Commits · 63955548e942e574e055e3064791940338049cbf · tsoc / openmm

10 Apr, 2013 1 commit
- 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
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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

30 Mar, 2013 1 commit

Completed support for serialization of all integrator types. Modified... · a6882a28

Yutong Zhao authored Mar 30, 2013

Completed support for serialization of all integrator types. Modified Assertion utilities to allow ASSERT_EQUAL to work on strings. Updated unit tests for testSerializeIntegrators.

a6882a28

29 Mar, 2013 3 commits
- Fixed failing test cases · 0ea02ab9
  Peter Eastman authored Mar 29, 2013
  
  0ea02ab9
- Improved test cases: use symmetric difference to approximate force instead of one sided difference · aefe9a9f
  Peter Eastman authored Mar 29, 2013
  
  aefe9a9f
- GromacsTopFile processes [pairs] lines correctly · fb13fc68
  Peter Eastman authored Mar 29, 2013
  
  fb13fc68
28 Mar, 2013 3 commits
- Added platform properties to report the CUDA/OpenCL device name and OpenCL platform name · 0f83704f
  Peter Eastman authored Mar 28, 2013
  
  0f83704f
- Added Context::setState() · 4d75af9f
  Peter Eastman authored Mar 28, 2013
  
  4d75af9f
- In double precision mode, compute erfc() exactly instead of approximating it · 403b2595
  Peter Eastman authored Mar 28, 2013
  
  403b2595
27 Mar, 2013 3 commits
- Fixed incorrect documentation · 0a1f4594
  Peter Eastman authored Mar 27, 2013
  
  0a1f4594
- Fixed errors in mixed precision mode · 613bd77b
  Peter Eastman authored Mar 27, 2013
  
  613bd77b
- Fixed bug reading PDB files with multiple locations for some atoms · 00e0bb96
  Peter Eastman authored Mar 27, 2013
  
  00e0bb96
26 Mar, 2013 1 commit
- Fixed compilation error on Windows · df265df8
  Peter Eastman authored Mar 26, 2013
  
  df265df8
25 Mar, 2013 3 commits
- Fixed error in mixed precision mode · 6f7c46b4
  Peter Eastman authored Mar 25, 2013
  
  6f7c46b4
- Explicitly check for the return code of nvcc in CUDA JIT compilation. · abf9bd6b
  Yutong Zhao authored Mar 25, 2013
  
  abf9bd6b
- Cleaned up Python API for XmlSerializer. Also ensure that deserialized... · 4f911c7a
  Peter Eastman authored Mar 25, 2013
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Cleaned up Python API for XmlSerializer.  Also ensure that deserialized objects are returned as the correct class (see bug 1827)
```
  4f911c7a