musica 0.11.1.3__tar.gz → 0.12.0__tar.gz

{musica-0.11.1.3 → musica-0.12.0}/.dockerignore

@@ -17,3 +17,4 @@
 !pyproject.toml
 !LICENSE
 !README.md
+!wheelhouse

{musica-0.11.1.3 → musica-0.12.0}/.github/workflows/windows.yml

@@ -13,7 +13,8 @@ concurrency:
 
 jobs:
   mingw:
-    runs-on: windows-2019
+    runs-on: windows-latest
+    continue-on-error: true 
     strategy:
       matrix:
         architecture: [x64]
@@ -24,10 +25,7 @@ jobs:
         uses: egor-tensin/setup-mingw@v2
         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 numpy
+          static: 0
 
       - name: Run Cmake 
         run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
@@ -40,8 +38,8 @@ jobs:
           cd build
           ctest -C Debug --rerun-failed --output-on-failure . --verbose
 
-  msvc2022:
-    runs-on: windows-2022
+  msvc:
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -58,10 +56,8 @@ jobs:
         python-version: '3.x'
         architecture: x86
 
-    - run: pip install numpy
-
     - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -70,11 +66,11 @@ jobs:
       run: cd build ; ctest -C ${{ matrix.build_type }} --output-on-failure  --verbose
 
   clang:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
-        version: [12.0.0, 13.0.0, 14.0.0, 15.0.0, 16.0.0, 17.0.1, 18.1.0, 19.1.0, 20.1.0]
+        version: [19.1.0, 20.1.0]
 
     steps:
       - uses: actions/checkout@v4
@@ -82,9 +78,6 @@ jobs:
       - name: Install Clang
         run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}/LLVM-${{ matrix.version }}-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM"
 
-      - uses: actions/setup-python@v5
-      - run: pip install numpy
-
       - 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" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
@@ -95,7 +88,7 @@ jobs:
         run: cd build ; ctest -C Debug --output-on-failure  --verbose
 
   clang-cl-11:
-    runs-on: windows-2019
+    runs-on: windows-latest
     continue-on-error: true 
     strategy:
       matrix:
@@ -111,11 +104,8 @@ jobs:
           python-version: '3.x'
           architecture: x86
 
-      - uses: actions/setup-python@v5
-      - run: pip install numpy
-
       - name: Run CMake
-        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel
@@ -125,6 +115,7 @@ jobs:
 
   fortran:
     runs-on: windows-latest
+    continue-on-error: true 
     strategy:
       fail-fast: false
       matrix:

{musica-0.11.1.3 → musica-0.12.0}/.gitignore

@@ -11,6 +11,8 @@ musica.cpython-*
 musica.egg-info
 **/*.mod
 
+.venv
+.pytest_cache
 **/*__pycache__*
 **/*.pyc
 wheelhouse

musica-0.12.0/.zenodo.json

@@ -0,0 +1,80 @@
+{
+  "title": "MUSICA: Multi-Scale Infrastructure for Chemistry and Aerosols",
+  "description": "MUSICA is a multi-language library for performing computational simulations in atmospheric chemistry.",
+  "license": {
+    "id": "Apache-2.0"
+  },
+  "creators": [
+    {
+      "name": "Dawson, Matthew",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Gim, Jiwon",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Fillmore, David",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Shores, Kyle",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": "0000-0002-4272-5187"
+    },
+    {
+      "name": "Thind, Montek",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    },
+    {
+      "name": "Jian Sun",
+      "affiliation": "National Center for Atmospheric Research (NCAR)",
+      "orcid": ""
+    }
+  ],
+  "contributors": [
+    {
+      "name": "ACOM MUSICA Development Team",
+      "type": "ResearchGroup"
+    },
+    {
+      "name": "Angela Pak",
+      "type": "ProjectMember"
+    },
+    {
+      "name": "Aidan Winney",
+      "type": "ProjectMember"
+    },
+    {
+      "name": "Dee Grant",
+      "type": "Other"
+    },
+    {
+      "name": "Ward Fisher",
+      "type": "Other"
+    },
+    {
+      "name": "Qina Tan",
+      "type": "ProjectMember"
+    }
+  ],
+  "keywords": [
+    "atmospheric chemistry",
+    "chemical mechanisms",
+    "air quality modeling",
+    "photolysis",
+    "MICM",
+    "TUV-x"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "10.1175/BAMS-D-19-0331.1",
+      "relation": "cites",
+      "description": "The foundational MUSICA paper describing the scientific vision"
+    }
+  ]
+}

