musica 0.12.2__tar.gz → 0.13.0__tar.gz

{musica-0.12.2 → musica-0.13.0}/.github/workflows/mac.yml

@@ -13,15 +13,16 @@ concurrency:
 
 jobs:
   c_cxx:
-    runs-on: macos-latest
+    runs-on: macos-15
     continue-on-error: true 
     strategy:
       matrix:
+        xcode: ['16.4']
+        build_type: [Release]
         compiler:
           - { cpp: g++-13, c: gcc-13, fc: gfortran-13}
           - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
           - { cpp: clang++, c: clang, fc: gfortran-14}
-        build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
       CXX: ${{ matrix.compiler.cpp }}
@@ -32,7 +33,7 @@ jobs:
 
       - uses: maxim-lobanov/setup-xcode@v1
         with:
-          xcode-version: '16.4'
+          xcode-version: ${{ matrix.xcode }}
 
       - name: Install dependencies
         run: brew install netcdf netcdf-fortran

{musica-0.12.2 → musica-0.13.0}/.github/workflows/ubuntu.yml

@@ -18,7 +18,6 @@ jobs:
     strategy:
       matrix:
         compiler:
-          - { cpp: g++-12, c: gcc-12, fc: gfortran-12}
           - { cpp: g++-13, c: gcc-13, fc: gfortran-13}
           - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
           - { cpp: clang++, c: clang, fc: gfortran-12}

{musica-0.12.2 → musica-0.13.0}/.gitignore

@@ -21,3 +21,7 @@ error.json
 
 .ipynb_checkpoints
 configs/tuvx/output/
+
+node_modules/
+musica_env/
+.env

{musica-0.12.2 → musica-0.13.0}/CITATION.cff

@@ -64,4 +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: 0.12.2
+version: 0.13.0

{musica-0.12.2 → musica-0.13.0}/CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # must be on the same line so that pyproject.toml can correctly identify the version
-project(musica-distribution VERSION 0.12.2)
+project(musica-distribution VERSION 0.13.0)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/SetDefaults.cmake)
@@ -33,6 +33,7 @@ option(MUSICA_ENABLE_CARMA "Enable CARMA" ON)
 option(MUSICA_ENABLE_PIC "Build the library with position independent code" OFF)
 option(MUSICA_ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(MUSICA_BUNDLE_DEPENDENCIES "Bundle dependencies with the library" ON)
+option(MUSICA_ENABLE_JAVASCRIPT "Build the JavaScript addon" OFF)
 
 set(MUSICA_GPU_TYPE "None" CACHE STRING "The GPU type being targeted")
 
@@ -154,6 +155,13 @@ if(MUSICA_ENABLE_PYTHON_LIBRARY)
   add_subdirectory(musica)
 endif()
 
+################################################################################
+
+# Musica JavaScript Addon
+if(MUSICA_ENABLE_JAVASCRIPT)
+  add_subdirectory(javascript)
+endif()
+
 ################################################################################
 ###
 # Configure and display a summary file for how musica was built.

{musica-0.12.2 → musica-0.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.12.2
+Version: 0.13.0
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>, Montek Thind <mthind@ucar.edu>
 Maintainer-Email: ACOM MUSICA Developers <musica-support@ucar.edu>
@@ -208,24 +208,24 @@ License:                                  Apache License
          
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
 Requires-Python: >=3.9
+Requires-Dist: numpy>=2.0.0
 Requires-Dist: pyyaml>=6.0.2
-Requires-Dist: xarray>=2022.3.0
 Requires-Dist: ussa1976>=v0.3.4
+Requires-Dist: xarray>=2022.3.0
 Provides-Extra: test
-Requires-Dist: numpy; extra == "test"
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: matplotlib; extra == "test"
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: matplotlib>=3.6.0; extra == "test"
 Provides-Extra: gpu
-Requires-Dist: nvidia-cublas-cu12; extra == "gpu"
-Requires-Dist: nvidia-cuda-runtime-cu12; extra == "gpu"
+Requires-Dist: nvidia-cublas-cu12>=12.6.4.1; extra == "gpu"
+Requires-Dist: nvidia-cuda-runtime-cu12>=12.6.68; extra == "gpu"
 Provides-Extra: tutorial
-Requires-Dist: pandas; extra == "tutorial"
-Requires-Dist: matplotlib; extra == "tutorial"
-Requires-Dist: numpy; extra == "tutorial"
-Requires-Dist: scipy; extra == "tutorial"
-Requires-Dist: seaborn; extra == "tutorial"
-Requires-Dist: dask[distributed]; extra == "tutorial"
-Requires-Dist: dask-jobqueue; extra == "tutorial"
+Requires-Dist: dask-jobqueue>=0.8.0; extra == "tutorial"
+Requires-Dist: dask[distributed]>=2022.3.0; extra == "tutorial"
+Requires-Dist: matplotlib>=3.6.0; extra == "tutorial"
+Requires-Dist: numpy>=2.0.0; extra == "tutorial"
+Requires-Dist: pandas>=2.2.0; extra == "tutorial"
+Requires-Dist: scipy>=1.10.0; extra == "tutorial"
+Requires-Dist: seaborn>=0.12.0; extra == "tutorial"
 Description-Content-Type: text/markdown
 
