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Creation ofOpenFOAM simulation models from given input images usingGmsh.

You will first need to install

• OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-12)
• Gmsh (https://gmsh.info) (tested with Gmsh 4.13.1)

To install thepymm executable from the development version:

pip install git+https://github.com/cssr-tools/pymm.git

If you are interested in a specific version (e.g., v2024.10) or in modifying the source code, then you can clone the repository and install the Python requirements in a virtual environment with the following commands:

# Clone the repogit clone https://github.com/cssr-tools/pymm.git# Get inside the foldercd pymm# For a specific version (e.g., v2024.10), or skip this step (i.e., edge version)git checkout v2024.10# Create virtual environment (to specific Python, python3.12 -m venv vpycopm)python3 -m venv vpymm# Activate virtual environmentsource vpymm/bin/activate# Upgrade pip, setuptools, and wheelpip install --upgrade pip setuptools wheel# Install the pymm packagepip install -e.# For contributions/testing/linting, install the dev-requirementspip install -r dev-requirements.txt

See theOpenFOAM page, where from OpenFOAM-12 the simulator is available via apt get.

You can runpymm as a single command line:

pymm -i input_image.png -p input_parameters.toml -o output_folder

Runpymm --help to see all possible command line argument options. Inside theinput_parameters.toml file you provide the framework parameters such as the dimensions of the microsystem, mesh size, inlet pressure, and more. See the .toml files in theexamples andtests folders.

See theexamples in thedocumentation.

• Landa-Marbán, D. 2023. An open-source image-based framework for CFD in microsystems.https://doi.org/10.5281/zenodo.8430988.

The following is a list of journal papers in whichpymm is used:

1. Liu, N., Haugen, M., Benali, B., Landa-Marbán, D., Fernø, M.A., 2023. Pore-scale spatiotemporal dynamics of microbial-induced calcium carbonate growth and distribution in porous media. Int. J. Greenh. Gas Control 125, 103885.https://doi.org/10.1016/j.ijggc.2023.103885
2. Liu, N., Haugen, M., Benali, B., Landa-Marbán, D., Fernø, M.A., 2023. Pore-scale kinetics of calcium dissolution and secondary precipitation during geological carbon storage. Chem. Geol. 641, 121782.https://doi.org/10.1016/j.chemgeo.2023.121782.

pymm, an image-based Python package for computational fluid dynamics, is funded byCenter for Sustainable Subsurface Resources [project no. 331841] andNORCE Norwegian Research Centre As [project number 101070].Contributions are more than welcome using the fork and pull request approach.For a new feature, please request this by raising an issue.