readme.md

Overview

OpenDiHu is a software framework to solve 1D, 2D, and 3D multi-physics problems in parallel with the Finite Element Method. It is used in the domain of skeletal muscle simulations: Electrophysiology, contraction, neuro-chemo-electro-mechanics. Design goals are usability, performance and extensibility.

The software is developed at SGS and IANS at the University of Stuttgart.

OpenDiHu has moved!

Important

OpenDiHu has moved to its own GitHub Organization where it continues to be actively maintained and developed as OpenDiHu version 2.x.

• Go to the new opendihu repo
• Read the new documentation page

You are on the repo of the previous codebase as of 01/2024, containing the stable OpenDiHu version 1.4 and the Documentation for version 1.4.

Installation

Refer to the documentation for detailed installation instructions.

However, if you usually skip instructions, do the following:

git clone https://github.com/maierbn/opendihu.git && cd opendihu && make

If there are error messages, have a look at the log file config.log.

Literature

At 01/2024, the following literature written by the authors is available.

• (Open-access) Benjamin's PhD thesis. This is the most comprehensive literature about OpenDiHu and contains details of the implemented models as well as some documentation about the software architecture.

  Maier, B. (2021). Scalable Biophysical Simulations of the Neuromuscular System.

• (Open-access) Journal paper about mesh generation and simulations:

  Maier, B, Schulte, M. (2022) Mesh generation and multi-scale simulation of a contracting muscle–tendon complex, Journal of Computational Science

• Article about computational performance, in proceedings of the HLRS:

  Krämer, A.; Maier, B.; Rau, T.; Huber, F.; Klotz, T.; Ertl, T.; Göddeke, D.; Mehl, M.; Reina, G.; Röhrle, O. (2020): Multi-physics multi-scale HPC simulations of skeletal muscles, High Performance Computing in Science and Engineering ’20, Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2020, ed. by Nagel, W.; Kröner, D.; Resch, M., Springer International Publishing, 2021

• First conference paper:

  Maier, B., Emamy, N., Krämer, A., & Mehl, M. (2019). Highly parallel multi-physics simulation of muscular activation and EMG. In COUPLED VIII: proceedings of the VIII International Conference on Computational Methods for Coupled Problems in Science and Engineering (pp. 610-621). CIMNE