Scientific Computing at Simula Research Laboratory

This page contains information about Scientific Computing at Simula Research Laboratory.

For information related to the projects at Department of Computational Physiology go here.

Software¶

A list scientific software (and corresponding publication) developed by personnel in the Scientific Computing Department.

FEniCS¶

• MuscleX Muscle-growth Devold et al. (2025)
• 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)
• Non-conforming 3D-1D modelling in FEniCSx FEniCSx_ii
• Network models for FEniCSx: networks_fenicsx
• 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 Kjeldsberg et al. (2019)
• 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 Kjeldsberg et al. (2023)

FSI¶

• A collection of tools for pre-processing, simulating, and post-processing vascular fluid-structure-interaction problems VaSP Yamamoto et al. (2025)
• 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 FEnICS
• beat - Cardiac electrophysiology solver in FEniCSx and FEnICS
• ldrb - Library for creating rule-based fiber orientations in FEniCSx and FEniCS

Other¶

• General ODE translator gotranx Finsberg & Hake (2024)
• A tool for visualizing dependencies between different components of your ODE model modelgraph

Missing a package?¶

If you package is missing from the list, go to Add new package

Reproducibility¶

We think reproducibility is important and we have created some guidelines for reproducible research.

On this web-page we discuss what is needed when you want to publish a paper that contains some code, and we are created two example papers that follows these guidelines

• Simple example paper
• Example paper using FEniCS
• Example Python Package

We provide repositories that can generate a repository structure automatically by using Cookiecutter

• Generate Paper
• Generate Python Package