diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index e424a5c8..de9e059a 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -1,6 +1,11 @@ name: Docker -on: [push, pull_request] +on: + push: + branches: + - main + pull_request: + workflow_dispatch: concurrency: group: ${{ github.workflow }}-${{ github.ref || github.run_id }} @@ -8,7 +13,6 @@ concurrency: jobs: docker-build-and-test: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name name: Build and Test - ${{ matrix.dockerfile }} runs-on: ubuntu-latest strategy: diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml index 54130b99..247d035b 100644 --- a/.github/workflows/mac.yml +++ b/.github/workflows/mac.yml @@ -1,6 +1,11 @@ name: Mac -on: [push, pull_request] +on: + push: + branches: + - main + pull_request: + workflow_dispatch: concurrency: group: ${{ github.workflow }}-${{ github.ref || github.run_id }} @@ -8,7 +13,6 @@ concurrency: jobs: c_cxx: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: macos-latest strategy: matrix: @@ -17,7 +21,7 @@ jobs: - { cpp: g++-12, c: gcc-12} - { cpp: g++-13, c: gcc-13} - { cpp: clang++, c: clang} - build_type: [Debug, Release] + build_type: [Release] env: CC: ${{ matrix.compiler.c }} CXX: ${{ matrix.compiler.cpp }} @@ -25,23 +29,25 @@ jobs: steps: - uses: actions/checkout@v3 + - uses: actions/setup-python@v5 + - run: pip install -r python/requirements.txt + - name: Run Cmake - run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} + run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON - name: Build - run: cmake --build build --parallel 10 + run: cmake --build build --parallel - name: Run tests run: | cd build ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10 fortran: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: macos-latest strategy: matrix: gcc_version: [11, 12, 13] - build_type: [Debug, Release] + build_type: [Release] env: FC: gfortran-${{ matrix.gcc_version }} @@ -55,7 +61,7 @@ jobs: run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON - name: Build - run: cmake --build build --parallel 10 + run: cmake --build build --parallel - name: Run tests run: | diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml index 973e7cec..b4ad40e4 100644 --- a/.github/workflows/ubuntu.yml +++ b/.github/workflows/ubuntu.yml @@ -1,6 +1,11 @@ name: Ubuntu -on: [push, pull_request] +on: + push: + branches: + - main + pull_request: + workflow_dispatch: concurrency: group: ${{ github.workflow }}-${{ github.ref || github.run_id }} @@ -8,7 +13,6 @@ concurrency: jobs: c_cxx: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: ubuntu-latest strategy: matrix: @@ -17,7 +21,7 @@ jobs: - { cpp: g++-12, c: gcc-12} - { cpp: g++-13, c: gcc-13} - { cpp: clang++, c: clang} - build_type: [Debug, Release] + build_type: [Release] env: CC: ${{ matrix.compiler.c }} CXX: ${{ matrix.compiler.cpp }} @@ -25,23 +29,25 @@ jobs: steps: - uses: actions/checkout@v3 + - uses: actions/setup-python@v5 + - run: pip install -r python/requirements.txt + - name: Run Cmake - run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} + run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON - name: Build - run: cmake --build build --verbose + run: cmake --build build --verbose --parallel - name: Run tests run: | cd build ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10 fortran: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: ubuntu-latest strategy: matrix: gcc_version: [11, 12, 13] - build_type: [Debug, Release] + build_type: [Release] env: FC: gfortran-${{ matrix.gcc_version }} @@ -57,7 +63,7 @@ jobs: run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON - name: Build - run: cmake --build build --parallel 10 + run: cmake --build build --parallel - name: Run tests run: | diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 50f44a3d..f29de4a3 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -1,6 +1,11 @@ name: Windows -on: [push, pull_request] +on: + push: + branches: + - main + pull_request: + workflow_dispatch: concurrency: group: ${{ github.workflow }}-${{ github.ref || github.run_id }} @@ -8,7 +13,6 @@ concurrency: jobs: mingw: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: windows-2019 strategy: matrix: @@ -21,12 +25,15 @@ jobs: with: platform: ${{ matrix.architecture }} version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14 + + - uses: actions/setup-python@v5 + - run: pip install -r python/requirements.txt - name: Run Cmake - run: cmake -S . -B build -G "MinGW Makefiles" + run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_ENABLE_PYTHON_LIBRARY=ON - name: Build - run: cmake --build build --parallel 10 + run: cmake --build build --parallel - name: Run tests run: | @@ -34,70 +41,61 @@ jobs: ctest -C Debug --rerun-failed --output-on-failure . --verbose msvc2019: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: windows-2019 strategy: matrix: - build_type: [Debug, Release] + build_type: [Release] architecture: [Win32, x64] steps: - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v5 + if: ${{ matrix.architecture == 'Win32' }} + with: + python-version: '3.x' + architecture: x86 + - run: pip install -r python/requirements.txt + - name: Run CMake - run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} + run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON - name: Build - run: cmake --build build --config ${{ matrix.build_type }} --parallel 10 + run: cmake --build build --config ${{ matrix.build_type }} --parallel - name: Test run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure - msvc2019_latest: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name - runs-on: windows-2019 - - steps: - - uses: actions/checkout@v3 - - name: Run CMake - run: cmake -S . -B build -G "Visual Studio 16 2019" - - name: Build - run: cmake --build build --config Release --parallel 10 - - name: Test - run: cd build ; ctest -j 10 -C Release --output-on-failure - msvc2022: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: windows-2022 strategy: matrix: - build_type: [Debug, Release] + build_type: [Release] architecture: [Win32, x64] steps: - uses: actions/checkout@v3 - - name: Run CMake - run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} - - name: Build - run: cmake --build build --config ${{ matrix.build_type }} --parallel 10 - - name: Test - run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure - msvc2022_latest: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name - runs-on: windows-2022 + - name: Set up Python + uses: actions/setup-python@v5 + if: ${{ matrix.architecture == 'Win32' }} + with: + python-version: '3.x' + architecture: x86 + + - run: pip install -r python/requirements.txt - steps: - - uses: actions/checkout@v3 - name: Run CMake - run: cmake -S . -B build -G "Visual Studio 17 2022" + run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON + - name: Build - run: cmake --build build --config Release --parallel 10 + run: cmake --build build --config ${{ matrix.build_type }} --parallel + - name: Test - run: cd build ; ctest -j 10 -C Release --output-on-failure + run: cd build ; ctest -j 10 -C ${{ matrix.build_type }} --output-on-failure clang: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: windows-2019 strategy: matrix: @@ -105,17 +103,23 @@ jobs: steps: - uses: actions/checkout@v3 + - name: Install Clang run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}.0.0/LLVM-${{ matrix.version }}.0.0-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM" + + - uses: actions/setup-python@v5 + - run: pip install -r python/requirements.txt + - name: Run CMake - run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -DCMAKE_BUILD_TYPE=Debug + run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_ENABLE_PYTHON_LIBRARY=ON + - name: Build - run: cmake --build build --parallel 10 + run: cmake --build build --parallel + - name: Test run: cd build ; ctest -j 10 -C Debug --exclude-regex "test-unicode" --output-on-failure clang-cl-11: - if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name runs-on: windows-2019 strategy: matrix: @@ -123,9 +127,22 @@ jobs: steps: - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + if: ${{ matrix.architecture == 'Win32' }} + with: + python-version: '3.x' + architecture: x86 + + - uses: actions/setup-python@v5 + - run: pip install -r python/requirements.txt + - name: Run CMake - run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL + run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_ENABLE_PYTHON_LIBRARY=ON + - name: Build - run: cmake --build build --config Debug --parallel 10 + run: cmake --build build --config Debug --parallel + - name: Test run: cd build ; ctest -j 10 -C Debug --exclude-regex "test-unicode" --output-on-failure \ No newline at end of file diff --git a/.gitignore b/.gitignore index 474cb91d..512992b6 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,6 @@ CMakeCache.txt CMakeFiles .DS_Store .vscode +dist/ +musica.cpython-* +musica.egg-info \ No newline at end of file diff --git a/.gitmodules b/.gitmodules index cf939edf..79edeeb8 100644 --- a/.gitmodules +++ b/.gitmodules @@ -4,3 +4,7 @@ [submodule "lib/tuv-x"] path = lib/tuv-x url = https://github.com/NCAR/tuv-x +[submodule "lib/pybind11"] + path = lib/pybind11 + url = https://github.com/pybind/pybind11 + branch = stable diff --git a/CITATION.cff b/CITATION.cff index 76eee6b3..e93959e7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ cff-version: 1.2.0 -message: "This Citation File Format (CFF) record describes a software paper." +message: "This Citation File Format (CFF) record describes how to cite MUSICA software." authors: - family-names: Pfister given-names: Gabriele G. @@ -64,3 +64,4 @@ number: 10 page: "E1743 - E1760" doi: "10.1175/BAMS-D-19-0331.1" url: "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml" +version: 