Commits · 456b8a0538539d1e7d6bf7aae6a91b6e1c7c9680 · tsoc / openmm

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16 Apr, 2013 2 commits
- Updated version number to 5.1. · 456b8a05
  Peter Eastman authored Apr 16, 2013
  
  456b8a05
- Fixed bug that caused some TOP files to fail · 681f601b
  Peter Eastman authored Apr 16, 2013
  
  681f601b
15 Apr, 2013 5 commits
- Context constructor now uses const System&, guaranteeing that System won't be modified. · 0307a0db
  Yutong Zhao authored Apr 15, 2013
  
  0307a0db
- Fixes a minor windows compiler invocation issue where C:\Program Files becomes... · 19757775
  Yutong Zhao authored Apr 15, 2013
```
Fixes a minor windows compiler invocation issue where C:\Program Files becomes delimited by the space. Also enables debugging libraries to be built in debug mode for WIN32 + Visual Studio. 
```
  19757775
- CMakeLists now includes .cl and .cu kernel files as part of the project in Visual Studio. · 5c4abf73
  Yutong Zhao authored Apr 15, 2013
  
  5c4abf73
- Fixed bug that prevented constraints being applied when computing kinetic energy · 37b86c10
  Peter Eastman authored Apr 15, 2013
  
  37b86c10
- Fixes a race condition in buffer status in findBlocksWithInteractions() · 29256dfe
  Yutong Zhao authored Apr 15, 2013
  
  29256dfe
12 Apr, 2013 4 commits
- Updated version number to 5.1 · cbc21173
  Peter Eastman authored Apr 12, 2013
  
  cbc21173
- Call cudaProfilerStop() when destroying a context so profiling will work correctly · 11b86e0d
  Peter Eastman authored Apr 12, 2013
  
  11b86e0d
- Fixed errors in mixed precision mode · a106d7d1
  Peter Eastman authored Apr 12, 2013
  
  a106d7d1
- When computing kinetic energy, make sure the shifted velocities are... · 820a6baa
  Peter Eastman authored Apr 12, 2013
```
When computing kinetic energy, make sure the shifted velocities are perpendicular to the constraints
```
  820a6baa
11 Apr, 2013 1 commit
- Changed workgroup size to work around NVIDIA bug. This also improves performance slightly. · 01afee8b
  Peter Eastman authored Apr 11, 2013
  
  01afee8b
10 Apr, 2013 3 commits
- Added volatile keyword to fix crashes on some GPUs · 83284ce6
  Peter Eastman authored Apr 10, 2013
  
  83284ce6
- RPMD supports virtual sites · 3e7616fc
  Peter Eastman authored Apr 10, 2013
  
  3e7616fc
- Added some PDB residue and atom synonyms used by Tinker · 63955548
  Peter Eastman authored Apr 10, 2013
  
  63955548
09 Apr, 2013 2 commits
- RPMDIntegrator throws an exception if the System includes virtual sites · d5b80604
  Peter Eastman authored Apr 09, 2013
  
  d5b80604
- Bug fix · 703842be
  Peter Eastman authored Apr 09, 2013
  
  703842be
08 Apr, 2013 3 commits
- Reduced memory use for random numbers, eliminated unnecessary calculation when... · 54b7eec9
  Peter Eastman authored Apr 08, 2013
```
Reduced memory use for random numbers, eliminated unnecessary calculation when generating random numbers
```
  54b7eec9
- Added getPeriodicBoxVolume() to State · 9b083022
  Peter Eastman authored Apr 08, 2013
  
  9b083022
- Use peer to peer copying between GPUs when available · 41bcc20f
  Peter Eastman authored Apr 08, 2013
  
  41bcc20f
05 Apr, 2013 4 commits
- Improved performance of CCMA · c0a43bfc
  Peter Eastman authored Apr 05, 2013
  
  c0a43bfc
- Made some test cases (hopefully) more robust · 022a0190
  Peter Eastman authored Apr 05, 2013
  
  022a0190
- Ensure the build directory really gets created, so copying pthreads library doesn't fail · 8fe900c7
  Peter Eastman authored Apr 05, 2013
  
  8fe900c7
- RPMDIntegrator::getState() applies periodic boundary conditions based on copy 0 (see bug 1833) · 9a55eeec
  Peter Eastman authored Apr 05, 2013
  
  9a55eeec
04 Apr, 2013 1 commit
- Ensure that CUDA is chosen over OpenCL when both are available · 4e50d721
  Peter Eastman authored Apr 04, 2013
  
  4e50d721
03 Apr, 2013 11 commits
- Fixed reorderAtoms so that it always uses double precision periodicBoxSizeDouble. · aee19db2
  Yutong Zhao authored Apr 03, 2013
  
  aee19db2
- Bug fix · fea6769a
  Peter Eastman authored Apr 03, 2013
  
  fea6769a
- Replaced hydrogenDefinitions argument with a loadHydrogenDefinitions() method · c4e08591
  Peter Eastman authored Apr 03, 2013
  
  c4e08591
- Added Topology.loadBondDefinitions() · a700032d
  Peter Eastman authored Apr 03, 2013
  
  a700032d
- Modeller.addHydrogens() allows the user to provide an XML file with additional residue definitions · cd68d924
  Peter Eastman authored Apr 03, 2013
  
  cd68d924
- Modeller.addHydrogens() returns a list of what variants were used · 47b2ac75
  Peter Eastman authored Apr 03, 2013
  
  47b2ac75
- Reduced default constraint tolerance to 1e-5 · 293eccf9
  Peter Eastman authored Apr 03, 2013
  
  293eccf9
- Improved "no template found" error message to suggest possible causes. · a29ebb6f
  Peter Eastman authored Apr 03, 2013
  
  a29ebb6f
- Robert's refactoring of StateDataReporter to let subclasses add new reported values · 886533b9
  Peter Eastman authored Apr 03, 2013
  
  886533b9
- Copied Lee-Ping's fixes to the CUDA test over to the reference one · b8618886
  Peter Eastman authored Apr 03, 2013
  
  b8618886
- Modified TestCudaAmoebaMultipoleForce to agree with unit-correction. · 9a59374e
  Lee-Ping Wang authored Apr 03, 2013
  
  9a59374e
02 Apr, 2013 3 commits
- Modified some stochastic test cases to fail less often · 9b2b0cad
  Peter Eastman authored Apr 02, 2013
  
  9b2b0cad
- Modified some stochastic test cases to fail less often · 0529f325
  Peter Eastman authored Apr 02, 2013
  
  0529f325
- GromacsTopFile supports all terms needed for CHARMM force field · 8e995a20
  Peter Eastman authored Apr 02, 2013
  
  8e995a20
01 Apr, 2013 1 commit

Removed redundant overload of == operator in AssertionUtilities.h. Removed... · 84165803

Yutong Zhao authored Apr 01, 2013

Removed redundant overload of == operator in AssertionUtilities.h. Removed extraneous version check for serialized integrators and state. Updated unit test to include more details.

84165803