Filename: AtomMap.h | |||
Revision 1.1018 | jim | 2017/03/30 20:06:17 | +10 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1017 and 1.1018 |
Filename: BOCgroup.h | |||
Revision 1.1034 | jim | 2016/09/29 20:31:46 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1033 and 1.1034 | |||
Revision 1.1033 | jim | 2016/09/14 15:47:31 | +4 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1032 and 1.1033 |
Filename: BackEnd.C | |||
Revision 1.80 | jim | 2017/04/01 19:43:04 | +3 -1 |
Suspend to finish creating groups, allowing use of CkLoop during startup. | |||
Show difference between Revision 1.79 and 1.80 | |||
Revision 1.79 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.78 and 1.79 | |||
Revision 1.78 | jim | 2016/09/14 15:47:31 | +4 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.77 and 1.78 |
Filename: ComputeAngles.C | |||
Revision 1.1038 | jim | 2016/06/08 22:06:20 | +2 -3 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1037 and 1.1038 |
Filename: ComputeBondedCUDA.C | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: ComputeBondedCUDA.h | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: ComputeBondedCUDAKernel.cu | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: ComputeBondedCUDAKernel.h | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: ComputeBonds.C | |||
Revision 1.1035 | jim | 2016/06/08 22:06:21 | +2 -3 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1034 and 1.1035 |
Filename: ComputeCUDAMgr.C | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +45 -2 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputeCUDAMgr.ci | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputeCUDAMgr.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +12 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputeConsForce.C | |||
Filename: ComputeDihedrals.C | |||
Revision 1.1038 | jim | 2016/06/08 22:06:21 | +2 -3 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1037 and 1.1038 |
Filename: ComputeGBIS.inl | |||
Revision 1.6 | jim | 2016/09/14 15:47:31 | +21 -21 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.5 and 1.6 |
Filename: ComputeGridForce.C | |||
Revision 1.28 | ryanmcgreevy | 2016/09/21 20:40:42 | +1 -1 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.27 and 1.28 |
Filename: ComputeHomeTuples.h | |||
Revision 1.1065 | jim | 2017/03/30 20:06:17 | +240 -2 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1064 and 1.1065 |
Filename: ComputeImpropers.C | |||
Revision 1.1035 | jim | 2016/06/08 22:06:21 | +4 -3 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1034 and 1.1035 |
Filename: ComputeLCPO.C | |||
Revision 1.14 | jim | 2016/12/06 21:31:46 | +1 -1 |
Fix apparent error in SASA gradient calculation noticed by Kecheng Yang. | |||
Show difference between Revision 1.13 and 1.14 |
Filename: ComputeMap.h | |||
Revision 1.1060 | jim | 2017/03/30 20:06:17 | +3 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1059 and 1.1060 | |||
Revision 1.1059 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1058 and 1.1059 | |||
Revision 1.1058 | jim | 2016/09/14 15:47:31 | +4 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1057 and 1.1058 |
Filename: ComputeMgr.C | |||
Revision 1.1133 | jim | 2017/03/30 20:06:17 | +369 -40 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1132 and 1.1133 | |||
Revision 1.1132 | jim | 2017/03/20 19:52:17 | +2 -2 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.1131 and 1.1132 | |||
Revision 1.1131 | jim | 2016/09/29 20:31:47 | +11 -2 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1130 and 1.1131 | |||
Revision 1.1130 | jim | 2016/09/14 15:47:31 | +191 -4 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1129 and 1.1130 | |||
Revision 1.1129 | jim | 2016/09/06 19:50:45 | +19 -0 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.1128 and 1.1129 |
Filename: ComputeMgr.ci | |||
Revision 1.1024 | jim | 2017/03/30 20:06:17 | +13 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1023 and 1.1024 | |||
Revision 1.1023 | jim | 2016/09/14 15:47:31 | +14 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1022 and 1.1023 | |||
Revision 1.1022 | jim | 2016/09/06 19:50:45 | +1 -0 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.1021 and 1.1022 |
Filename: ComputeMgr.h | |||
Revision 1.1047 | jim | 2017/03/30 20:06:17 | +21 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1046 and 1.1047 | |||
Revision 1.1046 | jim | 2016/09/14 15:47:31 | +23 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1045 and 1.1046 | |||
Revision 1.1045 | jim | 2016/09/06 19:50:45 | +2 -0 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.1044 and 1.1045 |
Filename: ComputeMsm.C | |||
Revision 1.73 | dhardy | 2017/04/21 21:15:13 | +18 -2 |
Split MSM initialization into two phases to avoid race conditions. Phase 1 initializes the overall Map object that, in part, indicates the PE for each chare. Phase 2 creates the chares. | |||
Show difference between Revision 1.72 and 1.73 | |||
Revision 1.72 | dhardy | 2017/03/29 19:25:55 | +1 -0 |
Added another comment | |||
Show difference between Revision 1.71 and 1.72 | |||
Revision 1.71 | dhardy | 2017/03/29 19:03:04 | +2 -0 |
Added comment to test mail from CVS check-in | |||
Show difference between Revision 1.70 and 1.71 |
Filename: ComputeMsmMgr.ci | |||
Revision 1.21 | dhardy | 2017/04/21 21:15:13 | +1 -0 |
Split MSM initialization into two phases to avoid race conditions. Phase 1 initializes the overall Map object that, in part, indicates the PE for each chare. Phase 2 creates the chares. | |||
Show difference between Revision 1.20 and 1.21 |
Filename: ComputeNonbondedBase.h | |||
Revision 1.1192 | jim | 2016/09/29 20:31:47 | +48 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1191 and 1.1192 | |||
Revision 1.1191 | jim | 2016/09/22 22:14:01 | +13 -9 |
Change temporary pairlists from short to int and use simple pairlist loops on KNL. | |||
Show difference between Revision 1.1190 and 1.1191 | |||
Revision 1.1190 | jim | 2016/08/29 22:15:45 | +47 -127 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.1189 and 1.1190 | |||
Revision 1.1189 | jim | 2016/08/23 21:29:08 | +85 -3 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1188 and 1.1189 |
Filename: ComputeNonbondedBase2.h | |||
Revision 1.55 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.54 and 1.55 | |||
Revision 1.54 | jim | 2016/09/09 21:10:40 | +2 -0 |
Disable pragma simd assert for Go forces kernels | |||
Show difference between Revision 1.53 and 1.54 | |||
Revision 1.53 | jim | 2016/08/29 22:15:45 | +2 -31 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.52 and 1.53 |
Filename: ComputeNonbondedBase2KNL.h | |||
Revision 1.6 | jim | 2016/10/21 21:49:56 | +33 -12 |
Implement MARTINI switching function for Lennard-Jones in KNL kernel. | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2016/09/08 19:35:05 | +4 -0 |
Work around segfault in Intel 2017 compiler (the compiler itself segfaults). | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/08/29 22:15:46 | +8 -21 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/08/29 04:40:09 | +4 -4 |
Fix KNL kernel for PME without multiple timestepping. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/08/26 16:18:42 | +2 -1 |
Eliminate emulated gather by storing vdwType as int. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/08/23 21:29:08 | None |
Optimized kernel for KNL. |
Filename: ComputeNonbondedCUDA.C | |||
Revision 1.102 | jim | 2016/10/27 21:12:14 | +4 -4 |
Require CUDA compute capability 3.0 or higher. | |||
Show difference between Revision 1.101 and 1.102 | |||
Revision 1.101 | jim | 2016/09/14 15:47:31 | +23 -26 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.100 and 1.101 | |||
Revision 1.100 | jim | 2016/09/06 19:50:46 | +6 -0 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.99 and 1.100 |