musica-0.12.0/AUTHORS.md

@@ -0,0 +1,59 @@
+# MUSICA Authors and Contributors
+
+This file acknowledges all individuals who have contributed to the MUSICA project.
+
+## Core Development Team
+
+The following individuals are the primary developers and maintainers of the MUSICA software:
+
+- **Matthew Dawson** (mattdawson@ucar.edu) - Core Developer
+- **Jiwon Gim** (jiwongim@ucar.edu) - Core Developer  
+- **David Fillmore** (fillmore@ucar.edu) - Core Developer
+- **Kyle Shores** (kshores@ucar.edu) - Core Developer
+- **Montek Thind** (mthind@ucar.edu) - Core Developer
+- **Jian Sun** - Core Developer
+
+## Scientific Leadership and Vision
+
+The scientific leadership and vision for MUSICA are provided by the authors of the [foundational paper](https://doi.org/10.1175/BAMS-D-19-0331.1). 
+This software implements that vision. For a full list of scientific authors, 
+please refer to our [CITATION.cff](CITATION.cff) file. To cite the software, use the Zenodo DOI from our latest release.
+
+## Additional Contributors
+
+<!-- Contributors will be added here as they join the project -->
+<!-- Format: -->
+<!-- - **Name** (affiliation) - Brief description of contribution -->
+
+- **Aidan Winney** - Documentation and Tutorials
+- **Angela Pak** - Documentation and Tutorials
+- **Dee Grant** - Improving the Python API
+- **Qina Tan** - Implementing the CUDA-based Rosenbrock solver
+
+## Recognition Policy
+
+We recognize contributors at different levels based on their involvement:
+
+- **Core Development Team**: Listed in `pyproject.toml`, `.zenodo.json` (creators), and this file
+- **Additional Contributors**: Listed in `.zenodo.json` (contributors) and this file
+- **All Contributors**: Automatically tracked by GitHub's contributor statistics
+
+See our [Contributing Guide](CONTRIBUTING.md) for more details on how contributions are recognized.
+
+## How to Contribute
+
+We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.
+
+## Acknowledgments
+
+We thank the broader atmospheric chemistry modeling community for their feedback, testing, and contributions to making MUSICA a robust and useful tool for scientific research.
+
+---
+
+## Citation Information
+
+For citation purposes, please refer to our [CITATION.cff](CITATION.cff) file for the appropriate citations based on your use case. The main citations are:
+
+1. **For the MUSICA vision and scientific framework**: [Pfister et al., 2020](https://doi.org/10.1175/BAMS-D-19-0331.1)
+2. **For the MUSICA software evaluation**: [Schwantes et al., 2022](https://doi.org/10.1029/2021MS002889)
+3. **For the software itself**: Use the Zenodo DOI from our latest release

{musica-0.11.1.3 → musica-0.12.0}/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: 0.10.0
+version: 0.12.0

{musica-0.11.1.3 → musica-0.12.0}/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 0.11.1.3)
+project(musica-distribution VERSION 0.12.0)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${PROJECT_SOURCE_DIR}/cmake/SetDefaults.cmake)
@@ -89,6 +89,13 @@ if(MUSICA_BUILD_C_CXX_INTERFACE)
   endif()
 endif()
 