0.6.0 \ No newline at end of file diff --git a/CMakeLists.txt b/CMakeLists.txt index 7a7beadd..01b714f7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.21) project( musica-distribution - VERSION 0.6.0 + VERSION 0.6.1 ) set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${CMAKE_CURRENT_LIST_DIR}/cmake) @@ -36,6 +36,9 @@ cmake_dependent_option( cmake_dependent_option( MUSICA_ENABLE_MICM "Adds MICM, a model independent chemical mechanism solver" ON "MUSICA_BUILD_C_CXX_INTERFACE" OFF) +cmake_dependent_option( + MUSICA_ENABLE_PYTHON_LIBRARY "Adds pybind11, a lightweight header-only library that exposes C++ types in Python and vice versa" OFF "MUSICA_BUILD_C_CXX_INTERFACE" OFF) + cmake_dependent_option( MUSICA_CREATE_ENVIRONMENT_MODULE "Creates an Lmod environment module file that can be installed on the same machine this library is installed to." OFF "MUSICA_BUILD_C_CXX_INTERFACE" OFF) @@ -46,6 +49,13 @@ if(MUSICA_CREATE_ENVIRONMENT_MODULE) endif() endif() +# shared libraries are required for python, but for some reason setting +# BUILD_SHARED_LIBS to ON doesn't work on windows +if (MUSICA_ENABLE_PYTHON_LIBRARY AND NOT WIN32) + message(STATUS "Python requires shared libraries to be built. Enabling shared libraries.") + set(BUILD_SHARED_LIBS ON) +endif() + ################################################################################ # Projet wide setup variables set(MUSICA_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR}) @@ -75,6 +85,11 @@ endif() ################################################################################ # Dependencies +include(musica_util) + +# Add submodules +checkout_submodules() + include(dependencies) if(MUSICA_BUILD_DOCS) @@ -98,3 +113,9 @@ endif() if(MUSICA_BUILD_FORTRAN_INTERFACE) add_subdirectory(fortran) endif() + +################################################################################ +# Musica python +if(MUSICA_ENABLE_PYTHON_LIBRARY) + add_subdirectory(python) +endif() \ No newline at end of file diff --git a/cmake/dependencies.cmake b/cmake/dependencies.cmake index a8600f8c..93bbeda0 100644 --- a/cmake/dependencies.cmake +++ b/cmake/dependencies.cmake @@ -48,4 +48,10 @@ if (MUSICA_ENABLE_TUVX) GIT_TAG 0.8.0 ) FetchContent_MakeAvailable(yaml-cpp) +endif() + +################################################################################ +# pybind11 +if(MUSICA_ENABLE_PYTHON_LIBRARY) + add_subdirectory(${CMAKE_SOURCE_DIR}/lib/pybind11) endif() \ No newline at end of file diff --git a/cmake/musica_util.cmake b/cmake/musica_util.cmake index 4d879455..aa33afa8 100644 --- a/cmake/musica_util.cmake +++ b/cmake/musica_util.cmake @@ -1,17 +1,22 @@ function(checkout_submodules) find_package(Git) - if(GIT_FOUND AND EXISTS "${CMAKE_SOURCE_DIR}/.git") - # Update submodules as needed + if(GIT_FOUND) + message(STATUS "Source dir: ${CMAKE_CURRENT_LIST_DIR}") + if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/.git") + # Update submodules as needed option(GIT_SUBMODULE "Check submodules during build" ON) if(GIT_SUBMODULE) message(STATUS "Submodule update") execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} RESULT_VARIABLE GIT_SUBMOD_RESULT) if(NOT GIT_SUBMOD_RESULT EQUAL "0") message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules") endif() endif() + else() + message(FATAL_ERROR "Unable to find .git directory and cannot checkout submodules") + endif() else() message(FATAL_ERROR "Git was not found") endif() diff --git a/configs/TS1/config.json b/configs/TS1/config.json new file mode 100644 index 00000000..04d0ef28 --- /dev/null +++ b/configs/TS1/config.json @@ -0,0 +1,6 @@ +{ + "camp-files": [ + "species.json", + "reactions.json" + ] +} diff --git a/configs/TS1/initial_conditions.csv b/configs/TS1/initial_conditions.csv new file mode 100644 index 00000000..fa2a0ec1 --- /dev/null +++ b/configs/TS1/initial_conditions.csv @@ -0,0 +1,343 @@ +CONC.O2,8.90261411 +CONC.N2,33.1007671 +CONC.ALKNIT,8.72E-10 +CONC.BZOOH,2.68E-11 +CONC.C6H5OOH,4.20E-10 +CONC.COF2,5.24E-11 +CONC.COFCL,7.92E-12 +CONC.HF,1.81E-11 +CONC.F,3.89E-28 +CONC.BENZO2,2.09E-13 +CONC.BZOO,8.81E-13 +CONC.PAN,4.25E-08 +CONC.MVK,2.61E-08 +CONC.MACROOH,1.21E-09 +CONC.SOAG0,3.33E-11 +CONC.SOAG1,2.14E-10 +CONC.SOAG2,1.40E-09 +CONC.SOAG3,4.27E-09 +CONC.SOAG4,2.25E-08 +CONC.ISOPNITB,1.05E-09 +CONC.SO3,1.75E-17 +CONC.OCS,1.96E-08 +CONC.SO,1.22E-20 +CONC.S,1.10E-26 +CONC.H,9.67E-18 +CONC.MEK,1.04E-08 +CONC.MTERP,1.09E-09 +CONC.N2O5,1.00E-11 +CONC.HCN,1.90E-08 +CONC.SVOC,1.98E-10 +CONC.ISOPNO3,5.35E-13 +CONC.RO2,7.13E-12 +CONC.PHENO2,2.54E-13 +CONC.IVOC,2.06E-09 +CONC.TERPNIT,8.28E-10 +CONC.HNO3,1.04E-07 +CONC.ACBZO2,3.54E-13 +CONC.CH3COOOH,7.19E-09 +CONC.SO2,6.15E-08 +CONC.CH4,7.03E-05 +CONC.CH3CL,2.07E-08 +CONC.CH3CO3,8.32E-11 +CONC.C6H5O2,6.23E-12 +CONC.TERPROD1,1.68E-09 +CONC.HYAC,4.88E-08 +CONC.HPALD,3.56E-10 +CONC.H2O,7.46E-01 +CONC.NO2,6.37E-08 +CONC.EOOH,3.56E-09 +CONC.NTERPOOH,9.37E-11 +CONC.CCL4,2.96E-09 +CONC.CF2CLBR,1.24E-10 +CONC.CF3BR,1.26E-10 +CONC.CFC11,8.50E-09 +CONC.CFC113,2.66E-09 +CONC.CFC114,6.19E-10 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100644 index 00000000..6ca324c6 --- /dev/null +++ b/configs/TS1/reactions.json @@ -0,0 +1,7124 @@ +{ + "__comments": [ "This mechanism may contain refactored reactions based on custom", + "rate constant functions in mo_usrrxt.F90 in the CAM source code.", + "As this file could change at any time, it is important that you", + "do an md5 checksum of mo_usrrxt.F90 from the version of CAM you", + "are using. The value should be: 9783938d6c5977f1c3603cadfe254987" ], + "camp-data": [ + { + "name": "MZ327_TS1.2_20230307", + "type": "MECHANISM", + "reactions": [ + { + "type": "TROE", + "k0_A": 5.5e-30, + "kinf_A": 8.3e-13, + "kinf_B": 2, + "reactants": { + "C2H2": { }, + "OH": { } + }, + "products": { + "GLYOXAL": { "yield": 0.65 }, + "OH": { "yield": 0.65 }, + "HCOOH": { "yield": 0.35 }, + "HO2": { "yield": 0.35 }, + "CO": { "yield": 0.35 } + } + }, + { + "type": "ARRHENIUS", + "A": 2.0e-12, + "Ea": -6.90325e-21, + "reactants": { + "CH3O2": { }, + "TERPO2": { } + }, + "products": { + "TERPROD1": { }, + "CH2O": { "yield": 0.95 }, + "CH3OH": { "yield": 0.25 }, + "HO2": { }, + "CH3COCH3": { "yield": 0.025 } + } + }, + { + "type": "ARRHENIUS", + "A": 3.8e-12, + "Ea": -2.7613e-21, + "reactants": { + "C3H7OOH": { }, + "OH": { } + }, + "products": { + "H2O": { }, + "C3H7O2": { } + } + }, + { + "type": "PHOTOLYSIS", + "MUSICA name": "jterpnit", + "reactants": { + "TERPNIT": { } + }, + "products": { + "TERPROD1": { }, + "NO2": { }, + "HO2": { } + } + }, + { + "type": "ARRHENIUS", + "A": 1.45e-12, + "Ea": -3.03743e-21, + "reactants": { + "N": { }, + "NO2": { } + }, + "products": { + "N2": { }, + "O2": { } + } + }, + { + "type": "ARRHENIUS", + "A": 3.4e-11, + "Ea": 2.20904e-20, + "reactants": { + "O": { }, + "CH2O": { } + }, + "products": { + "HO2": { }, + "OH": { }, + "CO": { } + } + }, + { + "type": "ARRHENIUS", + "A": 7.5e-13, + "Ea": -9.66454e-21, + "reactants": { + "TOLUO2VBS": { }, + "HO2": { } + }, + "products": { + "HO2": { }, + "SOAG0": { "yield": 0.1364 }, + "SOAG1": { "yield": 0.0101 }, + "SOAG2": { "yield": 0.0763 }, + "SOAG3": { "yield": 0.2157 }, + "SOAG4": { "yield": 0.0738 } + } + }, + { + "type": "PHOTOLYSIS", + "MUSICA name": "jo2_b", + "reactants": { + "O2": { } + }, + "products": { + "O": { "yield": 2 } + } + }, + { + "type": "ARRHENIUS", + "A": 1.3e-12, + "Ea": 2.44375e-20, + "reactants": { + "OH": { }, + "HCFC142B": { } + }, + "products": { + "CL": { }, + "COF2": 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"__description": "", + "molecular weight [kg mol-1]": 0.153822 + }, + { + "name": "CF2CLBR", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.165365 + }, + { + "name": "CF3BR", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.14891 + }, + { + "name": "CFC11", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.137368 + }, + { + "name": "CFC113", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.187375 + }, + { + "name": "CFC114", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.170921 + }, + { + "name": "CFC115", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.154467 + }, + { + "name": "CFC12", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.120913 + }, + { + "name": "CH2BR2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.173834 + }, 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"", + "molecular weight [kg mol-1]": 0.0709054 + }, + { + "name": "CL2O2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.102904 + }, + { + "name": "CLO", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0514521 + }, + { + "name": "CLONO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0974576 + }, + { + "name": "HCOOH", + "type": "CHEM_SPEC", + "__description": "formic acid", + "molecular weight [kg mol-1]": 0.0460246 + }, + { + "name": "HBR", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0809114 + }, + { + "name": "HOBR", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0969108 + }, + { + "name": "HOCL", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0524595 + }, + { + "name": "N", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0140067 + }, + { + "name": "BIGENE", + "type": "CHEM_SPEC", + "__description": "lumped alkenes C>3", + "molecular weight [kg mol-1]": 0.0561032 + }, + { + "name": "C2H4", + "type": "CHEM_SPEC", + "__description": "ethene", + "molecular weight [kg mol-1]": 0.0280516 + }, + { + "name": "C2H5O2", + "type": "CHEM_SPEC", + "__description": "ethylperoxy radical", + "molecular weight [kg mol-1]": 0.0610578 + }, + { + "name": "CH3COCHO", + "type": "CHEM_SPEC", + "__description": "methyl glyoxal", + "molecular weight [kg mol-1]": 0.0720614 + }, + { + "name": "CH3COCH3", + "type": "CHEM_SPEC", + "__description": "acetone", + "molecular