Update CMake for Soot, Spray, and Radiation

.clang-tidy

@@ -19,6 +19,8 @@ Checks: 'bugprone-*,
          -readability-static-accessed-through-instance,
          -readability-identifier-length,
          -readability-function-cognitive-complexity,
+         -readability-convert-member-functions-to-static,
+         -readability-make-member-function-const,
          -readability-function-size'
 WarningsAsErrors: ''
 HeaderFilterRegex: 'PeleLMeX\/Source|PeleLMeX\/Exec|PeleLMeX\/Submodules\/PelePhysics\/Source|PeleLMeX\/Submodules\/PelePhysics\/Mechanism'

.github/workflows/ci.yml

@@ -160,11 +160,10 @@ jobs:
             -DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
             -DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
             -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
-            -DPELELMEX_DIM:STRING=${DIM} \
-            -DPELELMEX_ENABLE_MPI:BOOL=ON \
-            -DPELELMEX_ENABLE_EB:BOOL=${{matrix.use_eb}} \
-            -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
-            -DPELELMEX_ENABLE_MASA:BOOL=OFF \
+            -DPELE_DIM:STRING=${DIM} \
+            -DPELE_ENABLE_MPI:BOOL=ON \
+            -DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
+            -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
             -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
             ${{github.workspace}}; \
             if [ $? -ne 0 ]; then exit 1; fi \
@@ -254,8 +253,8 @@ jobs:
           cmake -Bbuild-${{matrix.cuda_pkg}} \
             -DCMAKE_BUILD_TYPE:STRING=Release \
             -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
-            -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-            -DPELELMEX_ENABLE_CUDA:BOOL=ON \
+            -DPELE_ENABLE_MPI:BOOL=OFF \
+            -DPELE_ENABLE_CUDA:BOOL=ON \
             -DAMReX_CUDA_ERROR_CAPTURE_THIS:BOOL=ON \
             -DCMAKE_CUDA_ARCHITECTURES:STRING=70 \
             -DCMAKE_CUDA_COMPILER_LAUNCHER:STRING=ccache \
@@ -319,14 +318,14 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
           -DCMAKE_CXX_COMPILER:STRING=$(which clang++) \
           -DCMAKE_C_COMPILER:STRING=$(which clang) \
-          -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-          -DPELELMEX_ENABLE_HIP:BOOL=ON \
+          -DPELE_ENABLE_MPI:BOOL=OFF \
+          -DPELE_ENABLE_HIP:BOOL=ON \
           -DAMReX_AMD_ARCH:STRING=gfx90a \
           -DCMAKE_HIP_ARCHITECTURES:STRING=gfx90a \
           -DAMDGPU_TARGETS:STRING=gfx90a \
           -DGPU_TARGETS:STRING=gfx90a \
           -DAMReX_GPU_RDC:BOOL=OFF \
-          -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
+          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
           -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
           ${{github.workspace}}
       - name: Build
@@ -388,10 +387,9 @@ jobs:
             -DCMAKE_CXX_COMPILER:STRING=$(which icpx) \
             -DCMAKE_C_COMPILER:STRING=$(which icx) \
             -DCMAKE_CXX_FLAGS:STRING=-fsycl \
-            -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-            -DPELELMEX_ENABLE_MASA:BOOL=OFF \
-            -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
-            -DPELELMEX_ENABLE_SYCL:BOOL=ON \
+            -DPELE_ENABLE_MPI:BOOL=OFF \
+            -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
+            -DPELE_ENABLE_SYCL:BOOL=ON \
             -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
             ${{github.workspace}}
       - name: Build
@@ -447,11 +445,10 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
           -DCMAKE_CXX_COMPILER:STRING=clang++ \
           -DCMAKE_C_COMPILER:STRING=clang \
-          -DPELELMEX_ENABLE_EB:BOOL=${{matrix.use_eb}} \
-          -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-          -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
-          -DPELELMEX_ENABLE_MASA:BOOL=OFF \
-          -DPELELMEX_ENABLE_CLANG_TIDY:BOOL=ON \
+          -DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
+          -DPELE_ENABLE_MPI:BOOL=OFF \
+          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
+          -DPELE_ENABLE_CLANG_TIDY:BOOL=ON \
           -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
           ${{github.workspace}}
       - name: Check
@@ -499,10 +496,9 @@ jobs:
           -DCMAKE_BUILD_TYPE:STRING=Debug \
           -DCMAKE_CXX_COMPILER:STRING=clang++ \
           -DCMAKE_C_COMPILER:STRING=clang \
-          -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-          -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
-          -DPELELMEX_ENABLE_MASA:BOOL=OFF \
-          -DPELELMEX_ENABLE_CLANG_TIDY:BOOL=OFF \
+          -DPELE_ENABLE_MPI:BOOL=OFF \
+          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
+          -DPELE_ENABLE_CLANG_TIDY:BOOL=OFF \
           ${{github.workspace}}
       - name: Build
         run: |

