Merge branch 'development' of github.com:seahorce-scidac/REMORA into …

…docs

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

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)

Docs/sphinx_doc/Verification.rst

@@ -47,7 +47,7 @@ Ideal Mini Grid
 
 This small idealized grid is used to test netCDF-provided initial and boundary conditions. The ocean is initialized with zero velocity and a constant temperature and salinity. Time-varying boundary conditions are then applied for velocity, temperature, or salinity (provided by netCDF file). The default is to used a clamped boundary condition for all quantities, but options for Chapman-Flather and radiation conditions are available. This test also verifies correct behavior with land-sea masking when using the ``_masked`` grid file.
 
-The netCDF files needed to run these tests can be found in the `remora-data <https://github.com/seahorce-scidac/remora-data`_ repository under the ``IdealMiniGrid`` directory.
+The netCDF files needed to run these tests can be found in the `remora-data <https://github.com/seahorce-scidac/remora-data>`_ repository under the ``IdealMiniGrid`` directory.
 
 .. _particlesseamount:
 

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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