInterface.cpp
+                   ${SRC_DIR}/IO/REMORA_NCPlotFile.cpp
+                   ${SRC_DIR}/IO/REMORA_NCFile.cpp
+                   ${SRC_DIR}/IO/REMORA_ReadFromInitNetcdf.cpp
+                   ${SRC_DIR}/IO/REMORA_ReadFromBdryNetcdf.cpp
+                   ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp
                    ${SRC_DIR}/Initialization/REMORA_init_from_netcdf.cpp)
     target_compile_definitions(${remora_lib_name} PUBLIC REMORA_USE_NETCDF)
   endif()
@@ -51,25 +46,25 @@ function(build_remora_lib remora_lib_name)
 
   target_sources(${remora_lib_name}
      PRIVATE
-       ${SRC_DIR}/Derive.cpp
+       ${SRC_DIR}/REMORA_Derive.cpp
        ${SRC_DIR}/REMORA.cpp
        ${SRC_DIR}/REMORA_SumIQ.cpp
        ${SRC_DIR}/REMORA_Tagging.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/REMORA_BoundaryConditions_cons.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_xvel.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_yvel.cpp
+       ${SRC_DIR}/BoundaryConditions/REMORA_BoundaryConditions_zvel.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_FillPatch.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_FillPatcher.cpp
        ${SRC_DIR}/BoundaryConditions/REMORA_PhysBCFunct.cpp
        ${SRC_DIR}/Initialization/REMORA_init.cpp
        ${SRC_DIR}/Initialization/REMORA_init1d.cpp
        ${SRC_DIR}/Initialization/REMORA_init_bcs.cpp
        ${SRC_DIR}/Initialization/REMORA_make_new_level.cpp
-       ${SRC_DIR}/IO/Checkpoint.cpp
-       ${SRC_DIR}/IO/Plotfile.cpp
-       ${SRC_DIR}/IO/writeJobInfo.cpp
-       ${SRC_DIR}/IO/console_io.cpp
+       ${SRC_DIR}/IO/REMORA_Checkpoint.cpp
+       ${SRC_DIR}/IO/REMORA_Plotfile.cpp
+       ${SRC_DIR}/IO/REMORA_writeJobInfo.cpp
+       ${SRC_DIR}/IO/REMORA_console_io.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_Advance.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_advance_2d.cpp
        ${SRC_DIR}/TimeIntegration/REMORA_advance_2d_onestep.cpp

diff --git a/CMake/SetAmrexOptions.cmake b/CMake/SetAmrexOptions.cmake
@@ -6,7 +6,7 @@ set(AMReX_MPI ${REMORA_ENABLE_MPI})
 set(AMReX_OMP ${REMORA_ENABLE_OPENMP})
 set(AMReX_PRECISION "${REMORA_PRECISION}" CACHE STRING "Floating point precision" FORCE)
 set(AMReX_EB OFF)
-set(AMReX_FORTRAN_INTREMORAACES OFF)
+set(AMReX_FORTRAN_INTERFACES OFF)
 set(AMReX_LINEAR_SOLVERS OFF)
 set(AMReX_AMRDATA OFF)
 set(AMReX_PARTICLES OFF)

diff --git a/Exec/Advection/prob.cpp b/Exec/Advection/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/Channel_Test/prob.cpp b/Exec/Channel_Test/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/DoubleGyre/prob.cpp b/Exec/DoubleGyre/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/DoublyPeriodic/prob.cpp b/Exec/DoublyPeriodic/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/IdealMiniGrid/prob.cpp b/Exec/IdealMiniGrid/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/OCCAMS/prob.cpp b/Exec/OCCAMS/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/ParticlesOverSeaMount/prob.cpp b/Exec/ParticlesOverSeaMount/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/Seamount/prob.cpp b/Exec/Seamount/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/Upwelling/prob.cpp b/Exec/Upwelling/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Exec/Upwelling_ML/prob.cpp b/Exec/Upwelling_ML/prob.cpp
@@ -1,11 +1,10 @@
 #include "prob.H"
-#include "prob_common.H"
+#include "REMORA_prob_common.H"
 
