Work on an open-source tool for EM stimulation chambers and other tools. The entire package is developed and tested on Ubuntu 18.04.
To install the external packages, just run:
sudo install.sh
This should give you all dependencies and correct setting of the environment.
Simply run:
python3 setup.py install
or if you want to have a local installation:
python3 setup.py install --user
The files 'meshconvert.py' and 'xml_writer.py' from the site-package 'dolfin_utils' of dolfin. They can be found in 'emstimtools/utils' and the first file was modified slightly (change indicated in file header). It is licensed under the GNU Lesser General Public License (LGPL) version 3, which can be found in the file LICENSE-3RD-PARTY.txt.
The package works with:
- Python 3
- Salome 8.3.0 (to be downloaded here)
- GMSH SDK 4.0.2 (to be download from gmsh site)
- FEniCS 2018.1.0 (from official Ubuntu PPA, see details on FEniCS site)
Optional:
- ParaView > V5.5 (https://www.paraview.org/) for postprocessing (XDMF support needed).
Note
For SALOME and GMSH certain manual installations are needed. Those are specified in the documentation.
The package takes a user-prepared geometry and input file, where all details about the (multi-)physics model are described. Then a fully-automated workflow yields the desired output data and files, which can be readily visualized in e.g. ParaView.
This code is documented by the help of Sphinx. For a good user experience, install sphinx on your machine and run
make latexpdf
in the doc directory. It will give you a good overview of the capabilities of this tool. Also, certain bugs ('features') are explained in case an error occurs during execution.
In the examples directory, a few published as well as unpublished examples are given. Please feel free to add some on your own!