v3.6.0

.github/workflows/mac.yml

@@ -26,7 +26,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Build
         run: cmake --build build --parallel 10
@@ -51,7 +51,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Build
         run: cmake --build build --parallel 10
@@ -67,7 +67,7 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-14, c: gcc-14}
           - { cpp: g++-12, c: gcc-12}
           - { cpp: clang++, c: clang}
         build_type: [Release]
@@ -79,7 +79,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Build
         run: cmake --build build --parallel 10

.github/workflows/ubuntu.yml

@@ -25,7 +25,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Build
         run: cmake --build build --parallel 10
@@ -48,7 +48,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
       - name: Build
         run: cmake --build build --verbose

.github/workflows/windows.yml

@@ -27,7 +27,7 @@ jobs:
           version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -G "MinGW Makefiles"
+        run: cmake -S . -B build -G "MinGW Makefiles"
 
       - name: Build
         run: cmake --build build --parallel 10
@@ -48,7 +48,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Run CMake
-      run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -G "Visual Studio 17 2022" -A ${{ matrix.architecture }}
+      run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -G "Visual Studio 17 2022" -A ${{ matrix.architecture }}
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
     - name: Test
@@ -66,7 +66,7 @@ jobs:
       - name: Install Clang
         run: curl -fsSL -o LLVM${{ 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"
       - name: Run CMake
-        run: cmake -S . -B build -DMICM_ENABLE_PROFILE=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -G"MinGW Makefiles"
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -G"MinGW Makefiles"
       - name: Build
         run: cmake --build build --parallel 10
       - name: Test
@@ -82,7 +82,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Run CMake
-        run: cmake -S . -B build -D MICM_ENABLE_PROFILE=ON -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
       - name: Build
         run: cmake --build build --config Debug --parallel 10
       - name: Test

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 title: Model Independent Chemistry Model (MICM)
-version: v3.5.0
+version: v3.6.0
 doi: "10.5281/zenodo.10472189"
 authors:
   - family-names: Dawson

CMakeLists.txt

@@ -3,7 +3,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # project and version must be on the same line so that the docs can extract it
-project(micm VERSION 3.5.0 LANGUAGES CXX)
+project(micm VERSION 3.6.0 LANGUAGES CXX)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING
@@ -29,7 +29,7 @@ option(MICM_ENABLE_MPI "Enable MPI parallel support" OFF)
 option(MICM_ENABLE_OPENMP "Enable OpenMP support" OFF)
 option(MICM_ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(MICM_ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
-option(MICM_ENABLE_JSON "Enable json configuration file reading" ON)
+option(MICM_ENABLE_CONFIG_READER "Enable yaml configuration file reading" ON)
 option(MICM_BUILD_DOCS "Build the documentation" OFF)
 option(MICM_ENABLE_LLVM "Build with LLVM support for JIT-compiling" OFF)
 option(MICM_ENABLE_TESTS "Build the tests" ON)
@@ -99,7 +99,7 @@ endif()
 ################################################################################
 # Command-line driver examples / Command-line profiler
 
-if(PROJECT_IS_TOP_LEVEL AND MICM_ENABLE_JSON AND (MICM_ENABLE_EXAMPLES OR MICM_ENABLE_PROFILE))
+if(PROJECT_IS_TOP_LEVEL AND MICM_ENABLE_CONFIG_READER AND (MICM_ENABLE_EXAMPLES OR MICM_ENABLE_PROFILE))
   add_subdirectory(examples)
 endif()
 

cmake/dependencies.cmake

@@ -92,14 +92,14 @@ if(MICM_ENABLE_TESTS)
 endif()
 
 ################################################################################
-# nlohmann::json
+# yaml-cpp
 
