Commits · 644cc275ab5a549a82cce4d49680da729c2051e6 · tsoc / openmm

21 Apr, 2009 1 commit
- Moved header files into an openmm subdirectory · 644cc275
  Peter Eastman authored Apr 21, 2009
  
  644cc275
17 Apr, 2009 4 commits
- CUDA platform would fail if you had a GBSAOBCForce but no NonbondedForce. · b2c89feb
  Peter Eastman authored Apr 17, 2009
  
  b2c89feb
- Fixed a test case that failed on some GPUs. · 11eab27d
  Peter Eastman authored Apr 17, 2009
  
  11eab27d
- Modified the API for lots of classes so that the number of... · 64493da6
  Peter Eastman authored Apr 17, 2009
```
Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.
```
  64493da6
- Redesigned the API for specifying exclusions and 1-4 interactions. · 29e3fa57
  Peter Eastman authored Apr 17, 2009
  
  29e3fa57
16 Apr, 2009 1 commit
- Optimized LINCS by merging kernels and implementing a syncAllThreads() function. · afd06645
  Peter Eastman authored Apr 16, 2009
  
  afd06645
11 Apr, 2009 2 commits
- Modified CMakeLists to not assume the C: drive on Windows. · bf7a968c
  Peter Eastman authored Apr 11, 2009
  
  bf7a968c
- Modified some parameter names and doxygen comments to reduce confusion · e9dc1983
  Peter Eastman authored Apr 11, 2009
  
  e9dc1983
10 Apr, 2009 1 commit
- Improved LINCS performance by eliminating some uncoalesced memory access · 95d1c382
  Peter Eastman authored Apr 10, 2009
  
  95d1c382
09 Apr, 2009 2 commits
- Reference code for GB/VI · 297538f7
  Mark Friedrichs authored Apr 09, 2009
  
  297538f7
- Fixed several bugs in LINCS · 04b90973
  Peter Eastman authored Apr 09, 2009
  
  04b90973
08 Apr, 2009 3 commits
- Fixed thread synchronization problem in LINCS kernel · 8a83a2fb
  Peter Eastman authored Apr 08, 2009
  
  8a83a2fb
- Enhancements to CUDAStream to reduce the risk of bugs and make debugging easier · 306d99e8
  Peter Eastman authored Apr 08, 2009
  
  306d99e8
- Continuing implementation of LINCS for Cuda platform · 968cb132
  Peter Eastman authored Apr 08, 2009
  
  968cb132
07 Apr, 2009 1 commit
- Real space Ewald (direct summation) is now in kCalculateCDLJForces.h,... · 1b9ab82b
  Rossen Apostolov authored Apr 07, 2009
```
Real space Ewald (direct summation) is now in kCalculateCDLJForces.h, reciprocal summation is done in a separate kernel
```
  1b9ab82b
06 Apr, 2009 1 commit
- Implemented the Ewald summation method in the reference platform. Preliminary... · d3b512ad
  Rossen Apostolov authored Apr 06, 2009
```
Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.
```
  d3b512ad
02 Apr, 2009 1 commit
- Converted lots of ints to unsigned ints (might help performance a little by avoiding conversions) · 5b017677
  Peter Eastman authored Apr 02, 2009
  
  5b017677
01 Apr, 2009 1 commit
- Added file that got missed in last commit · e85347d1
  Peter Eastman authored Apr 01, 2009
  
  e85347d1
31 Mar, 2009 1 commit
- Preliminary implementation of LINCS (both reference and Cuda) · 72872e97
  Peter Eastman authored Mar 31, 2009
  
  72872e97
24 Mar, 2009 2 commits
- Keep atom coordinates in the first periodic cell to maintain precision. · 389563ef
  Peter Eastman authored Mar 24, 2009
  
  389563ef
- Deleted lots of obsolete code. · ff0a69f9
  Peter Eastman authored Mar 24, 2009
  
  ff0a69f9
17 Mar, 2009 1 commit
- Fixed compilation warning under Windows. · a56ce87d
  Peter Eastman authored Mar 17, 2009
  
  a56ce87d
10 Mar, 2009 1 commit
- Implemented finer grained neighbor list. Also various minor optimizations. · e04283fe
  Peter Eastman authored Mar 10, 2009
  
  e04283fe
06 Mar, 2009 1 commit
- Use Hilbert curve for reordering water molecules · 56d7ed02
  Peter Eastman authored Mar 06, 2009
  
  56d7ed02
28 Feb, 2009 1 commit
- Reduced memory use for random numbers. Also reduced the frequency of reordering water molecules. · aeb2f4ac
  Peter Eastman authored Feb 28, 2009
  
  aeb2f4ac
27 Feb, 2009 2 commits
- Reduced memory use for exclusions. Also deleted some obsolete files. · 8055a541
  Peter Eastman authored Feb 27, 2009
  
  8055a541
- Minor speed optimization to neighbor list building · b98859ec
  Peter Eastman authored Feb 27, 2009
  
  b98859ec
25 Feb, 2009 1 commit
- Added Linux version of CUDPP library · 66255407
  Peter Eastman authored Feb 25, 2009
  
  66255407
20 Feb, 2009 3 commits
- Implemented setting random seed for reference platform, as well as adding it... · eb0bba22
  Peter Eastman authored Feb 20, 2009
```
Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.
```
  eb0bba22
- Added other files that somehow got ommitted from earlier checkin · 630bdd40
  Peter Eastman authored Feb 20, 2009
  
  630bdd40
- Added missing header file · 9b7a9f65
  Peter Eastman authored Feb 20, 2009
  
  9b7a9f65
19 Feb, 2009 8 commits
- Checking in Cuda implementation of explicit solvent · 1010df33
  Peter Eastman authored Feb 19, 2009
  
  1010df33
- Checked in explicit solvent implementation for Cuda platform (cutoffs,... · df4b64cb
  Peter Eastman authored Feb 19, 2009
```
Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)
```
  df4b64cb
- Added preprocessor flag, OPENMM_BUILDING_SHARED_LIBRARY, to Cuda shared lib build · 08d6cc4c
  Mark Friedrichs authored Feb 19, 2009
  
  08d6cc4c
- Mods for preprocessor flags for shared/static libs · 2b5402dc
  Mark Friedrichs authored Feb 19, 2009
  
  2b5402dc
- Change for static lib and handling of OPENMM_EXPORT · d9de3c8a
  Mark Friedrichs authored Feb 19, 2009
  
  d9de3c8a
- Added changes to get Static libs to work w/ OPENMM_EXPORT setting · c87fe8a3
  Mark Friedrichs authored Feb 19, 2009
  
  c87fe8a3
- If seed <=1, then use time() to generate seed · 84dda6a7
  Mark Friedrichs authored Feb 19, 2009
  
  84dda6a7
- RNG seed mods for LangevinIntegrator · 8c0b4073
  Mark Friedrichs authored Feb 19, 2009
  
  8c0b4073
18 Feb, 2009 1 commit
- Reactivated dupfac dynamic setting · 73f248e7
  Mark Friedrichs authored Feb 18, 2009
```
Made setting of RNG seed consistent w/ logic used for Cuda 
```
  73f248e7