+# since sources are collected so that python libraries can target them directly,
+# we need to know if we are targeting Fortran before we collect the sources
+# otherwise cmake freaks out, and I don't know why, but this fixes it
+if(MUSICA_ENABLE_TUVX)
+    enable_language(Fortran)
+endif()
+
 # Add flags when using the ClangCL toolset
 if(CMAKE_GENERATOR_TOOLSET STREQUAL "ClangCL")
   list(APPEND musica_compile_definitions MUSICA_USING_CLANGCL)

musica-0.12.0/CONTRIBUTING.md

@@ -0,0 +1,98 @@
+# Contributing to MUSICA
+
+We welcome contributions from the community! This guide outlines how you can contribute to the MUSICA project.
+
+## Getting Started
+
+### Development Setup
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/NCAR/musica.git
+   cd musica
+   ```
+
+2. **Build the project:**
+   ```bash
+   mkdir build && cd build
+   ccmake ..
+   make
+   ```
+
+3. **Python development setup:**
+   ```bash
+   pip install -e .
+   ```
+
+For detailed developer options and dependency management, see our [Software Development Plan](docs/Software%20Development%20Plan.pdf).
+
+## Types of Contributions
+
+We appreciate all types of contributions:
+
+### Code Contributions
+- Bug fixes
+- New features
+- Performance improvements
+- Test coverage improvements
+
+### Documentation
+- README improvements
+- Code documentation
+- Tutorial and example updates
+- Wiki contributions
+
+### Testing and Validation
+- Bug reports with reproducible examples
+- Testing on different platforms
+- Validation against known results
+
+### Scientific Contributions
+- New chemical mechanisms
+- Algorithm improvements
+- Performance optimizations
+
+## Contribution Process
+
+1. **Fork the repository** and create a feature branch
+2. **Make your changes** following our coding standards
+3. **Add tests** for new functionality
+4. **Update documentation** as needed
+5. **Submit a pull request** with a clear description
+
+## Recognition Policy
+
+We believe in recognizing all contributors appropriately:
+
+### Core Development Team
+Contributors who make substantial, ongoing contributions to the codebase, architecture, or project direction will be listed as authors in:
+- `pyproject.toml` (for Python package metadata)
+- `.zenodo.json` (as "creators" for software citations)
+- `AUTHORS.md` (as core developers)
+
+### Additional Contributors  
+Contributors who make valuable but smaller contributions will be acknowledged in:
+- `.zenodo.json` (as "contributors" with appropriate type)
+- `AUTHORS.md` (in the Additional Contributors section)
+- GitHub's contributor list (automatic)
+
+## Development Guidelines
+
+### Code Standards
+- Follow existing code style and conventions
+- Include appropriate tests for new functionality
+- Document new features and APIs
+
+### Dependency Management
+We use CMake for C++ dependencies and pip for Python dependencies. See our [README](README.md#developer-options) for information about specifying dependency versions during development.
+
+### GPU Support
+If contributing GPU-related code, please test on appropriate hardware and follow our GPU build guidelines.
+
+## Questions?
+
+- Check our [documentation](https://ncar.github.io/musica/index.html)
+- Read our [Software Development Plan](docs/Software%20Development%20Plan.pdf)
+- Contact the maintainers at musica-support@ucar.edu
+
+Thank you for your interest in contributing to MUSICA!

{musica-0.11.1.3 → musica-0.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.11.1.3
+Version: 0.12.0
 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>
@@ -207,6 +207,7 @@ License:                                  Apache License
             limitations under the License.
          
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
+Requires-Dist: pyyaml>=6.0.2
 Provides-Extra: test
 Requires-Dist: numpy; extra == "test"
 Requires-Dist: pytest; extra == "test"
@@ -233,24 +234,132 @@ Multi-Scale Infrastructure for Chemistry and Aerosols
 MUSICA is a collection of modeling software, tools, and grids, that
 allow for robust modeling of chemistry in Earth's atmosphere.
 
-At present the project encompasses these components
+At present the project encompasses these core components
 - [TUV-x](https://github.com/NCAR/tuv-x)
     - A photolysis rate calculator 
 
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
-## Available grids
+- [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration)
+    - The standardized format to describe atmospheric chemistry
 
-Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
+These components are used to drive the MUSICA software ecosystem. This is a snapshot of how MUSICA can be used with different
+models.
+
+![MUSICA Ecosystem](docs/source/_static/ecosystem.png)
+
+# Installation
+MUSICA is installable via pip for Python or CMake for C++. 
+
+## Pip
+```
+pip install musica
+```
+
+## CMake
+```
+$ git clone https://github.com/NCAR/musica.git
