APBS 1.0.0 (2008-04)

New features

  • Changed license to New BSD style open source license (see http://www.opensource.org/licenses/bsd-license.php) for more information
  • Added in a feature limited version of PMG (Aqua) that reduces the memory footprint of an APBS run by 2-fold
  • Modified several routines to boost the speed of APBS calculations by approximately 10% when combined with the low memory version of APBS
  • Simplified parameter input for ION and SMPBE keywords (key-value pairs)
  • Examples and documentation for size-modified PBE code (Vincent Chu et al)
  • Added in “fast” compile-time option that uses optimized parameters for multigrid calculations
  • mg-dummy calculations can be run with any number (n>3) of grid points
  • Updated PMG license to LGPL
  • Added per-atom SASA information output from APOLAR calculations
  • Added per-atom verbosity to APOLAR calculation outputs
  • Ability to read-in MCSF-format finite element meshes (e.g., as produced by Holst group GAMER software)
  • Updated installation instructions in user guide
  • Updated inputgen.py to write out the electrostatic potential for APBS input file.

Bug fixes

  • Updated tools/python/apbslib* for new NOsh functionality
  • Clarified ELEC/DIME and ELEC/PDIME documentation
  • Added more transparent warnings/error messages about path lengths which exceed the 80-character limit
  • Fixed small typo in user guide in installation instructions
  • Fixed memory leaks throughout the APBS code
  • Fixed NOsh_parseREAD errors for input files with r line feeds.
  • Fixed a variable setting error in the test examples
  • Fixed a bug where memory usage is reported incorrectly for large allocations on 64-bit systems
  • Added DTRSV to APBS-supplied BLAS to satisfy FEtk SuperLU dependency
  • Fixed a small bug in routines.c to print out uncharged molecule id
  • Limited calculation of forces when surface maps are read in