.github/workflows/linux.yml

@@ -28,7 +28,7 @@ jobs:
   #    env:
   #       AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
   #       PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
-  #       PELELMEX_HOME: ${GITHUB_WORKSPACE}
+  #       PELE_HOME: ${GITHUB_WORKSPACE}
   #       AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
   #       SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
   #    working-directory: ./Exec/RegTests/EB_FlowPastCylinder/

Build/cmake.sh

@@ -7,17 +7,17 @@ cmake -DCMAKE_INSTALL_PREFIX:PATH=./install \
       -DCMAKE_C_COMPILER:STRING=clang \
       -DMPIEXEC_PREFLAGS:STRING=--oversubscribe \
       -DCMAKE_BUILD_TYPE:STRING=Release \
-      -DPELELMEX_DIM:STRING=3 \
-      -DPELELMEX_ENABLE_MPI:BOOL=OFF \
-      -DPELELMEX_ENABLE_FCOMPARE:BOOL=OFF \
-      -DPELELMEX_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
-      -DPELELMEX_ENABLE_MASA:BOOL=OFF \
-      -DPELELMEX_ENABLE_CPPCHECK:BOOL=OFF \
-      -DPELELMEX_ENABLE_CLANG_TIDY:BOOL=OFF \
-      -DPELELMEX_ENABLE_CUDA:BOOL=OFF \
+      -DPELE_DIM:STRING=3 \
+      -DPELE_ENABLE_MPI:BOOL=OFF \
+      -DPELE_ENABLE_FCOMPARE:BOOL=OFF \
+      -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
+      -DPELE_ENABLE_MASA:BOOL=OFF \
+      -DPELE_ENABLE_CPPCHECK:BOOL=OFF \
+      -DPELE_ENABLE_CLANG_TIDY:BOOL=OFF \
+      -DPELE_ENABLE_CUDA:BOOL=OFF \
       -DAMReX_CUDA_ARCH=Volta \
       -DPYTHON_EXECUTABLE=$(which python3) \
-      -DPELELMEX_PRECISION:STRING=DOUBLE \
+      -DPELE_PRECISION:STRING=DOUBLE \
       ..
 #make
 cmake --build . --parallel $(sysctl -n hw.ncpu) #&> output.txt

CMake/BuildExeAndLib.cmake

@@ -1,7 +1,7 @@
 get_filename_component(DIR_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
-set(pelelmex_lib_name PelePhysics-Lib-${PELELMEX_EOS_MODEL}-${PELELMEX_CHEMISTRY_MODEL}-${PELELMEX_TRANSPORT_MODEL})
-set(pelelmex_exe_name ${PROJECT_NAME}-${DIR_NAME})
-include(BuildPeleLMeXLib)
-include(BuildPeleLMeXExe)
-build_pelelmex_lib(${pelelmex_lib_name})
-build_pelelmex_exe(${pelelmex_exe_name} ${pelelmex_lib_name})
+set(pele_physics_lib_name "PelePhysicsLib-${PELE_PHYSICS_EOS_MODEL}-${PELE_PHYSICS_CHEMISTRY_MODEL}-${PELE_PHYSICS_TRANSPORT_MODEL}-Spray${PELE_PHYSICS_ENABLE_SPRAY}-Soot${PELE_PHYSICS_ENABLE_SOOT}-Radiation${PELE_PHYSICS_ENABLE_RADIATION}")
+set(pele_exe_name "${PROJECT_NAME}-${DIR_NAME}")
+include(BuildPelePhysicsLib)
+include(BuildPeleExe)
+build_pele_physics_lib(${pele_physics_lib_name})
+build_pele_exe(${pele_exe_name} ${pele_physics_lib_name})

