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Jan Habscheid
fxdgm_testing
Commits
7400a756
Verified
Commit
7400a756
authored
6 months ago
by
Lambert Theisen
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Add Docker setup and document it in Readme (for macOS)
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Dockerfile
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Dockerfile
README.md
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README.md
docker-compose.yml
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docker-compose.yml
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40 additions
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3 deletions
Dockerfile
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7400a756
# Start with a base image that includes conda
FROM
continuumio/miniconda3
# Set environment variables
ENV
CONDA_DEFAULT_ENV=fenicsx-env
ENV
PATH /opt/conda/envs/${CONDA_DEFAULT_ENV}/bin:$PATH
ENV
HOME /root
# Create the environment and install packages
RUN
conda create
--name
${
CONDA_DEFAULT_ENV
}
python
=
3.12.3
-y
&&
\
conda
install
-n
${
CONDA_DEFAULT_ENV
}
-c
conda-forge fenics-dolfinx
=
0.8.0
mpich
=
4.2.1
pyvista
=
0.43.10
matplotlib
=
3.8.4
numpy
=
1.26.4
scipy
=
1.14.0
gcc
=
12.4.0
sphinx
=
7.3.7 myst-parser
=
4.0.0 sphinx-copybutton
=
0.5.2 sphinx-rtd-theme
=
3.0.1
-y
# Activate environment
SHELL
["conda", "run", "-n", "fenicsx-env", "/bin/bash", "-c"]
WORKDIR
/root
# Set the default environment on container start
# ENTRYPOINT ["conda", "run", "-n", "fenicsx-env", "/bin/bash", "-c"]
CMD
["bash"]
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README.md
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# Reproducibility Repository for Numerical Treatment of a Thermodynamically Consistent Electrolyte Model (B.Sc. Thesis - Jan Habscheid)
[

](https://git.rwth-aachen.de/Jan.Habscheid/bsc-electrolytemodels/pipelines)
[

](https://git.rwth-aachen.de/Jan.Habscheid/bsc-electrolytemodels/pipelines)
[

](https://janhab.pages.rwth-aachen.de/bsc-electrolytemodels/)
[

](https://doi.org/10.5281/zenodo.13645296)
[

](https://git.rwth-aachen.de/jan.habscheid/bsc-electrolytemodels/-/tags)
...
...
@@ -40,9 +40,16 @@ Use the "environment.yml" file to install all necessary environments
conda env create -f environment.yml
```
### macOS installation using Docker
```
docker compose build
docker compose run solver
```
## Usage
Find the visualizations from the thesis and some extra calculations in the "examples" folder.
Find the visualizations from the thesis and some extra calculations in the "examples" folder.
In the subfolder "ReproducableCode" is the code, to execute the calculations with some first visualizations.
The subfolder "Data" stores the data for all the simulations in a
*
.npz file, which can be read with numpy
`np.load(file.npz)`
.
"Visualizations" creates the necessary figures from the thesis and stores them in
*
.svg format in "Figures".
...
...
@@ -66,4 +73,4 @@ In "src" there are the generic FEniCSx implementations, that were used to calcul
-
Prof. Dr. Manuel Torrilhon
-
ACoM - Applied and Computational Mathematics
-
RWTH Aachen University
-
mt@acom.rwth-aachen.de
\ No newline at end of file
-
mt@acom.rwth-aachen.de
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docker-compose.yml
0 → 100644
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7400a756
services
:
solver
:
build
:
context
:
.
dockerfile
:
Dockerfile
volumes
:
-
.:/root/solver
stdin_open
:
true
# Equivalent to -i for interactive mode
tty
:
true
# Equivalent to -t for a terminal interface
command
:
[
"
/bin/bash"
]
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