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Merge branch 'main' into release
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‎.github/workflows/mac.yml‎

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@@ -12,13 +12,13 @@ concurrency:
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cancel-in-progress: true
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jobs:
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xcode_macos_13:
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runs-on: macos-13
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xcode_macos_15_intel:
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runs-on: macos-15-intel
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continue-on-error: true
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strategy:
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matrix:
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# all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-13-Readme.md#xcode
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xcode: ['14.1', '15.0']
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# all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-15-Readme.md#xcode
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xcode: ['16.0', '16.1', '16.2']
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build_type: [Release]
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env:
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DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer

‎.github/workflows/runner.yml‎

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name: Designated GPU Runner
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on:
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
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cancel-in-progress: true
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jobs:
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cuda_tests:
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runs-on: gha-runner-micm
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runs-on:
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group: CIRRUS-4x16-gpu
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container:
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image: nvcr.io/nvidia/nvhpc:23.7-devel-cuda12.2-ubuntu22.04
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image: nvcr.io/nvidia/nvhpc:25.9-devel-cuda13.0-ubuntu24.04
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options: --gpus all
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steps:
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- uses: actions/checkout@v4
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apt update
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apt install -y cmake g++
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- name: Run Cmake
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- name: Run Cmake
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run: cmake -S . -B build -DMICM_GPU_TYPE="a10"
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- name: Copy cublas headers
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run: |
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cp -r /opt/nvidia/hpc_sdk/*/23.7/cuda/include/* /usr/include/
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cp -r /opt/nvidia/hpc_sdk/*/25.9/cuda/include/* /usr/include/
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- name: Build
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run: cmake --build build --parallel 10

‎CITATION.cff‎

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cff-version: 1.2.0
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message: If you use this software, please cite it as below.
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title: Model Independent Chemistry Module (MICM)
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version: v3.10.0
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version: v3.11.0
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doi: "10.5281/zenodo.10472189"
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authors:
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- family-names: Dawson

‎CMakeLists.txt‎

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@@ -3,7 +3,7 @@
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cmake_minimum_required(VERSION 3.21)
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# project and version must be on the same line so that the docs can extract it
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project(micm VERSION 3.10.0 LANGUAGES CXX)
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project(micm VERSION 3.11.0 LANGUAGES CXX)
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if(NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE "Release" CACHE STRING

‎README.md‎

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@@ -115,7 +115,7 @@ int main(const int argc, const char *argv[])
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auto bar = Species{ "Bar" };
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auto baz = Species{ "Baz" };
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Phase gas_phase{ std::vector<Species>{ foo, bar, baz } };
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Phase gas_phase{ "gas", std::vector<PhaseSpecies>{ foo, bar, baz } };
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System chemical_system{ SystemParameters{ .gas_phase_ = gas_phase } };
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@@ -161,7 +161,7 @@ int main(const int argc, const char *argv[])
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To build and run the example using GNU (assuming the default install location):
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```
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g++ -o foo_chem foo_chem.cpp -I/usr/local/micm-3.10.0/include -std=c++20
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g++ -o foo_chem foo_chem.cpp -I/usr/local/micm-3.11.0/include -std=c++20
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./foo_chem
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```
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‎cmake/dependencies.cmake‎

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@@ -77,18 +77,27 @@ if(MICM_ENABLE_TESTS)
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FetchContent_Declare(googletest
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GIT_REPOSITORY https://github.com/google/googletest.git
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GIT_TAG be03d00f5f0cc3a997d1a368bee8a1fe93651f48
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FIND_PACKAGE_ARGS NAMES GTest
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)
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set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
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set(BUILD_GMOCK OFF CACHE BOOL "" FORCE)
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FetchContent_MakeAvailable(googletest)
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# don't run clang-tidy on google test
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set_target_properties(gtest PROPERTIES CXX_CLANG_TIDY "")
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set_target_properties(gtest_main PROPERTIES CXX_CLANG_TIDY "")
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# set_target_properties(gmock PROPERTIES CXX_CLANG_TIDY "")
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# set_target_properties(gmock_main PROPERTIES CXX_CLANG_TIDY "")
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# don't run clang-tidy on google test (only when fetched, not when using system install)
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if(TARGET gtest)
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set_target_properties(gtest PROPERTIES CXX_CLANG_TIDY "")
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endif()
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if(TARGET gtest_main)
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set_target_properties(gtest_main PROPERTIES CXX_CLANG_TIDY "")
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endif()
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if(TARGET gmock)
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set_target_properties(gmock PROPERTIES CXX_CLANG_TIDY "")
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endif()
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if(TARGET gmock_main)
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set_target_properties(gmock_main PROPERTIES CXX_CLANG_TIDY "")
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endif()
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endif()
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################################################################################

‎docker/Dockerfile.coverage‎

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@@ -27,7 +27,6 @@ RUN mkdir /build \
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-D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
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-D MICM_ENABLE_COVERAGE:BOOL=TRUE \
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-D MICM_ENABLE_LLVM:BOOL=TRUE \
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-D MICM_ENABLE_PROFILE:BOOL=TRUE \
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# -D MICM_ENABLE_MPI:BOOL=TRUE \
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# -D MICM_ENABLE_OPENMP:BOOL=TRUE \
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../micm \

‎docker/Dockerfile.nvhpc‎

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#
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# Container versions, and sizes, can be found at https://catalog.ngc.nvidia.com/orgs/nvidia/containers/nvhpc/tags
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#
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FROM nvcr.io/nvidia/nvhpc:23.7-devel-cuda12.2-ubuntu22.04
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from nvcr.io/nvidia/nvhpc:25.1-devel-cuda12.6-ubuntu24.04
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RUN apt update \
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&& apt -y install \
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COPY . /micm/
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# copy headers needed for cublas to /usr/include
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RUN cp -r /opt/nvidia/hpc_sdk/*/23.7/cuda/include/* /usr/include/
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RUN cp -r /opt/nvidia/hpc_sdk/*/25.1/cuda/include/* /usr/include/
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# build the library and run the tests
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RUN mkdir /build \

‎docs/source/_static/switcher.json‎

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[
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{
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"name": "v3.10.0 (stable)",
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"version": "v3.10.0 (stable)",
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"name": "v3.11.0 (stable)",
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"version": "v3.11.0 (stable)",
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"url": "https://ncar.github.io/micm"
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},
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{
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"version": "3.10.0",
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"url": "https://ncar.github.io/micm/versions/3.10.0"
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},
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{
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"name": "v3.11.0",
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"version": "3.11.0",
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"url": "https://ncar.github.io/micm/versions/3.11.0"
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},
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{
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"name": "dev",
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"version": "dev",

‎docs/source/user_guide/user_defined_rate_constant_tutorial.rst‎

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while (elapsed_solve_time < time_step)
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{
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auto result = solver.Solve(time_step - elapsed_solve_time, state);
152-
elapsed_solve_time = result.final_time_;
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elapsed_solve_time = result.stats_.final_time_;;
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}
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print_state(time_step * (i + 1), state);
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while (elapsed_solve_time < time_step)
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{
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auto result = solver.Solve(time_step - elapsed_solve_time, state);
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elapsed_solve_time = result.final_time_;
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elapsed_solve_time = result.stats_.final_time_;;
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}
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print_state(time_step * (i + 1), state);

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