weight [kg mol-1]": 0.0580768 + }, + { + "name": "O", + "type": "CHEM_SPEC", + "__description": "ground state atomic oxygen", + "molecular weight [kg mol-1]": 0.0159994 + }, + { + "name": "OCLO", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0674515 + }, + { + "name": "O1D", + "type": "CHEM_SPEC", + "__description": "excited state atomic oxygen", + "molecular weight [kg mol-1]": 0.0159994 + }, + { + "name": "PHENO", + "type": "CHEM_SPEC", + "__description": "phenoxy radical", + "molecular weight [kg mol-1]": 0.159115 + }, + { + "name": "HCFC141B", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.116948 + }, + { + "name": "HCFC142B", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.100494 + }, + { + "name": "HCFC22", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0864679 + }, + { + "name": "DMS", + "type": "CHEM_SPEC", + "__description": "dimethyl sulfide", + "molecular weight [kg mol-1]": 0.0621324 + }, + { + "name": "C2H5OH", + "type": "CHEM_SPEC", + "__description": "ethanol", + "molecular weight [kg mol-1]": 0.0460658 + }, + { + "name": "HCL", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0364601 + }, + { + "name": "BEPOMUC", + "type": "CHEM_SPEC", + "__description": "unsaturated dialdehydic epoxide from OH + benzene", + "molecular weight [kg mol-1]": 0.126109 + }, + { + "name": "CHBR3", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.25273 + }, + { + "name": "H2402", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.259824 + }, + { + "name": "CO2", + "type": "CHEM_SPEC", + "__description": "carbon dioxide", + "molecular weight [kg mol-1]": 0.0440098 + }, + { + "name": "BZALD", + "type": "CHEM_SPEC", + "__description": "benzaldehyde", + "molecular weight [kg mol-1]": 0.106121 + }, + { + "name": "BENZENE", + "type": "CHEM_SPEC", + "__description": "benzene", + "molecular weight [kg mol-1]": 0.0781104 + }, + { + "name": "C3H7O2", + "type": "CHEM_SPEC", + "__description": "propylperoxy radical", + "molecular weight [kg mol-1]": 0.0750836 + }, + { + "name": "CH3O2", + "type": "CHEM_SPEC", + "__description": "methylperoxy radical", + "molecular weight [kg mol-1]": 0.047032 + }, + { + "name": "BCARY", + "type": "CHEM_SPEC", + "__description": "beta-caryophyllene", + "molecular weight [kg mol-1]": 0.204343 + }, + { + "name": "BIGALD", + "type": "CHEM_SPEC", + "__description": "lumped aldehyde from terpene ozonolysis", + "molecular weight [kg mol-1]": 0.0980982 + }, + { + "name": "BIGALD2", + "type": "CHEM_SPEC", + "__description": "4-oxy-2-pentenal, a product of aromatic oxidation", + "molecular weight [kg mol-1]": 0.0980982 + }, + { + "name": "BIGALD3", + "type": "CHEM_SPEC", + "__description": "2-methyl butenedial, a product of aromatic oxidation", + "molecular weight [kg mol-1]": 0.0980982 + }, + { + "name": "BIGALD4", + "type": "CHEM_SPEC", + "__description": "2-methyl-4-oxo-2-pentenal, a product of aromatic oxidation", + "molecular weight [kg mol-1]": 0.112124 + }, + { + "name": "BIGALK", + "type": "CHEM_SPEC", + "__description": "lumped alkanes C>3", + "molecular weight [kg mol-1]": 0.0721438 + }, + { + "name": "H2O2", + "type": "CHEM_SPEC", + "__description": "hydrogen peroxide", + "molecular weight [kg mol-1]": 0.0340136 + }, + { + "name": "C2H5OOH", + "type": "CHEM_SPEC", + "__description": "ethyl hydroperoxide", + "molecular weight [kg mol-1]": 0.0620652 + }, + { + "name": "C2H6", + "type": "CHEM_SPEC", + "__description": "ethane", + "molecular weight [kg mol-1]": 0.0300664 + }, + { + "name": "C3H8", + "type": "CHEM_SPEC", + "__description": "propane", + "molecular weight [kg mol-1]": 0.0440922 + }, + { + "name": "C3H6", + "type": "CHEM_SPEC", + "__description": "propene", + "molecular weight [kg mol-1]": 0.0420774 + }, + { + "name": "CH2O", + "type": "CHEM_SPEC", + "__description": "formaldehyde", + "molecular weight [kg mol-1]": 0.0300252 + }, + { + "name": "CH3CN", + "type": "CHEM_SPEC", + "__description": "acetonitrile", + "molecular weight [kg mol-1]": 0.0410509 + }, + { + "name": "C2H2", + "type": "CHEM_SPEC", + "__description": "ethyne", + "molecular weight [kg mol-1]": 0.0260368 + }, + { + "name": "CH3OH", + "type": "CHEM_SPEC", + "__description": "methanol", + "molecular weight [kg mol-1]": 0.03204 + }, + { + "name": "CH3OOH", + "type": "CHEM_SPEC", + "__description": "methyl hydroperoxide", + "molecular weight [kg mol-1]": 0.0480394 + }, + { + "name": "CRESOL", + "type": "CHEM_SPEC", + "__description": "lumped cresols (hydroxymethylbenzenes)", + "molecular weight [kg mol-1]": 0.108136 + }, + { + "name": "ENEO2", + "type": "CHEM_SPEC", + "__description": "lumped hydroxyperoxy radical from OH + large alkenes", + "molecular weight [kg mol-1]": 0.105109 + }, + { + "name": "MACRO2", + "type": "CHEM_SPEC", + "__description": "peroxy radical from methacrolein oxidation", + "molecular weight [kg mol-1]": 0.119093 + }, + { + "name": "ISOPAO2", + "type": "CHEM_SPEC", + "__description": "1,2-isomer of isoprene peroxy radical", + "molecular weight [kg mol-1]": 0.11712 + }, + { + "name": "MALO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.115064 + }, + { + "name": "ISOPBO2", + "type": "CHEM_SPEC", + "__description": "1,4-isomer of isoprene peroxy radical", + "molecular weight [kg mol-1]": 0.11712 + }, + { + "name": "MCO3", + "type": "CHEM_SPEC", + "__description": "peroxy radical from OH abstraction reaction with MACR", + "molecular weight [kg mol-1]": 0.101079 + }, + { + "name": "MDIALO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.117079 + }, + { + "name": "MEKO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.103094 + }, + { + "name": "EO2", + "type": "CHEM_SPEC", + "__description": "hydroxyperoxy radical from OH + ethene chemistry", + "molecular weight [kg mol-1]": 0.0770572 + }, + { + "name": "EO", + "type": "CHEM_SPEC", + "__description": "hydroxyalkoxy radical from OH + ethene chemistry", + "molecular weight [kg mol-1]": 0.0610578 + }, + { + "name": "GLYOXAL", + "type": "CHEM_SPEC", + "__description": "glyoxal", + "molecular weight [kg mol-1]": 0.0580356, + "diffusion coefficient [m2 s-1]": 1e300 + }, 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"molecular weight [kg mol-1]": 0.0020148 + }, + { + "name": "HYDRALD", + "type": "CHEM_SPEC", + "__description": "lumped unsturated hydroxycarbonyl", + "molecular weight [kg mol-1]": 0.100113 + }, + { + "name": "ISOP", + "type": "CHEM_SPEC", + "__description": "isoprene", + "molecular weight [kg mol-1]": 0.0681142 + }, + { + "name": "NTERPO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.230232 + }, + { + "name": "TOLO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.173141 + }, + { + "name": "TERP2O2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.199219 + }, + { + "name": "XYLENO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.187166 + }, + { + "name": "TERPO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.185234 + }, + { + "name": "XYLOLO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.203166 + }, + { + "name": "PBZNIT", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.183118 + }, + { + "name": "XYLENES", + "type": "CHEM_SPEC", + "__description": "lumped xylenes", + "molecular weight [kg mol-1]": 0.106162 + }, + { + "name": "PO2", + "type": "CHEM_SPEC", + "__description": "propene peroxy radical", + "molecular weight [kg mol-1]": 0.091083 + }, + { + "name": "TOLUENE", + "type": "CHEM_SPEC", + "__description": "toluene", + "molecular weight [kg mol-1]": 0.0921362 + }, + { + "name": "XO2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.149119 + }, + { + "name": "XOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.150126 + }, + { + "name": "TERPROD2", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.154201 + }, + { + "name": "MEKOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.104101 + }, + { + "name": "MACR", + "type": "CHEM_SPEC", + "__description": "methacrolein", + "molecular weight [kg mol-1]": 0.0700878 + }, + { + "name": "HONITR", + "type": "CHEM_SPEC", + "__description": "lumped hydroxynitrates from various compounds (formula updated 2017-04-06)", + "molecular weight [kg mol-1]": 0.1331, + "diffusion coefficient [m2 s-1]": 1000.0 + }, + { + "name": "ISOPNITA", + "type": "CHEM_SPEC", + "__description": "1,2-hydroxynitrate from OH+isoprene chemistry", + "molecular weight [kg mol-1]": 0.147126, + "diffusion coefficient [m2 s-1]": 1000.0 + }, + { + "name": "ISOPNOOH", + "type": "CHEM_SPEC", + "__description": "nitroxy-hydroperoxide from NO3+isoprene chemistry", + "molecular weight [kg mol-1]": 0.163125 + }, + { + "name": "IEPOX", + "type": "CHEM_SPEC", + "__description": "isoprene epoxide", + "molecular weight [kg mol-1]": 0.118127 + }, + { + "name": "ONITR", + "type": "CHEM_SPEC", + "__description": "lumped hydroxynitrates (formula updated 2017-04-06)", + "molecular weight [kg mol-1]": 0.147126, + "diffusion coefficient [m2 s-1]": 1000.0 + }, + { + "name": "H2SO4", + "type": "CHEM_SPEC", + "__description": "sulfuric acid", + "molecular weight [kg mol-1]": 0.0980784 + }, + { + "name": "N2O", + "type": "CHEM_SPEC", + "__description": "nitrous oxide", + "molecular weight [kg mol-1]": 0.0440129 + }, + { + "name": "NO3", + "type": "CHEM_SPEC", + "__description": "nitrate radical", + "molecular weight [kg mol-1]": 0.0620049, + "diffusion coefficient [m2 s-1]": 1000.0 + }, + { + "name": "OH", + "type": "CHEM_SPEC", + "__description": "hydroxyl radical", + "molecular weight [kg mol-1]": 0.0170068 + }, + { + "name": "PHENOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.176122 + }, + { + "name": "PHENOL", + "type": "CHEM_SPEC", + "__description": "phenol, product of benzene chemistry", + "molecular weight [kg mol-1]": 0.0941098 + }, + { + "name": "XYLOL", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.122161 + }, + { + "name": "ROOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0900756 + }, + { + "name": "O3", + "type": "CHEM_SPEC", + "__description": "ozone", + "molecular weight [kg mol-1]": 0.0479982 + }, + { + "name": "TERPOOH", + "type": "CHEM_SPEC", + "__description": "Hydroxy hydroperoxide from terpene 0 double bonds", + "molecular weight [kg mol-1]": 0.186241 + }, + { + "name": "TOLOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.174148 + }, + { + "name": "XYLENOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.188174 + }, + { + "name": "XYLOLOOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.204173 + }, + { + "name": "CO", + "type": "CHEM_SPEC", + "__description": "carbon monoxide", + "molecular weight [kg mol-1]": 0.0280104 + }, + { + "name": "CH3COOH", + "type": "CHEM_SPEC", + "__description": "acetic acid", + "molecular weight [kg mol-1]": 0.0600504 + }, + { + "name": "CH3CHO", + "type": "CHEM_SPEC", + "__description": "acetaldehyde", + "molecular weight [kg mol-1]": 0.044051 + }, + { + "name": "BIGALD1", + "type": "CHEM_SPEC", + "__description": "butenedial, a product of aromatic oxidation", + "molecular weight [kg mol-1]": 0.0840724 + }, + { + "name": "ALKOOH", + "type": "CHEM_SPEC", + "__description": "lumped alkane peroxide", + "molecular weight [kg mol-1]": 0.104143 + }, + { + "name": "DICARBO2", + "type": "CHEM_SPEC", + "__description": "acylperoxy radical formed from aromatic oxidation, via unsaturated dicarbonyl chemistry", + "molecular weight [kg mol-1]": 0.12909 + }, + { + "name": "BENZOOH", + "type": "CHEM_SPEC", + "__description": "bicyclic hydroperoxide from OH + benzene", + "molecular weight [kg mol-1]": 0.160122 + }, + { + "name": "ALKO2", + "type": "CHEM_SPEC", + "__description": "lumped alkane peroxy radical from BIGALK", + "molecular weight [kg mol-1]": 0.103135 + }, + { + "name": "HO2NO2", + "type": "CHEM_SPEC", + "__description": "pernitric acid", + "molecular weight [kg mol-1]": 0.0790117 + }, + { + "name": "C3H7OOH", + "type": "CHEM_SPEC", + "__description": "propyl hydrogen peroxide", + "molecular weight [kg mol-1]": 0.076091 + }, + { + "name": "NH3", + "type": "CHEM_SPEC", + "__description": "ammonia", + "molecular weight [kg mol-1]": 0.017031 + }, + { + "name": "TERP2OOH", + "type": "CHEM_SPEC", + "__description": "2nd generation terpene hydroperoxide", + "molecular weight [kg mol-1]": 0.200226 + }, + { + "name": "POOH", + "type": "CHEM_SPEC", + "__description": "", + "molecular weight [kg mol-1]": 0.0920904 + }, + { + "name": "NOA", + "type": "CHEM_SPEC", + "__description": "nitrooxyacetone, largely from NO3+propene chemistry", + "molecular weight [kg mol-1]": 0.119074 + }, + { + "name": "NC4CHO", + "type": "CHEM_SPEC", + "__description": "nitrooxy-aldehyde from NO3+isoprene chemistry", + "molecular weight [kg mol-1]": 0.145111, + "diffusion coefficient [m2 s-1]": 1000.0 + }, + { + "name": "TEPOMUC", + "type": "CHEM_SPEC", + "__description": "toluene, xylenes product", + "molecular weight [kg mol-1]": 0.140134 + }, + { + "name": "NH4", + "type": "CHEM_SPEC", + "__description": "Ammonium", + "molecular weight [kg mol-1]": 0 + }, + { + "name": "M", + "type": "CHEM_SPEC", + "__description": "third-body species" + } + + ] +} diff --git a/configs/analytical/config.json b/configs/analytical/config.json new file mode 100644 index 00000000..03622f15 --- /dev/null +++ b/configs/analytical/config.json @@ -0,0 +1 @@ +{"camp-files": ["species.json", "reactions.json"]} \ No newline at end of file diff --git a/configs/analytical/reactions.json b/configs/analytical/reactions.json new file mode 100644 index 00000000..b44350a3 --- /dev/null +++ b/configs/analytical/reactions.json @@ -0,0 +1 @@ +{"camp-data": [{"type": "MECHANISM", "name": "music box interactive configuration", "reactions": [{"type": "ARRHENIUS", "A": 0.00012, "B": 7, "C" : 75, "D": 50, "E": 0.5, "reactants": {"B": {"qty": 1}}, "products": {"C": {"yield": 1}, "irr__089f1f45-4cd8-4278-83d5-d638e98e4315": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 0.004, "C" : 50, "reactants": {"A": {"qty": 1}}, "products": {"B": {"yield": 1}, "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7": {"yield": 1}}}]}]} \ No newline at end of file diff --git a/configs/analytical/species.json b/configs/analytical/species.json new file mode 100644 index 00000000..58ede0a7 --- /dev/null +++ b/configs/analytical/species.json @@ -0,0 +1 @@ +{"camp-data": [{"name": "A", "type": "CHEM_SPEC"}, {"name": "B", "type": "CHEM_SPEC"}, {"name": "C", "type": "CHEM_SPEC"}, {"name": "irr__089f1f45-4cd8-4278-83d5-d638e98e4315", "type": "CHEM_SPEC"}, {"name": "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7", "type": "CHEM_SPEC"}]} \ No newline at end of file diff --git a/configs/carbon_bond_5/config.json b/configs/carbon_bond_5/config.json new file mode 100644 index 00000000..d046530b --- /dev/null +++ b/configs/carbon_bond_5/config.json @@ -0,0 +1,7 @@ +{ + "camp-files": [ + "species.json", + "reactions.json" + ] + } + \ No newline at end of file diff --git a/configs/carbon_bond_5/initial_conditions.csv b/configs/carbon_bond_5/initial_conditions.csv new file mode 100644 index 00000000..3e5cc918 --- /dev/null +++ b/configs/carbon_bond_5/initial_conditions.csv @@ -0,0 +1,66 @@ +CONC.NO,0.000000001 +CONC.NO2,0.00000001 +CONC.HNO3,0.00000001 +CONC.O3,0.000002 +CONC.H2O2,0.00000005 +CONC.CO,0.000006 +CONC.SO2,0.00000003 +CONC.HCL,0.00000009 +CONC.CH4,0.00009 +CONC.ETHA,0.00000001 +CONC.FORM,0.00000009 +CONC.MEOH,0.000000009 +CONC.MEPX,0.00000002 +CONC.ALD2,0.00000001 +CONC.PAR,0.00000002 +CONC.ETH,0.000000002 +CONC.OLE,0.0000000004 +CONC.IOLE,0.00000000003 +CONC.TOL,0.000000001 +CONC.XYL,0.000000001 +CONC.NTR,0.000000001 +CONC.PAN,0.00000003 +CONC.AACD,0.000000002 +CONC.ROOH,0.000000001 +CONC.ISOP,0.0000002 +CONC.O2,56 +CONC.H2,0.00003 +CONC.H2O,128 +EMIS.NO,0.000000000144 +EMIS.NO2,0.00000000000756 +EMIS.CO,0.00000000196 +EMIS.SO2,0.00000000106 +EMIS.FORM,0.0000000000102 +EMIS.MEOH,0.000000000000592 +EMIS.ALD2,0.00000000000425 +EMIS.PAR,0.000000000427 +EMIS.ETH,0.0000000000462 +EMIS.OLE,0.0000000000149 +EMIS.IOLE,0.0000000000149 +EMIS.TOL,0.0000000000153 +EMIS.XYL,0.000000000014 +EMIS.ISOP,0.00000000000603 +PHOTO.NO2,0.00477 +PHOTO.O3->O1D,0.00000226 +PHOTO.O3->O3P,0.000252999999999999 +PHOTO.NO3->NO2,0.116999999999999 +PHOTO.NO3->NO,0.0144 +PHOTO.HONO,0.000918 +PHOTO.H2O2,0.00000259 +PHOTO.PNA,0.00000189 +PHOTO.HNO3,0.0000000861 +PHOTO.NTR,0.000000477 +PHOTO.ROOH,0.00000181 +PHOTO.MEPX,0.00000181 +PHOTO.FORM->HO2,0.00000793 +PHOTO.FORM->CO,0.000022 +PHOTO.ALD2,0.0000022 +PHOTO.PACD,0.00000181 +PHOTO.ALDX,0.0000022 +PHOTO.OPEN,0.000645 +PHOTO.MGLY,0.0000764 +PHOTO.ISPD,0.00000000198 +ENV.temperature,287.45 +ENV.pressure,101319.9 +ENV.air_density,42.3934005 +ENV.time_step,60.0 \ No newline at end of file diff --git a/configs/carbon_bond_5/reactions.json b/configs/carbon_bond_5/reactions.json new file mode 100644 index 00000000..763c7c01 --- /dev/null +++ b/configs/carbon_bond_5/reactions.json @@ -0,0 +1,4766 @@ +{ + "camp-data": [ + { + "type": "MECHANISM", + "name": "music box interactive configuration", + "reactions": [ + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "NO2", + "reactants": { + "NO2": {} + }, + "products": { + "NO": { + "yield": 1 + }, + "O": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 6e-34, + "Ea": 0, + "B": -2.4, + "D": 300, + "E": 0, + "reactants": { + "O": { + "qty": 1 + }, + "O2": { + "qty": 1 + }, + "M": { + "qty": 1 + } + }, + "products": { + "O3": { + "yield": 1 + }, + "M": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 3e-12, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O3": { + "qty": 1 + }, + "NO": { + "qty": 1 + } + }, + "products": { + "NO2": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 5.6e-12, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O": { + "qty": 1 + }, + "NO2": { + "qty": 1 + } + }, + "products": { + "NO": { + "yield": 1 + } + } + }, + { + "type": "TROE", + "k0_A": 2.5e-31, + "k0_B": -1.8, + "k0_C": 0, + "kinf_A": 2.2e-11, + "kinf_B": -0.7, + "kinf_C": 0, + "Fc": 0.6, + "N": 1, + "reactants": { + "O": { + "qty": 1 + }, + "NO2": { + "qty": 1 + } + }, + "products": { + "NO3": { + "yield": 1 + } + } + }, + { + "type": "TROE", + "k0_A": 9e-32, + "k0_B": -1.5, + "k0_C": 0, + "kinf_A": 3e-11, + "kinf_B": 0, + "kinf_C": 0, + "Fc": 0.6, + "N": 1, + "reactants": { + "O": { + "qty": 1 + }, + "NO": { + "qty": 1 + } + }, + "products": { + "NO2": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1.2e-13, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "NO2": { + "qty": 1 + }, + "O3": { + "qty": 1 + } + }, + "products": { + "NO3": { + "yield": 1 + } + } + }, + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "O3->O3P", + "reactants": { + "O3": {} + }, + "products": { + "O": { + "yield": 1 + } + } + }, + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "O3->O1D", + "reactants": { + "O3": {} + }, + "products": { + "O1D": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 2.1e-11, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O1D": { + "qty": 1 + }, + "M": { + "qty": 1 + } + }, + "products": { + "O": { + "yield": 1 + }, + "M": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 2.2e-10, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O1D": { + "qty": 1 + }, + "H2O": { + "qty": 1 + } + }, + "products": { + "OH": { + "yield": 2 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1.7e-12, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O3": { + "qty": 1 + }, + "OH": { + "qty": 1 + } + }, + "products": { + "HO2": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1e-14, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "O3": { + "qty": 1 + }, + "HO2": { + "qty": 1 + } + }, + "products": { + "OH": { + "yield": 1 + } + } + }, + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "NO3->NO2", + "reactants": { + "NO3": {} + }, + "products": { + "NO2": { + "yield": 1 + }, + "O": { + "yield": 1 + } + } + }, + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "NO3->NO", + "reactants": { + "NO3": {} + }, + "products": { + "NO": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1.5e-11, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "NO3": { + "qty": 1 + }, + "NO": { + "qty": 1 + } + }, + "products": { + "NO2": { + "yield": 2 + } + } + }, + { + "type": "ARRHENIUS", + "A": 4.5e-14, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "NO3": { + "qty": 1 + }, + "NO2": { + "qty": 1 + } + }, + "products": { + "NO": { + "yield": 1 + }, + "NO2": { + "yield": 1 + } + } + }, + { + "type": "TROE", + "k0_A": 2e-30, + "k0_B": -4.4, + "k0_C": 0, + "kinf_A": 1.4e-12, + "kinf_B": -0.7, + "kinf_C": 0, + "Fc": 0.6, + "N": 1, + "reactants": { + "NO3": { + "qty": 1 + }, + "NO2": { + "qty": 1 + } + }, + "products": { + "N2O5": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 2.5e-22, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "N2O5": { + "qty": 1 + }, + "H2O": { + "qty": 1 + } + }, + "products": { + "HNO3": { + "yield": 2 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1.8e-39, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "N2O5": { + "qty": 1 + }, + "H2O": { + "qty": 2 + } + }, + "products": { + "HNO3": { + "yield": 2 + } + } + }, + { + "type": "TROE", + "k0_A": 0.001, + "k0_B": -3.5, + "k0_C": -11000, + "kinf_A": 970000000000000, + "kinf_B": 0.1, + "kinf_C": -11080, + "Fc": 0.45, + "N": 1, + "reactants": { + "N2O5": { + "qty": 1 + } + }, + "products": { + "NO3": { + "yield": 1 + }, + "NO2": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 3.3e-39, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + 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"type": "ARRHENIUS", + "A": 1.97e-10, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "SESQ": { + "qty": 1 + }, + "OH": { + "qty": 1 + } + }, + "products": { + "OH": { + "yield": 1 + } + } + }, + { + "type": "ARRHENIUS", + "A": 1.9e-11, + "Ea": 0, + "B": 0, + "D": 300, + "E": 0, + "reactants": { + "SESQ": { + "qty": 1 + }, + "NO3": { + "qty": 1 + } + }, + "products": { + "NO3": { + "yield": 1 + } + } + }, + { + "type": "PHOTOLYSIS", + "scaling factor": 1, + "MUSICA name": "O2", + "reactants": { + "O2": {} + }, + "products": { + "O": { + "yield": 2 + } + } + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "NO", + "species": "NO" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "NO2", + "species": "NO2" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "CO", + "species": "CO" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "SO2", + "species": "SO2" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "FORM", + "species": "FORM" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "MEOH", + "species": "MEOH" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "ALD2", + "species": "ALD2" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "PAR", + "species": "PAR" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "ETH", + "species": "ETH" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "OLE", + "species": "OLE" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "IOLE", + "species": "IOLE" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "TOL", + "species": "TOL" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "XYL", + "species": "XYL" + }, + { + "type": "EMISSION", + "scaling factor": 1, + "MUSICA name": "ISOP", + "species": "ISOP" + } + ] + } + ] +} \ No newline at end of file diff --git a/configs/carbon_bond_5/species.json b/configs/carbon_bond_5/species.json new file mode 100644 index 00000000..94c41675 --- /dev/null +++ b/configs/carbon_bond_5/species.json @@ -0,0 +1,272 @@ +{ + "camp-data": [ + { + "name": "AACD", + "type": "CHEM_SPEC" + }, + { + "name": "ALD2", + "type": "CHEM_SPEC" + }, + { + "name": "ALDX", + "type": "CHEM_SPEC" + }, + { + "name": "BENZENE", + "type": "CHEM_SPEC" + }, + { + "name": "BENZRO2", + "type": "CHEM_SPEC" + }, + { + "name": "C2O3", + "type": "CHEM_SPEC" + }, + { + "name": "CH4", + "type": "CHEM_SPEC" + }, + { + "name": "CL", + "type": "CHEM_SPEC" + }, + { + "name": "CL2", + "type": "CHEM_SPEC" + }, + { + "name": "CLO", + "type": "CHEM_SPEC" + }, + { + "name": "CO", + "type": "CHEM_SPEC" + }, + { + "name": "CRES", + "type": "CHEM_SPEC" + }, + { + "name": "CRO", + "type": "CHEM_SPEC" + }, + { + "name": "CXO3", + "type": "CHEM_SPEC" + }, + { + "name": "ETH", + "type": "CHEM_SPEC" + }, + { + "name": "ETHA", + "type": "CHEM_SPEC" + }, + { + "name": "ETOH", + "type": "CHEM_SPEC" + }, + { + "name": "FACD", + "type": "CHEM_SPEC" + }, + { + "name": "FMCL", + "type": "CHEM_SPEC" + }, + { + "name": "FORM", + "type": "CHEM_SPEC" + }, + { + "name": "H2", + "type": "CHEM_SPEC" + }, + { + "name": "H2O", + "type": "CHEM_SPEC" + }, + { + "name": "H2O2", + "type": "CHEM_SPEC" + }, + { + "name": "HCL", + "type": "CHEM_SPEC" + }, + { + "name": "HCO3", + "type": "CHEM_SPEC" + }, + { + "name": "HNO3", + "type": "CHEM_SPEC" + }, + { + "name": "HO2", + "type": "CHEM_SPEC" + }, + { + "name": "HOCL", + "type": "CHEM_SPEC" + }, + { + "name": "HONO", + "type": "CHEM_SPEC" + }, + { + "name": "IOLE", + "type": "CHEM_SPEC" + }, + { + "name": "ISOP", + "type": "CHEM_SPEC" + }, + { + "name": "ISPD", + "type": "CHEM_SPEC" + }, + { + "name": "M", + "type": "CHEM_SPEC" + }, + { + "name": "MEO2", + "type": "CHEM_SPEC" + }, + { + "name": "MEOH", + "type": "CHEM_SPEC" + }, + { + "name": "MEPX", + "type": "CHEM_SPEC" + }, + { + "name": "MGLY", + "type": "CHEM_SPEC" + }, + { + "name": "N2O5", + "type": "CHEM_SPEC" + }, + { + "name": "NO", + "type": "CHEM_SPEC" + }, + { + "name": "NO2", + "type": "CHEM_SPEC" + }, + { + "name": "NO3", + "type": "CHEM_SPEC" + }, + { + "name": "NTR", + "type": "CHEM_SPEC" + }, + { + "name": "O", + "type": "CHEM_SPEC" + }, + { + "name": "O1D", + "type": "CHEM_SPEC" + }, + { + "name": "O3", + "type": "CHEM_SPEC" + }, + { + "name": "OH", + "type": "CHEM_SPEC" + }, + { + "name": "O2", + "type": "CHEM_SPEC" + }, + { + "name": "OLE", + "type": "CHEM_SPEC" + }, + { + "name": "OPEN", + "type": "CHEM_SPEC" + }, + { + "name": "PACD", + "type": "CHEM_SPEC" + }, + { + "name": "PAN", + "type": "CHEM_SPEC" + }, + { + "name": "PANX", + "type": "CHEM_SPEC" + }, + { + "name": "PAR", + "type": "CHEM_SPEC" + }, + { + "name": "PNA", + "type": "CHEM_SPEC" + }, + { + "name": "ROOH", + "type": "CHEM_SPEC" + }, + { + "name": "ROR", + "type": "CHEM_SPEC" + }, + { + "name": "SESQ", + "type": "CHEM_SPEC" + }, + { + "name": "SO2", + "type": "CHEM_SPEC" + }, + { + "name": "SULF", + "type": "CHEM_SPEC" + }, + { + "name": "TERP", + "type": "CHEM_SPEC" + }, + { + "name": "TO2", + "type": "CHEM_SPEC" + }, + { + "name": "TOL", + "type": "CHEM_SPEC" + }, + { + "name": "TOLRO2", + "type": "CHEM_SPEC" + }, + { + "name": "XO2", + "type": "CHEM_SPEC" + }, + { + "name": "XO2N", + "type": "CHEM_SPEC" + }, + { + "name": "XYL", + "type": "CHEM_SPEC" + }, + { + "name": "XYLRO2", + "type": "CHEM_SPEC" + } + ] +} \ No newline at end of file diff --git a/configs/chapman/config.json b/configs/chapman/config.json index 04d0ef28..2b5917a0 100644 --- a/configs/chapman/config.json +++ b/configs/chapman/config.json @@ -3,4 +3,4 @@ "species.json", "reactions.json" ] -} +} \ No newline at end of file diff --git a/configs/chapman/initial_conditions.csv b/configs/chapman/initial_conditions.csv new file mode 100644 index 00000000..eb291c26 --- /dev/null +++ b/configs/chapman/initial_conditions.csv @@ -0,0 +1,9 @@ +CONC.O2,0.75 +CONC.O3,8.1e-6 +ENV.temperature,206.6374207 +ENV.pressure,6152.049805 +ENV.air_density,3.580772136E+00 +ENV.time_step,60 +PHOTO.R1,2.42e-17 +PHOTO.R3,1.15e-5 +PHOTO.R5,6.61e-9 \ No newline at end of file diff --git a/configs/robertson/config.json b/configs/robertson/config.json new file mode 100644 index 00000000..514d1124 --- /dev/null +++ b/configs/robertson/config.json @@ -0,0 +1,6 @@ +{ + "camp-files": [ + "species.json", + "reactions.json" + ] + } \ No newline at end of file diff --git a/configs/robertson/initial_conditions.csv b/configs/robertson/initial_conditions.csv new file mode 100644 index 00000000..b9edac99 --- /dev/null +++ b/configs/robertson/initial_conditions.csv @@ -0,0 +1,10 @@ +CONC.A,1 +CONC.B,0 +CONC.C,0 +ENV.temperature,272.5 +ENV.pressure,101253.3 +ENV.air_density,1e6 +ENV.time_step,200.0 +PHOTO.r1,0.04 +PHOTO.r2,3e7 +PHOTO.r3,1e4 \ No newline at end of file diff --git a/configs/robertson/reactions.json b/configs/robertson/reactions.json new file mode 100644 index 00000000..cbffae84 --- /dev/null +++ b/configs/robertson/reactions.json @@ -0,0 +1,43 @@ +{ + "camp-data": [ + { + "name": "reaction rates no user defined", + "type": "MECHANISM", + "reactions": [ + { + "type": "PHOTOLYSIS", + "reactants": { + "A": {} + }, + "products": { + "B": {} + }, + "MUSICA name": "r1" + }, + { + "type": "PHOTOLYSIS", + "reactants": { + "B": { "qty": 2} + }, + "products": { + "B": {}, + "C": {} + }, + "MUSICA name": "r2" + }, + { + "type": "PHOTOLYSIS", + "reactants": { + "B": {}, + "C": {} + }, + "products": { + "A": {}, + "C": {} + }, + "MUSICA name": "r3" + } + ] + } + ] +} \ No newline at end of file diff --git a/configs/robertson/species.json b/configs/robertson/species.json new file mode 100644 index 00000000..5a1a8db6 --- /dev/null +++ b/configs/robertson/species.json @@ -0,0 +1,16 @@ +{ + "camp-data": [ + { + "name": "A", + "type": "CHEM_SPEC" + }, + { + "name": "B", + "type": "CHEM_SPEC" + }, + { + "name": "C", + "type": "CHEM_SPEC" + } + ] +} \ No newline at end of file diff --git a/docker/Dockerfile b/docker/Dockerfile index e6104d97..42880400 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -10,6 +10,7 @@ RUN dnf -y update \ make \ netcdf-fortran-devel \ json-devel \ + python \ valgrind \ && dnf clean all diff --git a/docker/Dockerfile.fortran-intel b/docker/Dockerfile.fortran-intel index 8e90f135..e3bd63d7 100644 --- a/docker/Dockerfile.fortran-intel +++ b/docker/Dockerfile.fortran-intel @@ -33,7 +33,7 @@ RUN cd musica \ -B build \ -D MUSICA_ENABLE_TESTS=ON \ -D MUSICA_ENABLE_TUVX=OFF \ - -D CMAKE_BUILD_TYPE=Debug \ + -D CMAKE_BUILD_TYPE=Release \ && cd build \ && make install @@ -45,7 +45,7 @@ ENV FC=ifx RUN cd musica/fortran/test/fetch_content_integration \ && mkdir build && cd build \ && cmake .. \ - -D CMAKE_BUILD_TYPE=Debug \ + -D CMAKE_BUILD_TYPE=Release \ && make RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build diff --git a/docker/Dockerfile.fortran-nvhpc b/docker/Dockerfile.fortran-nvhpc index 9c21239a..b86296b8 100644 --- a/docker/Dockerfile.fortran-nvhpc +++ b/docker/Dockerfile.fortran-nvhpc @@ -38,7 +38,7 @@ RUN cd musica \ -B build \ -D MUSICA_ENABLE_TESTS=ON \ -D MUSICA_ENABLE_TUVX=OFF \ - -D CMAKE_BUILD_TYPE=Debug \ + -D CMAKE_BUILD_TYPE=Release \ && cd build \ && make install @@ -50,7 +50,7 @@ ENV FC=nvfortran RUN cd musica/fortran/test/fetch_content_integration \ && mkdir build && cd build \ && cmake .. \ - -D CMAKE_BUILD_TYPE=Debug \ + -D CMAKE_BUILD_TYPE=Release \ && make RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build diff --git a/fortran/CMakeLists.txt b/fortran/CMakeLists.txt index 15d04347..69974314 100644 --- a/fortran/CMakeLists.txt +++ b/fortran/CMakeLists.txt @@ -35,8 +35,8 @@ target_include_directories(musica-fortran ) target_link_libraries(musica-fortran - PUBLIC - musica + INTERFACE + musica::musica ) target_sources(musica-fortran diff --git a/fortran/micm_core.F90 b/fortran/micm_core.F90 index 80d3cc18..35760999 100644 --- a/fortran/micm_core.F90 +++ b/fortran/micm_core.F90 @@ -1,11 +1,16 @@ module micm_core - use iso_c_binding, only: c_ptr, c_char, c_int, c_double, c_null_char + use iso_c_binding, only: c_ptr, c_char, c_int, c_double, c_null_char, c_size_t, c_f_pointer implicit none public :: micm_t private + type, bind(c) :: Mapping + character(kind=c_char, len=1) :: name(256) + integer(c_size_t) :: index + end type Mapping + interface function create_micm_c(config_path, error_code) bind(C, name="create_micm") import c_ptr, c_int, c_char @@ -28,11 +33,26 @@ subroutine micm_solve_c(micm, time_step, temperature, pressure, num_concentratio integer(kind=c_int), value, intent(in) :: num_concentrations real(kind=c_double), intent(inout) :: concentrations(num_concentrations) end subroutine micm_solve_c + + function get_species_ordering(micm, array_size) bind(c, name="get_species_ordering") + import :: c_ptr, c_size_t + type(c_ptr), value :: micm + integer(kind=c_size_t), intent(out) :: array_size + type(c_ptr) :: get_species_ordering + end function get_species_ordering + + type(c_ptr) function get_user_defined_reaction_rates_ordering(micm, array_size) & + bind(c, name="get_user_defined_reaction_rates_ordering") + import :: c_ptr, c_size_t + type(c_ptr), value :: micm + integer(kind=c_size_t), intent(out) :: array_size + end function get_user_defined_reaction_rates_ordering end interface type :: micm_t - private - type(c_ptr) :: ptr + type(Mapping), pointer :: species_ordering(:), reaction_rates_ordering(:) + integer(kind=c_size_t) :: species_ordering_length, reaction_rates_ordering_length + type(c_ptr), private :: ptr contains ! Solve the chemical system procedure :: solve @@ -52,9 +72,11 @@ function constructor(config_path, errcode) result( this ) integer, intent(out) :: errcode character(len=1, kind=c_char) :: c_config_path(len_trim(config_path)+1) integer :: n, i + type(c_ptr) :: mappings_ptr allocate( this ) + print *, "Config Path:", config_path n = len_trim(config_path) do i = 1, n c_config_path(i) = config_path(i:i) @@ -66,6 +88,15 @@ function constructor(config_path, errcode) result( this ) if (errcode /= 0) then return end if + + mappings_ptr = get_species_ordering(this%ptr, this%species_ordering_length) + call c_f_pointer(mappings_ptr, this%species_ordering, [this%species_ordering_length]) + + ! this%reaction_rates_ordering = get_user_defined_reaction_rates_ordering(this%ptr, this%reaction_rates_ordering_length) + + ! do i = 1, this%reaction_rates_ordering_length + ! print *, "Reaction Rate Name:", this%reaction_rates_ordering(i)%name, ", Index:", this%reaction_rates_ordering(i)%index + ! end do end function constructor subroutine solve(this, time_step, temperature, pressure, num_concentrations, concentrations) diff --git a/fortran/test/fetch_content_integration/CMakeLists.txt b/fortran/test/fetch_content_integration/CMakeLists.txt index 8ca09407..10ffe012 100644 --- a/fortran/test/fetch_content_integration/CMakeLists.txt +++ b/fortran/test/fetch_content_integration/CMakeLists.txt @@ -11,7 +11,7 @@ include(FetchContent) FetchContent_Declare(musica-fortran GIT_REPOSITORY https://github.com/NCAR/musica.git - GIT_TAG main + GIT_TAG 79-allow-updates-to-custom-rate-constant-parameters-and-mapping-by-name ) set(MUSICA_BUILD_C_CXX_INTERFACE OFF) @@ -33,7 +33,11 @@ add_executable(test_micm_fort_api test_micm_fort_api.F90) target_link_libraries(test_micm_fort_api PRIVATE musica::musica-fortran - stdc++ +) + +set_target_properties(test_micm_fort_api + PROPERTIES + LINKER_LANGUAGE Fortran ) add_test( @@ -47,11 +51,15 @@ add_executable(test_micm_fort_api_invalid test_micm_fort_api_invalid.F90) target_link_libraries(test_micm_fort_api_invalid PRIVATE musica::musica-fortran - stdc++ ) add_test( NAME test_micm_fort_api_invalid COMMAND $ WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} +) + +set_target_properties(test_micm_fort_api_invalid + PROPERTIES + LINKER_LANGUAGE Fortran ) \ No newline at end of file diff --git a/fortran/test/unit/CMakeLists.txt b/fortran/test/unit/CMakeLists.txt index f67af53f..4e3062c2 100644 --- a/fortran/test/unit/CMakeLists.txt +++ b/fortran/test/unit/CMakeLists.txt @@ -1,5 +1,7 @@ include(test_util) +create_standard_test_fortran(NAME musica_fortran_interface SOURCES test_musica_fortran_interface.F90) + if (MUSICA_ENABLE_TUVX) create_standard_test_fortran(NAME connect_to_tuvx SOURCES tuvx.F90) if (MUSICA_ENABLE_OPENMP) diff --git a/fortran/test/unit/test_musica_fortran_interface.F90 b/fortran/test/unit/test_musica_fortran_interface.F90 new file mode 100644 index 00000000..f7d6ca2e --- /dev/null +++ b/fortran/test/unit/test_musica_fortran_interface.F90 @@ -0,0 +1,40 @@ +program test_micm_fort_api + use iso_c_binding + use micm_core, only: micm_t + + implicit none + + type(micm_t), pointer :: micm + real(c_double) :: time_step + real(c_double) :: temperature + real(c_double) :: pressure + integer(c_int) :: num_concentrations + real(c_double), dimension(5) :: concentrations + integer :: errcode + character(len=7) :: config_path + + time_step = 200 + temperature = 272.5 + pressure = 101253.3 + num_concentrations = 5 + concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /) + config_path = "configs/chapman" + + write(*,*) "[test micm fort api] Creating MICM solver..." + micm => micm_t(config_path, errcode) + + if (errcode /= 0) then + write(*,*) "[test micm fort api] Failed in creating solver." + stop 3 + endif + + write(*,*) "[test micm fort api] Initial concentrations", concentrations + + write(*,*) "[test micm fort api] Solving starts..." + call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations) + + write(*,*) "[test micm fort api] After solving, concentrations", concentrations + + write(*,*) "[test micm fort api] Finished." + +end program diff --git a/include/musica/micm.hpp b/include/musica/micm.hpp index 4a680363..e4418df9 100644 --- a/include/musica/micm.hpp +++ b/include/musica/micm.hpp @@ -2,7 +2,7 @@ * This file contains the defintion of the MICM class, which represents a multi-component * reactive transport model. It also includes functions for creating and deleting MICM instances with c binding * Copyright (C) 2023-2024 National Center for Atmospheric Research, - * + * * SPDX-License-Identifier: Apache-2.0* creating solvers, and solving the model. */ #pragma once @@ -15,13 +15,22 @@ class MICM; +struct Mapping +{ + char *name; + size_t index; +}; + #ifdef __cplusplus -extern "C" { +extern "C" +{ #endif -MICM* create_micm(const char* config_path, int* error_code); -void delete_micm(const MICM* micm); -void micm_solve(MICM* micm, double time_step, double temperature, double pressure, int num_concentrations, double* concentrations); + MICM *create_micm(const char *config_path, int *error_code); + void delete_micm(const MICM *micm); + void micm_solve(MICM *micm, double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters); + Mapping *get_species_ordering(MICM *micm, size_t *array_size); + Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size); #ifdef __cplusplus } @@ -39,8 +48,8 @@ class MICM /// @brief Create a solver by reading and parsing configuration file /// @param config_path Path to configuration file or directory containing configuration file /// @return 0 on success, 1 on failure in parsing configuration file - int create_solver(const std::string& config_path); - + int create_solver(const std::string &config_path); + /// @brief Solve the system /// @param time_step Time [s] to advance the state by /// @para/ @briefm temperature Temperature [K] @@ -48,7 +57,10 @@ class MICM /// @param config_path Path to configuration file or directory containing configuration file /// @return 0 on success, 1 on failure in parsing species' concentrations /// @param concentrations Species's concentrations - void solve(double time_step, double temperature, double pressure, int num_concentrations, double* concentrations); + void solve(double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters); + + std::map