Filename: ComputeNonbondedCUDA.h | |||
Revision 1.25 | jim | 2016/09/14 15:47:31 | +9 -1 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2016/09/06 19:50:46 | +1 -1 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.23 and 1.24 |
Filename: ComputeNonbondedCUDAKernel.cu | |||
Revision 1.39 | jim | 2016/09/14 15:47:31 | +1 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.38 and 1.39 | |||
Revision 1.38 | jim | 2016/09/06 19:50:46 | +15 -4 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.37 and 1.38 |
Filename: ComputeNonbondedInl.h | |||
Revision 1.16 | jim | 2016/08/23 21:29:08 | +77 -2 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.15 and 1.16 |
Filename: ComputeNonbondedPair.C | |||
Revision 1.1070 | jim | 2016/09/04 11:07:22 | +4 -0 |
Eliminate aggregate virial calculation overhead for CUDA builds. | |||
Show difference between Revision 1.1069 and 1.1070 | |||
Revision 1.1069 | jim | 2016/08/29 22:15:46 | +4 -4 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.1068 and 1.1069 | |||
Revision 1.1068 | jim | 2016/08/23 21:29:08 | +9 -28 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1067 and 1.1068 |
Filename: ComputeNonbondedSelf.C | |||
Revision 1.1064 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1063 and 1.1064 | |||
Revision 1.1063 | jim | 2016/09/04 11:07:22 | +4 -0 |
Eliminate aggregate virial calculation overhead for CUDA builds. | |||
Show difference between Revision 1.1062 and 1.1063 | |||
Revision 1.1062 | jim | 2016/08/29 22:15:46 | +4 -4 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.1061 and 1.1062 | |||
Revision 1.1061 | jim | 2016/08/23 21:29:08 | +6 -0 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1060 and 1.1061 |
Filename: ComputeNonbondedUtil.C | |||
Revision 1.1126 | jim | 2017/03/30 20:06:17 | +2 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1125 and 1.1126 | |||
Revision 1.1125 | jim | 2016/10/21 21:49:56 | +25 -0 |
Implement MARTINI switching function for Lennard-Jones in KNL kernel. | |||
Show difference between Revision 1.1124 and 1.1125 | |||
Revision 1.1124 | jim | 2016/09/29 20:31:47 | +3 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1123 and 1.1124 | |||
Revision 1.1123 | jim | 2016/09/14 20:13:26 | +1 -2 |
Remove unused static alchLambda. | |||
Show difference between Revision 1.1122 and 1.1123 | |||
Revision 1.1122 | jim | 2016/09/14 15:47:31 | +3 -1 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1121 and 1.1122 | |||
Revision 1.1121 | jim | 2016/08/23 21:29:08 | +106 -8 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1120 and 1.1121 |
Filename: ComputeNonbondedUtil.h | |||
Revision 1.1094 | jim | 2017/03/30 20:06:17 | +1 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1093 and 1.1094 | |||
Revision 1.1093 | jim | 2016/10/21 21:49:57 | +7 -0 |
Implement MARTINI switching function for Lennard-Jones in KNL kernel. | |||
Show difference between Revision 1.1092 and 1.1093 | |||
Revision 1.1092 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1091 and 1.1092 | |||
Revision 1.1091 | jim | 2016/09/22 22:14:01 | +5 -5 |
Change temporary pairlists from short to int and use simple pairlist loops on KNL. | |||
Show difference between Revision 1.1090 and 1.1091 | |||
Revision 1.1090 | jim | 2016/09/14 20:13:26 | +0 -1 |
Remove unused static alchLambda. | |||
Show difference between Revision 1.1089 and 1.1090 | |||
Revision 1.1089 | jim | 2016/08/29 22:11:58 | +1 -1 |
Tweak KNL interpolation table size to have grid point at 8/10/12 A cutoff distances. | |||
Show difference between Revision 1.1088 and 1.1089 | |||
Revision 1.1088 | jim | 2016/08/23 21:29:08 | +39 -2 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1087 and 1.1088 |
Filename: ComputePme.C | |||
Revision 1.229 | jim | 2017/02/19 15:19:58 | +75 -16 |
Use CkLoop parallelization on slab PME trans, untrans, and ungrid sends. | |||
Show difference between Revision 1.228 and 1.229 | |||
Revision 1.228 | jim | 2017/02/17 17:19:05 | +5 -5 |
Change "Bool useCkLoop" to "int useCkLoop". | |||
Show difference between Revision 1.227 and 1.228 | |||
Revision 1.227 | jim | 2016/11/04 01:25:07 | +1 -1 |
Fix bug that was enabling PME k-space CkLoop code on too few pes. | |||
Show difference between Revision 1.226 and 1.227 | |||
Revision 1.226 | jim | 2016/10/30 22:50:00 | +40 -13 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.225 and 1.226 | |||
Revision 1.225 | jim | 2016/10/27 18:17:29 | +5 -2 |
Make old CUDA PME (PMEOffload) compatible with new CUDA nonbonded kernels (useCUDA2). | |||
Show difference between Revision 1.224 and 1.225 | |||
Revision 1.224 | jim | 2016/10/10 19:52:01 | +2 -2 |
Work around CUDA errors during PME force calculation by using stream 0 for potential upload. | |||
Show difference between Revision 1.223 and 1.224 | |||
Revision 1.223 | jim | 2016/09/29 20:31:47 | +81 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.222 and 1.223 | |||
Revision 1.222 | jim | 2016/09/14 15:47:31 | +9 -1 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.221 and 1.222 | |||
Revision 1.221 | jim | 2016/09/07 18:09:58 | +14 -14 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.220 and 1.221 | |||
Revision 1.220 | jim | 2016/08/22 16:26:55 | +15 -4 |
Enable vectorization of recv_grid. | |||
Show difference between Revision 1.219 and 1.220 |
Filename: ComputePme.h | |||
Revision 1.37 | jim | 2016/09/29 20:31:47 | +11 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.36 and 1.37 | |||
Revision 1.36 | jim | 2016/09/07 18:09:59 | +1 -1 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.35 and 1.36 |
Filename: ComputePmeCUDA.C | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +67 -23 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputePmeCUDA.h | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputePmeCUDAKernel.cu | |||
Filename: ComputePmeCUDAMgr.C | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +0 -1 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputePmeCUDAMgr.ci | |||
Revision 1.2 | jim | 2017/03/28 19:45:55 | +2 -2 |
Only call ckNew() on pe 0. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:31 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputePmeCUDAMgr.h | |||
Revision 1.3 | jim | 2017/03/30 20:06:17 | +1 -1 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/09/27 20:51:27 | +15 -29 |
Fix from Antti-Pekka Hynninen for usePMECUDA hangs on Windows, other cleanup. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: ComputePmeMgr.ci | |||
Revision 1.39 | jim | 2016/08/22 16:26:56 | +1 -0 |
Enable vectorization of recv_grid. | |||
Show difference between Revision 1.38 and 1.39 |
Filename: ComputeQM.C | |||
Revision 1.4 | jim | 2016/11/24 00:49:52 | +50 -29 |
From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/11/14 20:24:40 | +26 -13 |
From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/09/29 21:10:34 | +20 -23 |
Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/29 20:31:47 | None |
QM/MM interface from Marcelo Melo. |
Filename: ComputeQM.h | |||
Revision 1.1 | jim | 2016/09/29 20:31:47 | None |
QM/MM interface from Marcelo Melo. |
Filename: ComputeQMMgr.ci | |||
Revision 1.1 | jim | 2016/09/29 20:31:47 | None |
QM/MM interface from Marcelo Melo. |
Filename: ComputeRestraints.C | |||
Filename: ComputeSelfTuples.h | |||
Revision 1.27 | jim | 2017/03/30 20:06:17 | +138 -2 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.26 and 1.27 |
Filename: ComputeTclBC.C | |||
Revision 1.9 | jim | 2016/08/09 21:43:24 | +2 -2 |
Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. | |||
Show difference between Revision 1.8 and 1.9 |
Filename: ConfigList.h | |||
Revision 1.1011 | jim | 2016/09/14 17:10:20 | +9 -0 |
Fix Tcl parameter introspection for structure and coordinates. | |||
