Visualization¶

GPos output data can be analysed using the Python (version 3 or higher) example scripts present in the example repo folder:

gpos_funcs.py: Script that includes the functions to read, analyse and plot GPos data files of selected species and positions.
gpos_test.py (python gpos_test.py <path to folder containing openPMD files> <array of species>): Script that uses the necessary functions of gpos_funcs.py to compare selected GPos output particle data and species properties.
gpos_plot.py (python gpos_test.py <path to folder containing openPMD files> <array of species>): Script that generates plots of the overlap of the 2D distributions of selected species at selected positions and stores them under a new “Plots” folder.

The packages required to run those scripts are:

numpy
openPMD-api (installed with python)
matplotlib
scipy

To install them with pip (for Python 3.9) you can use the command:

$ pip install -r <package_name>
$ python ...

To install using the spack package manager the use of an environment is highly recommended:

$ git clone https://github.com/spack/spack.git
$ source spack/share/spack/setup-env.sh
$ spack env create vis
$ spack env activate vis
$ spack add python@3.8.10 py-scipy@1.6.3  py-matplotlib@3.4.2  py-numpy@1.20.3
$ spack add openpmd-api@0.13.4 +python
$ spack concretize
$ spack install
$ spack activate py-scipy@1.6.3  py-matplotlib@3.4.2  py-numpy@1.20.3
$ spack load openpmd-api
$ python ...
$ spack env deactivate

Note

Syntax of all Python scripts is tested at each Pull Request and Push in the linux workflow of the GitHub repo and gpos_test.py is executed to confirm accuracy of results.