dolfin_mech
A set of FEniCS-based python tools for Computational Mechanics.
The library has notably been used in:
- [Genet (2019). A relaxed growth modeling framework for controlling growth-induced residual stresses. Clinical Biomechanics.]
- [Álvarez-Barrientos, Hurtado & Genet (2021). Pressure-driven micro-poro-mechanics: A variational framework for modeling the response of porous materials. International Journal of Engineering Science.]
- [Patte, Genet & Chapelle (2022). A quasi-static poromechanical model of the lungs. Biomechanics and Modeling in Mechanobiology.]
- [Patte, Brillet, Fetita, Gille, Bernaudin, Nunes, Chapelle & Genet (2022). Estimation of regional pulmonary compliance in idiopathic pulmonary fibrosis based on personalized lung poromechanical modeling. Journal of Biomechanical Engineering.]
- [Tueni, Allain & Genet (2023). On the structural origin of the anisotropy in the myocardium: Multiscale modeling and analysis. Journal of the Mechanical Behavior of Biomedical Materials.]
- [Laville, Fetita, Gille, Brillet, Nunes, Bernaudin & Genet (2023). Comparison of optimization parametrizations for regional lung compliance estimation using personalized pulmonary poromechanical modeling. Biomechanics and Modeling in Mechanobiology.]
- [Peyraut & Genet (2024). A model of mechanical loading of the lungs including gravity and a balancing heterogeneous pleural pressure. Biomechanics and Modeling in Mechanobiology.]
- [Peyraut & Genet (2025). Finite strain formulation of the discrete equilibrium gap principle: application to direct parameter estimation from large full-fields measurements. Comptes Rendus Mécanique.]
- [Manoochehrtayebi, Bel-Brunon & Genet (2025). Finite strain micro-poro-mechanics: Formulation and compared analysis with macro-poro-mechanics. International Journal of Solids and Structures.]
- [Peyraut & Genet (2025). Inverse Uncertainty Quantification for Personalized Biomechanical Modeling: Application to Pulmonary Poromechanical Digital Twins. Journal of Biomechanical Engineering.]
- [Manoochehrtayebi, Genet & Bel-Brunon (2025). Micro-poro-mechanical modeling of lung parenchyma: Theoretical modeling and parameters identification. Journal of Biomechanical Engineering.]
Installation
A working installation of FEniCS (version 2019.1.0) is required to run dolfin_mech.
To setup a system, the simplest is to use conda: first install miniconda (note that for Microsoft Windows machines you first need to install WSL, the Windows Subsystem for Linux, and then install miniconda for linux inside the WSL), and then install the necessary packages:
conda create -y -c conda-forge -n dolfin_mech fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23 pandas=1.3 pip python=3.10 vtk=9.2
conda activate dolfin_mech
Now, if you only need to use the library, you can install it with:
pip install dolfin_mech
But if you need to develop within the library, you need to install an editable version of the sources:
git clone https://github.com/mgenet/dolfin_mech.git
pip install -e dolfin_mech/.
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