Commits · 8b44287eb527fae6af8618438035add9158ed59e · tsoc / openmm

07 Jan, 2014 2 commits
- Merge branch 'master' of https://github.com/SimTk/openmm · 8b44287e
  Jason Swails authored Jan 06, 2014
  
  8b44287e
- Merge pull request #274 from peastman/sfmt · 291484f2
  peastman authored Jan 06, 2014
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Ensure SFMT data array is correctly aligned
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  291484f2
06 Jan, 2014 9 commits
- Merge pull request #264 from rmcgibbo/reset-dlopen-flags · 9f957758
  peastman authored Jan 06, 2014
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Fix weird import segfault with RTLD_GLOBAL
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  9f957758
- Ensure SFMT data array is correctly aligned · 64b0a6c8
  peastman authored Jan 06, 2014
  
  64b0a6c8
- Merged changes between repositories by hand · 2e83bfc8
  Peter Eastman authored Jan 06, 2014
  
  2e83bfc8
- Improved logic for selecting a platform to better deal with exceptions in context initialization · d91e3f19
  peastman authored Jan 06, 2014
  
  d91e3f19
- Merge pull request #272 from peastman/master · 5e2170ff
  peastman authored Jan 06, 2014
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Fixed some bugs identified by Valgrind
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  5e2170ff
- Fixed some bugs identified by Valgrind · fc1d0b5c
  peastman authored Jan 06, 2014
  
  fc1d0b5c
- Merge pull request #271 from peastman/master · 192fe4ca
  peastman authored Jan 06, 2014
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Workaround for compilation error on some compilers
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  192fe4ca
- Workaround for compilation error on some compilers · 29bfe077
  peastman authored Jan 06, 2014
  
  29bfe077
- Merge pull request #270 from peastman/host · 742ab844
  peastman authored Jan 06, 2014
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Added option for setting CUDA host compiler
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  742ab844
05 Jan, 2014 1 commit
- Merge pull request #268 from jchodera/minor-context-fixes · d3734248
  peastman authored Jan 04, 2014
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Added missing required kernel names to check of platform capabilities.
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  d3734248
04 Jan, 2014 1 commit

Added missing required kernel names (ApplyConstraintsKernel and... · 9bb2259d

John Chodera authored Jan 04, 2014

Added missing required kernel names (ApplyConstraintsKernel and VirtualSitesKernel) to check for platform capabilities, since these kernels are initialized in the next code block.

9bb2259d

01 Jan, 2014 1 commit
- Fix misplacement of "kappa" in cutoff-GB expression. · 25580770
  Jason Swails authored Jan 01, 2014
  
  25580770
31 Dec, 2013 3 commits
- Just remove the whole nonsense · 98ffd5fe
  Robert McGibbon authored Dec 30, 2013
  
  98ffd5fe
- unused variables · d5115033
  Robert McGibbon authored Dec 30, 2013
  
  d5115033
- Reset the dlopen flags · bb628e2e
  Robert McGibbon authored Dec 30, 2013
  
  bb628e2e
28 Dec, 2013 1 commit
- Correct treatment of kappa when kappa == 0 and when there is a cutoff. · 2410cbef
  Jason Swails authored Dec 27, 2013
  
  2410cbef
27 Dec, 2013 1 commit

Merge pull request #260 from swails/master · a99915ba

peastman authored Dec 27, 2013

Add GBn2 to the simtk.openmm.app namespace and correct unit handling of implicitSolventKappa

a99915ba

25 Dec, 2013 2 commits

Apparently 1/u.nanometers is a quantity rather than a unit, so the command: · 4c24a43e

Jason Swails authored Dec 25, 2013

implicitSolventKappa = implicitSolventKappa.value_in_unit(1/units.nanometers)

will always fail. The only solution I've found is to take the unit of the
quantity. i.e.:

implicitSolventKappa = implicitSolventKappa.value_in_unit((1/units.nanometers).unit)

4c24a43e

Bring GBn2 into the simtk.openmm.app namespace. Also remove some redundant · ce46b9b0
Jason Swails authored Dec 25, 2013
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references.
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ce46b9b0

22 Dec, 2013 5 commits
- Merge pull request #249 from swails/master · 5219d2a5
  peastman authored Dec 22, 2013
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Add a salt concentration term to the custom GB forces
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  5219d2a5
- Unit-ify the 0 in implicitSolventKappa. · 38f286e5
  Jason Swails authored Dec 22, 2013
  
  38f286e5
- Oops, 1/length, not length. · 3ca3fe54
  Jason Swails authored Dec 21, 2013
  
  3ca3fe54
- Merge branch 'master' of https://github.com/SimTk/openmm · caefd490
  Jason Swails authored Dec 21, 2013
  
  caefd490
- Allow implicitSolventKappa to have units (it has dimensions of length) and · 508f989d
  Jason Swails authored Dec 21, 2013
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convert the number to pure nanometers before using it in the GB code.
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  508f989d
21 Dec, 2013 4 commits
- Fixed quotes in command line when using CudaHostCompiler option · cc11a449
  peastman authored Dec 20, 2013
  
  cc11a449
- Merge pull request #255 from peastman/master · 0b35240d
  peastman authored Dec 20, 2013
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Parallelized summing the forces from different threads
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  0b35240d
- Parallelized summing the forces from different threads · 8bdf0829
  peastman authored Dec 20, 2013
  
  8bdf0829
- Merge pull request #254 from peastman/master · f1258fc3
  peastman authored Dec 20, 2013
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Parallelized LangevinIntegrator for CPU platform
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  f1258fc3
20 Dec, 2013 4 commits
- Merge branch 'master' of https://github.com/peastman/openmm · 83470b8e
  peastman authored Dec 20, 2013
  
  83470b8e
- Merge pull request #253 from peastman/master · 39d270d7
  peastman authored Dec 20, 2013
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Bug fixes
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  39d270d7
- Benchmark script did not set OpenCLPrecision correctly · 92b12c5d
  peastman authored Dec 20, 2013
  
  92b12c5d
- Fixed a compilation error on gcc 4.4 · 3366382d
  peastman authored Dec 20, 2013
  
  3366382d
19 Dec, 2013 4 commits
- Parallelized LangevinIntegrator for CPU platform · ddf1216d
  peastman authored Dec 19, 2013
  
  ddf1216d
- Merge pull request #251 from peastman/avx · da998c51
  peastman authored Dec 19, 2013
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CPU platform can use AVX when available
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  da998c51
- Fixed bug in detecting if AVX is supported · 6cde1860
  peastman authored Dec 19, 2013
  
  6cde1860
- Automatically select whether to use the SSE or AVX version of CpuNonbondedForce · d4af8747
  peastman authored Dec 18, 2013
  
  d4af8747
18 Dec, 2013 2 commits
- Improved vectorization of CpuNonbondedForce · 5cd23acb
  peastman authored Dec 18, 2013
  
  5cd23acb
- kappa -> implicitSolventKappa · a727539a
  Jason Swails authored Dec 18, 2013
  
  a727539a