Commits · 065e084b563ee90653b468662f27fb34b19b94be · tsoc / openmm

"platforms/common/vscode:/vscode.git/clone" did not exist on "cdc0789a1b4d82266419d469c951470ef78fd1d0"

03 Dec, 2009 3 commits
- Replace Platform::getPlatform by Platform::getPlatformByName where necessary,... · 065e084b
  John Chodera authored Dec 03, 2009
```
Replace Platform::getPlatform by Platform::getPlatformByName where necessary, due to recently changed interface.
```
  065e084b
- Modified softcore equation to conform w/ Shirts and Pande, JCP 122:134508, 2005. · 8f017de1
  Mark Friedrichs authored Dec 03, 2009
```
Removed cruft from Cmake file
Modified the way platform is specified in TstFreeEnergyCudaUsingParameterFile.cpp
```
  8f017de1
- Fixed plugin initialization for CUDA free energy plugin · 19c403f2
  Peter Eastman authored Dec 03, 2009
  
  19c403f2
01 Dec, 2009 1 commit
- Changed how plugin initialization is done to avoid initialization order problems · 32946009
  Peter Eastman authored Dec 01, 2009
  
  32946009
26 Nov, 2009 3 commits
- Removal of CudaFreeEnergyPlatform · ffc44a95
  Mark Friedrichs authored Nov 26, 2009
  
  ffc44a95
- Removal of CudaFreeEnergyPlatform · 844a0bf6
  Mark Friedrichs authored Nov 26, 2009
  
  844a0bf6
- Removal of ReferenceFreeEnergyPlatform · 3f9a1d9d
  Mark Friedrichs authored Nov 26, 2009
  
  3f9a1d9d
23 Nov, 2009 1 commit
- Mods to remove VC 8 warnings · ca21532c
  Mark Friedrichs authored Nov 23, 2009
  
  ca21532c
20 Nov, 2009 1 commit
- bornRadiusScaleFactors were not included in second GB/VI force loop · ab09b522
  Mark Friedrichs authored Nov 20, 2009
```
removed some cruft
```
  ab09b522
19 Nov, 2009 3 commits
- Inactivated static tests · 8428a88f
  Mark Friedrichs authored Nov 19, 2009
  
  8428a88f
- Activated static tests · d80ba38f
  Mark Friedrichs authored Nov 19, 2009
```
Fixed bug: was calling kReduceObcGbsaSoftcoreBornForces instead of kReduceGBVISoftcoreBornForces in GB/VI force calculation
```
  d80ba38f
- Missing include file · 8fc504ed
  Mark Friedrichs authored Nov 19, 2009
  
  8fc504ed
18 Nov, 2009 4 commits
- Added extern' to SetCalculateLocalSoftcoreGpuSim definition · e6bd8433
  Mark Friedrichs authored Nov 18, 2009
  
  e6bd8433
- Mods to get Free energy plugin libs to compile on Windows; still problem w/... · 98c26853
  Mark Friedrichs authored Nov 18, 2009
```
Mods to get Free energy plugin libs to compile on Windows; still problem w/ kCalculateLocalSoftcoreForces.cu
and hence OpenMMFreeEnergyCuda lib
```
  98c26853
- 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 1 commit
- 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
12 Nov, 2009 1 commit
- gpuSetObcSoftcoreParameters was not returning GpuObcGbsaSoftcore reference · 45cbddce
  Mark Friedrichs authored Nov 12, 2009
  
  45cbddce
11 Nov, 2009 2 commits
- 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
10 Nov, 2009 1 commit
- Added missing kReduceObcGbsaSoftcoreBornForces · f3aa6be9
  Mark Friedrichs authored Nov 10, 2009
  
  f3aa6be9
09 Nov, 2009 3 commits
- 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
06 Nov, 2009 1 commit
- Added TestReferenceGBVISoftcoreForce and repaired TestCudaGBVISoftcoreForce · 50f8b9fa
  Mark Friedrichs authored Nov 06, 2009
```
Removed print cruft
```
  50f8b9fa
03 Nov, 2009 3 commits

Fixes to make Windows happier · fb249907
Mark Friedrichs authored Nov 03, 2009

fb249907
Removed annoying message · bdc4754a
Mark Friedrichs authored Nov 03, 2009

bdc4754a

Mark Friedrichs authored Nov 03, 2009

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail

7a36f461