-if(MICM_ENABLE_JSON)
-  FetchContent_Declare(json
-      GIT_REPOSITORY https://github.com/nlohmann/json.git
-      GIT_TAG v3.11.2
+if(MICM_ENABLE_CONFIG_READER)
+  FetchContent_Declare(yaml-cpp
+    GIT_REPOSITORY https://github.com/jbeder/yaml-cpp.git
+    GIT_TAG 0.8.0
   )
-  FetchContent_MakeAvailable(json)
+  FetchContent_MakeAvailable(yaml-cpp)
 endif()
 
 ################################################################################
@@ -115,19 +115,28 @@ endif()
 
 if(NOT ${MICM_GPU_TYPE} STREQUAL "None")
   string(TOLOWER ${MICM_GPU_TYPE} MICM_GPU_TYPE_LOWER)
+  # Data center GPUs
   set(cuda_arch_map_a100 80)
   set(cuda_arch_map_v100 70)
   set(cuda_arch_map_h100 90a)
   set(cuda_arch_map_h200 90a)
   set(cuda_arch_map_b100 95)
   set(cuda_arch_map_b200 95)
+  # Consumer grade GPUs
+  set(cuda_arch_map_turing 75)
+
   set(cuda_arch_map_all_major all-major)
   # Setting CUDAARCHS does not override CMAKE_CUDA_ARCHITECTURES or CUDA_ARCHITECTURES
   # until the current process has returned to the caller site in CMake.
   set(ENV{CUDAARCHS} ${cuda_arch_map_${MICM_GPU_TYPE_LOWER}})
 
   if("$ENV{CUDAARCHS}" STREQUAL "")
-    message(FATAL_ERROR "${MICM_GPU_TYPE_LOWER} unsupported, current options are a100,v100,h{1,2}00, b{1,2}00.")
+    # dynamically create the current options
+    set(arch_options "")
+    foreach(arch IN ITEMS a100 v100 h100 h200 b100 b200 turing)
+      list(APPEND arch_options ${arch})
+    endforeach()
+    message(FATAL_ERROR "${MICM_GPU_TYPE_LOWER} unsupported, current options are ${arch_options}.")
   endif()
 
   message(STATUS "GPU architecture found: $ENV{CUDAARCHS}")

cmake/test_util.cmake

@@ -4,7 +4,7 @@
 if(MICM_ENABLE_MEMCHECK)
   if(MICM_ENABLE_CUDA)
     find_program(MEMORYCHECK_COMMAND "compute-sanitizer")
-    set(MEMORYCHECK_COMMAND_OPTIONS "--error-exitcode=1 --show-backtrace device --tool=memcheck --launch-timeout=0")
+    set(MEMORYCHECK_COMMAND_OPTIONS "--error-exitcode=1 --leak-check full --show-backtrace device --launch-timeout=0")
     set(CUDA_MEMORY_CHECK TRUE)
   else()
     find_program(MEMORYCHECK_COMMAND "valgrind")
@@ -26,7 +26,11 @@ function(create_standard_test)
 
   add_executable(test_${TEST_NAME} ${TEST_SOURCES})
 
-  target_link_libraries(test_${TEST_NAME} PUBLIC musica::micm GTest::gtest_main)
+  if(TEST_IS_CUDA_TEST)
+    target_link_libraries(test_${TEST_NAME} PUBLIC musica::micm cuda_gtest_main)
+  else()
+    target_link_libraries(test_${TEST_NAME} PUBLIC musica::micm GTest::gtest_main)
+  endif()
 
   # link additional libraries
   foreach(library ${TEST_LIBRARIES})

docker/Dockerfile.memcheck

@@ -19,7 +19,6 @@ RUN mkdir /build \
         -D CMAKE_BUILD_TYPE=release \
         -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
         -D MICM_ENABLE_MEMCHECK:BOOL=TRUE \
-        -D MICM_ENABLE_PROFILE:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.openmp

