Commits · c775bd19961fe05b606a2b8e0213f2eea27c41af · tsoc / openmm

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27 Jan, 2012 1 commit
- Renamed math functions in Cuda kernels to single-precision equivalent [cos() -> cosf()] · 470c9b7f
  Mark Friedrichs authored Jan 27, 2012
  
  470c9b7f
12 Dec, 2011 1 commit
- Modified threadsPerBlock for several kernels and added launch_bounds · 77742df8
  Mark Friedrichs authored Dec 12, 2011
  
  77742df8
23 Nov, 2011 1 commit
- Edits to remove some VC9 warnings · 36762962
  Mark Friedrichs authored Nov 23, 2011
  
  36762962
10 Nov, 2011 1 commit

Mark Friedrichs authored Nov 10, 2011

In Born radii calculation for particle i, removed factor of lambda associated w/ particle i

032e18de

26 Oct, 2011 2 commits
- Moved gpuSetNonbondedSoftcoreParameters() to freeEnergyCudaGpu.cpp · 0308dbf8
  Mark Friedrichs authored Oct 26, 2011
  
  0308dbf8
- Added missing iostream header · 2c708e02
  Mark Friedrichs authored Oct 26, 2011
  
  2c708e02
25 Oct, 2011 3 commits
- Temp fix for tempBuffers used w/ cutoffs · efe4025d
  Mark Friedrichs authored Oct 25, 2011
  
  efe4025d
- 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
24 Oct, 2011 1 commit
- Extened Free energy plugin to allow cutoffs; cleaned up code and added tests · bc85b9f0
  Mark Friedrichs authored Oct 24, 2011
  
  bc85b9f0
09 Aug, 2011 1 commit
- Added missing lambda factor in second OBC force loop of free energy plugin · 2141605b
  Mark Friedrichs authored Aug 09, 2011
  
  2141605b
03 Mar, 2011 1 commit
- Modified number of threeads used in Born sum reduction · c7a1ae89
  Mark Friedrichs authored Mar 03, 2011
  
  c7a1ae89
29 Jun, 2010 1 commit
- Added static to __device__ declarations to allow compilation w/ CUDA 3.1 · 2833fb44
  Mark Friedrichs authored Jun 29, 2010
  
  2833fb44
05 Apr, 2010 1 commit
- Modified pForce4a -> pForce4 · 2db43eae
  Mark Friedrichs authored Apr 05, 2010
  
  2db43eae
04 Dec, 2009 1 commit

Edits to address potential thread-safety issues: · b0e45e86

Mark Friedrichs authored Dec 04, 2009

Removed static variables in CudaFreeEnergyKernels.cpp
Moved declaration of global feSim to within method where actually used  in kCalculateNonbondedSoftcore.cu

b0e45e86

03 Dec, 2009 1 commit
- 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
26 Nov, 2009 1 commit
- Removal of CudaFreeEnergyPlatform · 844a0bf6
  Mark Friedrichs authored Nov 26, 2009
  
  844a0bf6
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 2 commits
- 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 3 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
- 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 1 commit
- 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 2 commits
- 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 2 commits

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

fb249907

dded GB/VI to Cuda platform · 7a36f461

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