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Setup CMake (#364)
* Add CMakeLists in the various subfolders. * First pass at setting up cmake compilation and targets. * Add the right include folder for the selected mechanism. * A few fixes in CMakeLists.txt. * Update to have CUDA working. Self build of lib functions. * Jon's suggestions. * Fixes related to updated cmake minimum version. * Remove *_api and a few fixes. Tested as a subdir in LMeX with MPI, MPI+CUDA and MPI+HIP.
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‎CMake/PelePhysicsConfig.cmake.in

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@PACKAGE_INIT@
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set(PELEPHYSICS_SPACEDIM @PELEPHYSICS_SPACEDIM@)
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set(PELEPHYSICS_CHEMISTRY_MODEL @PELEPHYSICS_CHEMISTRY_MODEL@)
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set(PELEPHYSICS_EOS_MODEL @PELEPHYSICS_EOS_MODEL@)
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set(PELEPHYSICS_TRANSPORT_MODEL @PELEPHYSICS_TRANSPORT_MODEL@)
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set(PELEPHYSICS_MPI @PELEPHYSICS_MPI@)
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set(PELEPHYSICS_OMP @PELEPHYSICS_OMP@)
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set(PELEPHYSICS_CUDA @PELEPHYSICS_CUDA@)
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set(PELEPHYSICS_HIP @PELEPHYSICS_HIP@)
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set(PELEPHYSICS_SYCL @PELEPHYSICS_SYCL@)
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find_package(AMReX QUIET REQUIRED @AMREX_REQUIRED_COMPONENTS@)
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find_package(SUNDIALS QUIET REQUIRED)
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include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@Targets.cmake")
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set(@PROJECT_NAME@_INCLUDE_DIRS "${PROJECT_PREFIX_DIR}/@CMAKE_INSTALL_INCLUDEDIR@")
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set(@PROJECT_NAME@_LIBRARY_DIRS "${PROJECT_PREFIX_DIR}/@CMAKE_INSTALL_LIBDIR@")
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set(@PROJECT_NAME@_LIBRARIES "@PROJECT_NAME@::PelePhysics-@PELEPHYSICS_CHEMISTRY_MODEL@-@PELEPHYSICS_EOS_MODEL@-@PELEPHYSICS_TRANSPORT_MODEL@")
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set(@PROJECT_NAME@_FOUND TRUE)
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check_required_components(@PROJECT_NAME@)