Show difference between Revision 1.1010 and 1.1011 |
Filename: Controller.C | |||
Revision 1.1326 | jim | 2017/03/29 21:29:03 | +3 -3 |
Minimal change for testing billion-atom systems. | |||
Show difference between Revision 1.1325 and 1.1326 | |||
Revision 1.1325 | jim | 2017/02/03 21:39:23 | +453 -46 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
Show difference between Revision 1.1324 and 1.1325 | |||
Revision 1.1324 | jim | 2016/10/14 16:12:12 | +5 -5 |
From Brian Radak, alchemical output format tweaks and make TI output behave more like FEP output. | |||
Show difference between Revision 1.1323 and 1.1324 | |||
Revision 1.1323 | jim | 2016/09/29 22:29:50 | +53 -29 |
From Brian Radak: cumulative alchemical work is now printed out in the TI log when alchemical switching is on; energy evaluations at alchLambda2 are now printed in their own FEP log during FEP. | |||
Show difference between Revision 1.1322 and 1.1323 | |||
Revision 1.1322 | jim | 2016/09/29 20:31:47 | +6 -4 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1321 and 1.1322 | |||
Revision 1.1321 | jim | 2016/09/14 20:22:03 | +184 -178 |
From Brian Radak, move TI stdout to separate lines, change PARTITION format in alchOutFile, and other alchemical output fixes. | |||
Show difference between Revision 1.1320 and 1.1321 | |||
Revision 1.1320 | jim | 2016/09/05 18:25:42 | +2 -3 |
Alchemical cleanup from Brian Radak. | |||
Show difference between Revision 1.1319 and 1.1320 | |||
Revision 1.1319 | jim | 2016/06/08 22:06:21 | +94 -96 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1318 and 1.1319 |
Filename: Controller.h | |||
Revision 1.1093 | jim | 2017/03/29 21:29:03 | +1 -1 |
Minimal change for testing billion-atom systems. | |||
Show difference between Revision 1.1092 and 1.1093 | |||
Revision 1.1092 | jim | 2017/02/03 21:39:23 | +16 -0 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
Show difference between Revision 1.1091 and 1.1092 | |||
Revision 1.1091 | jim | 2016/09/29 22:29:50 | +7 -0 |
From Brian Radak: cumulative alchemical work is now printed out in the TI log when alchemical switching is on; energy evaluations at alchLambda2 are now printed in their own FEP log during FEP. | |||
Show difference between Revision 1.1090 and 1.1091 | |||
Revision 1.1090 | jim | 2016/09/14 20:22:03 | +16 -0 |
From Brian Radak, move TI stdout to separate lines, change PARTITION format in alchOutFile, and other alchemical output fixes. | |||
Show difference between Revision 1.1089 and 1.1090 | |||
Revision 1.1089 | jim | 2016/06/08 22:06:21 | +2 -5 |
Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. | |||
Show difference between Revision 1.1088 and 1.1089 |
Filename: CudaComputeGBISKernel.cu | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +10 -10 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaComputeGBISKernel.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +3 -3 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaComputeNonbonded.C | |||
Revision 1.3 | jim | 2017/03/30 20:06:17 | +177 -178 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/10/27 18:16:41 | +3 -1 |
Comment out code to avoid PME pes because it delays results for those pes. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaComputeNonbonded.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +4 -6 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaComputeNonbondedKernel.cu | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +16 -197 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaComputeNonbondedKernel.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +4 -35 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaNonbondedTables.C | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: CudaNonbondedTables.h | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: CudaPmeSolver.C | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +2 -6 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolver.ci | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolver.h | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolverUtil.C | |||
Revision 1.3 | jim | 2017/03/30 20:06:17 | +65 -116 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/10/27 22:04:05 | +4 -4 |
Fix spelling of "orthorhombic". | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolverUtil.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +3 -6 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolverUtilKernel.cu | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +155 -749 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaPmeSolverUtilKernel.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +10 -20 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaTileListKernel.cu | |||
Revision 1.3 | jim | 2017/03/30 20:06:17 | +7 -6 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/12/05 22:20:43 | +2 -2 |
Remove unnecessary safety check. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaTileListKernel.h | |||
Revision 1.2 | jim | 2017/03/30 20:06:17 | +1 -1 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: CudaUtils.C | |||
Revision 1.2 | jim | 2016/09/14 15:47:32 | +175 -73 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1 and 1.2 |
Filename: CudaUtils.h | |||
Revision 1.4 | jim | 2017/03/30 20:06:17 | +0 -4 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/09/14 15:47:32 | +274 -33 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.2 and 1.3 |
Filename: DeviceCUDA.C | |||
Revision 1.6 | jim | 2017/03/30 20:06:17 | +0 -6 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2016/10/27 21:12:14 | +4 -4 |
Require CUDA compute capability 3.0 or higher. | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/09/14 15:47:32 | +152 -75 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.3 and 1.4 |
Filename: DeviceCUDA.h | |||
Revision 1.5 | jim | 2017/03/30 20:06:17 | +0 -4 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/09/14 15:47:32 | +33 -4 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.3 and 1.4 |
Filename: DeviceCUDAkernel.cu | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: DumpBench.C | |||
Filename: GlobalMasterIMD.C | |||
Revision 1.10 | jim | 2017/03/20 19:52:17 | +10 -4 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.9 and 1.10 |
Filename: GlobalMasterIMD.h | |||
Revision 1.6 | jim | 2017/03/20 19:52:17 | +4 -1 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.5 and 1.6 |
Filename: GlobalMasterTcl.C | |||
Revision 1.24 | jim | 2016/08/09 21:43:24 | +2 -2 |
Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. | |||
Show difference between Revision 1.23 and 1.24 |
Filename: GridForceGrid.C | |||
Revision 1.24 | ryanmcgreevy | 2016/09/21 20:40:48 | +8 -2 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.23 and 1.24 |
Filename: GridForceGrid.h | |||
Revision 1.17 | ryanmcgreevy | 2016/09/21 20:40:51 | +13 -2 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.16 and 1.17 |
Filename: HomePatch.C | |||
Revision 1.1238 | jim | 2016/09/29 21:30:47 | +1 -1 |
Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. | |||
Show difference between Revision 1.1237 and 1.1238 | |||
Revision 1.1237 | jim | 2016/09/29 20:31:47 | +64 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1236 and 1.1237 | |||
Revision 1.1236 | jim | 2016/09/07 20:54:04 | +7 -0 |
Regenerate rattle list etc. after checkpoint load or atom exchange. | |||
Show difference between Revision 1.1235 and 1.1236 | |||
Revision 1.1235 | jim | 2016/09/06 18:17:54 | +1 -3 |
Tweak rattle list regeneration flag. | |||
Show difference between Revision 1.1234 and 1.1235 | |||
Revision 1.1234 | jim | 2016/09/06 17:58:38 | +11 -3 |
Fix bond checksum error after reinitatoms with single-patch non-periodic simulation. | |||
Show difference between Revision 1.1233 and 1.1234 |