-#include "EOS.H"
 #include "AMReX_ParmParse.H"
 #include "AMReX_MultiFab.H"
-#include "IndexDefines.H"
-#include "DepthStretchTransform.H"
+#include "REMORA_IndexDefines.H"
+#include "REMORA_DepthStretchTransform.H"
 
 using namespace amrex;
 

diff --git a/Source/BoundaryConditions/Make.package b/Source/BoundaryConditions/Make.package
@@ -1,10 +1,10 @@
-CEXE_sources += BoundaryConditions_xvel.cpp
-CEXE_sources += BoundaryConditions_yvel.cpp
-CEXE_sources += BoundaryConditions_zvel.cpp
-CEXE_sources += BoundaryConditions_cons.cpp
+CEXE_sources += REMORA_BoundaryConditions_xvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_yvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_zvel.cpp
+CEXE_sources += REMORA_BoundaryConditions_cons.cpp
 
 ifeq ($(USE_PNETCDF), TRUE)
-CEXE_sources += BoundaryConditions_netcdf.cpp
+CEXE_sources += REMORA_BoundaryConditions_netcdf.cpp
 endif
 
 CEXE_sources += REMORA_FillPatch.cpp
@@ -14,4 +14,4 @@ CEXE_sources += REMORA_PhysBCFunct.cpp
 CEXE_headers += REMORA_PhysBCFunct.H
 
 CEXE_headers += REMORA_FillPatcher.H
-CEXE_headers += TimeInterpolatedData.H
+CEXE_headers += REMORA_TimeInterpolatedData.H
diff --git a/...aryConditions/BoundaryConditions_cons.cpp → ...itions/REMORA_BoundaryConditions_cons.cpp b/...aryConditions/BoundaryConditions_cons.cpp → ...itions/REMORA_BoundaryConditions_cons.cpp
diff --git a/...yConditions/BoundaryConditions_netcdf.cpp → ...ions/REMORA_BoundaryConditions_netcdf.cpp b/...yConditions/BoundaryConditions_netcdf.cpp → ...ions/REMORA_BoundaryConditions_netcdf.cpp
diff --git a/...aryConditions/BoundaryConditions_xvel.cpp → ...itions/REMORA_BoundaryConditions_xvel.cpp b/...aryConditions/BoundaryConditions_xvel.cpp → ...itions/REMORA_BoundaryConditions_xvel.cpp
diff --git a/...aryConditions/BoundaryConditions_yvel.cpp → ...itions/REMORA_BoundaryConditions_yvel.cpp b/...aryConditions/BoundaryConditions_yvel.cpp → ...itions/REMORA_BoundaryConditions_yvel.cpp
diff --git a/...aryConditions/BoundaryConditions_zvel.cpp → ...itions/REMORA_BoundaryConditions_zvel.cpp b/...aryConditions/BoundaryConditions_zvel.cpp → ...itions/REMORA_BoundaryConditions_zvel.cpp
@@ -1,6 +1,6 @@
 #include "AMReX_PhysBCFunct.H"
 #include <REMORA_PhysBCFunct.H>
-#include <prob_common.H>
+#include <REMORA_prob_common.H>
 
 using namespace amrex;
 

diff --git a/Source/BoundaryConditions/REMORA_FillPatch.cpp b/Source/BoundaryConditions/REMORA_FillPatch.cpp
@@ -1,7 +1,7 @@
 #include <REMORA.H>
 #include <REMORA_PhysBCFunct.H>
-#include <IndexDefines.H>
-#include <TimeInterpolatedData.H>
+#include <REMORA_IndexDefines.H>
+#include <REMORA_TimeInterpolatedData.H>
 
 using namespace amrex;
 

diff --git a/Source/BoundaryConditions/REMORA_PhysBCFunct.H b/Source/BoundaryConditions/REMORA_PhysBCFunct.H
@@ -12,9 +12,9 @@
 #include "AMReX_TypeTraits.H"
 #include "AMReX_Orientation.H"
 
-#include <TimeInterpolatedData.H>
-#include <IndexDefines.H>
-#include <DataStruct.H>
+#include <REMORA_TimeInterpolatedData.H>
+#include <REMORA_IndexDefines.H>
+#include <REMORA_DataStruct.H>
 
 using PlaneVector = amrex::Vector<amrex::FArrayBox>;
 

diff --git a/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp b/Source/BoundaryConditions/REMORA_PhysBCFunct.cpp
@@ -1,5 +1,5 @@
 #include "AMReX_PhysBCFunct.H"
-#include "IndexDefines.H"
+#include "REMORA_IndexDefines.H"
 #include <REMORA_PhysBCFunct.H>
 
 using namespace amrex;

diff --git a/...BoundaryConditions/TimeInterpolatedData.H → ...yConditions/REMORA_TimeInterpolatedData.H b/...BoundaryConditions/TimeInterpolatedData.H → ...yConditions/REMORA_TimeInterpolatedData.H
diff --git a/Source/EOS.H b/Source/EOS.H
diff --git a/Source/IO/Make.package b/Source/IO/Make.package
@@ -1,17 +1,17 @@
 