+$ cd musica
+$ mkdir build
+$ cd build
+$ ccmake ..
+$ make
+$ make install
+```
+
+# Using the MUSICA Python API
+MUSICA makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the [official documentation](https://ncar.github.io/musica/index.html) for further tutorials and examples.
+```
+# --- Import Musica ---
+import musica
+import musica.mechanism_configuration as mc
+
+# --- 1. Define the chemical system of interest ---
+A = mc.Species(name="A")
+B = mc.Species(name="B")
+C = mc.Species(name="C")
+species = [A, B, C]
+gas = mc.Phase(name="gas", species=species)
+
+# --- 2. Define a mechanism of interest ---
+# Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.
+
+r1 = mc.Arrhenius(name="A->B", A=4.0e-3, C=50, reactants=[A], products=[B], gas_phase=gas)
+r2 = mc.Arrhenius(name="B->C", A=1.2e-4, B=2.5, C=75, D=50, E=0.5, reactants=[B], products=[C], gas_phase=gas)
+
+mechanism = mc.Mechanism(name="musica_example", species=species, phases=[gas], reactions=[r1, r2])
+
+# --- 3. Create MICM solver ---
+# A solver must be initialized with either a configuration file or a mechanism:
+
+solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)
+
+# --- 4. Define environmental conditions ---
+temperature=300.0
+pressure=101000.0
+
+# --- 5. Create and initialize State ---
+# In the model, conditions represent the starting environment for the reactions and are assigned by modifying the state.
+
+state = solver.create_state()
+state.set_concentrations({"A": 1.0, "B": 3.0, "C": 5.0})
+state.set_conditions(temperature, pressure)
+initial_pressure = state.get_conditions()['air_density'][0] # store for visualization and output
+
+# --- 6. Time parameters ---
+time_step = 4  # stepping
+sim_length = 20  # total simulation time
+
+# --- (Optional) 7. Save initial state (t=0) for output visualization ---
+initial_row = {"time.s": 0.0, "ENV.temperature.K": temperature, "ENV.pressure.Pa": pressure, "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]}
+initial_row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+
+# --- 8. Solve through time loop only ---
+# The following loop simply solves the model per each time step:
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    concentrations = state.get_concentrations()
+    curr_time += time_step
 
-# Contributors guide
-Checkout our [software development plan](docs/Software%20Development%20Plan.pdf)
-to see how you can contribute new science to MUSICA software.
+# --- 9. Solve and create DataFrame ---
+# It is likely more useful to solve at each time step and store the associated data:
+import pandas as pd
+
+output_data = [] # prepare to store output per time step
+output_data.append(initial_row) # save t=0 data
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    row = {
+        "time.s": curr_time,
+        "ENV.temperature.K": state.get_conditions()['temperature'][0],
+        "ENV.pressure.Pa": state.get_conditions()['pressure'][0],
+        "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]
+    }
+    row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+    output_data.append(row)
+    curr_time += time_step
+
+df = pd.DataFrame(output_data)
+print(df)
+
+# --- 10. Visualize Specific Results ---
+import matplotlib.pyplot as plt
+
+df.plot(x='time.s', y=['CONC.A.mol m-3', 'CONC.B.mol m-3', 'CONC.C.mol m-3'], title='Concentration over time', ylabel='Concentration (mol m-3)', xlabel='Time (s)')
+plt.show()
+```
+
+# Available grids
+Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
 
 ## Developer Options
 
-### Specifying dependency versions via paramaterization at configure time
+### Specifying dependency versions via parameterization at configure time
 
 Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it is possible for developers to specify which versions of various dependencies should be used. These options are currently limited to those dependencies managed via `FetchContent`.  This change allows for more easily testing `musica` against changes committed in different repositories and branches.  The environmental variables introduced are outlined in the following table. 
 
@@ -262,6 +371,7 @@ Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it i
 | [MICM](https://github.com/NCAR/mcim.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
 | [TUV-X](https://github.com/NCAR/tuv-x.git)             | TUVX_GIT_REPOSITORY       | TUVX_GIT_TAG       |
 | [PyBind11](https://github.com/pybind/pybind11)         | PYBIND11_GIT_REPOSITORY   | PYBIND11_GIT_TAG   |
+| [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration.git) | MECH_CONFIG_GIT_REPOSITORY | MECH_CONFIG_GIT_TAG |
 
 #### Example Usage
 
@@ -282,54 +392,80 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
 ### Python build
 Musica has python bindings. If you want to install the python package, you may `pip install musica`.
 
-To build the package locally,
+#### PyPi
+If you only want to use the CPU components, 
 