Filename: HomePatch.h | |||
Revision 1.1090 | jim | 2016/09/29 20:31:47 | +4 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1089 and 1.1090 | |||
Revision 1.1089 | jim | 2016/09/06 17:58:39 | +2 -0 |
Fix bond checksum error after reinitatoms with single-patch non-periodic simulation. | |||
Show difference between Revision 1.1088 and 1.1089 |
Filename: IMDOutput.C | |||
Revision 1.15 | jim | 2017/03/20 19:52:17 | +1 -1 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.14 and 1.15 |
Filename: InfoStream.C | |||
Revision 1.1020 | jim | 2017/03/30 16:09:59 | +3 -0 |
Fix int64 output on Mac. | |||
Show difference between Revision 1.1019 and 1.1020 |
Filename: InfoStream.h | |||
Revision 1.1021 | jim | 2017/03/30 16:02:54 | +3 -0 |
Fix int64 output on Mac. | |||
Show difference between Revision 1.1020 and 1.1021 |
Filename: LJTable.h | |||
Revision 1.1012 | jim | 2016/08/23 21:29:08 | +4 -0 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1011 and 1.1012 |
Filename: Lattice.h | |||
Revision 1.1036 | jim | 2017/03/30 20:06:17 | +15 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1035 and 1.1036 |
Filename: LdbCoordinator.C | |||
Revision 1.128 | jim | 2017/03/30 20:06:17 | +57 -23 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.127 and 1.128 |
Filename: MGridforceParams.C | |||
Revision 1.5 | ryanmcgreevy | 2016/09/21 20:40:51 | +29 -5 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.4 and 1.5 |
Filename: MGridforceParams.h | |||
Revision 1.5 | ryanmcgreevy | 2016/09/21 20:40:51 | +3 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.4 and 1.5 |
Filename: Molecule.C | |||
Revision 1.1266 | jim | 2017/04/02 18:33:13 | +24 -9 |
Speed up dihedral parameter assignment when reading from js file. | |||
Show difference between Revision 1.1265 and 1.1266 | |||
Revision 1.1265 | jim | 2016/11/14 20:24:41 | +5 -1 |
From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). | |||
Show difference between Revision 1.1264 and 1.1265 | |||
Revision 1.1264 | jim | 2016/09/30 18:35:12 | +27 -0 |
Initialize QM/MM pointers to zero to avoid crash when reloading structure. | |||
Show difference between Revision 1.1263 and 1.1264 | |||
Revision 1.1263 | jim | 2016/09/29 20:31:47 | +227 -15 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1262 and 1.1263 | |||
Revision 1.1262 | jim | 2016/09/16 18:22:20 | +14 -17 |
From Brian Radak, small fix to LJcorrection calculation. | |||
Show difference between Revision 1.1261 and 1.1262 | |||
Revision 1.1261 | jim | 2016/09/07 18:09:59 | +113 -115 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.1260 and 1.1261 |
Filename: Molecule.h | |||
Revision 1.1121 | jim | 2017/03/29 21:29:03 | +6 -6 |
Minimal change for testing billion-atom systems. | |||
Show difference between Revision 1.1120 and 1.1121 | |||
Revision 1.1120 | jim | 2016/09/29 20:31:47 | +194 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1119 and 1.1120 |
Filename: MoleculeQM.C | |||
Revision 1.5 | jim | 2017/01/10 22:35:34 | +1 -1 |
Add space in nested template to appease xlC compiler. | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/11/24 00:49:53 | +5 -4 |
From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/11/14 20:24:41 | +1 -1 |
From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/09/29 21:30:47 | +25 -25 |
Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/29 20:31:47 | None |
QM/MM interface from Marcelo Melo. |
Filename: MsmMacros.h | |||
Filename: NamdCentLB.C | |||
Revision 1.125 | jim | 2017/03/30 20:06:17 | +4 -4 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.124 and 1.125 |
Filename: NamdHybridLB.C | |||
Revision 1.40 | jim | 2017/03/30 20:06:17 | +4 -4 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.39 and 1.40 |
Filename: NamdState.C | |||
Revision 1.1092 | jim | 2017/03/29 21:29:04 | +2 -2 |
Minimal change for testing billion-atom systems. | |||
Show difference between Revision 1.1091 and 1.1092 | |||
Revision 1.1091 | jim | 2016/11/24 00:49:54 | +4 -0 |
From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. | |||
Show difference between Revision 1.1090 and 1.1091 | |||
Revision 1.1090 | jim | 2016/09/29 20:31:47 | +21 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1089 and 1.1090 | |||
Revision 1.1089 | jim | 2016/09/07 18:09:59 | +2 -2 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.1088 and 1.1089 |
Filename: NamdTypes.h | |||
Revision 1.1055 | jim | 2016/09/14 15:47:32 | +8 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1054 and 1.1055 | |||
Revision 1.1054 | jim | 2016/08/26 16:18:43 | +1 -6 |
Eliminate emulated gather by storing vdwType as int. | |||
Show difference between Revision 1.1053 and 1.1054 | |||
Revision 1.1053 | jim | 2016/08/23 21:29:08 | +15 -0 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1052 and 1.1053 |
Filename: Node.C | |||
Revision 1.1159 | dhardy | 2017/04/21 21:15:13 | +6 -0 |
Split MSM initialization into two phases to avoid race conditions. Phase 1 initializes the overall Map object that, in part, indicates the PE for each chare. Phase 2 creates the chares. | |||
Show difference between Revision 1.1158 and 1.1159 | |||
Revision 1.1158 | dhardy | 2017/04/12 16:15:08 | +33 -33 |
Rearranged startup order so that MSM is started BEFORE CUDA. This seems to fix the bug that Jim found where MSM startup for tutorial (non-periodic sphere) crashes when using a CUDA device with multiple CPU cores. | |||
Show difference between Revision 1.1157 and 1.1158 | |||
Revision 1.1157 | jim | 2017/03/30 20:06:17 | +1 -1 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1156 and 1.1157 | |||
Revision 1.1156 | jim | 2017/03/28 19:45:55 | +2 -1 |
Only call ckNew() on pe 0. | |||
Show difference between Revision 1.1155 and 1.1156 | |||
Revision 1.1155 | dhardy | 2017/03/24 18:08:24 | +2 -2 |
Fixed bug: MSM not getting initialized whenever CUDA2 is active | |||
Show difference between Revision 1.1154 and 1.1155 | |||
Revision 1.1154 | jim | 2016/10/30 22:50:02 | +2 -0 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.1153 and 1.1154 | |||
Revision 1.1153 | jim | 2016/09/27 22:26:15 | +12 -2 |
Preliminary fix for reloading structure with extraBonds. | |||
Show difference between Revision 1.1152 and 1.1153 | |||
Revision 1.1152 | ryanmcgreevy | 2016/09/21 20:40:51 | +42 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.1151 and 1.1152 | |||
Revision 1.1151 | jim | 2016/09/14 15:47:32 | +56 -7 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1150 and 1.1151 | |||
Revision 1.1150 | jim | 2016/09/06 19:50:46 | +1 -0 |
Rebuild CUDA exclusion list after reloading structure. | |||
Show difference between Revision 1.1149 and 1.1150 |
Filename: Node.ci | |||
Revision 1.1035 | ryanmcgreevy | 2016/09/21 20:40:51 | +1 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.1034 and 1.1035 |
Filename: Node.h | |||
Revision 1.1054 | ryanmcgreevy | 2016/09/21 20:40:52 | +4 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.1053 and 1.1054 |
Filename: Parameters.C | |||
Revision 1.1058 | jim | 2017/03/31 18:16:03 | +20 -3 |
Only modify dihedral/improper multiplicity from psf for ancient X-PLOR parameters. | |||
Show difference between Revision 1.1057 and 1.1058 |
Filename: Patch.C | |||
Revision 1.1071 | jim | 2016/09/14 15:47:32 | +10 -2 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1070 and 1.1071 | |||
Revision 1.1070 | jim | 2016/09/04 11:07:23 | +6 -0 |
Eliminate aggregate virial calculation overhead for CUDA builds. | |||
Show difference between Revision 1.1069 and 1.1070 | |||
Revision 1.1069 | jim | 2016/08/29 22:15:46 | +54 -0 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.1068 and 1.1069 | |||
Revision 1.1068 | jim | 2016/08/26 16:18:44 | +2 -0 |
Eliminate emulated gather by storing vdwType as int. | |||