get_species_ordering(); + std::map get_user_defined_reaction_rates_ordering(); static constexpr size_t NUM_GRID_CELLS = 1; diff --git a/lib/micm b/lib/micm index a94cc96e..9993cd95 160000 --- a/lib/micm +++ b/lib/micm @@ -1 +1 @@ -Subproject commit a94cc96e7bd8dbba6c9eb88d73ade6e5437703b6 +Subproject commit 9993cd953aa33e96d677c6ba532e6e660bc0a43b diff --git a/lib/pybind11 b/lib/pybind11 new file mode 160000 index 00000000..8b03ffa7 --- /dev/null +++ b/lib/pybind11 @@ -0,0 +1 @@ +Subproject commit 8b03ffa7c06cd9c8a38297b1c8923695d1ff1b07 diff --git a/lib/tuv-x b/lib/tuv-x index a5c71420..d43b16d2 160000 --- a/lib/tuv-x +++ b/lib/tuv-x @@ -1 +1 @@ -Subproject commit a5c71420b5e72bf24570b34f28d43656772d1e76 +Subproject commit d43b16d29e26ee1b29085b3c0b6f5d56ec122751 diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt new file mode 100644 index 00000000..0b457c15 --- /dev/null +++ b/python/CMakeLists.txt @@ -0,0 +1,27 @@ +pybind11_add_module(musica_python wrapper.cpp) + +set_target_properties(musica_python PROPERTIES OUTPUT_NAME musica) + +target_include_directories(musica_python + PUBLIC + $ + $ +) + +target_link_libraries(musica_python PUBLIC musica::musica) + + +if(WIN32) + # makefiles on windows don't need the config directory + if (${CMAKE_GENERATOR} MATCHES "MinGW Makefiles") + set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}") + else() + # but visual studio does + set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}/$") + endif() +else() + set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}") +endif() + + +add_subdirectory(test) \ No newline at end of file diff --git a/python/requirements.txt b/python/requirements.txt new file mode 100644 index 00000000..296d6545 --- /dev/null +++ b/python/requirements.txt @@ -0,0 +1 @@ +numpy \ No newline at end of file diff --git a/python/test/CMakeLists.txt b/python/test/CMakeLists.txt new file mode 100644 index 00000000..04fd7ac9 --- /dev/null +++ b/python/test/CMakeLists.txt @@ -0,0 +1,9 @@ +add_test(NAME musica_python_chapman_test + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${PYTHON_MODULE_PATH} + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/chapman.py) + +add_test(NAME musica_python_analytical_test + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${PYTHON_MODULE_PATH} + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/analytical.py) \ No newline at end of file diff --git a/python/test/analytical.py b/python/test/analytical.py new file mode 100644 index 00000000..685e2519 --- /dev/null +++ b/python/test/analytical.py @@ -0,0 +1,60 @@ +import unittest +import numpy as np +import musica + +class TestAnalyticalSimulation(unittest.TestCase): + def test_simulation(self): + time_step = 200.0 + temperature = 272.5 + pressure = 101253.3 + + solver = musica.create_micm("configs/analytical") + + rates = musica.user_defined_reaction_rates(solver) + ordering = musica.species_ordering(solver) + + self.assertEqual(rates, {}) + self.assertEqual(ordering['A'], 0) + self.assertEqual(ordering['B'], 1) + self.assertEqual(ordering['C'], 2) + + # Initalizes concentrations + initial_concentrations = [1, 0, 0] + + model_concentrations = [initial_concentrations[:]] + analytical_concentrations = [initial_concentrations[:]] + + k1 = 4.0e-3 * np.exp(50 / temperature) + k2 = 1.2e-4 * np.exp(75 / temperature) * (temperature / 50)**7* (1.0 + 0.5 * pressure) + + time_step = 1 + sim_length = 100 + + curr_time = time_step + + idx_A = 0 + idx_B = 1 + idx_C = 2 + + concentrations = initial_concentrations + + # Gets analytical concentrations + while curr_time <= sim_length: + musica.micm_solve(solver, time_step, temperature, pressure, concentrations, None) + model_concentrations.append(concentrations[:]) + + initial_A = analytical_concentrations[0][idx_A] + A_conc = initial_A * np.exp(-(k1)* curr_time) + B_conc = initial_A * (k1 / (k2 - k1)) * (np.exp(-k1 * curr_time) - np.exp(-k2 * curr_time)) + C_conc = initial_A * (1.0 + (k1 * np.exp(-k2 * curr_time) - k2 * np.exp(-k1 * curr_time)) / (k2 - k1)) + + analytical_concentrations.append([A_conc, B_conc, C_conc]) + curr_time += time_step + + for i in range(len(model_concentrations)): + self.assertAlmostEqual(model_concentrations[i][idx_A], analytical_concentrations[i][idx_A], places=8) + self.assertAlmostEqual(model_concentrations[i][idx_B], analytical_concentrations[i][idx_B], places=8) + self.assertAlmostEqual(model_concentrations[i][idx_C], analytical_concentrations[i][idx_C], places=8) + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/python/test/chapman.py b/python/test/chapman.py new file mode 100644 index 00000000..87b46ec8 --- /dev/null +++ b/python/test/chapman.py @@ -0,0 +1,38 @@ +import unittest +import musica + +class TestChapman(unittest.TestCase): + def test_micm_solve(self): + time_step = 200.0 + temperature = 272.5 + pressure = 101253.3 + concentrations = [0.75, 0.4, 0.8, 0.01, 0.02] + + solver = musica.create_micm("configs/chapman") + rate_constant_ordering = musica.user_defined_reaction_rates(solver) + ordering = musica.species_ordering(solver) + + rate_constants = { + "PHOTO.R1" : 2.42e-17, + "PHOTO.R3" : 1.15e-5, + "PHOTO.R5" : 6.61e-9 + } + + ordered_rate_constants = len(rate_constants.keys()) * [0.0] + + for key, value in rate_constants.items(): + ordered_rate_constants[rate_constant_ordering[key]] = value + + musica.micm_solve(solver, time_step, temperature, pressure, concentrations, ordered_rate_constants) + + self.assertEqual(ordering, {'M': 0, 'O': 2, 'O1D': 1, 'O2': 3, 'O3': 4}) + self.assertEqual(rate_constant_ordering, {'PHOTO.R1': 0, 'PHOTO.R3': 1, 'PHOTO.R5': 2}) + + self.assertEqual(concentrations[0], 0.75) + self.assertNotEqual(concentrations[1], 0.4) + self.assertNotEqual(concentrations[2], 0.8) + self.assertNotEqual(concentrations[3], 0.01) + self.assertNotEqual(concentrations[4], 0.02) + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/python/wrapper.cpp b/python/wrapper.cpp new file mode 100644 index 00000000..b1cec1a8 --- /dev/null +++ b/python/wrapper.cpp @@ -0,0 +1,59 @@ +#include +#include +#include + +namespace py = pybind11; + +// Wraps micm.cpp +PYBIND11_MODULE(musica, m) +{ + py::class_(m, "MICM") + .def(py::init<>()) + .def("create_solver", &MICM::create_solver) + .def("solve", &MICM::solve) + .def("__del__", [](MICM &micm) {}); + + m.def("create_micm", [](const char *config_path) + { + int error_code; + MICM* micm = create_micm(config_path, &error_code); + return micm; }); + + m.def("delete_micm", &delete_micm); + + m.def( + "micm_solve", [](MICM *micm, double time_step, double temperature, double pressure, py::list concentrations, py::object custom_rate_parameters = py::none()) + { + std::vector concentrations_cpp; + for (auto item : concentrations) { + concentrations_cpp.push_back(item.cast()); + } + + std::vector custom_rate_parameters_cpp; + if (!custom_rate_parameters.is_none()) { + py::list parameters = custom_rate_parameters.cast(); + for (auto item : parameters) { + custom_rate_parameters_cpp.push_back(item.cast()); + } + } + + micm_solve(micm, time_step, temperature, pressure, + concentrations_cpp.size(), concentrations_cpp.data(), + custom_rate_parameters_cpp.size(), custom_rate_parameters_cpp.data()); + + // Update the concentrations list after solving + for (size_t i = 0; i < concentrations_cpp.size(); ++i) { + concentrations[i] = concentrations_cpp[i]; + } }, + "Solve the system"); + + m.def( + "species_ordering", [](MICM *micm) + { return micm->get_species_ordering(); }, + "Return map of get_species_ordering rates"); + + m.def( + "user_defined_reaction_rates", [](MICM *micm) + { return micm->get_user_defined_reaction_rates_ordering(); }, + "Return map of reaction rates"); +} \ No newline at end of file diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..f9ce0ef5 --- /dev/null +++ b/setup.py @@ -0,0 +1,132 @@ +import os +import re +import subprocess +import sys +from pathlib import Path + +from setuptools import Extension, setup +from setuptools.command.build_ext import build_ext + +# Convert distutils Windows platform specifiers to CMake -A arguments +PLAT_TO_CMAKE = { + "win32": "Win32", + "win-amd64": "x64", + "win-arm32": "ARM", + "win-arm64": "ARM64", +} + + +# A CMakeExtension needs a sourcedir instead of a file list. +# The name must be the _single_ output extension from the CMake build. +# If you need multiple extensions, see scikit-build. +class CMakeExtension(Extension): + def __init__(self, name: str, sourcedir: str = "") -> None: + super().