Commits · f816d961426b17b5d083de6d300e61960c5d5a29 · tsoc / openmm

25 Feb, 2015 4 commits
- Merge pull request #834 from peastman/pvec · f816d961
  peastman authored Feb 25, 2015
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Further improvements to PNaCl vectors
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  f816d961
- Further improvements to PNaCl vectors · 49cc84c4
  peastman authored Feb 25, 2015
  
  49cc84c4
- Merge pull request #831 from peastman/pvec · 57045028
  peastman authored Feb 24, 2015
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Optimizations to PNaCl vectors
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  57045028
- Optimizations to PNaCl vectors · d51ad3c3
  peastman authored Feb 24, 2015
  
  d51ad3c3
24 Feb, 2015 5 commits
- Merge pull request #830 from peastman/pnacl · 8f39837a
  peastman authored Feb 24, 2015
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Fixed problems running in PNaCl
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  8f39837a
- Fixed problems running in PNaCl · aa7bd1cf
  peastman authored Feb 24, 2015
  
  aa7bd1cf
- Merge pull request #829 from peastman/state · e670188b
  peastman authored Feb 23, 2015
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Avoid throwing exceptions internally when serializing States
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  e670188b
- Avoid throwing exceptions internally when serializing States · e18eb785
  peastman authored Feb 23, 2015
  
  e18eb785
- Merge pull request #828 from peastman/cleanup · f11bafd9
  peastman authored Feb 23, 2015
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Cleanup to AMOEBA code
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  f11bafd9
23 Feb, 2015 2 commits
- Cleaned up formatting in AMOEBA code · d95b90b9
  peastman authored Feb 23, 2015
  
  d95b90b9
- Deleted more debugging code · a568bb12
  peastman authored Feb 23, 2015
  
  a568bb12
21 Feb, 2015 6 commits
- Merge pull request #827 from peastman/reference · 162d69a2
  peastman authored Feb 20, 2015
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Lots of cleanup to reference platform
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  162d69a2
- Deleted lots of debugging code · c44c956d
  peastman authored Feb 20, 2015
  
  c44c956d
- Cleaned up formatting of AMOEBA reference code · 41cd79a5
  peastman authored Feb 20, 2015
  
  41cd79a5
- Moved AMOEBA reference code into OpenMM namespace · 25a308e6
  peastman authored Feb 20, 2015
  
  25a308e6
- Deleted obsolete debugging code · f72062af
  peastman authored Feb 20, 2015
  
  f72062af
- Combined subfolders in reference source, and renamed a couple of badly named classes · 3d69185a
  peastman authored Feb 20, 2015
  
  3d69185a
20 Feb, 2015 16 commits
- Elimininated obsolete SimTKOpenMMCommon files · 0671c7b0
  peastman authored Feb 20, 2015
  
  0671c7b0
- Cleaned up lots of formatting to be more consistent with the rest of OpenMM · 7fb10336
  peastman authored Feb 20, 2015
  
  7fb10336
- Deleted obsolete logging class · 1d3ffd7b
  peastman authored Feb 20, 2015
  
  1d3ffd7b
- Moved reference platform classes into OpenMM namespace · 9111cca0
  peastman authored Feb 20, 2015
  
  9111cca0
- Merge pull request #826 from peastman/angles · 2379b982
  peastman authored Feb 20, 2015
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Fixed an incorrect unit conversion when constraining angles with AMOEBA
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  2379b982
- Fixed an incorrect unit conversion when constraining angles with AMOEBA · 89ab01de
  peastman authored Feb 20, 2015
  
  89ab01de
- Merge pull request #825 from peastman/remove · 8148f51d
  peastman authored Feb 20, 2015
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Added removeForce() and removeConstraint() to System
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  8148f51d
- Merge pull request #824 from swails/master · 252e03de
  peastman authored Feb 20, 2015
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Fix `unitcell.py`
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  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
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mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.
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  fd1827e0
- Fix bug in unitcell.py (computeLengthsAndAngles), which resulted in a NameError. · 1004e6e5
  Jason Swails authored Feb 19, 2015
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Also added a test suite for them.
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  1004e6e5
- Merge pull request #823 from peastman/tinker · b43e3f12
  peastman authored Feb 19, 2015
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Regenerated AMOEBA2013 based on Tinker 7.0.1
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  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
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Fixed some test cases that were failing
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  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
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Minor changes to speed up some test cases
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  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
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Modeller preserves chain, residue, and atom ids when reasonable
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  1c271535
- Modeller preserves chain, residue, and atom ids when reasonable · f025c5f4
  peastman authored Feb 17, 2015
  
  f025c5f4
17 Feb, 2015 2 commits
- Merge pull request #814 from peastman/cuda7 · 828706cd
  peastman authored Feb 17, 2015
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Workaround for Nvidia bug on Maxwell in CUDA 6
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  828706cd
- Merge pull request #813 from peastman/ids · 37811976
  peastman authored Feb 17, 2015
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Topology records PDB ids for chains, residues, and atoms
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  37811976