Show difference between Revision 1.1067 and 1.1068 | |||
Revision 1.1067 | jim | 2016/08/23 21:29:08 | +19 -0 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1066 and 1.1067 |
Filename: Patch.h | |||
Revision 1.1047 | jim | 2016/08/29 22:15:46 | +3 -1 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.1046 and 1.1047 | |||
Revision 1.1046 | jim | 2016/08/23 21:29:08 | +6 -0 |
Optimized kernel for KNL. | |||
Show difference between Revision 1.1045 and 1.1046 |
Filename: PatchTypes.h | |||
Revision 1.25 | jim | 2016/09/04 11:07:24 | +6 -2 |
Eliminate aggregate virial calculation overhead for CUDA builds. | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2016/08/29 22:15:46 | +1 -1 |
Switch virial calculation to use aggregate rather than pairwise forces. | |||
Show difference between Revision 1.23 and 1.24 |
Filename: PmeKSpace.C | |||
Revision 1.23 | jim | 2016/11/05 15:42:09 | +2 -0 |
Limit CkLoop minimum grainsize. | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2016/11/05 15:14:11 | +4 -3 |
Fix bad CkLoop code that was assuming one part per chunk. | |||
Show difference between Revision 1.21 and 1.22 | |||
Revision 1.21 | jim | 2016/10/30 22:50:02 | +2 -3 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.20 and 1.21 | |||
Revision 1.20 | jim | 2016/09/14 15:47:32 | +1 -1 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.19 and 1.20 |
Filename: PmeKSpace.h | |||
Revision 1.14 | jim | 2016/10/30 22:50:02 | +1 -1 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.13 and 1.14 |
Filename: PmeSolver.C | |||
Revision 1.1 | jim | 2016/09/14 15:47:32 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: PmeSolver.ci | |||
Revision 1.1 | jim | 2016/09/14 15:47:33 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: PmeSolver.h | |||
Revision 1.1 | jim | 2016/09/14 15:47:33 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: PmeSolverUtil.h | |||
Revision 1.1 | jim | 2016/09/14 15:47:33 | None |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
Filename: Pointer.h | |||
Filename: ProxyMgr.C | |||
Revision 1.1114 | jim | 2017/03/30 20:06:17 | +2 -0 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1113 and 1.1114 |
Filename: ResizeArrayRaw.h | |||
Revision 1.26 | jim | 2016/08/22 16:16:02 | +4 -4 |
Align data to 64-byte boundaries. | |||
Show difference between Revision 1.25 and 1.26 |
Filename: ScriptTcl.C | |||
Revision 1.123 | jim | 2017/03/21 20:15:50 | +20 -17 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.122 and 1.123 | |||
Revision 1.122 | jim | 2016/09/27 15:40:41 | +4 -0 |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. | |||
Show difference between Revision 1.121 and 1.122 | |||
Revision 1.121 | ryanmcgreevy | 2016/09/21 20:40:53 | +33 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.120 and 1.121 | |||
Revision 1.120 | jim | 2016/09/19 21:11:38 | +4 -4 |
Provide better error messages for config parameter processing called via Tcl unknown proc. | |||
Show difference between Revision 1.119 and 1.120 | |||
Revision 1.119 | jim | 2016/09/19 20:31:54 | +6 -0 |
Pass long and double from Python to Tcl as objects instead of strings. | |||
Show difference between Revision 1.118 and 1.119 | |||
Revision 1.118 | jim | 2016/09/18 22:24:32 | +40 -0 |
Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". | |||
Show difference between Revision 1.117 and 1.118 | |||
Revision 1.117 | jim | 2016/09/15 20:56:12 | +1 -1 |
Return bools to Python from Tcl. | |||
Show difference between Revision 1.116 and 1.117 | |||
Revision 1.116 | jim | 2016/09/15 18:35:37 | +5 -2 |
Tcl exit command only initializes if multiple replicas are active. | |||
Show difference between Revision 1.115 and 1.116 | |||
Revision 1.115 | jim | 2016/09/15 17:45:29 | +2 -2 |
For Python interface, make tcl.call() and tcl.eval() use the local Tcl context from which python was called rather than the global Tcl context. | |||
Show difference between Revision 1.114 and 1.115 | |||
Revision 1.114 | jim | 2016/09/14 17:10:20 | +16 -0 |
Fix Tcl parameter introspection for structure and coordinates. | |||
Show difference between Revision 1.113 and 1.114 | |||
Revision 1.113 | jim | 2016/09/05 18:25:42 | +1 -1 |
Alchemical cleanup from Brian Radak. | |||
Show difference between Revision 1.112 and 1.113 | |||
Revision 1.112 | jim | 2016/08/09 21:43:25 | +3 -3 |
Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. | |||
Show difference between Revision 1.111 and 1.112 | |||
Revision 1.111 | jim | 2016/06/20 22:21:01 | +20 -2 |
Improve typing of values returned from Tcl to Python. | |||
Show difference between Revision 1.110 and 1.111 | |||
Revision 1.110 | jim | 2016/06/20 21:19:21 | +4 -4 |
Hide Python helper classes with leading underscore. | |||
Show difference between Revision 1.109 and 1.110 | |||
Revision 1.109 | jim | 2016/06/13 20:11:30 | +1 -1 |
Run until numsteps if run/minimize were never called, even if initialization was triggered. | |||
Show difference between Revision 1.108 and 1.109 |
Filename: ScriptTcl.h | |||
Revision 1.51 | jim | 2017/03/21 20:15:50 | +1 -1 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.50 and 1.51 | |||
Revision 1.50 | ryanmcgreevy | 2016/09/21 20:40:53 | +1 -0 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.49 and 1.50 | |||
Revision 1.49 | jim | 2016/09/18 22:24:33 | +2 -0 |
Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". | |||
Show difference between Revision 1.48 and 1.49 |
Filename: Sequencer.C | |||
Revision 1.1230 | jim | 2016/08/26 19:40:32 | +39 -71 |
Integrator cleanup from Brian Radak. | |||
Show difference between Revision 1.1229 and 1.1230 |
Filename: Sequencer.h | |||
Revision 1.1063 | jim | 2016/08/26 19:40:33 | +3 -2 |
Integrator cleanup from Brian Radak. | |||
Show difference between Revision 1.1062 and 1.1063 |
Filename: SimParameters.C | |||
Revision 1.1478 | jim | 2017/03/30 20:06:17 | +20 -17 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1477 and 1.1478 | |||
Revision 1.1477 | jim | 2017/03/20 19:52:17 | +11 -5 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.1476 and 1.1477 | |||
Revision 1.1476 | jim | 2017/02/03 21:39:23 | +109 -9 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
Show difference between Revision 1.1475 and 1.1476 | |||
Revision 1.1475 | jim | 2016/11/14 20:24:41 | +12 -6 |
From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). | |||
Show difference between Revision 1.1474 and 1.1475 | |||
Revision 1.1474 | jim | 2016/11/07 20:26:15 | +3 -3 |
From Brian Radak per discussion with Chris Chipot, change the default for alchBondLambdaEnd to be 0 (i.e. no scaling). | |||
Show difference between Revision 1.1473 and 1.1474 | |||
Revision 1.1473 | jim | 2016/10/30 22:50:02 | +8 -3 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.1472 and 1.1473 | |||
Revision 1.1472 | jim | 2016/10/27 22:05:36 | +17 -2 |
Disable new CUDA kernels for non-orthorhombic cells. | |||
Show difference between Revision 1.1471 and 1.1472 | |||
Revision 1.1471 | jim | 2016/10/27 20:26:29 | +8 -4 |
By default enable new CUDA nonbonded kernel always (disable with useCUDA2 off) and for 1-4 physical nodes also new CUDA PME kernel (disable with usePMECUDA off). | |||
Show difference between Revision 1.1470 and 1.1471 | |||
Revision 1.1470 | jim | 2016/09/29 21:30:48 | +25 -25 |
Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. | |||
Show difference between Revision 1.1469 and 1.1470 | |||
Revision 1.1469 | jim | 2016/09/29 20:31:47 | +395 -5 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1468 and 1.1469 | |||
Revision 1.1468 | ryanmcgreevy | 2016/09/21 20:40:53 | +34 -4 |
Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. | |||
Show difference between Revision 1.1467 and 1.1468 | |||
Revision 1.1467 | jim | 2016/09/19 17:39:17 | +3 -2 |
