I want to replace some 3D coulomb integrals with poisson's eq solution. The grid I am using has a structure but I bet it is not easy to find a Poisson solver for that grid. So I was wondering if there is a Poisson solver available preferably open source that can handle any arbitrary grid (with limitations of course) and can find for example the electrostatic potential at grid points given the charge density at those points. Grid can be big enough to have V=0 on the boundary.
In case you are still in Juelich , you should talk to Paul Baumeister
Try using FEniCS:
http://fenicsproject.org/documentation/dolfin/dev/python/demo/pde/poisson/python/documentation.html
The charges etc could be represented on the RHS of the eqn.
You can have a look at these two references; they are used in implementation of the method for biomolecular systems.
M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
You can have a look a reference: http://people.sc.fsu.edu/~jburkardt/f77_src/fishpack/fishpack.html
A Poisson Equation Solver
FISHPACK is a FORTRAN77 library which solves several forms of Poisson's equation, by John Adams, Paul Swarztraube, Roland Sweet.
I can add LIBMESH ( http://libmesh.sourceforge.net/) to the list of the already suggested packages. We use it routinely to solve Poisson equation in electronic devices with arbitrary shape.
Hello,
I think the following paper can propose you a good starting point:
http://www-user.tu-chemnitz.de/~potts/paper/poissonnfft.pdf
It depends also on what you want: do you want a method or just an algorithm that you can use "blindly"?
Cheers,
Michele
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