trevortrevor/gmpnp

Finite element implementation of 1D and 3D generalized modified PNP system of equations using FEniCS project in Python.

1D and 3D GMPNP

This repository contains the implementation of generalised modified Poisson-Nernst-Planck (GMPNP) for a CO2 electrocatalysis system using the FEniCS finite element package in Python. The implementation is available for

1. a 1D system with CO2 dissolved in electrolyte (H-cell type) and
2. a 3D cylindrical catalytic pore for a GDE-based system.

The parameter and mesh files for both the 1D and 3D cases can be found in the utilities folder. The script for the Stern layer solves the Poisson equation in the Stern region using the results obtained from the GMPNP model. Additionally, scripts to solve the reaction diffusion system for both 1D and 3D cases are available for comparison.

The 1D scripts were used to derive the results published in https://pubs.rsc.org/en/content/articlelanding/2019/ee/c9ee02485a#!divAbstract.

The environment.yml file can be used with conda to create the python environment needed to run the script using the command:

conda env create -f environment.yml

The environment name is the first line in the yaml file and is currently set as FEniCS.

Once the environment is created, activate it using:

conda activate FEniCS

To see the packages installed in the new environment, use:

conda env list

See https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html# for further help regarding managing enviroments using conda.

In order to run the scripts (both 1D and 3D), please check the basepath and basepath_utilities variables according to the location of the python file and the utilities folder on your local machine.

Activate the FEniCS virtual environment and run the MPNP script from the "1D" directory (as an example) using:

python MPNP_CO2ER_EDL.py

As you will see in the scripts, you can vary all relevant parameters using command line arguements like in the example below. This makes it simpler to submit multiple jobs on a computational cluster.

python MPNP_CO2ER_EDL.py --voltage_multiplier=-10.0 --cation='Cs'

The 3D pore scripts can be run following a similar procedure.

And you are good to go!

If you find this code useful, please cite it using the DOI: 10.5281/zenodo.4106373 or use the following BibTeX entry:

@software{divya_bohra_2020, author = {Divya Bohra}, title = {{divyabohra/GMPNP: First release of 1D and 3D GMPNP for CO2 electrocatalysis}}, month = oct, year = 2020, publisher = {Zenodo}, version = {v1.0.0}, doi = {10.5281/zenodo.4106373}, url = {https://doi.org/10.5281/zenodo.4106373} }