APBS 3.0 CHANGELOG

These are notes for APBS version 3.0

Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS. PBSAM is currently only available in the Linux and OS X distributions.
- Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
- More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
- Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
- Included NanoShaper alternative to MSMS.
- More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
Added binary DX format support to the appropriate APBS tools.
Test suite amended and expanded.
Removed hard-coded limitation to number of grid points used to determine surface accessibility.

PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

PB(S)AM now requires the key work 'pos' for the term argument.
PB(S)AM 'surf' keyword has been replaced with the 'usemesh' keyword.
PB(S)AM 'salt' keyword has been replaced with the 'ion' keyword.
PB(S)AM dynamics parameters are no longer accepted in the ELEC section.
PB(S)AM now has only one type of ELEC method: pb(s)am_auto.
PB(S)AM 'gridpts' keyword has been replaced with 'dime' keyword.
PB(S)AM 'dx' and '3dmap' keywords are deprecated to use the 'write' one instead.
BEM mesh keyword now requires method names instead of just integer values.
GEOFLOW ELEC type has been change from 'geoflow-auto' to 'geoflow'.
Fixed miscellaneous Windows build issues.
Update the build configurations for the Pythons libraries.