-CEXE_sources += Plotfile.cpp
-CEXE_sources += Checkpoint.cpp
-CEXE_sources += writeJobInfo.cpp
+CEXE_sources += REMORA_Plotfile.cpp
+CEXE_sources += REMORA_Checkpoint.cpp
+CEXE_sources += REMORA_writeJobInfo.cpp
 
-CEXE_sources += console_io.cpp
+CEXE_sources += REMORA_console_io.cpp
 
 ifeq ($(USE_PNETCDF), TRUE)
-  CEXE_sources += ReadFromInitNetcdf.cpp
-  CEXE_sources += ReadFromBdryNetcdf.cpp
-  CEXE_sources += NCInterface.cpp
-  CEXE_sources += NCPlotFile.cpp
-  CEXE_sources += NCFile.cpp
-  CEXE_headers += NCInterface.H
-  CEXE_headers += NCPlotFile.H
-  CEXE_headers += NCFile.H
+  CEXE_sources += REMORA_ReadFromInitNetcdf.cpp
+  CEXE_sources += REMORA_ReadFromBdryNetcdf.cpp
+  CEXE_sources += REMORA_NCInterface.cpp
+  CEXE_sources += REMORA_NCPlotFile.cpp
+  CEXE_sources += REMORA_NCFile.cpp
+  CEXE_headers += REMORA_NCInterface.H
+  CEXE_headers += REMORA_NCPlotFile.H
+  CEXE_headers += REMORA_NCFile.H
 endif
diff --git a/Source/IO/NCPlotFile.H b/Source/IO/NCPlotFile.H
diff --git a/Source/IO/Checkpoint.cpp → Source/IO/REMORA_Checkpoint.cpp b/Source/IO/Checkpoint.cpp → Source/IO/REMORA_Checkpoint.cpp
diff --git a/Source/IO/NCFile.H → Source/IO/REMORA_NCFile.H b/Source/IO/NCFile.H → Source/IO/REMORA_NCFile.H
@@ -1,5 +1,5 @@
-#ifndef _NCFILE_H_
-#define _NCFILE_H_
+#ifndef _REMORA_NCFILE_H_
+#define _REMORA_NCFILE_H_
 
 #include <sstream>
 #include <string>
@@ -9,7 +9,7 @@
 #include "AMReX_FArrayBox.H"
 #include "AMReX_IArrayBox.H"
 // this includes pnetcdf.h, and mpi.h
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 
 using PlaneVector = amrex::Vector<amrex::FArrayBox>;
 

diff --git a/Source/IO/NCFile.cpp → Source/IO/REMORA_NCFile.cpp b/Source/IO/NCFile.cpp → Source/IO/REMORA_NCFile.cpp
@@ -1,7 +1,7 @@
 #include <string>
 
-#include "NCFile.H"
-#include "NCInterface.H"
+#include "REMORA_NCFile.H"
+#include "REMORA_NCInterface.H"
 
 
 std::string ReadNetCDFVarAttrStr (const std::string& fname,

diff --git a/Source/IO/NCInterface.H → Source/IO/REMORA_NCInterface.H b/Source/IO/NCInterface.H → Source/IO/REMORA_NCInterface.H
@@ -6,8 +6,8 @@
  *  OOP-like manner.
  */
 
-#ifndef NC_INTREMORAACE_H
-#define NC_INTREMORAACE_H
+#ifndef REMORA_NC_INTERFACE_H
+#define REMORA_NC_INTERFACE_H
 
 #ifdef REMORA_USE_NETCDF
 #include <string>
@@ -382,4 +382,4 @@ public:
 
 #endif
 
-#endif /* NC_INTREMORAACE_H */
+#endif /* NC_INTERFACE_H */
diff --git a/Source/IO/NCInterface.cpp → Source/IO/REMORA_NCInterface.cpp b/Source/IO/NCInterface.cpp → Source/IO/REMORA_NCInterface.cpp
@@ -1,6 +1,6 @@
 #include <cstdio>
 
-#include "NCInterface.H"
+#include "REMORA_NCInterface.H"
 #include <AMReX.H>
 #include <AMReX_Print.H>
 

diff --git a/Source/IO/REMORA_NCPlotFile.H b/Source/IO/REMORA_NCPlotFile.H
@@ -0,0 +1,4 @@
+#ifndef _REMORA_NCPLOTFILE_H_
+#define _REMORA_NCPLOTFILE_H_
+extern std::string inputs_name;
+#endif