https://github.com/cssr-tools/pymm
Open-source image-based framework for computational fluid dynamics on microsystems
https://github.com/cssr-tools/pymm
cfd gmsh microsystems navier-stokes openfoam python
Last synced: about 1 month ago
JSON representation
Open-source image-based framework for computational fluid dynamics on microsystems
- Host: GitHub
- URL: https://github.com/cssr-tools/pymm
- Owner: cssr-tools
- License: gpl-3.0
- Created: 2024-02-16T17:42:42.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-11-03T16:50:24.000Z (5 months ago)
- Last Synced: 2025-11-03T18:32:40.744Z (5 months ago)
- Topics: cfd, gmsh, microsystems, navier-stokes, openfoam, python
- Language: Python
- Homepage: https://cssr-tools.github.io/pymm/
- Size: 88 MB
- Stars: 5
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Security: SECURITY.md
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README
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[](https://doi.org/10.5281/zenodo.8430989)
# pymm: An open-source image-based framework for CFD in microsystems
## Main feature
Creation of [_OpenFOAM_](https://www.openfoam.com) simulation models from given input images using [_Gmsh_](https://gmsh.info).
## Installation
You will first need to install
* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-13)
* Gmsh (https://gmsh.info) (tested with Gmsh 4.15.0)
To install the _pymm_ executable from the development version:
```bash
pip install git+https://github.com/cssr-tools/pymm.git
```
If you are interested in a specific version (e.g., v2025.10) 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:
```bash
# Clone the repo
git clone https://github.com/cssr-tools/pymm.git
# Get inside the folder
cd pymm
# For a specific version (e.g., v2025.10), or skip this step (i.e., edge version)
git checkout v2025.10
# 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_](https://openfoam.org/download/13-ubuntu/), where from OpenFOAM-12 the simulator is available via apt get, and OpenFOAM-13 is the latest release.
## Running pymm
You can run _pymm_ as a single command line:
```
pymm -i input_image.png -p input_parameters.toml -o output_folder
```
Run `pymm --help` to see all possible command line argument options. Inside the `input_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 the [_examples_](https://github.com/cssr-tools/pymm/tree/main/examples) and [_tests_](https://github.com/cssr-tools/pymm/tree/main/tests/configs) folders.
## Getting started
See the [_examples_](https://cssr-tools.github.io/pymm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pymm/introduction.html).
## Citing
* Landa-Marbán, D. 2023. pymm: 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
1. 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_](https://cssr.no) [project no. 331841] and [_NORCE Research As_](https://www.norceresearch.no) [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.