 # MUSICA

{musica-0.12.2 → musica-0.13.0}/cmake/dependencies.cmake

@@ -25,7 +25,7 @@ endif()
 
 if(MUSICA_BUILD_C_CXX_INTERFACE)
   set_git_default(MECH_CONFIG_GIT_REPOSITORY https://github.com/NCAR/MechanismConfiguration.git)
-  set_git_default(MECH_CONFIG_GIT_TAG a3ef728c69f619f80c272d634bc2a17ca5ab4de9)
+  set_git_default(MECH_CONFIG_GIT_TAG v1.0.0)
 
   FetchContent_Declare(mechanism_configuration
       GIT_REPOSITORY ${MECH_CONFIG_GIT_REPOSITORY}
@@ -75,7 +75,7 @@ endif()
 
 if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
   set_git_default(MICM_GIT_REPOSITORY https://github.com/NCAR/micm.git)
-  set_git_default(MICM_GIT_TAG d1c22955dc6af62cb4b2deb09d10bf19324e2340)
+  set_git_default(MICM_GIT_TAG e9123958129f34920491e61b79cd8b6baba28915)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -104,7 +104,7 @@ if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
   set(TUVX_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
   set_git_default(TUVX_GIT_REPOSITORY https://github.com/NCAR/tuv-x.git)
-  set_git_default(TUVX_GIT_TAG 1e8c99b4d206829c030b9f5315bf6afb3e970e3c)
+  set_git_default(TUVX_GIT_TAG v0.13.0)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}
@@ -142,7 +142,7 @@ if(MUSICA_ENABLE_PYTHON_LIBRARY)
   set(PYBIND11_NEWPYTHON ON)
 
   set_git_default(PYBIND11_GIT_REPOSITORY https://github.com/pybind/pybind11)
-  set_git_default(PYBIND11_GIT_TAG v2.12.0)
+  set_git_default(PYBIND11_GIT_TAG v3.0.0)
 
   FetchContent_Declare(pybind11
       GIT_REPOSITORY ${PYBIND11_GIT_REPOSITORY}

{musica-0.12.2 → musica-0.13.0}/cmake/musica.settings.in

@@ -7,6 +7,7 @@ Configured On:	    @BUILD_CONFIG_DATE@
 Host System:	    @CMAKE_SYSTEM_PROCESSOR@-@CMAKE_SYSTEM_NAME@-@CMAKE_SYSTEM_VERSION@
 Build Directory:    @CMAKE_BINARY_DIR@
 Install Prefix:     @CMAKE_INSTALL_PREFIX@
+Build type: @CMAKE_BUILD_TYPE@
 
 ## Compilers and Flags
 ----------------------

{musica-0.12.2 → musica-0.13.0}/configs/tuvx/data/dose_rates.json

@@ -3,7 +3,6 @@
      "The original TUV 5.4 source code and data sets can be found here: https://www2.acom.ucar.edu/modeling/tuv-download"
    ],
    "dose rates": {
-      "enable diagnostics": true,
       "rates": [
          {
             "name": "RB Meter, model 501",

{musica-0.12.2 → musica-0.13.0}/configs/tuvx/data/photolysis_rate_constants.json

@@ -3,7 +3,6 @@
       "The original TUV 5.4 source code and data sets can be found here: https://www2.acom.ucar.edu/modeling/tuv-download"
     ],
    "photolysis": {
-      "enable diagnostics" : true,
       "reactions": [
          {
             "name": "O2+hv->O+O",

{musica-0.12.2 → musica-0.13.0}/configs/tuvx/tuv_5_4.json

@@ -87,7 +87,6 @@
       },
       {
          "name": "extraterrestrial flux",
-         "enable diagnostics" : true,
          "type": "extraterrestrial flux",
          "units": "photon cm-2 s-1",
          "file path": ["data/profiles/solar/susim_hi.flx",
@@ -130,7 +129,6 @@
       ],
       "radiators": [
          {
-            "enable diagnostics" : true,
             "name": "air",
             "type": "base",
             "treat as air": true,
@@ -139,7 +137,6 @@
             "vertical profile units": "molecule cm-3"
          },
          {
-            "enable diagnostics" : true,
             "name": "O2",
             "type": "base",
             "cross section": "O2",
@@ -147,7 +144,6 @@
             "vertical profile units": "molecule cm-3"
          },
          {
-            "enable diagnostics" : true,
             "name": "O3",
             "type": "base",
             "cross section": "O3",
@@ -155,7 +151,6 @@
             "vertical profile units": "molecule cm-3"
          },
          {
-            "enable diagnostics" : true,
             "name": "aerosols",
             "type": "aerosol",
             "optical depths": [2.40e-01, 1.06e-01, 4.56e-02, 1.91e-02, 1.01e-02, 7.63e-03,
@@ -174,7 +169,6 @@
       ]
    },
    "photolysis": {
-      "enable diagnostics" : false,
       "reactions": [
          {
             "name": "O2+hv->O+O",
@@ -1598,7 +1592,6 @@
       ]
    },
    "dose rates": {
-      "enable diagnostics": true,
       "rates": [
          {
             "name": "RB Meter, model 501",