‎CMakeLists.txt

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cmake_minimum_required(VERSION 3.23)
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project( PelePhysics
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DESCRIPTION "A respository of physics databases and implementation code for use with the Pele suite of of codes"
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HOMEPAGE_URL "https://github.com/AMReX-Combustion/PelePhysics"
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LANGUAGES CXX
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)
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message(STATUS "CMake version: ${CMAKE_VERSION}")
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#
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# Options for model selection
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#
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set( PELEPHYSICS_SPACEDIM 3 CACHE STRING "Spatial dimension")
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set( PELEPHYSICS_PRECISION "DOUBLE" CACHE STRING "Floating point precision")
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set( PELEPHYSICS_CHEMISTRY_MODEL drm19 CACHE STRING "Chemical mechanism")
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set( PELEPHYSICS_EOS_MODEL Fuego CACHE STRING "Eq. of state model")
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set( PELEPHYSICS_TRANSPORT_MODEL Simple CACHE STRING "Transport model")
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#
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# Options for library content
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#
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option( PELEPHYSICS_REACTIONS "Enable Reaction" ON)
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option( PELEPHYSICS_TRANSPORT "Enable Transport" ON)
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option( PELEPHYSICS_EOS "Enable EOS" ON)
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option( PELEPHYSICS_UTILS "Enable Utilities" ON)
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#
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# Options for HPC
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#
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option( PELEPHYSICS_MPI "Enable MPI" OFF)
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option( PELEPHYSICS_OMP "Enable OpenMP" OFF)
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option( PELEPHYSICS_CUDA "Enable CUDA" OFF)
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option( PELEPHYSICS_HIP "Enable HIP" OFF)
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option( PELEPHYSICS_SYCL "Enable SYCL" OFF)
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set(PELEPHYSICS_GPU_BACKEND NONE)
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if (PELEPHYSICS_CUDA)
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enable_language(CUDA)
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set(PELEPHYSICS_GPU_BACKEND CUDA)
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endif ()
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if (PELEPHYSICS_HIP)
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enable_language(HIP)
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set(PELEPHYSICS_GPU_BACKEND HIP)
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endif ()
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if (PELEPHYSICS_SYCL)
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enable_language(SYCL)
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set(PELEPHYSICS_GPU_BACKEND SYCL)
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endif ()
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set(AMREX_HOME "" CACHE PATH "Path to AMReX top-level source directory")
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if (AMREX_HOME) # SUPERBUILD MODE
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message(STATUS "AMReX top-level source directory path: ${AMREX_HOME}")
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# Add AMReX module path
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list(APPEND CMAKE_MODULE_PATH ${AMREX_HOME}/Tools/CMake)
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set(AMREX_BINARY_DIR "${CMAKE_BINARY_DIR}/amrex" CACHE INTERNAL "Path to AMReX top-level binary directory")
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# Set required settings for AMReX
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set(USE_XSDK_DEFAULTS ON CACHE INTERNAL "")
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set(XSDK_ENABLE_Fortran OFF CACHE INTERNAL "")
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set(XSDK_PRECISION ${PELEPHYSICS_PRECISION} CACHE INTERNAL "")
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set(AMReX_SPACEDIM ${PELEPHYSICS_SPACEDIM} CACHE INTERNAL "")
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set(AMReX_MPI ${PELEPHYSICS_MPI} CACHE INTERNAL "")
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set(AMReX_OMP ${PELEPHYSICS_OMP} CACHE INTERNAL "")
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set(AMReX_GPU_BACKEND ${PELEPHYSICS_GPU_BACKEND} CACHE INTERNAL "")
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set(AMReX_SUNDIALS ON CACHE INTERNAL "")
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set(AMReX_EB OFF CACHE INTERNAL "")
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set(AMReX_FORTRAN OFF CACHE INTERNAL "")
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set(AMReX_LINEAR_SOLVERS OFF CACHE INTERNAL "")
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set(AMReX_AMRLEVEL OFF CACHE INTERNAL "")
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set(AMReX_BUILD_TUTORIALS OFF CACHE INTERNAL "")
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# Add AMReX as a sub-project: incflo inherits all AMReX options
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add_subdirectory(${AMREX_HOME} ${AMREX_BINARY_DIR})
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message(STATUS "AMReX binary directory: ${AMREX_BINARY_DIR}")
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else ()
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#
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# if AMReX::amrex is not part of the targets, use find_package
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#
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if (NOT TARGET AMReX::amrex)
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set(AMREX_REQUIRED_COMPONENTS ${PELEPHYSICS_SPACEDIM}D ${PELEPHYSICS_PRECISION})
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if (PELEPHYSICS_MPI)
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list(APPEND AMREX_REQUIRED_COMPONENTS MPI)
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endif ()
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if (PELEPHYSICS_OMP)
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list(APPEND AMREX_REQUIRED_COMPONENTS OMP)
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endif ()
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if (NOT PELEPHYSICS_GPU_BACKEND STREQUAL "NONE")
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list(APPEND AMREX_REQUIRED_COMPONENTS ${PELEPHYSICS_GPU_BACKEND})
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endif ()
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find_package(AMReX CONFIG REQUIRED ${AMREX_REQUIRED_COMPONENTS} )
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endif ()
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endif ()
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set(SUNDIALS_HOME "" CACHE PATH "Path to SUNDIALS top-level source directory")
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if (SUNDIALS_HOME) # SUPERBUILD MODE
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message(STATUS "SUNDIALS top-level source directory path: ${SUNDIALS_HOME}")
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# Add SUNDIALS module path
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list(APPEND CMAKE_MODULE_PATH ${SUNDIALS_HOME}/cmake)
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set(SUNDIALS_BINARY_DIR "${CMAKE_BINARY_DIR}/sundials" CACHE INTERNAL "Path to SUNDIALS top-level binary directory")
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# Set required settings for SUNDIALS
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set(SUNDIALS_PRECISION ${PELEPHYSICS_PRECISION} CACHE STRING "Floating point precision" FORCE)
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set(BUILD_ARKODE ON CACHE INTERNAL "")
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set(BUILD_CVODE ON CACHE INTERNAL "")
