A list scientific software (and corresponding publication) developed by personnel in the Scientific Computing Department.
FEniCS¶
- Scientific finite element toolbox scifem
- ADIOS4DOLFINx: A framework for checkpointing in FEniCS ADIOS4DOLFINx Dokken (2024)
- Multi-point constraints with DOLFINx: DOLFINx_MPC
Simulation¶
- SMART: Spatial Modeling Algorithms for Reactions and Transport smart Laughlin et al. (2023)
- Network models for FEniCS: Graphnics
- Software Components for Multiphysics Problems: HAZniCS Budisa et al. (2022)
Meshing¶
- Surface Volume Meshing ToolKit: SVMTK Mardal et al. (2022)
- Tool for creating idealised cardiac geometries and microstructure in FEniCS: cardiac-geometries
- Tool for creating idealised cardiac geometries and microstructure in FEniCSx: cardiac-geometriesx
- A collection of tools for manipulation of morphological features in patient-specific geometries morphMan
- Generate meshes from UK Biobank atlas ukb-atlas
Fluid Dynamics¶
- Next generation Open Source Navier Stokes solver using FEniCSx oasisx
- A verified and validated Python/FEniCS-based CFD solver for moving domains OasisMove
- A collection of tools for pre-processing, simulating, and post-processing vascular morphologies VaMPy
FSI¶
- A collection of tools for pre-processing, simulating, and post-processing vascular fluid-structure-interaction problems VaSP
- Monolithic Fluid-Structure Interaction (FSI) solver turtleFSI
Brain¶
- Intracranial Pulsation: brainpulse Causemann et al. (2022)
Heart¶
- Simula Cardiac ElectroMechanics Solver simcardems Finsberg et al. (2023)
- Tools for working with microphysiological data mps
- Library for tracking motion in cardiac mps data mps-motion
- Library for extracting action potential features ap-features
- Cardiac Circulation Models: circulation
pulse- Cardiac mechanics solver in FEniCSx and FEnICSbeat- Cardiac electrophysiology solver in FEniCSx and FEnICSldrb- Library for creating rule-based fiber orientations in FEniCSx and FEniCS
Other¶
- General ODE translator gotranx Finsberg & Hake (2024)
Missing a package?¶
If you package is missing from the list, go to Add new package
- Dokken, J. S. (2024). ADIOS4DOLFINx: A framework for checkpointing in FEniCS. Journal of Open Source Software, 9(96), 6451. 10.21105/joss.06451
- Laughlin, J. G., Dokken, J. S., Finsberg, H. N. t., Francis, E. A., Lee, C. T., Rognes, M. E., & Rangamani, P. (2023). SMART: Spatial Modeling Algorithms for Reactions and Transport. Journal of Open Source Software, 8(90), 5580. 10.21105/joss.05580
- Budisa, A., Hu, X., Kuchta, M., Mardal, K.-A., & Zikatanov, L. (2022). HAZniCS – Software Components for Multiphysics Problems. arXiv. 10.48550/ARXIV.2210.13274
- Mardal, K.-A., Rognes, M. E., Thompson, T. B., & Valnes, L. M. (2022). Getting started: from T1 images to simulation. In Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation (pp. 23–46). Springer International Publishing. 10.1007/978-3-030-95136-8_3
- Causemann, M., Vinje, V., & Rognes, M. E. (2022). Human intracranial pulsatility during the cardiac cycle: a computational modelling framework. bioRxiv. 10.1101/2022.05.19.492650