CMake/BuildPeleExe.cmake

@@ -0,0 +1,112 @@
+function(build_pele_exe pele_exe_name pele_physics_lib_name)
+
+  set(SRC_DIR ${CMAKE_SOURCE_DIR}/Source)
+
+  add_executable(${pele_exe_name} "")
+
+  if(CLANG_TIDY_EXE)
+    set_target_properties(${pele_exe_name} PROPERTIES CXX_CLANG_TIDY
+                          "${CLANG_TIDY_EXE};--config-file=${CMAKE_SOURCE_DIR}/.clang-tidy")
+  endif()
+
+  target_sources(${pele_exe_name}
+     PRIVATE
+       pelelmex_prob_parm.H
+       pelelmex_prob.H
+       pelelmex_prob.cpp
+  )
+
+  target_include_directories(${pele_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+  target_include_directories(${pele_exe_name} PRIVATE ${SRC_DIR})
+  target_include_directories(${pele_exe_name} PRIVATE ${CMAKE_BINARY_DIR})
+
+  target_sources(${pele_exe_name}
+     PRIVATE
+       ${SRC_DIR}/PeleLMeX_DeriveUserDefined.cpp
+       ${SRC_DIR}/PeleLMeX_DiffusionOp.H
+       ${SRC_DIR}/PeleLMeX_DiffusionOp.cpp
+       ${SRC_DIR}/PeleLMeX_EBUserDefined.H
+       ${SRC_DIR}/PeleLMeX_FlowControllerData.H
+       ${SRC_DIR}/PeleLMeX.H
+       ${SRC_DIR}/PeleLMeX.cpp
+       ${SRC_DIR}/PeleLMeX_Advance.cpp
+       ${SRC_DIR}/PeleLMeX_Advection.cpp
+       ${SRC_DIR}/PeleLMeX_BC.cpp
+       ${SRC_DIR}/PeleLMeX_BCfill.H
+       ${SRC_DIR}/PeleLMeX_Data.cpp
+       ${SRC_DIR}/PeleLMeX_Derive.H
+       ${SRC_DIR}/PeleLMeX_Derive.cpp
+       ${SRC_DIR}/PeleLMeX_DeriveFunc.H
+       ${SRC_DIR}/PeleLMeX_DeriveFunc.cpp
+       ${SRC_DIR}/PeleLMeX_Diagnostics.cpp
+       ${SRC_DIR}/PeleLMeX_Diffusion.cpp
+       ${SRC_DIR}/PeleLMeX_EB.cpp
+       ${SRC_DIR}/PeleLMeX_Eos.cpp
+       ${SRC_DIR}/PeleLMeX_Evaluate.cpp
+       ${SRC_DIR}/PeleLMeX_Evolve.cpp
+       ${SRC_DIR}/PeleLMeX_FlowController.cpp
+       ${SRC_DIR}/PeleLMeX_Forces.cpp
+       ${SRC_DIR}/PeleLMeX_Init.cpp
+       ${SRC_DIR}/PeleLMeX_Plot.cpp
+       ${SRC_DIR}/PeleLMeX_Projection.cpp
+       ${SRC_DIR}/PeleLMeX_Reactions.cpp
+       ${SRC_DIR}/PeleLMeX_Regrid.cpp
+       ${SRC_DIR}/PeleLMeX_Setup.cpp
+       ${SRC_DIR}/PeleLMeX_Tagging.cpp
+       ${SRC_DIR}/PeleLMeX_Temporals.cpp
+       ${SRC_DIR}/PeleLMeX_Timestep.cpp
+       ${SRC_DIR}/PeleLMeX_TransportProp.cpp
+       ${SRC_DIR}/PeleLMeX_UMac.cpp
+       ${SRC_DIR}/PeleLMeX_UserKeys.H
+       ${SRC_DIR}/PeleLMeX_Utils.H
+       ${SRC_DIR}/PeleLMeX_Utils.cpp
+       ${SRC_DIR}/PeleLMeX_Index.H
+       ${SRC_DIR}/PeleLMeX_K.H
+       ${SRC_DIR}/main.cpp
+  )
+
+  if(PELE_PHYSICS_ENABLE_SOOT)
+    target_sources(${pele_exe_name}
+      PRIVATE
+        ${SRC_DIR}/PeleLMeX_Soot.cpp)
+  endif()
+
+  if(PELE_PHYSICS_ENABLE_SPRAY)
+    target_sources(${pele_exe_name}
+      PRIVATE
+        ${SRC_DIR}/PeleLMeX_SprayParticles.cpp
+        SprayParticlesInitInsert.cpp)
+  endif()
+
+  if(PELE_PHYSICS_ENABLE_RADIATION)
+    target_sources(${pele_exe_name}
+      PRIVATE
+        ${SRC_DIR}/PeleLMeX_Radiation.cpp)
+  endif()
+
+  if(NOT "${pele_exe_name}" STREQUAL "${PROJECT_NAME}-UnitTests")
+    target_sources(${pele_exe_name}
+       PRIVATE
+         ${CMAKE_SOURCE_DIR}/Source/main.cpp
+    )
+  endif()
+
+  if(PELE_ENABLE_CUDA)
+    set(pctargets "${pele_exe_name};${pele_physics_lib_name}")
+    foreach(tgt IN LISTS pctargets)
+      get_target_property(PELE_SOURCES ${tgt} SOURCES)
+      list(FILTER PELE_SOURCES INCLUDE REGEX "\\.cpp")
+      set_source_files_properties(${PELE_SOURCES} PROPERTIES LANGUAGE CUDA)
+    endforeach()
+    set_target_properties(${pele_exe_name} PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
+    target_compile_options(${pele_exe_name} PRIVATE $<$<COMPILE_LANGUAGE:CUDA>:-Xptxas --disable-optimizer-constants>)
+  endif()
+
+  target_link_libraries(${pele_exe_name} PRIVATE ${pele_physics_lib_name} AMReX-Hydro::amrex_hydro_api AMReX::amrex)
+
+  install(TARGETS ${pele_exe_name}
+          RUNTIME DESTINATION bin
+          ARCHIVE DESTINATION lib
+          LIBRARY DESTINATION lib)
+
+endfunction()