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set(SUNDIALS_INDEX_SIZE 32 CACHE INTERNAL "")
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set(BUILD_CVODES OFF CACHE INTERNAL "")
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set(BUILD_IDA OFF CACHE INTERNAL "")
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set(BUILD_IDAS OFF CACHE INTERNAL "")
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set(BUILD_KINSOL OFF CACHE INTERNAL "")
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set(BUILD_CPODES OFF CACHE INTERNAL "")
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set(BUILD_EXAMPLES OFF CACHE INTERNAL "")
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set(_BUILD_EXAMPLES OFF CACHE INTERNAL "")
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set(BUILD_TESTING OFF CACHE INTERNAL "")
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set(EXAMPLES_ENABLE_C OFF CACHE INTERNAL "")
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set(EXAMPLES_ENABLE_CXX OFF CACHE INTERNAL "")
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set(EXAMPLES_INSTALL OFF CACHE INTERNAL "")
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set(ENABLE_CUDA ${PELEPHYSICS_CUDA} CACHE INTERNAL "")
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set(ENABLE_HIP ${PELEPHYSICS_HIP} CACHE INTERNAL "")
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set(ENABLE_SYCL ${PELEPHYSICS_SYCL} CACHE INTERNAL "")
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set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
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add_subdirectory(${SUNDIALS_HOME} ${SUNDIALS_BINARY_DIR})
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message(STATUS "SUNDIALS binary directory: ${SUNDIALS_BINARY_DIR}")
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else ()
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#
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# Find SUNDIALS, check for required components
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#
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if (NOT TARGET SUNDIALS::cvode)
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# Check if we can require components
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find_package(SUNDIALS)
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endif ()
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endif ()
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#
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# Enable CUDA if requested
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#
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if (PELEPHYSICS_GPU_BACKEND STREQUAL "CUDA")
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include(AMReXTargetHelpers)
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endif ()
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#
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# Define the object library to compile
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#
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set(pelephysics_lib_name PelePhysics-${PELEPHYSICS_CHEMISTRY_MODEL}-${PELEPHYSICS_EOS_MODEL}-${PELEPHYSICS_TRANSPORT_MODEL})
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add_library(${pelephysics_lib_name} OBJECT)
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target_link_libraries(${pelephysics_lib_name} PUBLIC AMReX::amrex)
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target_link_libraries(${pelephysics_lib_name} PUBLIC SUNDIALS::cvode SUNDIALS::arkode)
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add_subdirectory(Source)
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set(PELEPHYSICS_MECH_DIR "Support/Mechanism/")
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add_subdirectory(${PELEPHYSICS_MECH_DIR})
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if (PELEPHYSICS_UTILS)
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add_subdirectory(Utility/PMF)
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add_subdirectory(Utility/TurbInflow)
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add_subdirectory(Utility/PltFileManager)
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endif ()
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if (PELEPHYSICS_TRANSPORT)
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add_subdirectory(Transport)
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endif ()
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if (PELEPHYSICS_EOS)
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add_subdirectory(Eos)
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endif ()
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if (PELEPHYSICS_REACTIONS)
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add_subdirectory(Reactions)
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endif ()
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if (PELEPHYSICS_GPU_BACKEND STREQUAL "CUDA")
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setup_target_for_cuda_compilation(${pelephysics_lib_name})
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endif ()
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if ( NOT CMAKE_CXX_FLAGS )
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target_link_libraries(${pelephysics_lib_name} PUBLIC AMReX::Flags_CXX)
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endif ()
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# Installation rules
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include(CMakePackageConfigHelpers)
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include(GNUInstallDirs)
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message( STATUS "PelePhysics configuration summary: ")
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message( STATUS " Build type = ${CMAKE_BUILD_TYPE}")
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message( STATUS " Install directory = ${CMAKE_INSTALL_PREFIX}")
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message( STATUS " CMake target = ${pelephysics_lib_name}")
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# Collect all headers and make them installable with the target
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get_target_property(PELEPHYSICS_INCLUDES ${pelephysics_lib_name} SOURCES)
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list(FILTER PELEPHYSICS_INCLUDES INCLUDE REGEX "\\.H")
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set_target_properties(
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${pelephysics_lib_name} PROPERTIES PUBLIC_HEADER "${PELEPHYSICS_INCLUDES}")
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# Install PelePhysics
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install(
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TARGETS ${pelephysics_lib_name}
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EXPORT ${PROJECT_NAME}Targets
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RUNTIME DESTINATION bin
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ARCHIVE DESTINATION lib
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LIBRARY DESTINATION lib
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INCLUDES DESTINATION include
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PUBLIC_HEADER DESTINATION include
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)
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# Make PelePhysics discoverable using `find_package`
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install(
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EXPORT ${PROJECT_NAME}Targets
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NAMESPACE ${PROJECT_NAME}::
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DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}
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)
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configure_package_config_file(
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CMake/${PROJECT_NAME}Config.cmake.in
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${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
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INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}
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)
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install(FILES
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${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
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DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}
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)

