Commits · b321a758e9bc0a91f35d301e1cbbc3e065217315 · tsoc / openmm

18 Nov, 2009 7 commits
- Clean up to remove warning · b321a758
  Mark Friedrichs authored Nov 18, 2009
  
  b321a758
- Mods for Windows · b8019839
  Mark Friedrichs authored Nov 18, 2009
  
  b8019839
- Mods to get rng to compile on Linux · 0d19a61c
  Mark Friedrichs authored Nov 18, 2009
  
  0d19a61c
- Mods to get rng to compile on Windows · 35daf780
  Mark Friedrichs authored Nov 18, 2009
  
  35daf780
- Change double to RealOpenMM to remove build warnings · c4b8ba2d
  Mark Friedrichs authored Nov 18, 2009
  
  c4b8ba2d
- Added #include <typeinfo> to see if it removes errors associated w/... · 9535bef7
  Mark Friedrichs authored Nov 18, 2009
```
Added #include <typeinfo> to see if it removes errors associated w/ std::bad_cast on Linux Ubuntu 4.3.2
```
  9535bef7
- Removed reference to cudaKernels.h · 7ca951d1
  Mark Friedrichs authored Nov 18, 2009
  
  7ca951d1
17 Nov, 2009 4 commits
- Created CUDA implementation of CustomExternalForce · 77d3b647
  Peter Eastman authored Nov 17, 2009
  
  77d3b647
- Put more reasonable tolerances into test case for random number generator · 20b02641
  Peter Eastman authored Nov 17, 2009
  
  20b02641
- Units of nonPolarPrefactor are now kJ/mol/nm^2 (were kcal/mol/A^2) · fd767c3d
  Mark Friedrichs authored Nov 17, 2009
```
Changed ReferenceFreeEnergyPlatform name to ReferenceFreeEnergy
Removed references to ParameterFileName in GB/VI
```
  fd767c3d
- Redesigned CustomNonbondedForce to eliminate combining rules and allow the... · 70015b75
  Peter Eastman authored Nov 17, 2009
```
Redesigned CustomNonbondedForce to eliminate combining rules and allow the expression to directly use parameters for individual particles.
```
  70015b75
13 Nov, 2009 1 commit
- Eliminated use of rand() and srand(), which are not thread safe · 37b2436e
  Peter Eastman authored Nov 13, 2009
  
  37b2436e
12 Nov, 2009 8 commits
- Created CUDA implementation of CustomBondForce · bcbd7dc1
  Peter Eastman authored Nov 12, 2009
  
  bcbd7dc1
- Disabled building static library for CUDA plugin · 0de2ac88
  Peter Eastman authored Nov 12, 2009
  
  0de2ac88
- Set private entries for integrators · 0a38a824
  Mark Friedrichs authored Nov 12, 2009
  
  0a38a824
- Initialized prevTemp, prevFriction, prevStepSize · 0d29e962
  Mark Friedrichs authored Nov 12, 2009
  
  0d29e962
- Removed reference to srand()/rand() due to thread-safety concerns; · c3c6724a
  Mark Friedrichs authored Nov 12, 2009
```
replaced w/ the "KISS" (Keep It Simple Stupid) random number generator implemented in rng.h & rng.cpp
```
  c3c6724a
- gpuSetObcSoftcoreParameters was not returning GpuObcGbsaSoftcore reference · 45cbddce
  Mark Friedrichs authored Nov 12, 2009
  
  45cbddce
- Optimization to evaluating integral powers in custom expressions · 1e52c490
  Peter Eastman authored Nov 12, 2009
  
  1e52c490
- Optimization to evaluating tabulated functions · d0ce27f1
  Peter Eastman authored Nov 12, 2009
  
  d0ce27f1
11 Nov, 2009 7 commits
- Added support for subexpressions · e1a7bc3d
  Peter Eastman authored Nov 11, 2009
  
  e1a7bc3d
- Remove doubling of nonbonded buffers for OBC & GB/VI · e09764b5
  Mark Friedrichs authored Nov 11, 2009
  
  e09764b5
- Inactivate diagnostic · 29fa0870
  Mark Friedrichs authored Nov 11, 2009
  
  29fa0870
- Mods to remove requirement that nonbonded force buffer size should be doubled for GB/VI and OBC · 7b89b1bf
  Mark Friedrichs authored Nov 11, 2009
  
  7b89b1bf
- Created OpenCL implementation of CustomExternalForce. Also fixed a bug. · 67b261f6
  Peter Eastman authored Nov 11, 2009
  
  67b261f6
- Fixed a broken test case · 20e2483b
  Peter Eastman authored Nov 11, 2009
  
  20e2483b
- Created CustomExternalForce, along with the reference implementation · dc556529
  Peter Eastman authored Nov 11, 2009
  
  dc556529
10 Nov, 2009 3 commits
- Created OpenCL implementation of CustomBondForce · 1f6802f9
  Peter Eastman authored Nov 10, 2009
  
  1f6802f9
- Created CustomBondForce, along with the reference implementation · 3eb561ad
  Peter Eastman authored Nov 10, 2009
  
  3eb561ad
- Added missing kReduceObcGbsaSoftcoreBornForces · f3aa6be9
  Mark Friedrichs authored Nov 10, 2009
  
  f3aa6be9
09 Nov, 2009 4 commits
- Bug fix · aa4f6c62
  Peter Eastman authored Nov 09, 2009
  
  aa4f6c62
- Added ReferenceFreeEnergyPlatform & CudaFreeEnergyPlatform · 6d1814ac
  Mark Friedrichs authored Nov 09, 2009
  
  6d1814ac
- NonPolarPrefactor for GBSA OBC was missing for CudaPlatform · 0d42a187
  Mark Friedrichs authored Nov 09, 2009
  
  0d42a187
- Softcore factor multiplying LJ eps is now lambda^4 instead of lambda^1 · c9e927a5
  Mark Friedrichs authored Nov 09, 2009
```
Removed references to softCoreLJLambda in NonbondedSoftcoreForce
```
  c9e927a5
07 Nov, 2009 1 commit
- Fixed two bugs · 8365dede
  Peter Eastman authored Nov 07, 2009
  
  8365dede
06 Nov, 2009 5 commits
- Created OpenCL implementations of AndersenThermostat and BrownianIntegrator. Also fixed some bugs. · cc5467e7
  Peter Eastman authored Nov 06, 2009
  
  cc5467e7
- Fixed compilation error on AMD's OpenCL implementation · 13d89753
  Peter Eastman authored Nov 06, 2009
  
  13d89753
- Bug fix · de04cdb3
  Peter Eastman authored Nov 06, 2009
  
  de04cdb3
- Created (not yet fully debugged) OpenCL implementation of... · 3cf5495a
  Peter Eastman authored Nov 06, 2009
```
Created (not yet fully debugged) OpenCL implementation of VariableVerletIntegrator and VariableLangevinIntegrator.
```
  3cf5495a
- Added TestReferenceGBVISoftcoreForce and repaired TestCudaGBVISoftcoreForce · 50f8b9fa
  Mark Friedrichs authored Nov 06, 2009
```
Removed print cruft
```
  50f8b9fa