fe-manual — APBS-PDB2PQR 1.6 documentation

# fe-manual

Manually-configured adaptive finite element Poisson-Boltzmann calculations.

This is a single-point PBE calculation performed by our adaptive finite element PBE solver. It requires that APBS be linked to the Michael Holst group FEtk finite element library during compilation. The finite element solver uses a “solve-estimate-refine” cycle. Specifically, starting from an initial mesh, it performs the following iteration:

1. solve the problem with the current mesh
2. estimate the error in the solution
3. adaptively refine the mesh to reduce the error

This iteration is repeated until a global error tolerance is reached.

Keywords for this calculation type include:

ELEC fe-manual keywords:

- akeyPRE
- akeySOLVE
- bcfl
- calcenergy
- calcforce
- chgm
- domainLength
- ekey
- etol
- ion
- lpbe
- lrpbe
- maxsolve
- maxvert
- mol
- npbe
- nrpbe
- pdie
- sdens
- sdie
- srad
- srfm (elec)
- swin
- targetNum
- targetRes
- temp
- usemesh
- write

Note

The finite element methods are currently most useful for a select set of problems which can benefit from adaptive refinement of the solution. Furthermore, this implementation is experimental. In general, the sequential and parallel focusing multigrid methods offer the most efficient solution of the PBE for most systems.