Commits · b2d5520dab305c089d30da42b996cf0f39d268d3 · tsoc / openmm

01 Aug, 2013 1 commit

Converted the routine for identifying molecules from a recursion to a loop. ... · b2d5520d

peastman authored Aug 01, 2013

Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.

b2d5520d

31 Jul, 2013 3 commits
- Handle extra particles correctly when guessing why no template matched a residue. · 16b5edb6
  peastman authored Jul 31, 2013
  
  16b5edb6
- ForceField tries to figure out why no residue matched a template · 9e09ca68
  peastman authored Jul 31, 2013
  
  9e09ca68
- Merge pull request #84 from peastman/cache · 818dc73b
  peastman authored Jul 31, 2013
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Cache the PTX files for compiled kernels
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  818dc73b
30 Jul, 2013 3 commits
- Can set OPENMM_CACHE_DIR to specify where PTX files should be cached · bf34e947
  peastman authored Jul 30, 2013
  
  bf34e947
- Eliminated some #defines to improve the efficiency of PTX caching · 50eb44c5
  peastman authored Jul 30, 2013
  
  50eb44c5
- Cache filename specifies whether it was compiled in 32 or 64 bit mode · 00f51540
  peastman authored Jul 29, 2013
  
  00f51540
29 Jul, 2013 2 commits
- Cache the PTX files for compiled kernels · d7aebd3a
  peastman authored Jul 29, 2013
  
  d7aebd3a
- Merge pull request #82 from rmcgibbo/setLength · 6144a88b
  peastman authored Jul 29, 2013
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Fix segfault when positions are not 3 dimensional.
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  6144a88b
27 Jul, 2013 3 commits
- Fix segfault when positions are not 3 dimensional. · 2ad438b7
  Robert McGibbon authored Jul 26, 2013
  
  2ad438b7
- Merge pull request #80 from peastman/master · 1c3d149d
  peastman authored Jul 26, 2013
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Lots of updates to documentation for new features in 5.2.
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  1c3d149d
- Lots of updates to documentation for new features in 5.2. · e1c332db
  peastman authored Jul 26, 2013
  
  e1c332db
26 Jul, 2013 7 commits
- Merge pull request #79 from peastman/master · 9076fe48
  peastman authored Jul 26, 2013
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Added an argument to addHydrogens() for selecting which Platform to use for minimization. Also marked convertWater() as deprecated.
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  9076fe48
- Merge branch 'master' of https://github.com/peastman/openmm · 927480f5
  Peter Eastman authored Jul 26, 2013
  
  927480f5
- Added an argument to addHydrogens() for selecting which Platform to use for... · 187ccbb8
  peastman authored Jul 26, 2013
```
Added an argument to addHydrogens() for selecting which Platform to use for minimization.  Also marked convertWater() as deprecated.
```
  187ccbb8
- Merge pull request #78 from peastman/master · adf78fa5
  peastman authored Jul 26, 2013
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Include process ID in temporary file names to avoid collisions
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  adf78fa5
- Include process ID in temporary file names to avoid collisions · 71b66a9b
  Peter Eastman authored Jul 26, 2013
  
  71b66a9b
- Merge pull request #76 from peastman/master · 80e35034
  peastman authored Jul 26, 2013
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Updated to newer version of cl.hpp
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  80e35034
- Updated to newer version of cl.hpp · cf99e9e7
  peastman authored Jul 26, 2013
  
  cf99e9e7
25 Jul, 2013 4 commits
- Merge pull request #75 from peastman/master · e8e7db31
  peastman authored Jul 25, 2013
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Added SWM4-NDP water model
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  e8e7db31
- Added SWM4-NDP water model · 09efc337
  peastman authored Jul 25, 2013
  
  09efc337
- Merge pull request #74 from peastman/master · 1cf3d58a
  peastman authored Jul 25, 2013
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Changed order of arguments to produce a simpler API
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  1cf3d58a
- Changed order of arguments to produce a simpler API · 843076ac
  peastman authored Jul 25, 2013
  
  843076ac
23 Jul, 2013 2 commits
- Merge pull request #72 from peastman/master · 3b2ee9b5
  peastman authored Jul 23, 2013
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__all__ should not include symbols that start with _
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  3b2ee9b5
- __all__ should not include symbols that start with _ · 73fdc083
  peastman authored Jul 23, 2013
  
  73fdc083
22 Jul, 2013 6 commits
- Merge pull request #66 from rmcgibbo/buffering · b788fdd6
  peastman authored Jul 22, 2013
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StateDataReporter buffering
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  b788fdd6
- add flush instructions · bc9f1c6a
  Robert McGibbon authored Jul 22, 2013
  
  bc9f1c6a
- Merge pull request #69 from rmcgibbo/pickle2-vec3 · 99df6758
  peastman authored Jul 22, 2013
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Add support for pickle protocol 2 for Vec3
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  99df6758
- Merge pull request #68 from rmcgibbo/getIntegrator-typemap2 · 1d1d1390
  peastman authored Jul 22, 2013
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return correct subtype for getIntegrator()
```
  1d1d1390
- Add support for pickle protocol 2 for Vec3 · d1334405
  Robert McGibbon authored Jul 21, 2013
  
  d1334405
- return correct subtype for getIntegrator() · 3c1bf2c3
  Robert McGibbon authored Jul 21, 2013
  
  3c1bf2c3
21 Jul, 2013 1 commit
- Changed statedatareporter to not buffer its outstream · cd4b69be
  Robert McGibbon authored Jul 20, 2013
  
  cd4b69be
20 Jul, 2013 1 commit
- Merge pull request #64 from peastman/bugs · 49cb91c5
  peastman authored Jul 19, 2013
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Minor bug fixes
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  49cb91c5
19 Jul, 2013 6 commits
- Improved logic for picking grid size · 1c6bea76
  peastman authored Jul 19, 2013
  
  1c6bea76
- Prevent test case from crashing if the CPU is not supported · dcee8145
  peastman authored Jul 19, 2013
  
  dcee8145
- Fixed error that caused testInstallation.py to fail when the GPU was configured in exclusive mode · 2413fd82
  peastman authored Jul 19, 2013
  
  2413fd82
- Merge pull request #63 from peastman/master · fdce64f7
  peastman authored Jul 19, 2013
```
Fixed a bug in CustomIntegrator related to atom reordering
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  fdce64f7
- Fixed a bug in CustomIntegrator related to atom reordering · 603683e2
  peastman authored Jul 19, 2013
  
  603683e2
- Merge pull request #60 from peastman/embedded · 3a2299a5
  peastman authored Jul 19, 2013
```
Lots of bug fixes, especially on low end or embedded devices, and on Windows
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  3a2299a5
18 Jul, 2013 1 commit
- Fix bug in CMake script · 958b6ec8
  peastman authored Jul 18, 2013
  
  958b6ec8