 ```
-pip install -e .
+pip install musica
 ```
 
-If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
-variable `BUILD_GPU`.
+Note that GPU support has only been tested on linux. If you have an NVIDIA GPU and would like to take 
+advantage of our GPU solver, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then install musica with our gpu option.
 
 ```
-BUILD_GPU=1 pip install -e .
+pip install --upgrade setuptools pip wheel
+pip install nvidia-pyindex
+pip install musica[gpu]
 ```
 
-## Citing MUSICA
+#### Local build
 
-MUSICA can be cited in at least two ways. The first is to cite [the paper](https://doi.org/10.1175/BAMS-D-19-0331.1) that defines the vision
-of the MUSICA software. The bibtex entry below can be used to generate a citaiton for this.
+Musica has python bindings. To build the package locally,
 
 ```
-@Article { acom.software.musica-vision,
-    author = "Gabriele G. Pfister and Sebastian D. Eastham and Avelino F. Arellano and Bernard Aumont and Kelley C. Barsanti and Mary C. Barth and Andrew Conley and Nicholas A. Davis and Louisa K. Emmons and Jerome D. Fast and Arlene M. Fiore and Benjamin Gaubert and Steve Goldhaber and Claire Granier and Georg A. Grell and Marc Guevara and Daven K. Henze and Alma Hodzic and Xiaohong Liu and Daniel R. Marsh and John J. Orlando and John M. C. Plane and Lorenzo M. Polvani and Karen H. Rosenlof and Allison L. Steiner and Daniel J. Jacob and Guy P. Brasseur",
-    title = "The Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA)",
-    journal = "Bulletin of the American Meteorological Society",
-    year = "2020",
-    publisher = "American Meteorological Society",
-    address = "Boston MA, USA",
-    volume = "101",
-    number = "10",
-    doi = "10.1175/BAMS-D-19-0331.1",
-    pages= "E1743 - E1760",
-    url = "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml"
-}
+pip install -e .
 ```
 
-At present MUSICA is on version zero. MUSICAv0 can be cited using the bibtex entry below.
-MUSICAv0 description and evaluation:
+If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
+variable `BUILD_GPU`.
 
