https://github.com/finsberg/ambit-beat-proof-of-concept

Simple example of how to couple ambit together with FEniCS-beat
https://github.com/finsberg/ambit-beat-proof-of-concept

Last synced: 3 days ago
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Simple example of how to couple ambit together with FEniCS-beat

• Host: GitHub
• URL: https://github.com/finsberg/ambit-beat-proof-of-concept
• Owner: finsberg
• License: mit
• Created: 2024-02-15T07:38:08.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-02-15T08:16:09.000Z (9 months ago)
• Last Synced: 2024-02-15T09:27:59.949Z (9 months ago)
• Language: Python
• Size: 338 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Coupling fenics-beat with ambit

This repository contains a proof of concept for coupling [`fenics-beat`](https://github.com/finsberg/fenics-beat) together with [`ambit`](https://github.com/marchirschvogel/ambit).

Note that `fenics-beat` uses legacy FEniCS while `ambit` uses dolfinx so the two simulators needs to be run independently.

The initial idea would be to first run a monodomain simulation using `fenics-beat` and then saving the resulting active tension in a format that can be read by `ambit`.

The we will use that active tension to drive the mechanics simulator in `ambit`.

For the time being we use the demo and mesh provided by `ambit` in the demo [solid_flow0d](https://github.com/marchirschvogel/ambit/tree/master/demos/solid_flow0d).

## Running the Mondodomain simulator

### Set up environment

We will use a docker image for legacy FEniCS

```

docker run --name beat -w /home/shared -v $PWD:/home/shared -it ghcr.io/scientificcomputing/fenics-gmsh:2023-11-15

```

Next we install the development version of `fenics-beat` and `gotranx`

```

python3 -m pip install git+https://github.com/finsberg/fenics-beat

python3 -m pip install git+https://github.com/finsberg/gotranx

```

Note that eventually we will converge on a specific version (or the latest stable version), but for the time being we will use the development version.

### Run

```

python3 main_beat.py

```

### Converting active tension to a format that can be read by `ambit`

```

python3 convert_Ta.py

```

## Running Mechanics Simulator

### Set up environment

Ambit currently works with `dolfinx` version 0.6, so we will use a docker image with this version

e.g

```

docker run --name ambit -w /home/shared -v $PWD:/home/shared -it ghcr.io/fenics/dolfinx/dolfinx:v0.6.0

```

Next we install the development version of `ambit`

```

python3 -m pip install git+git+https://github.com/marchirschvogel/ambit

```

### Run

```

python3 main_ambit.py

```