This module solves the Reaction-Diffusion PDEs for one or more species in one or two-dimensional domain. The Crank-Nicolson finite difference schema is implemented, and Periodic, Dirichlet, and Neumann boundary conditions are supported.
After downloading the project zip file and extracting its folder or cloning the project by git, go to its directory and install it by executing the following command line
pip install .
(Ensure you don't forget the dot at the end of the command). After that, you can import the module into your Python environment, like
from solvers.rd import *
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Check the HowTo.ipynb notebook to see an example of a Brusselator model solution.
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The Circuit_3954.ipynb explains the PDE of the three-node gene circuit, its topology, and how to load the sample parameters. Similar to the Brusselator in the HowTo.ipynb example, it provides the kinetic function for integration, but you need to write the rest yourself. Note that you need the "Pandas" to be able to load the sampled parameters.
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The source code is in the solvers folder if you need to delve into more details of how the solver works.