PyPNP is a solver for simulating charge-transport systems with an arbitrary number of charge-carrying species. These systems are modeled by the Poisson-Nernst-Planck (PNP) equations with the possibility of coupling to the Navier-Stokes (NS) equation to simulate electrokinetic phenomena.
The solver uses continuous piecewise linear finite elements for the PNP system, and div-conforming (discontinuous) finite elements for the NS system. The nonlinearities of the system are handled by implementing a monolithic Newton approach of the entire PNP (and NS) system. The linearized systems are stabilized by an edge-averaged finite element (EAFE) approximation.
This package is based on the FEniCS package for discretizing the differential equations. This permits the use of any compatible linear algebra solver for solving the resulting linear system of equations.
To ensure that the git hooks are properly being used (and creating a docker image for MacOS), run:
./scripts/init
When contributing, ensure code styling is consistent by running ./scripts/lint.
This script is automatically run whenever a commit is made.
Use git commit ... --no-verify to bypass linting, although this practice is strongly discouraged.
The FEniCS distribution uses Docker for simplicity. Install Docker by following these instructions. To run the project in a docker container, run
./scripts/start
The Docker container will open in a shared directory to the repository's root so that any updates to files in the repository are available from within the Docker container.
To exit the Docker container, simply run the exit command.
If FEniCS is not already installed or there are compatibility issues, follow the steps for MacOS to run FEniCS in a Docker container.