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APBS Changelog

What's new in APBS 1.4.0 Beta

Jul 26, 2012
  • Added in new read and write binary (gz) commands. Can read gzipped DX files directly.
  • Added new write format to output the atomic potentials to a flat file (see atompot)
  • Added new functionality for using a previously calculated potential map for a new calculation.
  • Added a new program for converting delphi potential maps to OpenDX format. tools/mesh/del2dx
  • Updated Doxygen manual with call/caller graphs. Replaced HTML with PDF.
  • Added tools/matlab/solver with simple Matlab LPBE solver for prototyping, teaching, etc.
  • Deprecated APBS XML output format.
  • Deprecated nlev keyword.
  • Added etol keyword, which allows user-defined error tolerance in LPBE and NPBE calculations (default errtol value is 1.0e-6).
  • Added more explanatory error messages for the case in which parm keyword is missing from APBS input file for apolar calculations.
  • Added a polar and apolor forces calculation example to examples/born/ .
  • Added warning messages for users who try to compile APBS with --enable-tinker flag and run APBS stand-alone execution.
  • Switched default Opal service urls from sccne.wustl.edu to NBCR.
  • Added a sanity check in routines.c: 'bcfl map' in the input file requires 'usemap pot' statement in the input file as well.
  • Introduced Vpmgp_size() routine to replace F77MGSZ call in vpmg.c
  • Updated test results for APBS-1.3 release.
  • BUGFIXES
  • Modified Vpmg_dbForce with some grid checking code provided by Matteo Rotter.
  • Fixed a bug in psize.py per Michael Lerner's suggestion. The old version of psize.py gives wrong cglen and fglen results in special cases (e.g., all y coordinates are negative values).
  • Fixed a bug in examples/scripts/checkforces.sh: the condition for "Passed with rounding error" is abs(difference) < errortol, not the other way around.
  • Fixed the help string in ApbsClient.py .
  • Fixed a bug in Vacc_atomdSASA(): the atom SASA needs to be reset to zero displacement after finite melement methods.
  • Fixed a bug in Vpmg_dbForce(): the initialization of rtot should appear before it is used.
  • Fixed a bug in initAPOL(): center should be initialized before used.
  • Fixed a bug in routines.c: eliminated spurious "Invalid data type for writing!" and "Invalid format for writing!" from outputs with "write atompot" statement in the input file.
  • Fixed a bug in vpmg.c: fixed zero potential value problem on eges and corners in non-focusing calculations.

New in APBS 1.2.1 Beta (Apr 1, 2010)

  • Added in warning into focusFillBound if there is a large value detected
  • in setting the boundary conditions during a focusing calculation
  • Added in a check and abort in Vpmg_qmEnergy if chopped values are
  • detected. This seems to occur under certain conditions for npbe calcs.
  • Fixed a bug in Vpmg_MolIon that causes npbe based calculaions
  • to return very large energies.

New in APBS 1.1.0 (Mar 10, 2009)

  • NEW FEATURES:
  • Moved APBS user guide and tutorial to MediaWiki
  • Added in support for OpenMPI for parallel calculations
  • Added in command line support for Opal job submissions (Code by Samir Unni)
  • Allowed pathname containing spaces in input file, as long as the whole pathname is in quotes ("")
  • Documented 'make test' and related features
  • MODIFICATIONS:
  • Modified the function bcCalc to march through the data array linearly when setting boundary conditions. This removes duplication of grid points on the edge of the array and corners.
  • Clarified documentation on the IDs assigned to input maps, PQRs, parameter files, etc.
  • Updated tutorial to warn against spaces in APBS working directory path in VMD; updated user guide to warn against spaces in APBS installation path on Windows
  • 'make test' has been reconfigured to run before issuing make install (can be run from top directory)
  • Removed tools/visualization/vmd from tools directory in lieu of built-in support in VMD
  • Path lengths can now be larger than 80 characters
  • Expanded authorship list
  • Added in 'make test-opal' as a post install test (run from the examples install directory)
  • Added additional concentrations to protein-rna test case to better encompass experimental conditions used by Garcia-Garcia and Draper; this improves agreement with the published data
  • BUG FIXES:
  • Fixed typos in User Guide (ion keyword) and clarified SMPBE keyword usage
  • Fixed typo in User Guide (writemat: poission -> poisson)
  • Updated psize.py with Robert's patch to fix inconsistent assignment of fine grid numbers in some (very) rare cases
  • Fixed bug with boundary condition assignment. This could potentially affect all calculations; however, probably has limited impact: many test cases gave identical results after the bug fix; the largest change in value was < 0.07%.

New in APBS 1.0 (Sep 6, 2008)

  • 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 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 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