From Brian Radak, make outputEnergies script-settable. | |||
Show difference between Revision 1.1466 and 1.1467 | |||
Revision 1.1466 | jim | 2016/09/14 15:47:33 | +5 -2 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1465 and 1.1466 | |||
Revision 1.1465 | jim | 2016/09/07 18:09:59 | +14 -9 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.1464 and 1.1465 | |||
Revision 1.1464 | jim | 2016/09/05 18:25:43 | +126 -166 |
Alchemical cleanup from Brian Radak. | |||
Show difference between Revision 1.1463 and 1.1464 | |||
Revision 1.1463 | jim | 2016/07/29 21:16:22 | +9 -9 |
Add config options for Intel Math Kernel Library. | |||
Show difference between Revision 1.1462 and 1.1463 |
Filename: SimParameters.h | |||
Revision 1.1248 | jim | 2017/03/30 20:06:17 | +3 -2 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1247 and 1.1248 | |||
Revision 1.1247 | jim | 2017/03/20 19:52:17 | +4 -2 |
From Joao Ribeiro, add IMDignoreForces option for QwikMD. | |||
Show difference between Revision 1.1246 and 1.1247 | |||
Revision 1.1246 | jim | 2017/02/03 21:39:23 | +14 -2 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
Show difference between Revision 1.1245 and 1.1246 | |||
Revision 1.1245 | jim | 2016/11/14 20:24:41 | +3 -2 |
From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). | |||
Show difference between Revision 1.1244 and 1.1245 | |||
Revision 1.1244 | jim | 2016/09/29 20:31:47 | +48 -2 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1243 and 1.1244 | |||
Revision 1.1243 | jim | 2016/09/07 18:09:59 | +3 -2 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.1242 and 1.1243 | |||
Revision 1.1242 | jim | 2016/09/05 18:25:43 | +3 -7 |
Alchemical cleanup from Brian Radak. | |||
Show difference between Revision 1.1241 and 1.1242 |
Filename: TupleTypesCUDA.h | |||
Revision 1.1 | jim | 2017/03/30 20:06:17 | None |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. |
Filename: UniqueSet.h | |||
Filename: WorkDistrib.C | |||
Revision 1.1291 | jim | 2017/03/30 20:06:17 | +10 -2 |
From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels. | |||
Show difference between Revision 1.1290 and 1.1291 | |||
Revision 1.1290 | jim | 2016/09/29 20:31:47 | +5 -2 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1289 and 1.1290 | |||
Revision 1.1289 | jim | 2016/09/14 15:47:33 | +35 -8 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1288 and 1.1289 | |||
Revision 1.1288 | jim | 2016/09/07 18:09:59 | +5 -6 |
From Brian Radak, alchemical cleanup and disable/re-enable alch in script. | |||
Show difference between Revision 1.1287 and 1.1288 |
Filename: colvar.C | |||
Revision 1.35 | jim | 2017/05/16 21:14:20 | +66 -45 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.34 and 1.35 | |||
Revision 1.34 | jim | 2017/03/21 20:15:50 | +7 -20 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.33 and 1.34 | |||
Revision 1.33 | jim | 2017/03/08 18:57:23 | +5 -5 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.32 and 1.33 | |||
Revision 1.32 | jim | 2017/03/01 14:34:00 | +19 -19 |
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 | |||
Show difference between Revision 1.31 and 1.32 | |||
Revision 1.31 | jim | 2017/02/08 16:58:30 | +248 -175 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.30 and 1.31 | |||
Revision 1.30 | jim | 2016/12/21 13:51:06 | +38 -26 |
Fixes from Jerome Henin to the total force calculation in ABF and wall potentials for extended-Lagrangian coordinates. | |||
Show difference between Revision 1.29 and 1.30 | |||
Revision 1.29 | jim | 2016/11/28 17:30:57 | +7 -4 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.28 and 1.29 | |||
Revision 1.28 | jim | 2016/10/24 21:15:57 | +9 -3 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.27 and 1.28 | |||
Revision 1.27 | jim | 2016/10/14 16:35:15 | +4 -4 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.26 and 1.27 | |||
Revision 1.26 | jim | 2016/10/07 16:14:05 | +689 -670 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.25 and 1.26 |
Filename: colvar.h | |||
Revision 1.19 | jim | 2017/05/16 21:14:20 | +8 -14 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.18 and 1.19 | |||
Revision 1.18 | jim | 2017/02/08 16:58:30 | +44 -6 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.17 and 1.18 | |||
Revision 1.17 | jim | 2016/10/07 16:14:07 | +108 -105 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.16 and 1.17 |
Filename: colvaratoms.C | |||
Revision 1.27 | jim | 2017/05/16 21:14:20 | +99 -24 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.26 and 1.27 | |||
Revision 1.26 | jim | 2017/03/21 20:15:50 | +23 -57 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.25 and 1.26 | |||
Revision 1.25 | jim | 2017/03/08 18:57:23 | +1 -1 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2017/02/08 16:58:30 | +14 -5 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.23 and 1.24 | |||
Revision 1.23 | jim | 2016/11/28 17:30:57 | +6 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2016/10/24 21:15:57 | +17 -7 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.21 and 1.22 | |||
Revision 1.21 | jim | 2016/10/14 16:35:15 | +23 -0 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.20 and 1.21 | |||
Revision 1.20 | jim | 2016/10/07 16:14:07 | +711 -412 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.19 and 1.20 |
Filename: colvaratoms.h | |||
Revision 1.17 | jim | 2017/05/16 21:14:20 | +8 -4 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/03/21 20:15:50 | +12 -15 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2017/02/08 16:58:30 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/11/28 17:30:57 | +3 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/10/14 16:35:16 | +2 -0 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2016/10/07 16:14:07 | +248 -120 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.11 and 1.12 |
Filename: colvarbias.C | |||
Revision 1.20 | jim | 2017/05/16 21:14:20 | +15 -5 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.19 and 1.20 | |||
Revision 1.19 | jim | 2017/02/08 16:58:30 | +161 -31 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.18 and 1.19 | |||
Revision 1.18 | jim | 2016/10/07 16:14:07 | +111 -36 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.17 and 1.18 |
Filename: colvarbias.h | |||
Revision 1.17 | jim | 2017/05/16 21:14:20 | +1 -1 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/02/08 16:58:30 | +93 -20 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/10/07 16:14:07 | +40 -7 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.14 and 1.15 |
Filename: colvarbias_abf.C | |||
Revision 1.24 | jim | 2017/05/16 21:14:20 | +10 -8 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.23 and 1.24 | |||
Revision 1.23 | jim | 2017/03/21 20:15:50 | +6 -6 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2017/02/08 16:58:30 | +25 -91 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.21 and 1.22 | |||
Revision 1.21 | jim | 2016/10/24 21:15:57 | +2 -1 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.20 and 1.21 | |||
Revision 1.20 | jim | 2016/10/07 16:14:07 | +239 -57 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.19 and 1.20 |
Filename: colvarbias_abf.h | |||
Revision 1.14 | jim | 2017/02/08 16:58:30 | +9 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/10/07 16:14:07 | +32 -8 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.12 and 1.13 |
Filename: colvarbias_alb.C | |||
Revision 1.7 | jim | 2017/03/21 20:15:50 | +0 -3 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.6 and 1.7 | |||
Revision 1.6 | jim | 2017/02/08 16:58:30 | +15 -49 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2016/10/07 16:14:07 | +33 -16 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.4 and 1.5 |
Filename: colvarbias_alb.h | |||
