Commits · 4e50d72141b60a7a37ce6f2ef94d49d85a1529b1 · tsoc / openmm

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
```
Cleaned up Python API for XmlSerializer.  Also ensure that deserialized objects are returned as the correct class (see bug 1827)
```
  4f911c7a
23 Mar, 2013 1 commit
- Fixed errors in mixed precision mode · 85f8a7e2
  Peter Eastman authored Mar 23, 2013
  
  85f8a7e2
22 Mar, 2013 4 commits
- Fixed test cases for serializing AMOEBA forces · c4e26638
  Peter Eastman authored Mar 22, 2013
  
  c4e26638
- Replaced lots of tabs with spaces · b723e4af
  Peter Eastman authored Mar 22, 2013
  
  b723e4af
- Merged 5.1Optimizations branch back to trunk · 93c467b2
  Peter Eastman authored Mar 22, 2013
  
  93c467b2
- Fixes nvcc terminals popping up during CUDA JIT compilation due to invoking... · f6d4557d
  Yutong Zhao authored Mar 22, 2013
```
Fixes nvcc terminals popping up during CUDA JIT compilation due to invoking system("nvcc ..."). Replaced with MSVC's native CreateProcess() function. 
```
  f6d4557d
19 Mar, 2013 1 commit
- Throw exception if an atom type is defined twice · bc90b216
  Peter Eastman authored Mar 19, 2013
  
  bc90b216
18 Mar, 2013 2 commits
- Accidentally added local copy of /docs as subfolder under /docs. Deleting subfolder and contents. · 248e8883
  Joy Ku authored Mar 18, 2013
  
  248e8883
- No commit message · 3050314a
  Joy Ku authored Mar 18, 2013
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No commit message
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  3050314a
17 Mar, 2013 1 commit

Fixed units for AMOEBA dipole and quadrupole moment (now returns Debye and... · 4386b1a8

Lee-Ping Wang authored Mar 17, 2013

Fixed units for AMOEBA dipole and quadrupole moment (now returns Debye and Debye * Angstrom, not Debye/10 and Debye*Angstrom/100.)  Rationale is that Debye/10 is not a common physical unit.  Note that CUDA platform still gets quadrupole to be incorrect.

4386b1a8

26 Feb, 2013 1 commit
- CudaApplyConstraintsKernel::apply() did not set the context as current,... · 624c878f
  Peter Eastman authored Feb 26, 2013
```
CudaApplyConstraintsKernel::apply() did not set the context as current, leading to errors when using multiple contexts
```
  624c878f