Commits · 79c0e60467949f9b83b0b2f71c0d2287b3552217 · tsoc / openmm

18 Nov, 2016 5 commits
- Optmized influence function and energy computations for PME and LJPME. · 79c0e604
  Andy Simmonett authored Aug 19, 2016
  
  79c0e604
- Initial fast reciprocal space LJPME implementation, with test. · a741138b
  Andy Simmonett authored Aug 19, 2016
  
  a741138b
- Implemented real space CPU LJPME terms. · 40a7363d
  Andy Simmonett authored Aug 17, 2016
```
o Only reference reciprocal space code works, for now.
o Vector lengths of 4 and 8 implemented and tested.
o Tests pass for Reference and CPU platforms.
```
  40a7363d
- Updated tests, to compare to Gromacs · 42e695c7
  Andy Simmonett authored Aug 15, 2016
```
o Added C12 shift term, to match GMX.
o Added tests to compare energies and forces directly to GMX, with and without exclusions.
o Modified set/get LJPME parameters to look similar to electrostatic equivalents.
```
  42e695c7
- Initial reference implementation of LJPME. · a919ab44
  Andy Simmonett authored Aug 11, 2016
  
  a919ab44
14 Nov, 2016 4 commits
- Merge pull request #1670 from jchodera/update-packaging-scripts · 81125231
  peastman authored Nov 14, 2016
```
Update build and packaging scripts
```
  81125231
- Merge pull request #1668 from peastman/bond · 5c646b02
  peastman authored Nov 14, 2016
```
Created Bond class that can store bond type and order
```
  5c646b02
- Build tests for packaging · 0087dcb8
  jchodera authored Nov 14, 2016
  
  0087dcb8
- Update build and packaging scripts. · b9e2844f
  jchodera authored Nov 14, 2016
  
  b9e2844f
11 Nov, 2016 6 commits
- Merge pull request #5 from swails/bond · ebb7a083
  peastman authored Nov 11, 2016
```
More singletons
```
  ebb7a083
- More singletons · 42686c7a
  Jason Swails authored Nov 11, 2016
  
  42686c7a
- Merge pull request #4 from swails/bond · ba924c54
  peastman authored Nov 11, 2016
```
namedtuple and singleton
```
  ba924c54
- Fix typo. · 8f8dbd12
  Jason Swails authored Nov 11, 2016
  
  8f8dbd12
- - Add a class to make what are intended to be Singletons really Singletons · 829792ef
  Jason Swails authored Nov 10, 2016
```
- Make Python 2.7 a minimum requirement per pandegroup/openmm#1656
- Make the bond classes as well as other forcefield.py singletons inherit from
  Singleton to make them pickleable
- Make class Bond inherit from namedtuple instead of tuple
```
  829792ef
- Add a test to make sure that the bond types are really singletons. · 311a2cff
  Jason Swails authored Nov 10, 2016
  
  311a2cff
10 Nov, 2016 2 commits
- Created Bond class that can store bond type and order · 7c7b945e
  peastman authored Nov 10, 2016
  
  7c7b945e
- Merge pull request #1665 from peastman/external · b465c982
  peastman authored Nov 10, 2016
```
Added ignoreExternalBonds option to createSystem()
```
  b465c982
09 Nov, 2016 4 commits
- Fixed failing test case · f3ce6720
  peastman authored Nov 09, 2016
  
  f3ce6720
- Added ignoreExternalBonds option to createSystem() · ff55a3a0
  peastman authored Nov 09, 2016
  
  ff55a3a0
- Merge pull request #1664 from peastman/dcd · f968bf99
  peastman authored Nov 09, 2016
```
Fixed error writing a DCD file for a very long trajectory
```
  f968bf99
- Fixed error writing a DCD file for a very long trajectory · 61293829
  peastman authored Nov 09, 2016
  
  61293829
08 Nov, 2016 1 commit
- Merge pull request #1663 from peastman/customswitch · 31c883b3
  peastman authored Nov 08, 2016
```
Fixed bug in switching functions with CustomNonbondedForce
```
  31c883b3
07 Nov, 2016 1 commit
- Fixed bug in switching functions with CustomNonbondedForce · c300870a
  Peter Eastman authored Nov 07, 2016
  
  c300870a
28 Oct, 2016 2 commits
- Merge pull request #1655 from peastman/checkaxis · 04b1a060
  peastman authored Oct 28, 2016
```
Added error checking to axis particle indices
```
  04b1a060
- Added error checking to axis particle indices · ba19d607
  peastman authored Oct 28, 2016
  
  ba19d607
25 Oct, 2016 1 commit
- Merge pull request #1652 from peastman/singular · ff270126
  peastman authored Oct 25, 2016
```
Handle singular matrix in DIIS
```
  ff270126
24 Oct, 2016 2 commits
- Handle singular matrix in DIIS · ca4bbc18
  Peter Eastman authored Oct 24, 2016
  
  ca4bbc18
- Merge pull request #1647 from peastman/polarizationzero · 5f509089
  peastman authored Oct 24, 2016
```
Support multipoles with polarization set to 0
```
  5f509089
20 Oct, 2016 3 commits
- Support multipoles with polarization set to 0 · effb1f57
  Peter Eastman authored Oct 20, 2016
  
  effb1f57
- Merge pull request #1646 from peastman/zonly · 9480ec98
  peastman authored Oct 20, 2016
```
Fixed errors with multipoles set to ZOnly mode
```
  9480ec98
- Fixed errors with multipoles set to ZOnly mode · f6d209af
  Peter Eastman authored Oct 20, 2016
  
  f6d209af
18 Oct, 2016 9 commits
- Merge pull request #1642 from peastman/radius · 1f78252a
  peastman authored Oct 18, 2016
```
Fixed bug computing neighbor list
```
  1f78252a
- Fixed bug in OpenCL as well · 2c47f7b2
  Peter Eastman authored Oct 18, 2016
  
  2c47f7b2
- Fixed bug computing neighbor list · 556dddb6
  Peter Eastman authored Oct 18, 2016
  
  556dddb6
- Merge pull request #1640 from peastman/diis · 5ea8680f
  peastman authored Oct 18, 2016
```
Solve DIIS matrix on GPU
```
  5ea8680f
- Merge pull request #1641 from jchodera/gb-cleanup · d1caf109
  peastman authored Oct 18, 2016
```
Change variable 'q' to 'charge' in custom gb models
```
  d1caf109
- Added a missing fabs() · c0538e1f
  Peter Eastman authored Oct 18, 2016
  
  c0538e1f
- Merge pull request #1639 from jchodera/update-docs · 38d967b2
  peastman authored Oct 18, 2016
```
Update docstrings to specify units and domain for torsions
```
  38d967b2
- Change variable 'q' to 'charge' in custom gb models · d02f75ff
  John Chodera (MSKCC) authored Oct 18, 2016
  
  d02f75ff
- Fix API docs · ef4e38b9
  John Chodera (MSKCC) authored Oct 17, 2016
  
  ef4e38b9