 ```
-@Article{acom.software.musica,
-    author = {Schwantes, Rebecca H. and Lacey, Forrest G. and Tilmes, Simone and Emmons, Louisa K. and Lauritzen, Peter H. and Walters, Stacy and Callaghan, Patrick and Zarzycki, Colin M. and Barth, Mary C. and Jo, Duseong S. and Bacmeister, Julio T. and Neale, Richard B. and Vitt, Francis and Kluzek, Erik and Roozitalab, Behrooz and Hall, Samuel R. and Ullmann, Kirk and Warneke, Carsten and Peischl, Jeff and Pollack, Ilana B. and Flocke, Frank and Wolfe, Glenn M. and Hanisco, Thomas F. and Keutsch, Frank N. and Kaiser, Jennifer and Bui, Thao Paul V. and Jimenez, Jose L. and Campuzano-Jost, Pedro and Apel, Eric C. and Hornbrook, Rebecca S. and Hills, Alan J. and Yuan, Bin and Wisthaler, Armin},
-    title = {Evaluating the Impact of Chemical Complexity and Horizontal Resolution on Tropospheric Ozone Over the Conterminous US With a Global Variable Resolution Chemistry Model},
-    journal = {Journal of Advances in Modeling Earth Systems},
-    volume = {14},
-    number = {6},
-    pages = {e2021MS002889},
-    doi = {https://doi.org/10.1029/2021MS002889},
-    url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002889},
-    eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021MS002889},
-    year = {2022}
-}
+BUILD_GPU=1 pip install -e .
 ```
+
+# Contributing
+
+We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.
+
+For a complete list of contributors and authors, see [AUTHORS.md](AUTHORS.md).
+
+# Citations
+
+MUSICA can be cited in at least two ways:
+
+1. **Cite the foundational paper** that defines the vision of the MUSICA software:
+    - [Pfister et al., 2020, Bulletin of the American Meteorological Society](https://doi.org/10.1175/BAMS-D-19-0331.1)
+    - Use the following BibTeX entry:
+      ```
+      @Article { acom.software.musica-vision,
+          author = "Gabriele G. Pfister and Sebastian D. Eastham and Avelino F. Arellano and Bernard Aumont and Kelley C. Barsanti and Mary C. Barth and Andrew Conley and Nicholas A. Davis and Louisa K. Emmons and Jerome D. Fast and Arlene M. Fiore and Benjamin Gaubert and Steve Goldhaber and Claire Granier and Georg A. Grell and Marc Guevara and Daven K. Henze and Alma Hodzic and Xiaohong Liu and Daniel R. Marsh and John J. Orlando and John M. C. Plane and Lorenzo M. Polvani and Karen H. Rosenlof and Allison L. Steiner and Daniel J. Jacob and Guy P. Brasseur",
+          title = "The Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA)",
+          journal = "Bulletin of the American Meteorological Society",
+          year = "2020",
+          publisher = "American Meteorological Society",
+          address = "Boston MA, USA",
+          volume = "101",
+          number = "10",
+          doi = "10.1175/BAMS-D-19-0331.1",
+          pages= "E1743 - E1760",
+          url = "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml"
+      }
+      ```
+
+2. **Cite the MUSICA software and its evaluation** (MUSICAv0):
+    - [Schwantes et al., 2022, Journal of Advances in Modeling Earth Systems](https://doi.org/10.1029/2021MS002889)
+    - Use the following BibTeX entry:
+      ```
+      @Article{acom.software.musica,
+          author = {Schwantes, Rebecca H. and Lacey, Forrest G. and Tilmes, Simone and Emmons, Louisa K. and Lauritzen, Peter H. and Walters, Stacy and Callaghan, Patrick and Zarzycki, Colin M. and Barth, Mary C. and Jo, Duseong S. and Bacmeister, Julio T. and Neale, Richard B. and Vitt, Francis and Kluzek, Erik and Roozitalab, Behrooz and Hall, Samuel R. and Ullmann, Kirk and Warneke, Carsten and Peischl, Jeff and Pollack, Ilana B. and Flocke, Frank and Wolfe, Glenn M. and Hanisco, Thomas F. and Keutsch, Frank N. and Kaiser, Jennifer and Bui, Thao Paul V. and Jimenez, Jose L. and Campuzano-Jost, Pedro and Apel, Eric C. and Hornbrook, Rebecca S. and Hills, Alan J. and Yuan, Bin and Wisthaler, Armin},
+          title = {Evaluating the Impact of Chemical Complexity and Horizontal Resolution on Tropospheric Ozone Over the Conterminous US With a Global Variable Resolution Chemistry Model},
+          journal = {Journal of Advances in Modeling Earth Systems},
+          volume = {14},
+          number = {6},
+          pages = {e2021MS002889},
+          doi = {https://doi.org/10.1029/2021MS002889},
+          url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002889},
+          eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021MS002889},
+          year = {2022}
+      }
+      ```