@@ -18,7 +18,7 @@ RUN mkdir /build \
       && cmake  \
         -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
         -D MICM_ENABLE_OPENMP:BOOL=TRUE \
-        -D MICM_ENABLE_JSON:BOOL=TRUE \
+        -D MICM_ENABLE_CONFIG_READER:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.publish

@@ -20,7 +20,7 @@ RUN mkdir /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
         -D MICM_ENABLE_LLVM:BOOL=TRUE \
-        -D MICM_ENABLE_JSON:BOOL=TRUE \
+        -D MICM_ENABLE_CONFIG_READER:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docs/source/_static/switcher.json

@@ -1,7 +1,7 @@
 [
   {
-      "name": "v3.5.0 (stable)",
-      "version": "v3.5.0 (stable)",
+      "name": "v3.6.0 (stable)",
+      "version": "v3.6.0 (stable)",
       "url": "https://ncar.github.io/micm"
   },
   {
@@ -29,6 +29,11 @@
     "version": "3.5.0",
     "url": "https://ncar.github.io/micm/versions/3.5.0"
   },
+  {
+    "name": "v3.6.0",
+    "version": "3.6.0",
+    "url": "https://ncar.github.io/micm/versions/3.6.0"
+  },
   {
     "name": "dev",
     "version": "dev",

docs/source/getting_started.rst

@@ -37,13 +37,13 @@ Options
 .. image:: _static/options.png
 
 
-MICM can optionally include support for json configuration reading, OpenMP,
+MICM can optionally include support for yaml configuration reading, OpenMP,
 JIT-compiled chemistry functions, and GPUs. Each of these requires an additional library. 
 Some of these libraries can be included automatically with cmake build options,
 others require that you have libraries installed on your system.
 
-- JSON configuration support
-  - When building micm, you need to enable the JSON option. This will download and configure the `nlohmann/jsoncpp library <https://github.com/nlohmann/json>`_  for you. For example: ``cmake -DMICM_ENABLE_JSON=ON ..``
+- YAML configuration support
+  - When building micm, you need to enable the YAML option. This will download and configure the `jbeder/yaml-cpp library <https://github.com/jbeder/yaml-cpp>`_  for you. For example: ``cmake -DMICM_ENABLE_CONFIG_READER=ON ..``
 - JIT-compiled chemistry functions 
   - This requires `LLVM <https://llvm.org/docs/index.html>`_ to be installed with on your system. Once it is, you can include the jit options with ``cmake -DENBABLE_LLVM=ON ..``
 - GPU support
@@ -73,7 +73,7 @@ MICM Executable Example
 A simple driver for MICM is built with the library and can be used to solve a
 chemical system for given initial conditions over one time step.
 
-Just pass the driver the path to the folder containing a valid JSON
+Just pass the driver the path to the folder containing a valid YAMl
 mechanism configuration and the path to a CSV file holding the initial
 conditions.
 

docs/source/user_guide/index.rst

@@ -30,7 +30,7 @@ If you would like to include the json examples, you must configure micm to build
 
 .. code-block:: console
 
-    $ cmake -DMICM_ENABLE_JSON=ON ..
+    $ cmake -DMICM_ENABLE_CONFIG_READER=ON ..
     $ make
     $ ./test_rate_constants_no_user_defined_example_with_config
     $ ./test_rate_constants_user_defined_example_with_config

examples/configs/TS1/species.json

@@ -1274,6 +1274,7 @@
     {
       "name": "M",
       "type": "CHEM_SPEC",
+      "tracer type": "THIRD_BODY",
       "__description": "third-body species"
     }
 

examples/configs/carbon_bond_5/species.json

@@ -130,7 +130,8 @@
     },
     {
       "name": "M",
-      "type": "CHEM_SPEC"
+      "type": "CHEM_SPEC",
+      "tracer type": "THIRD_BODY"
     },
     {
       "name": "MEO2",

examples/configs/chapman/config.yaml

@@ -0,0 +1,3 @@
+camp-files:
+  - species.yaml
+  - reactions.yaml