Commits · b9d12c46232671c10ade0e36ebd637a4f53bd50a · tsoc / openmm

25 Oct, 2011 5 commits
- Clean code and several bug fixes to GB/VI and Obc for nonbonded methods w/ cutoffs · b9d12c46
  Mark Friedrichs authored Oct 25, 2011
  
  b9d12c46
- More changes from Tony to reduce local memory use · ce74c6ae
  Peter Eastman authored Oct 25, 2011
  
  ce74c6ae
- GBSA OBC thread block size now based in part on available shared memory · 3f64d970
  Mark Friedrichs authored Oct 25, 2011
  
  3f64d970
- Threads per block for GB/VI kernels take into account required shared memory · 09c1460d
  Mark Friedrichs authored Oct 25, 2011
```
Padded atom entries in Born radii memory now initialized to zero
launch bounds guards now included for several kernels
```
  09c1460d
- Fix for GB/VI · dbea5152
  Mark Friedrichs authored Oct 25, 2011
  
  dbea5152
24 Oct, 2011 4 commits
- Edited and commented on draft · 805d4144
  Joy Ku authored Oct 24, 2011
  
  805d4144
- Removed diagnostic message · 2188d92a
  Mark Friedrichs authored Oct 24, 2011
  
  2188d92a
- Mods for additions/deletions to free energy plugin interface · 5baba853
  Mark Friedrichs authored Oct 24, 2011
  
  5baba853
- Extened Free energy plugin to allow cutoffs; cleaned up code and added tests · bc85b9f0
  Mark Friedrichs authored Oct 24, 2011
  
  bc85b9f0
20 Oct, 2011 3 commits
- Added Born radius scaling method and associated parameters · d4441c15
  Mark Friedrichs authored Oct 20, 2011
  
  d4441c15
- Beginning of application guide · ca9e8f8d
  Peter Eastman authored Oct 20, 2011
  
  ca9e8f8d
- Added some missing Windows EXPORTs · 7334bd9e
  Peter Eastman authored Oct 20, 2011
  
  7334bd9e
19 Oct, 2011 1 commit
- Removed unused parameters · 55678aa1
  Mark Friedrichs authored Oct 19, 2011
  
  55678aa1
18 Oct, 2011 2 commits
- Bug fixes to CustomGBForce · 906a0473
  Peter Eastman authored Oct 18, 2011
  
  906a0473
- Recognize all whitespace characters in expressions, not just spaces · 8b544e9c
  Peter Eastman authored Oct 18, 2011
  
  8b544e9c
17 Oct, 2011 2 commits
- Minor optimizations to reorderAtoms() · 73369ddd
  Peter Eastman authored Oct 17, 2011
  
  73369ddd
- Fixed compilation errors on Windows · 2927116e
  Peter Eastman authored Oct 17, 2011
  
  2927116e
15 Oct, 2011 1 commit
- Fixed some incorrect argument indices · b982b0e4
  Peter Eastman authored Oct 15, 2011
  
  b982b0e4
14 Oct, 2011 1 commit
- Created para-hydrogen test case for RPMD · 4e402990
  Peter Eastman authored Oct 14, 2011
  
  4e402990
13 Oct, 2011 2 commits
- Implemented == and != operators for Vec3 · 0ba49469
  Peter Eastman authored Oct 13, 2011
  
  0ba49469
- Bug fix to OpenCL RPMD · b7119534
  Peter Eastman authored Oct 13, 2011
  
  b7119534
12 Oct, 2011 1 commit
- Bug fixes to OpenCL RPMD · 49e268f1
  Peter Eastman authored Oct 12, 2011
  
  49e268f1
11 Oct, 2011 1 commit
- Tony Tye's optimization to reduce local memory use · 4405b165
  Peter Eastman authored Oct 11, 2011
  
  4405b165
07 Oct, 2011 2 commits
- Added "const" and "restrict" to lots of kernel arguments to let the compiler do more optimizations · 69e75377
  Peter Eastman authored Oct 07, 2011
  
  69e75377
- Fixed errors in GB on AMD GPUs · bf8b9f30
  Peter Eastman authored Oct 07, 2011
  
  bf8b9f30
06 Oct, 2011 3 commits
- Added a missing #include that caused compilation to fail · b475e127
  Peter Eastman authored Oct 06, 2011
  
  b475e127
- Add unit test for NonbondedSoftcoreForce · 9dd055eb
  Mark Friedrichs authored Oct 06, 2011
```
Cleanup code associated w/ NonbondedSoftcoreForce
```
  9dd055eb
- Fixed bug in OpenCL RPMD implementation · ab60bff4
  Peter Eastman authored Oct 06, 2011
  
  ab60bff4
05 Oct, 2011 6 commits
- Cleaned up code · 326627a8
  Mark Friedrichs authored Oct 05, 2011
  
  326627a8
- Minor mods · a587c652
  Mark Friedrichs authored Oct 05, 2011
  
  a587c652
- Cosmetic changes · 7f561d68
  Mark Friedrichs authored Oct 05, 2011
  
  7f561d68
- Add TestReferenceOBCSoftcoreForce · b64535d8
  Mark Friedrichs authored Oct 05, 2011
  
  b64535d8
- Mods for OBCSoftcore · 1d11610b
  Mark Friedrichs authored Oct 05, 2011
  
  1d11610b
- Code cleanup · 6718e0cc
  Mark Friedrichs authored Oct 05, 2011
  
  6718e0cc
04 Oct, 2011 2 commits
- Interface change for computeBornRadii() method · 1079a319
  Mark Friedrichs authored Oct 04, 2011
  
  1079a319
- Cleaned up code · 4d499572
  Mark Friedrichs authored Oct 04, 2011
  
  4d499572
03 Oct, 2011 2 commits
- Replaced references to usage of OBC algorithm for calculating Born radii in... · e9505f5b
  Mark Friedrichs authored Oct 03, 2011
```
Replaced references to usage of OBC algorithm for calculating Born radii in OpenMM/AMOEBA w/ the Grycuk algorithm
```
  e9505f5b
- Turn off diagnostics · cff89c54
  Mark Friedrichs authored Oct 03, 2011
  
  cff89c54
30 Sep, 2011 2 commits
- Replaced calculation of Born radii using OBC algorithm w/ Grycuk algorithm · 25058a77
  Mark Friedrichs authored Sep 30, 2011
```
TorsionTorsion grids reordered, if needed, so that first angle is the 'slow' index
Fixes for MonteCarloBarostat 
```
  25058a77
- Added enforcePeriodicBox flag to RPMDIntegrator::getState() · e772769e
  Peter Eastman authored Sep 30, 2011
  
  e772769e