Commits · 3628d973cb3ff739537ac7677ddcdf7379c3771f · tsoc / openmm

27 Jun, 2013 3 commits
- Created a dedicated test case for CPU based PME · 3628d973
  peastman authored Jun 27, 2013
  
  3628d973
- Created platform property for specifying whether to use the CPU based PME · d942ac2f
  peastman authored Jun 27, 2013
  
  d942ac2f
- Removed AVX code, since it had very little effect on performance and would... · 8ed07b6f
  peastman authored Jun 27, 2013
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Removed AVX code, since it had very little effect on performance and would have required a more complicated build process.  Also worked around a compilation error with clang.
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  8ed07b6f
26 Jun, 2013 2 commits
- Further optimizations to CPU based PME · e249751c
  peastman authored Jun 26, 2013
  
  e249751c
- Bug fixes and minor optimizations · 041f973f
  peastman authored Jun 26, 2013
  
  041f973f
25 Jun, 2013 1 commit
- Created AVX version of charge spreading. Also fixed incorrect energy computation. · f623f01a
  peastman authored Jun 25, 2013
  
  f623f01a
24 Jun, 2013 6 commits
- Optimized reciprocal space convolution by caching scale factors · dcfd5c02
  peastman authored Jun 24, 2013
  
  dcfd5c02
- Fixed compilation errors on Linux · 06fa0896
  peastman authored Jun 24, 2013
  
  06fa0896
- Merge branch 'pme' of https://github.com/peastman/openmm into pme · efee2f86
  Peter authored Jun 24, 2013
  
  efee2f86
- File missed in last checkin · 4eb72132
  peastman authored Jun 24, 2013
  
  4eb72132
- Merge branch 'pme' of https://github.com/peastman/openmm into pme · 68f8aed8
  Peter authored Jun 24, 2013
  
  68f8aed8
- Moved CPU based PME to a separate plugin · 5e0b0e3a
  peastman authored Jun 24, 2013
  
  5e0b0e3a
21 Jun, 2013 2 commits
- Connected CPU based PME to CUDA platform · 932a61b6
  peastman authored Jun 21, 2013
  
  932a61b6
- Fixed threading problems in CPU based PME · 56c071cc
  peastman authored Jun 21, 2013
  
  56c071cc
20 Jun, 2013 1 commit
- Continuing to implement CPU based PME · 823ad165
  peastman authored Jun 20, 2013
  
  823ad165
19 Jun, 2013 1 commit
- Parallelized charge spreading for CPU based PME. · 684ba725
  peastman authored Jun 19, 2013
  
  684ba725
18 Jun, 2013 1 commit
- Parallelized the reciprocal convolution and force interpolation. · 58e0996f
  peastman authored Jun 18, 2013
  
  58e0996f
17 Jun, 2013 1 commit
- Optimizations and bug fixes to CPU based PME · 54a93542
  peastman authored Jun 17, 2013
  
  54a93542
14 Jun, 2013 1 commit
- Continuing to implement CPU based PME · cf1070b6
  peastman authored Jun 14, 2013
  
  cf1070b6
13 Jun, 2013 4 commits
- Fixed bugs in addExtraParticles() · 84acc13d
  peastman authored Jun 13, 2013
  
  84acc13d
- Python wrapper for getVirtualSite() returns the correct subclass · ca74ebb8
  peastman authored Jun 13, 2013
  
  ca74ebb8
- Merge branch 'master' of https://github.com/SimTk/openmm · 82036a8c
  Peter Eastman authored Jun 13, 2013
  
  82036a8c
- Began implementing CPU based PME · 484472ca
  peastman authored Jun 13, 2013
  
  484472ca
12 Jun, 2013 3 commits
- Merge pull request #20 from rmcgibbo/pdb-overflow · 5f144c2c
  peastman authored Jun 12, 2013
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Avoid writing malformed PDBs when the positions are too large.
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  5f144c2c
- change error · b4c52477
  Robert McGibbon authored Jun 12, 2013
  
  b4c52477
- fix negative sign issue, and gracefully degrade precision by lopping off decimal places · 58786bc5
  Robert McGibbon authored Jun 12, 2013
  
  58786bc5
11 Jun, 2013 1 commit
- Avoid writing malformed output when the positions are too large. · 3261df63
  Robert McGibbon authored Jun 11, 2013
  
  3261df63
04 Jun, 2013 4 commits
- Merge branch 'master' of https://github.com/peastman/openmm · 4cf9f9d1
  Peter authored Jun 04, 2013
  
  4cf9f9d1
- Converted the array containing atom block indices for the neighbor list from... · 2ff0b0ae
  peastman authored Jun 04, 2013
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Converted the array containing atom block indices for the neighbor list from ushort2 to int.  This removes the hard limit of 2 million atoms.
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  2ff0b0ae
- Merge pull request #17 from peastman/master · 712a44cc
  Yutong Zhao authored Jun 04, 2013
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Bug fix to Modeller
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  712a44cc
- Fixed a bug caused by conflicting definitions of sum() · 7ae8e13a
  peastman authored Jun 04, 2013
  
  7ae8e13a
03 Jun, 2013 3 commits
- Merge pull request #15 from peastman/master · 07ef5c06
  Yutong Zhao authored Jun 03, 2013
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Improved error checking
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  07ef5c06
- Improved error messages when an invalid number of contracted beads is specified · e5cc38cf
  peastman authored Jun 03, 2013
  
  e5cc38cf
- Merge pull request #14 from peastman/contraction · bd4876cc
  Yutong Zhao authored Jun 03, 2013
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Implemented RPMD ring polymer contraction
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  bd4876cc
01 Jun, 2013 1 commit
- Created Python API for ring polymer contraction · ffdce362
  peastman authored May 31, 2013
  
  ffdce362
31 May, 2013 2 commits
- Created OpenCL implementation of ring polymer contraction · 8656e3ba
  peastman authored May 31, 2013
  
  8656e3ba
- Created CUDA implementation of ring polymer contraction · 863447a6
  peastman authored May 30, 2013
  
  863447a6
30 May, 2013 2 commits
- Merge branch 'master' of https://github.com/peastman/openmm · 2e0ebb67
  Peter Eastman authored May 30, 2013
  
  2e0ebb67
- Created API and reference implementation for ring polymer contraction · c0ccf9e3
  peastman authored May 30, 2013
  
  c0ccf9e3
29 May, 2013 1 commit
- Merge pull request #13 from proteneer/master · 5db397d0
  peastman authored May 29, 2013
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Add support for long long shuffle
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  5db397d0