__init__(name, sources=[]) + self.sourcedir = os.fspath(Path(sourcedir).resolve()) + + +class CMakeBuild(build_ext): + def build_extension(self, ext: CMakeExtension) -> None: + # Must be in this form due to bug in .resolve() only fixed in Python 3.10+ + ext_fullpath = Path.cwd() / self.get_ext_fullpath(ext.name) + extdir = ext_fullpath.parent.resolve() + + # Using this requires trailing slash for auto-detection & inclusion of + # auxiliary "native" libs + + debug = int(os.environ.get("DEBUG", 0)) if self.debug is None else self.debug + cfg = "Debug" if debug else "Release" + + # CMake lets you override the generator - we need to check this. + # Can be set with Conda-Build, for example. + cmake_generator = os.environ.get("CMAKE_GENERATOR", "") + + # Set Python_EXECUTABLE instead if you use PYBIND11_FINDPYTHON + # EXAMPLE_VERSION_INFO shows you how to pass a value into the C++ code + # from Python. + cmake_args = [ + f"-DMUSICA_ENABLE_PYTHON_LIBRARY=ON", + f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={extdir}{os.sep}", + f"-DPYTHON_EXECUTABLE={sys.executable}", + f"-DCMAKE_BUILD_TYPE={cfg}", # not used on MSVC, but no harm + ] + build_args = [] + # Adding CMake arguments set as environment variable + # (needed e.g. to build for ARM OSx on conda-forge) + if "CMAKE_ARGS" in os.environ: + cmake_args += [item for item in os.environ["CMAKE_ARGS"].split(" ") if item] + + if self.compiler.compiler_type != "msvc": + # Using Ninja-build since it a) is available as a wheel and b) + # multithreads automatically. MSVC would require all variables be + # exported for Ninja to pick it up, which is a little tricky to do. + # Users can override the generator with CMAKE_GENERATOR in CMake + # 3.15+. + if not cmake_generator or cmake_generator == "Ninja": + try: + import ninja + + ninja_executable_path = Path(ninja.BIN_DIR) / "ninja" + cmake_args += [ + "-GNinja", + f"-DCMAKE_MAKE_PROGRAM:FILEPATH={ninja_executable_path}", + ] + except ImportError: + pass + + else: + # Single config generators are handled "normally" + single_config = any(x in cmake_generator for x in {"NMake", "Ninja"}) + + # CMake allows an arch-in-generator style for backward compatibility + contains_arch = any(x in cmake_generator for x in {"ARM", "Win64"}) + + # Specify the arch if using MSVC generator, but only if it doesn't + # contain a backward-compatibility arch spec already in the + # generator name. + if not single_config and not contains_arch: + cmake_args += ["-A", PLAT_TO_CMAKE[self.plat_name]] + + # Multi-config generators have a different way to specify configs + if not single_config: + cmake_args += [ + f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{cfg.upper()}={extdir}" + ] + build_args += ["--config", cfg] + + if sys.platform.startswith("darwin"): + # Cross-compile support for macOS - respect ARCHFLAGS if set + archs = re.findall(r"-arch (\S+)", os.environ.get("ARCHFLAGS", "")) + if archs: + cmake_args += ["-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))] + + # Set CMAKE_BUILD_PARALLEL_LEVEL to control the parallel build level + # across all generators. + if "CMAKE_BUILD_PARALLEL_LEVEL" not in os.environ: + # self.parallel is a Python 3 only way to set parallel jobs by hand + # using -j in the build_ext call, not supported by pip or PyPA-build. + if hasattr(self, "parallel") and self.parallel: + # CMake 3.12+ only. + build_args += [f"-j{self.parallel}"] + + build_temp = Path(self.build_temp) / ext.name + if not build_temp.exists(): + build_temp.mkdir(parents=True) + + subprocess.run( + ["cmake", ext.sourcedir, *cmake_args], cwd=build_temp, check=True + ) + subprocess.run( + ["cmake", "--build", ".", *build_args], cwd=build_temp, check=True + ) + +setup( + name="musica", + version="0.1.0", + author="NCAR ACOM", + author_email="musica-support@ucar.edu", + description="Chemistry interface with python", + ext_modules=[CMakeExtension("musica")], + cmdclass={"build_ext": CMakeBuild}, + zip_safe=False, +) \ No newline at end of file diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 7e64cc37..0e1943d7 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -9,11 +9,6 @@ project( message (STATUS "CMake build configuration for ${PROJECT_NAME} (${CMAKE_BUILD_TYPE}) ${PROJECT_VERSION}") -include(musica_util) - -# Add submodules -checkout_submodules() - ############################################################################## # MUSICA targets @@ -86,4 +81,4 @@ endif() # Packaging if(MUSICA_ENABLE_INSTALL) add_subdirectory(packaging) -endif() \ No newline at end of file +endif() diff --git a/src/micm/CMakeLists.txt b/src/micm/CMakeLists.txt index 57442af7..90e75a3c 100644 --- a/src/micm/CMakeLists.txt +++ b/src/micm/CMakeLists.txt @@ -1,4 +1,5 @@ target_sources(musica PRIVATE micm.cpp -) \ No newline at end of file +) + diff --git a/src/micm/micm.cpp b/src/micm/micm.cpp index 4ae1ce98..8dded4cc 100644 --- a/src/micm/micm.cpp +++ b/src/micm/micm.cpp @@ -2,7 +2,7 @@ * This file contains the implementation of the MICM class, which represents a multi-component * reactive transport model. It also includes functions for creating and deleting MICM instances, * Copyright (C) 2023-2024 National Center for Atmospheric Research, - * + * * SPDX-License-Identifier: Apache-2.0* creating solvers, and solving the model. */ #include @@ -12,60 +12,111 @@ #include #include -MICM* create_micm(const char* config_path, int* error_code) +MICM *create_micm(const char *config_path, int *error_code) { - try { - MICM* micm = new MICM(); + try + { + MICM *micm = new MICM(); *error_code = micm->create_solver(std::string(config_path)); return micm; } - catch (const std::bad_alloc& e) { + catch (const std::bad_alloc &e) + { *error_code = 1; return nullptr; } } -void delete_micm(const MICM* micm) +void delete_micm(const MICM *micm) { delete micm; } -void micm_solve(MICM* micm, double time_step, double temperature, double pressure, int num_concentrations, double* concentrations) +void micm_solve(MICM *micm, double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters) { - micm->solve(time_step, temperature, pressure, num_concentrations, concentrations); + micm->solve(time_step, temperature, pressure, num_concentrations, concentrations, num_custom_rate_parameters, custom_rate_parameters); +} + +Mapping *get_species_ordering(MICM *micm, size_t *array_size) +{ + auto map = micm->get_species_ordering(); + Mapping *reactionRates = new Mapping[map.size()]; + + // Copy data from the map to the array of structs + size_t i = 0; + for (const auto &entry : map) + { + reactionRates[i].name = new char[entry.first.size() + 1]; // +1 for null terminator + std::strcpy(reactionRates[i].name, entry.first.c_str()); + reactionRates[i].index = entry.second; + ++i; + } + + // Set the size of the array + *array_size = map.size(); + + return reactionRates; +} + +Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size) +{ + auto map = micm->get_user_defined_reaction_rates_ordering(); + Mapping *reactionRates = new Mapping[map.size()]; + + // Copy data from the map to the array of structs + size_t i = 0; + for (const auto &entry : map) + { + reactionRates[i].name = new char[entry.first.size() + 1]; // +1 for null terminator + std::strcpy(reactionRates[i].name, entry.first.c_str()); + reactionRates[i].index = entry.second; + ++i; + } + + // Set the size of the array + *array_size = map.size(); + + return reactionRates; } MICM::MICM() : solver_(nullptr) {} MICM::~MICM() { - std::cout << "MICM destructor called" << std::endl; } int MICM::create_solver(const std::string &config_path) { int parsing_status = 0; // 0 on success, 1 on failure + try { + micm::SolverConfig<> solver_config; + micm::ConfigParseStatus status = solver_config.ReadAndParse(std::filesystem::path(config_path)); - micm::SolverConfig<> solver_config; - micm::ConfigParseStatus status = solver_config.ReadAndParse(std::filesystem::path(config_path)); - - if (status == micm::ConfigParseStatus::Success) - { - micm::SolverParameters solver_params = solver_config.GetSolverParams(); - auto params = micm::RosenbrockSolverParameters::three_stage_rosenbrock_parameters(NUM_GRID_CELLS); - solver_ = std::make_unique>(solver_params.system_, - solver_params.processes_, - params); + if (status == micm::ConfigParseStatus::Success) + { + micm::SolverParameters solver_params = solver_config.GetSolverParams(); + auto params = micm::RosenbrockSolverParameters::three_stage_rosenbrock_parameters(NUM_GRID_CELLS); + params.ignore_unused_species_ = true; + solver_ = std::make_unique>(solver_params.system_, + solver_params.processes_, + params); + } + else + { + parsing_status = 1; + } } - else + catch(std::exception &e) { + std::cerr << "Error: " << e.what() << std::endl; parsing_status = 1; } + return parsing_status; } -void MICM::solve(double time_step, double temperature, double pressure, int num_concentrations, double *concentrations) +void MICM::solve(double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters) { micm::State state = solver_->GetState(); @@ -77,10 +128,24 @@ void MICM::solve(double time_step, double temperature, double pressure, int num_ state.variables_.AsVector().assign(concentrations, concentrations + num_concentrations); + state.custom_rate_parameters_.AsVector().assign(custom_rate_parameters, custom_rate_parameters + num_custom_rate_parameters); + auto result = solver_->Solve(time_step, state); for (int i = 0; i < result.result_.AsVector().size(); i++) { concentrations[i] = result.result_.AsVector()[i]; } -} \ No newline at end of file +} + +std::map MICM::get_species_ordering() +{ + micm::State state = solver_->GetState(); + return state.variable_map_; +} + +std::map MICM::get_user_defined_reaction_rates_ordering() +{ + micm::State state = solver_->GetState(); + return state.custom_rate_parameter_map_; +} diff --git a/src/packaging/CMakeLists.txt b/src/packaging/CMakeLists.txt index 331b72ab..81b5945e 100644 --- a/src/packaging/CMakeLists.txt +++ b/src/packaging/CMakeLists.txt @@ -34,6 +34,7 @@ if (MUSICA_ENABLE_MICM) ) endif() + # install the cmake config files set(cmake_config_install_location "${CMAKE_INSTALL_LIBDIR}/cmake/musica") diff --git a/src/test/connections/micm_c_api.cpp b/src/test/connections/micm_c_api.cpp index c7ee270c..a58fce23 100644 --- a/src/test/connections/micm_c_api.cpp +++ b/src/test/connections/micm_c_api.cpp @@ -33,7 +33,14 @@ TEST_F(MicmCApiTest, SolveMicmInstance) { int num_concentrations = 5; double concentrations[] = {0.75, 0.4, 0.8, 0.01, 0.02}; - micm_solve(micm, time_step, temperature, pressure, num_concentrations, concentrations); + auto ordering = micm->get_user_defined_reaction_rates_ordering(); + int num_custom_rate_parameters = ordering.size(); + std::vector custom_rate_parameters(num_custom_rate_parameters, 0.0); + for(auto& entry : ordering) { + custom_rate_parameters[entry.second] = 0.0; + } + + micm_solve(micm, time_step, temperature, pressure, num_concentrations, concentrations, custom_rate_parameters.size(), custom_rate_parameters.data()); // Add assertions to check the solved concentrations ASSERT_EQ(concentrations[0], 0.75);