Revision 1.4 | jim | 2017/02/08 16:58:30 | +11 -3 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/10/07 16:14:07 | +4 -11 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.2 and 1.3 |
Filename: colvarbias_histogram.C | |||
Revision 1.4 | jim | 2017/03/21 20:15:50 | +2 -4 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2017/02/08 16:58:30 | +16 -62 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/10/07 16:14:07 | +40 -20 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.1 and 1.2 |
Filename: colvarbias_histogram.h | |||
Revision 1.3 | jim | 2017/02/08 16:58:30 | +9 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/10/07 16:14:07 | +6 -7 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.1 and 1.2 |
Filename: colvarbias_meta.C | |||
Revision 1.23 | jim | 2017/03/21 20:15:50 | +1 -5 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2017/02/08 16:58:30 | +358 -320 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.21 and 1.22 | |||
Revision 1.21 | jim | 2016/11/28 17:30:57 | +25 -2 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.20 and 1.21 | |||
Revision 1.20 | jim | 2016/10/24 21:15:57 | +52 -32 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.19 and 1.20 | |||
Revision 1.19 | jim | 2016/10/07 16:14:07 | +33 -20 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.18 and 1.19 |
Filename: colvarbias_meta.h | |||
Revision 1.16 | jim | 2017/02/08 16:58:30 | +35 -17 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/10/24 21:15:57 | +8 -0 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/10/07 16:14:08 | +5 -15 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.13 and 1.14 |
Filename: colvarbias_restraint.C | |||
Revision 1.8 | jim | 2017/05/16 21:14:20 | +7 -6 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.7 and 1.8 | |||
Revision 1.7 | jim | 2017/03/21 20:15:50 | +0 -1 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.6 and 1.7 | |||
Revision 1.6 | jim | 2017/03/01 14:34:00 | +33 -11 |
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2017/02/08 16:58:30 | +907 -356 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/10/07 16:14:08 | +333 -24 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.3 and 1.4 |
Filename: colvarbias_restraint.h | |||
Revision 1.6 | jim | 2017/03/01 14:34:00 | +6 -0 |
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2017/02/08 16:58:30 | +192 -66 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/10/07 16:14:08 | +80 -14 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.3 and 1.4 |
Filename: colvarcomp.C | |||
Revision 1.14 | jim | 2017/05/16 21:14:20 | +106 -91 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2017/03/21 20:15:50 | +22 -11 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2017/02/08 16:58:30 | +22 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.11 and 1.12 | |||
Revision 1.11 | jim | 2016/11/28 17:30:57 | +33 -4 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.10 and 1.11 | |||
Revision 1.10 | jim | 2016/10/24 21:15:58 | +3 -6 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.9 and 1.10 | |||
Revision 1.9 | jim | 2016/10/07 16:14:08 | +188 -92 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.8 and 1.9 |
Filename: colvarcomp.h | |||
Revision 1.26 | jim | 2017/05/16 21:14:20 | +67 -2 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.25 and 1.26 | |||
Revision 1.25 | jim | 2017/03/08 18:57:23 | +9 -0 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2017/02/08 16:58:30 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.23 and 1.24 | |||
Revision 1.23 | jim | 2016/11/28 17:30:57 | +70 -314 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2016/10/07 16:14:08 | +158 -63 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.21 and 1.22 |
Filename: colvarcomp_angles.C | |||
Revision 1.17 | jim | 2017/05/16 21:14:20 | +145 -0 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/03/21 20:15:50 | +4 -4 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2017/02/08 16:58:30 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/11/28 17:30:57 | +50 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/10/07 16:14:08 | +197 -112 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.12 and 1.13 |
Filename: colvarcomp_coordnums.C | |||
Revision 1.14 | jim | 2017/02/08 16:58:31 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/11/28 17:30:57 | +21 -10 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2016/10/07 16:14:08 | +194 -52 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.11 and 1.12 |
Filename: colvarcomp_distances.C | |||
Revision 1.21 | jim | 2017/05/16 21:14:20 | +14 -6 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.20 and 1.21 | |||
Revision 1.20 | jim | 2017/03/21 20:15:50 | +10 -10 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.19 and 1.20 | |||
Revision 1.19 | jim | 2017/03/08 18:57:23 | +21 -0 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.18 and 1.19 | |||
Revision 1.18 | jim | 2017/02/08 16:58:31 | +8 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.17 and 1.18 | |||
Revision 1.17 | jim | 2016/11/28 17:30:57 | +117 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2016/10/07 16:14:08 | +317 -351 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.15 and 1.16 |
Filename: colvarcomp_protein.C | |||
Revision 1.15 | jim | 2017/03/21 20:15:50 | +2 -2 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2017/02/08 16:58:31 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/11/28 17:30:57 | +23 -6 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2016/10/07 16:14:08 | +13 -3 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.11 and 1.12 |
Filename: colvarcomp_rotations.C | |||
Revision 1.18 | jim | 2017/02/08 16:58:31 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.17 and 1.18 | |||
Revision 1.17 | jim | 2016/11/28 17:30:57 | +73 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2016/10/07 16:14:08 | +45 -70 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.15 and 1.16 |
Filename: colvardeps.C | |||
Revision 1.7 | jim | 2017/05/16 21:14:20 | +207 -39 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.6 and 1.7 | |||
Revision 1.6 | jim | 2017/03/21 20:15:50 | +112 -96 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2017/03/08 18:57:23 | +21 -24 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2017/02/08 16:58:31 | +46 -21 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2016/11/28 17:30:57 | +5 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2016/10/24 21:15:58 | +4 -2 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/10/07 16:14:08 | None |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts |
Filename: colvardeps.h | |||
Revision 1.5 | jim | 2017/05/16 21:14:20 | +79 -28 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2017/03/21 20:15:50 | +39 -24 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.3 and 1.4 | |||
Revision 1.3 | jim | 2017/03/08 18:57:23 | +14 -5 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.2 and 1.3 | |||
Revision 1.2 | jim | 2017/02/08 16:58:31 | +16 -6 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/10/07 16:14:08 | None |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts |
Filename: colvargrid.C | |||
Revision 1.10 | jim | 2017/02/08 16:58:31 | +10 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.9 and 1.10 | |||
Revision 1.9 | jim | 2016/11/28 17:30:57 | +14 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.8 and 1.9 | |||
Revision 1.8 | jim | 2016/10/07 16:14:08 | +4 -5 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.7 and 1.8 |
Filename: colvargrid.h | |||
Revision 1.19 | jim | 2017/05/16 21:14:20 | +1 -1 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.18 and 1.19 | |||
Revision 1.18 | jim | 2017/03/21 20:15:50 | +0 -4 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.17 and 1.18 | |||
