Releases: Electrostatics/apbs
Releases · Electrostatics/apbs
v3.4.1
- Binary releases may be found in GitHub
releases.
Known Bugs and Limitations
- Automated build is only single threaded
- pb_solvers has been disabled; requires further development for full
integration - Support for the PYGBE solver is minimal so far; user needs to
install PYGBE (e.g. via [pip install pygbe]{.title-ref})
Minor Updates
- Updated Windows build to Windows 2022; Visual Studio updated to v17,
2022 - Specified Ubuntu build (20.04) and Mac build (11)
- Fixed CMake syntax error around Python detection
- Statically link Python in the Mac and Ubuntu builds
- Build arpack manually in the Mac build to get the static library
- Updated FETK to v1.9.3
- Updated installation documentation
- Added a CentOS Dockerfile; updated the Ubuntu Dockerfile
Notes
- The following are included in APBS:
- Geometric
Flow - FETk
- PBAM/PBSAM
- TABI-PB
v3.4.0
- Binary releases may be found in GitHub
releases.
New Features
- Revamped build system
- Most submodule switched to using CMake's FetchContent
- FETK is now required; currently using v1.9.2
- Automatic release processes implemented
- Cross-platform builds performed on GitHub Actions
- Pre-compiled binaries posted to each Release
- Binaries are currently single-threaded (no OpenMP)
Known Bugs and Limitations
- Automated build is only single threaded
- pb_solvers has been disabled; requires further development for full
integration - Support for the PYGBE solver is minimal so far; user needs to
install PYGBE (e.g., pip install pygbe) - Docker build was failing during tests and needs to be fixed
Notes
- The following are included in APBS:
- Geometric
Flow - FETk
- PBAM/PBSAM
- TABI-PB
3.3.0.alpha
Dec 10, 2021
- An amazing update
- Another amazing update
- A stupendous update
APBS-3.0.0
APBS 3.0 CHANGELOG
These are notes for APBS version 3.0
- Binary releases may be found on GitHub and on SourceForge.
New Features
- 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.
- 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.
Known Bugs / Limitations
- PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.
Minor Updates
- 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.
Notes
- The following are included in APBS as Git submodules:
APBS-1.5.0
APBS 1.5 CHANGELOG
These are notes for APBS version 1.5
- Binary releases may be found on GitHub and on SourceForge.
New Features
- 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.
- 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.
Known Bugs / Limitations
- PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.
Bug Fixes
- Build an iAPBS build bug.
- Fixed miscellaneous Windows build issues.
- OS X bundle problem on El Capitan.
Notes
- The following are included in APBS as Git submodules:
- Geometric Flow (link)
- FETk (link)
- PBAM/PBSAM (link)
- TABI-PB (link)
- To build on Windows from source, the root CMakeLists.txt file needs to be modified by un-commenting out the lines after "#if building on Windows" and commenting out the corresponding lines above.
APBS-1.4.2.1
APBS 1.4.2.1 CHANGELOG
These are notes for APBS version 1.4.2.1.
- Binary releases may be found on
GitHub and
on SourceForge.
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
mpeand 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
- the binary is called
- 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
APBS-1.4.2
APBS 1.4.2 CHANGELOG
These are notes for APBS version 1.4.2.
- Binary releases may be found on
GitHub and
on SourceForge.
New Features
- Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and built with APBS
- 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