musica-0.13.0/configs/v0/surface/config.json

@@ -0,0 +1,6 @@
+{
+  "camp-files": [
+    "species.json",
+    "reactions.json"
+  ]
+}

musica-0.13.0/configs/v0/surface/reactions.json

@@ -0,0 +1,24 @@
+{
+  "camp-data": [
+    {
+      "type": "MECHANISM",
+      "name": "music box interactive configuration",
+      "reactions": [
+        {
+          "type": "SURFACE",
+          "MUSICA name": "",
+          "reaction probability": 1.0,
+          "gas-phase reactant": "A",
+          "gas-phase products": {
+            "B": {
+              "yield": 1
+            },
+            "irr__241993b6-c109-44fc-97b0-bc0bc42fe945": {
+              "yield": 1
+            }
+          }
+        }
+      ]
+    }
+  ]
+}

musica-0.13.0/configs/v0/surface/species.json

@@ -0,0 +1,22 @@
+{
+  "camp-data": [
+    {
+      "name": "A",
+      "type": "CHEM_SPEC",
+      "diffusion coefficient [m2 s-1]": "2"
+    },
+    {
+      "name": "B",
+      "type": "CHEM_SPEC"
+    },
+    {
+      "name": "M",
+      "type": "CHEM_SPEC",
+      "tracer type": "THIRD_BODY"
+    },
+    {
+      "name": "irr__241993b6-c109-44fc-97b0-bc0bc42fe945",
+      "type": "CHEM_SPEC"
+    }
+  ]
+}

{musica-0.12.2 → musica-0.13.0}/configs/v1/chapman/config.json

@@ -4,24 +4,24 @@
   "species": [
     {
       "name": "M",
-      "tracer type": "THIRD_BODY"
+      "is third body": true
     },
     {
       "name": "O2",
-      "tracer type": "CONSTANT"
+      "__tracer type": "CONSTANT"
     },
     {
       "name": "O",
-      "absolute tolerance": 1e-12
+      "__absolute tolerance": 1e-12
     },
     {
       "name": "O1D",
-      "absolute tolerance": 1e-12
+      "__absolute tolerance": 1e-12
     },
     {
       "name": "O3",
-      "absolute tolerance": 1e-12,
       "molecular weight [kg mol-1]": 0.048,
+      "__absolute tolerance": 1e-12,
       "__long name": "ozone",
       "__atoms": 3,
       "__do advect": true

musica-0.13.0/configs/v1/chapman/config.yaml

@@ -0,0 +1,112 @@
+version: "1.0.0"
+name: Chapman
+species:
+  - name: M
+    is third body: true
+  - name: O2
+    __tracer type: CONSTANT
+  - name: O
+    __absolute tolerance: 1e-12
+  - name: O1D
+    __absolute tolerance: 1e-12
+  - name: O3
+    molecular weight [kg mol-1]: 0.048
+    __absolute tolerance: 1e-12
+    __long name: ozone
+    __atoms: 3
+    __do advect: true
+
+phases:
+  - name: gas
+    species:
+      - M
+      - O
+      - O2
+      - O3
+      - O1D
+
+reactions:
+  - type: PHOTOLYSIS
+    gas phase: gas
+    reactants:
+      - species name: O2
+    products:
+      - species name: O
+        coefficient: 2.0
+    name: jO2
+
+  - type: ARRHENIUS
+    gas phase: gas
+    reactants:
+      - species name: O
+        coefficient: 1
+      - species name: O2
+        coefficient: 1
+    products:
+      - species name: O3
+        coefficient: 1
+    A: 8.018e-17
+    name: R2
+
+  - type: PHOTOLYSIS
+    gas phase: gas
+    reactants:
+      - species name: O3
+    products:
+      - species name: O
+        coefficient: 1
+      - species name: O2
+        coefficient: 1
+    name: jO3->O
+
+  - type: ARRHENIUS
+    gas phase: gas
+    reactants:
+      - species name: O
+        coefficient: 1
+      - species name: O3
+        coefficient: 1
+    products:
+      - species name: O2
+        coefficient: 2.0
+    A: 1.576e-15
+    name: R4
+
+  - type: PHOTOLYSIS
+    gas phase: gas
+    reactants:
+      - species name: O3
+    products:
+      - species name: O1D
+        coefficient: 1
+      - species name: O2
+        coefficient: 1
+    name: jO3->O1D
+
+  - type: ARRHENIUS
+    gas phase: gas
+    reactants:
+      - species name: O1D
+        coefficient: 1
+      - species name: M
+        coefficient: 1
+    products:
+      - species name: O
+        coefficient: 1
+      - species name: M
+        coefficient: 1
+    A: 7.11e-11
+    name: R6
+
+  - type: ARRHENIUS
+    gas phase: gas
+    reactants:
+      - species name: O1D
+        coefficient: 1
+      - species name: O3
+        coefficient: 1
+    products:
+      - species name: O2
+        coefficient: 2.0
+    A: 1.2e-10
+    name: R7