Commits · 69d7dc4fa5a5dd4156ebb51a3cb67abc0c8b6486 · tsoc / openmm

"...reference/include/ReferenceVariableVerletDynamics.h" did not exist on "e561a67824a1a0ac544547ff4c08baa4853d1b5f"

19 Nov, 2015 2 commits
- Hopefully finished with supporting nucleotides in AMOEBA · 69d7dc4f
  peastman authored Nov 19, 2015
  
  69d7dc4f
- Fixed bugs that affected nucleotides in AMOEBA · 4daa1acb
  Peter Eastman authored Nov 19, 2015
  
  4daa1acb
29 Oct, 2015 1 commit
- Merge branch 'master' into nucleic · fd473eea
  Peter Eastman authored Oct 29, 2015
  
  fd473eea
28 Oct, 2015 5 commits
- Merge pull request #1182 from peastman/residueparams · 6a985cfd
  peastman authored Oct 28, 2015
```
[WIP] Per-atom parameters can be taken from residue templates
```
  6a985cfd
- Support residue template parameters for CustomManyParticleForce · 1f7985e7
  peastman authored Oct 28, 2015
  
  1f7985e7
- Added documentation for residue template parameters, plus other minor documentation updates · 5d9a166c
  peastman authored Oct 28, 2015
  
  5d9a166c
- Merge pull request #1219 from rmcgibbo/fastcopy · ef9a1050
  peastman authored Oct 28, 2015
```
Reinstate fast copy methods
```
  ef9a1050
- Reinstate fast copy methods · 9ff00fb0
  Robert McGibbon authored Oct 27, 2015
  
  9ff00fb0
27 Oct, 2015 11 commits
- Merge pull request #1216 from rmcgibbo/fix-segfault · 6d855c39
  peastman authored Oct 27, 2015
```
Fix segfault in swig wrappers
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  6d855c39
- Clean up some of the swig typemaps · 87ce9ccd
  Robert McGibbon authored Oct 27, 2015
  
  87ce9ccd
- Merge pull request #1199 from rmcgibbo/groups · 9314ff68
  peastman authored Oct 27, 2015
```
Modify Context.getState to accept a set of indices or bitmask
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  9314ff68
- Merge pull request #1205 from rmcgibbo/which-device · 433ca1ea
  peastman authored Oct 27, 2015
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Ensure context can be created when selecting CUDA device
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  433ca1ea
- Merge pull request #1217 from peastman/clcpubugs · dddc9e45
  peastman authored Oct 27, 2015
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Fixed test failures on OpenCL CPU device
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  dddc9e45
- Removed debug code · c95bd965
  peastman authored Oct 27, 2015
  
  c95bd965
- Increased a tolerance that was too small on some devices in single precision mode · d2453d1b
  peastman authored Oct 27, 2015
  
  d2453d1b
- Local memory array was wrong size with CPU device · 61ab8cb4
  peastman authored Oct 27, 2015
  
  61ab8cb4
- Fix segfault in swig wrappers · 381e8145
  Robert McGibbon authored Oct 27, 2015
  
  381e8145
- Merge pull request #1215 from peastman/cpuopt · ea15e2ba
  peastman authored Oct 27, 2015
```
Minor optimizations to CPU neighbor list
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  ea15e2ba
- Minor optimizations to CPU neighbor list · 6552f806
  peastman authored Oct 27, 2015
  
  6552f806
26 Oct, 2015 21 commits
- Modify Context.getState to accept a set of indices in addition to a bitmask · ecc7e011
  Robert McGibbon authored Oct 20, 2015
  
  ecc7e011
- Merge pull request #1210 from jchodera/top · 2c80cda8
  peastman authored Oct 26, 2015
```
Added getNumAtoms, getNumResidues, getNumChains to simtk.openmm.app.Topology
```
  2c80cda8
- Merge pull request #1211 from jchodera/deepcopy · 2049b1fe
  peastman authored Oct 26, 2015
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Fix force deepcopy bug
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  2049b1fe
- Force objects can now be pickled/unpickled · 1006797b
  John Chodera (MSKCC) authored Oct 26, 2015
  
  1006797b
- Merge pull request #1208 from rmcgibbo/cl-test-device · d4853aeb
  peastman authored Oct 26, 2015
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Control what device is used for OpenCL tests
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  d4853aeb
- Revert integrator deepcopy · cad8d293
  John Chodera (MSKCC) authored Oct 26, 2015
  
  cad8d293
- Rework and streamline deepcopy and pickle tests · 7a22ce95
  John Chodera (MSKCC) authored Oct 26, 2015
  
  7a22ce95
- Compare contents of deepcopy Force objects in Python tests. · 2b66a71b
  John Chodera (MSKCC) authored Oct 26, 2015
  
  2b66a71b
- Fix typo in getNumAtoms() and getNumResidues() implementation · d74e4789
  John Chodera (MSKCC) authored Oct 26, 2015
  
  d74e4789
- Grumble grumble · 59899650
  John Chodera (MSKCC) authored Oct 26, 2015
  
  59899650
- Simplify Topology.getNumChains() · b5330c31
  John Chodera (MSKCC) authored Oct 26, 2015
  
  b5330c31
- Merge pull request #1201 from rmcgibbo/gmx-include · 1d11b995
  peastman authored Oct 26, 2015
```
No GMX include directory in example
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  1d11b995
- Merge pull request #1209 from rmcgibbo/cl-custom-centroid-bond · 84cf2d08
  peastman authored Oct 26, 2015
```
Fix thread synchronization in customCentroidBond.cl
```
  84cf2d08
- Fix Topology Python test. · eb2f347a
  John Chodera (MSKCC) authored Oct 26, 2015
  
  eb2f347a
- Revert force deepcopy code to earlier working version. · a1372d52
  John Chodera (MSKCC) authored Oct 26, 2015
  
  a1372d52
- Update deepcopy test · c82f3c18
  John Chodera (MSKCC) authored Oct 26, 2015
  
  c82f3c18
- Fix typo in Python test · 1289d16d
  John Chodera (MSKCC) authored Oct 26, 2015
  
  1289d16d
- Add Python test to catch force deepcopy bug · 9639837c
  John Chodera (MSKCC) authored Oct 26, 2015
  
  9639837c
- Added Python test for Topology getters. · e5762fb2
  John Chodera (MSKCC) authored Oct 26, 2015
  
  e5762fb2
- Add getNumAtoms(), getNumResidues(), and getNumChains() to simtk.openmm.app.Topology · 73cfcd68
  John Chodera (MSKCC) authored Oct 26, 2015
  
  73cfcd68
- Fix thread synchronization in customCentroidBond.cl · 0d34441d
  Robert McGibbon authored Oct 25, 2015
  
  0d34441d