Commits · b0bda3a195365a5523da009034178b845e85d0df · tsoc / openmm

14 Jan, 2012 1 commit
- Bug fix to previous bug fix · b0bda3a1
  Peter Eastman authored Jan 14, 2012
  
  b0bda3a1
13 Jan, 2012 3 commits
- Fixed bug in CustomIntegrator when atoms get reordered · 69812ad7
  Peter Eastman authored Jan 13, 2012
  
  69812ad7
- Deleted a file that is no longer used. · 43e57ba0
  Peter Eastman authored Jan 13, 2012
  
  43e57ba0
- Tony Tye's optimizations to sorting. Also a couple of other very minor fixes. · c35407a8
  Peter Eastman authored Jan 13, 2012
  
  c35407a8
12 Jan, 2012 2 commits
- Implemented per-DOF uniform random numbers for OpenCL. Also fixed some bugs... · 052aea3e
  Peter Eastman authored Jan 12, 2012
```
Implemented per-DOF uniform random numbers for OpenCL.  Also fixed some bugs in getting and setting per-DOF variables.
```
  052aea3e
- Optimizations to CustomIntegrator: sum energy on the device, merge kernels when possible · 0d5f265c
  Peter Eastman authored Jan 12, 2012
  
  0d5f265c
11 Jan, 2012 8 commits
- Computing energy without forces caused the array of forces to be overwritten · b45e0d8e
  Peter Eastman authored Jan 11, 2012
  
  b45e0d8e
- Fixed bugs in velocity constraints · 5f95295e
  Peter Eastman authored Jan 11, 2012
  
  5f95295e
- The previous PDFs had markup showing · 25e868e1
  Peter Eastman authored Jan 11, 2012
  
  25e868e1
- Added warning about Windows "Program Compatibility Assistant" · 488b64f6
  Peter Eastman authored Jan 11, 2012
  
  488b64f6
- Fixed bug creating Python wrappers when the source code is inside a directory called "src" · b791d979
  Peter Eastman authored Jan 11, 2012
  
  b791d979
- Continuing to implement OpenCL CustomIntegrator: added velocity constraints... · 12c95e78
  Peter Eastman authored Jan 11, 2012
```
Continuing to implement OpenCL CustomIntegrator: added velocity constraints (not yet fully debugged)
```
  12c95e78
- Fixed incorrect comments · 08021b4e
  Peter Eastman authored Jan 11, 2012
  
  08021b4e
- Fixed bug in velocity constraints · 8819c217
  Peter Eastman authored Jan 11, 2012
  
  8819c217
09 Jan, 2012 4 commits
- Made it easier to stop a simulation by pressing control-c · 6c159d06
  Peter Eastman authored Jan 09, 2012
  
  6c159d06
- Fixed bug in Python wrapper generation · 01726081
  Peter Eastman authored Jan 09, 2012
  
  01726081
- Fixed compilation error when using double precision for CustomIntegrator · f820e172
  Peter Eastman authored Jan 09, 2012
  
  f820e172
- Continuing to implement OpenCL CustomIntegrator: added position constraints,... · 9e4cf579
  Peter Eastman authored Jan 09, 2012
```
Continuing to implement OpenCL CustomIntegrator: added position constraints, and use double precision where possible
```
  9e4cf579
06 Jan, 2012 7 commits
- Minor improvements to test script · ce6af5fd
  Peter Eastman authored Jan 06, 2012
  
  ce6af5fd
- Continuing implementation of OpenCL CustomIntegrator · dc8625a0
  Peter Eastman authored Jan 06, 2012
  
  dc8625a0
- Replaced exit() with exceptions · 36f6f9e6
  Mark Friedrichs authored Jan 06, 2012
  
  36f6f9e6
- Fixed bug in testInstallation script · 591c5f92
  Peter Eastman authored Jan 06, 2012
  
  591c5f92
- Created testInstallation.py script · 7dfc3aea
  Peter Eastman authored Jan 06, 2012
  
  7dfc3aea
- Minor fixes, added discussion of testInstallation.py script · 9c39f46e
  Peter Eastman authored Jan 06, 2012
  
  9c39f46e
- Beginnings of OpenCL implementation of CustomIntegrator · c7c13602
  Peter Eastman authored Jan 06, 2012
  
  c7c13602
05 Jan, 2012 3 commits
- Edits based on Joy's comments · b66c5425
  Mark Friedrichs authored Jan 05, 2012
  
  b66c5425
- Updated AMOEBA plug-in section and install instructions for 4.0 · d0aba41f
  Joy Ku authored Jan 05, 2012
  
  d0aba41f
- Updated application guide · b5964c70
  Joy Ku authored Jan 05, 2012
  
  b5964c70
04 Jan, 2012 3 commits
- File was not updated w/ r3053 · fbe20d20
  Mark Friedrichs authored Jan 04, 2012
  
  fbe20d20
- Minor API change to fix problem in wrapper generation · d5213882
  Peter Eastman authored Jan 04, 2012
  
  d5213882
- Python API generator no longer requires xpath library · 133b80e1
  Peter Eastman authored Jan 04, 2012
  
  133b80e1
03 Jan, 2012 3 commits
- Python examples only simulate 10,000 time steps instead of 100,000 · 3eff31f2
  Peter Eastman authored Jan 03, 2012
  
  3eff31f2
- Fixed bug in recognizing incomplete TER records in PDB files · 6c6161cb
  Peter Eastman authored Jan 03, 2012
  
  6c6161cb
- Added methods to set variables by name · 95093334
  Peter Eastman authored Jan 03, 2012
  
  95093334
17 Dec, 2011 1 commit
- Fixed Python API builder to handle CustomIntegrator · 4ca69ecc
  Peter Eastman authored Dec 17, 2011
  
  4ca69ecc
16 Dec, 2011 1 commit
- Implemented velocity constraints for CustomIntegrator · 50154b8b
  Peter Eastman authored Dec 16, 2011
  
  50154b8b
15 Dec, 2011 2 commits
- Created CustomIntegrator, including reference implementation · dfba24ea
  Peter Eastman authored Dec 15, 2011
  
  dfba24ea
- Memory leak fix · e9c5ab17
  Mark Friedrichs authored Dec 15, 2011
  
  e9c5ab17
13 Dec, 2011 2 commits
- Minor updates to installation instructions · d32d2920
  Peter Eastman authored Dec 13, 2011
  
  d32d2920
- Minor cleanup · c178e2c1
  Peter Eastman authored Dec 13, 2011
  
  c178e2c1