We need to update the manual pages for the old RD solver

[fyffep]

https://compucell3dreferencemanual.readthedocs.io/en/latest/reaction_diffusion_solver.html

Indicate all the options (like periodic boundary conditions, initial values, space-varying diffusion constant). We should add examples (Schanckenberg et. al).

Is it possible to define a global or local decay constant? Is it possible to have the field rules differ by cell type?

Otherwise probably the best way to exclude the field from a region is to

1. Define a frozen cell type where you want to exclude the field.
2. Define a diffusion constant of 0 in this cell type.
3. If you can't define decay in this region add an update term (does uptake work with frozen cells)?

If the reaction term does odd things when the field values are 0 then we have to introduce a non-diffusing auxiliary field with value 1 in the region of diffusion, 0 outside and multiply the reaction terms by this field. In this case you could draw an arbitrary shape from a file or in Python start function and see how the shape determined the final patterns. I'd also advocate having the random spot initial condition AND a Gaussian random noise initial condition as options. For all of that we'd need to do more in Python.

Does mu parser recognize and resolve symbols? I.e., could we define parameters in the XML <parameter = "7"/> and have terms like parameter*u in the auxiliary terms definition?

JAG