Commits · 9111cca092a59ae505625da07abf5c7d41a80925 · tsoc / openmm

"vscode:/vscode.git/clone" did not exist on "01ed382c95704d86bf74f71f7d6eba8fe60399c5"

20 Feb, 2015 11 commits
- Moved reference platform classes into OpenMM namespace · 9111cca0
  peastman authored Feb 20, 2015
  
  9111cca0
- Merge pull request #825 from peastman/remove · 8148f51d
  peastman authored Feb 20, 2015
```
Added removeForce() and removeConstraint() to System
```
  8148f51d
- Merge pull request #824 from swails/master · 252e03de
  peastman authored Feb 20, 2015
```
Fix `unitcell.py`
```
  252e03de
- Added removeForce() and removeConstraint() to System · 65d0449e
  peastman authored Feb 20, 2015
  
  65d0449e
- Fix names. · 7a60e434
  Jason Swails authored Feb 20, 2015
  
  7a60e434
- Merge branch 'master' of https://github.com/pandegroup/openmm · 245a7380
  Jason Swails authored Feb 19, 2015
  
  245a7380
- Add a reducePeriodicBoxVectors function, since many helpers (like the one in · fd1827e0
  Jason Swails authored Feb 19, 2015
```
mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.
```
  fd1827e0
- Fix bug in unitcell.py (computeLengthsAndAngles), which resulted in a NameError. · 1004e6e5
  Jason Swails authored Feb 19, 2015
```
Also added a test suite for them.
```
  1004e6e5
- Merge pull request #823 from peastman/tinker · b43e3f12
  peastman authored Feb 19, 2015
```
Regenerated AMOEBA2013 based on Tinker 7.0.1
```
  b43e3f12
- Regenerated AMOEBA2013 based on Tinker 7.0.1 · 9f5a02cd
  peastman authored Feb 19, 2015
  
  9f5a02cd
- Merge pull request #822 from peastman/master · bf03b073
  peastman authored Feb 19, 2015
```
Fixed some test cases that were failing
```
  bf03b073
19 Feb, 2015 3 commits
- Fixed some test cases that were failing · 1ce17590
  peastman authored Feb 19, 2015
  
  1ce17590
- Merge pull request #821 from peastman/tests · 7e4843fd
  peastman authored Feb 18, 2015
```
Minor changes to speed up some test cases
```
  7e4843fd
- Minor changes to speed up some test cases · f2958043
  peastman authored Feb 18, 2015
  
  f2958043
18 Feb, 2015 2 commits
- Merge pull request #815 from peastman/ids · 1c271535
  peastman authored Feb 17, 2015
```
Modeller preserves chain, residue, and atom ids when reasonable
```
  1c271535
- Modeller preserves chain, residue, and atom ids when reasonable · f025c5f4
  peastman authored Feb 17, 2015
  
  f025c5f4
17 Feb, 2015 4 commits
- Merge pull request #814 from peastman/cuda7 · 828706cd
  peastman authored Feb 17, 2015
```
Workaround for Nvidia bug on Maxwell in CUDA 6
```
  828706cd
- Merge pull request #813 from peastman/ids · 37811976
  peastman authored Feb 17, 2015
```
Topology records PDB ids for chains, residues, and atoms
```
  37811976
- Workaround for Nvidia bug on Maxwell in CUDA 6 · bfe7570e
  peastman authored Feb 17, 2015
  
  bfe7570e
- Topology records PDB ids for chains, residues, and atoms · e84f0727
  peastman authored Feb 17, 2015
  
  e84f0727
13 Feb, 2015 10 commits
- Merge pull request #809 from peastman/floor · 37ab709f
  peastman authored Feb 13, 2015
```
Custom expressions support floor() and ceil()
```
  37ab709f
- Tests for floor() and ceil(). · e0713aeb
  peastman authored Feb 13, 2015
  
  e0713aeb
- Custom expressions support floor() and ceil(). · dce6a437
  peastman authored Feb 13, 2015
  
  dce6a437
- Merge pull request #808 from peastman/parse · a0bdc698
  peastman authored Feb 13, 2015
```
Lepton exceptions have more informative messages
```
  a0bdc698
- Lepton exceptions have more informative messages · 418ceabd
  peastman authored Feb 13, 2015
  
  418ceabd
- Merge pull request #807 from peastman/compiler · e9b7c563
  peastman authored Feb 13, 2015
```
Support CUDA runtime compilation
```
  e9b7c563
- Cleanup to CUDA compiler plugin · 8fa08870
  Peter Eastman authored Feb 13, 2015
  
  8fa08870
- Created plugin for CUDA runtime compiler · 7e29671a
  Peter Eastman authored Feb 13, 2015
  
  7e29671a
- Merge pull request #806 from peastman/jit32 · 97ce448c
  peastman authored Feb 12, 2015
```
Updated to latest asmjit, which supports 32 bit mode
```
  97ce448c
- Updated to latest asmjit, which supports 32 bit mode · 01da1b51
  peastman authored Feb 12, 2015
  
  01da1b51
11 Feb, 2015 6 commits
- Merge pull request #802 from swails/fix-charmm-box-vecs · fabb38d1
  peastman authored Feb 11, 2015
```
Fix for unit cell vector calculation
```
  fabb38d1
- Fix AmberPrmtopFile for building with IFBOX != 1 or 2. Also Add tests for a · 918d17ac
  Jason Swails authored Feb 11, 2015
```
truncated octahedron inpcrd and prmtop file.
```
  918d17ac
- Add support for triclinic boxes to the Amber and CHARMM file parsers. · 0746deda
  Jason Swails authored Feb 11, 2015
  
  0746deda
- Beginnings of improvements for amber_file_parser and the CHARMM PSF file parser · 10be282a
  Jason Swails authored Feb 11, 2015
```
to support triclinic cells.

Also extend unitcell.computePeriodicBoxVectors to take Quantity inputs rather
than *just* scalars assumed to be nanometers.
```
  10be282a
- Merge branch 'master' into fix-charmm-box-vecs · 4570189f
  Jason Swails authored Feb 11, 2015
  
  4570189f
- Merge pull request #804 from peastman/xml · 26790496
  peastman authored Feb 10, 2015
```
Replaced TinyXML with irrXML
```
  26790496
10 Feb, 2015 4 commits
- Added irrXML to top level CMakeLists.txt · a165a094
  Peter Eastman authored Feb 10, 2015
  
  a165a094
- Replaced TinyXML with irrXML · 8aff3b74
  Peter Eastman authored Feb 10, 2015
  
  8aff3b74
- Merge pull request #803 from peastman/triclinic · 8bc8d184
  peastman authored Feb 10, 2015
```
Python layer supports triclinic boxes
```
  8bc8d184
- More support for triclinic boxes · 30a53702
  Peter Eastman authored Feb 10, 2015
  
  30a53702