‎Eos/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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EOS.H
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EOS.cpp
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Fuego.H
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GammaLaw.H
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SRK.H
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)
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if("${PELEPHYSICS_EOS_MODEL}" STREQUAL "GammaLaw")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_GAMMALAW_EOS)
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endif()
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if("${PELEPHYSICS_EOS_MODEL}" STREQUAL "Fuego")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_FUEGO_EOS)
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endif()
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if("${PELEPHYSICS_EOS_MODEL}" STREQUAL "Soave-Redlich-Kwong")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_SRK_EOS)
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endif()

‎Reactions/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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ReactorArkode.cpp
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ReactorArkode.H
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ReactorBase.H
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ReactorBase.cpp
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ReactorBDF.H
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ReactorBDF.cpp
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ReactorBDFsolver.H
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ReactorCvode.H
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ReactorCvode.cpp
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ReactorCvodeCustomLinSolver.H
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ReactorCvodeCustomLinSolver.cpp
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ReactorCvodeJacobian.H
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ReactorCvodeJacobian.cpp
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ReactorCvodePreconditioner.H
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ReactorCvodePreconditioner.cpp
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ReactorCvodeUtils.H
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ReactorCvodeUtils.cpp
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ReactorNull.H
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ReactorNull.cpp
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ReactorRK64.H
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ReactorRK64.cpp
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ReactorTypes.H
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ReactorUtils.H
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ReactorUtils.cpp
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)

‎Source/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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Factory.H
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PelePhysics.H
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PelePhysicsConstraints.H
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PhysicsConstants.H
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)

‎Support/Mechanism/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/Models/${PELEPHYSICS_CHEMISTRY_MODEL}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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Models/${PELEPHYSICS_CHEMISTRY_MODEL}/mechanism.H
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Models/${PELEPHYSICS_CHEMISTRY_MODEL}/mechanism.cpp
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)

‎Transport/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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Constant.H
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Simple.H
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Sutherland.H
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Transport.cpp
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Transport.H
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TransportParams.H
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TransportTypes.H
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)
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if("${PELEPHYSICS_TRANSPORT_MODEL}" STREQUAL "Constant")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_CONSTANT_TRANSPORT)
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endif()
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if("${PELEPHYSICS_TRANSPORT_MODEL}" STREQUAL "Simple")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_SIMPLE_TRANSPORT)
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endif()
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if("${PELEPHYSICS_TRANSPORT_MODEL}" STREQUAL "Sutherland")
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target_compile_definitions(${pelephysics_lib_name} PUBLIC USE_SUTHERLAND_TRANSPORT)
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endif()
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‎Utility/PMF/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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PMF.H
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PMFData.cpp
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PMFData.H
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)

‎Utility/PltFileManager/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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PltFileManager.cpp
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PltFileManager.H
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PltFileManagerBCFill.H
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)

‎Utility/TurbInflow/CMakeLists.txt

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target_include_directories(${pelephysics_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>)
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target_sources(${pelephysics_lib_name}
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PRIVATE
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turbinflow.cpp
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turbinflow.H
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)

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