pymm: An open-source image-based framework for CFD in microsystems

Main feature

Creation of OpenFOAM simulation models from given input images using Gmsh.

Installation

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 the pymm 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 repo
git clone https://github.com/cssr-tools/pymm.git
# Get inside the folder
cd 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 environment
source vpymm/bin/activate
# Upgrade pip, setuptools, and wheel
pip install --upgrade pip setuptools wheel
# Install the pymm package
pip install -e .
# For contributions/testing/linting, install the dev-requirements
pip install -r dev-requirements.txt

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

Running pymm

You can run pymm as a single command line:

pymm -i name_of_input_image.png -p input_parameters.txt -o output_folder

Run pymm --help to see all possible command line argument options. Inside the input_parameters.txt file you provide the framework parameters such as the dimensions of the microsystem, mesh size, inlet pressure, and more.

Getting started

See the examples in the documentation.

Citing

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

Journal papers using pymm

The following is a list of journal papers in which pymm 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.

About pymm

pymm, an image-based Python package for computational fluid dynamics, is funded by Center for Sustainable Subsurface Resources [project no. 331841] and NORCE 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.