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APBS-1.4.2.1
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@sobolevnrm sobolevnrm released this 31 May 14:15
· 4167 commits to master since this release
vAPBS-1.4.2.1
b4bd54a

APBS 1.4.2.1 CHANGELOG

These are notes for APBS version 1.4.2.1.

Changes from 1.4.2

  • Actually included PB-AM binary, examples and documentation -- note that this is Linux and OS X only!
  • Fixed Windows build so that it is not a Debug build, and ensured that no DLLs are missing

New Features

  • Poisson-Boltzmann Semi-Analytical Method (PB-AM) packaged and built with APBS
    • the binary is called mpe and colocated with the apbs binary
    • documentation is with the APBS documentation, and called PBE_Manual_V1.docx
    • examples are located with APBS examples in a pb-am directory
  • New Geometric flow API and improvements in speed (#235)
  • Support for BinaryDX file format (#216)
  • SOR solver added for mg-auto input file option
  • DXMath improvements (#168, #216)
  • Test suite improvements
    • APBS build in Travis-CI
    • Geometric Flow tests added
    • Protein RNA tests enabled (#149)
    • Intermetiate result testing (#64)
  • Example READMEs onverted to markdown and updated with latest results

Bug Fixes

  • OpenMPI (mg-para) functionality restored (#190)
  • Fixed parsing PQR files that contained records other than ATOM and HETATM (#77, #214)
  • Geometric Flow boundary indexing bug fixed
  • Build fixes:
    • Out of source CMake builds are again working
    • Python library may be built (#372)
    • CentOS 5 binary builds for glibc compatibility
    • Pull requests merged
  • Removed irrelevant warning messages (#378)

Notes

The following packages are treated as submodules in APBS:

  • Geometric Flow has been moved to it's own repository
  • FETk has been cloned so that we have could effect updates
  • PB-SAM lives here

Added chat feature for users. This can also be found from the support tab on http://www.poissonboltzmann.org/.

Known Bugs

  • Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that doth not support C++11. This is also an issue for CentOS 5
  • BEM is temprarily disabled due to build issues
  • Geometric Flow build is currently broken on Windows using Visual Studio
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