Revision 1.17 | jim | 2017/02/08 16:58:31 | +35 -24 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2016/11/28 17:30:57 | +41 -3 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/10/07 16:14:08 | +140 -84 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.14 and 1.15 |
Filename: colvarmodule.C | |||
Revision 1.32 | jim | 2017/05/16 21:14:20 | +52 -21 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.31 and 1.32 | |||
Revision 1.31 | jim | 2017/03/21 20:15:50 | +4 -2 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.30 and 1.31 | |||
Revision 1.30 | jim | 2017/03/08 18:57:23 | +11 -6 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.29 and 1.30 | |||
Revision 1.29 | jim | 2017/02/08 16:58:31 | +229 -94 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.28 and 1.29 | |||
Revision 1.28 | jim | 2016/11/28 17:30:57 | +1 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.27 and 1.28 | |||
Revision 1.27 | jim | 2016/10/24 21:15:58 | +6 -0 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.26 and 1.27 | |||
Revision 1.26 | jim | 2016/10/07 16:14:08 | +471 -152 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.25 and 1.26 |
Filename: colvarmodule.h | |||
Revision 1.30 | jim | 2017/05/16 21:14:20 | +11 -2 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.29 and 1.30 | |||
Revision 1.29 | jim | 2017/03/21 20:15:50 | +1 -3 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.28 and 1.29 | |||
Revision 1.28 | jim | 2017/03/08 18:57:23 | +4 -1 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.27 and 1.28 | |||
Revision 1.27 | jim | 2017/03/01 14:34:00 | +1 -1 |
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 | |||
Show difference between Revision 1.26 and 1.27 | |||
Revision 1.26 | jim | 2017/02/08 16:58:31 | +87 -30 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.25 and 1.26 | |||
Revision 1.25 | jim | 2016/12/21 13:51:06 | +1 -1 |
Fixes from Jerome Henin to the total force calculation in ABF and wall potentials for extended-Lagrangian coordinates. | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2016/11/28 17:30:57 | +3 -3 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.23 and 1.24 | |||
Revision 1.23 | jim | 2016/10/24 21:15:58 | +1 -1 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.22 and 1.23 | |||
Revision 1.22 | jim | 2016/10/14 16:35:16 | +4 -1 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.21 and 1.22 | |||
Revision 1.21 | jim | 2016/10/07 16:14:08 | +94 -46 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.20 and 1.21 |
Filename: colvarparse.C | |||
Revision 1.13 | jim | 2017/03/21 20:15:50 | +26 -27 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2017/02/08 16:58:31 | +11 -4 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.11 and 1.12 | |||
Revision 1.11 | jim | 2016/10/24 21:15:58 | +6 -6 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.10 and 1.11 | |||
Revision 1.10 | jim | 2016/10/07 16:14:08 | +397 -253 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.9 and 1.10 |
Filename: colvarparse.h | |||
Revision 1.11 | jim | 2017/03/21 20:15:50 | +4 -21 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.10 and 1.11 | |||
Revision 1.10 | jim | 2017/02/08 16:58:31 | +8 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.9 and 1.10 | |||
Revision 1.9 | jim | 2016/10/07 16:14:08 | +149 -55 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.8 and 1.9 |
Filename: colvarproxy.h | |||
Revision 1.18 | jim | 2017/03/21 20:15:50 | +5 -0 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.17 and 1.18 | |||
Revision 1.17 | jim | 2017/02/08 16:58:31 | +31 -6 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2016/11/28 17:30:57 | +1 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/10/24 21:15:58 | +5 -2 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/10/07 16:14:08 | +449 -113 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.13 and 1.14 |
Filename: colvarproxy_namd.C | |||
Revision 1.29 | jim | 2017/05/16 21:14:20 | +2 -2 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.28 and 1.29 | |||
Revision 1.28 | jim | 2017/03/21 20:15:50 | +10 -0 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.27 and 1.28 | |||
Revision 1.27 | jim | 2017/02/08 16:58:31 | +32 -12 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.26 and 1.27 | |||
Revision 1.26 | jim | 2016/11/28 17:30:57 | +1 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.25 and 1.26 | |||
Revision 1.25 | jim | 2016/10/24 21:15:58 | +3 -3 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2016/10/14 16:35:16 | +1 -1 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.23 and 1.24 | |||
Revision 1.23 | jim | 2016/10/07 16:14:08 | +541 -250 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.22 and 1.23 |
Filename: colvarproxy_namd.h | |||
Revision 1.17 | jim | 2017/03/21 20:15:50 | +14 -4 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/02/08 16:58:31 | +9 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/11/28 17:30:57 | +1 -1 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/10/24 21:15:58 | +5 -2 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/10/14 16:35:16 | +1 -1 |
From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. | |||
Show difference between Revision 1.12 and 1.13 | |||
Revision 1.12 | jim | 2016/10/07 16:14:08 | +125 -35 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.11 and 1.12 |
Filename: colvarproxy_namd_version.h | |||
Revision 1.1 | jim | 2017/03/21 20:17:09 | None |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
Filename: colvars_version.h | |||
Revision 1.2 | jim | 2017/05/16 21:14:20 | +1 -3 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2017/03/21 20:17:09 | None |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
Filename: colvarscript.C | |||
Revision 1.11 | jim | 2017/05/16 21:14:20 | +2 -5 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.10 and 1.11 | |||
Revision 1.10 | jim | 2017/03/21 20:15:50 | +71 -68 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.9 and 1.10 | |||
Revision 1.9 | jim | 2017/03/08 18:57:23 | +12 -1 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
Show difference between Revision 1.8 and 1.9 | |||
Revision 1.8 | jim | 2017/02/08 16:58:31 | +101 -12 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.7 and 1.8 | |||
Revision 1.7 | jim | 2016/10/24 21:15:58 | +30 -0 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
Show difference between Revision 1.6 and 1.7 | |||
Revision 1.6 | jim | 2016/10/07 16:14:08 | +76 -43 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.5 and 1.6 |
Filename: colvarscript.h | |||
Revision 1.7 | jim | 2017/05/16 21:14:20 | +1 -1 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.6 and 1.7 | |||
Revision 1.6 | jim | 2017/03/21 20:15:50 | +13 -5 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2017/02/08 16:58:31 | +11 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.4 and 1.5 | |||
Revision 1.4 | jim | 2016/10/07 16:14:08 | +2 -1 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.3 and 1.4 |
Filename: colvartypes.C | |||
Revision 1.6 | jim | 2017/02/08 16:58:31 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.5 and 1.6 | |||
Revision 1.5 | jim | 2016/10/07 16:14:08 | +50 -57 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.4 and 1.5 |
Filename: colvartypes.h | |||
Revision 1.17 | jim | 2017/05/16 21:14:20 | +5 -0 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/02/08 16:58:31 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2016/10/07 16:14:08 | +40 -6 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.14 and 1.15 |
Filename: colvarvalue.C | |||
Revision 1.12 | jim | 2017/05/16 21:14:20 | +2 -2 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.11 and 1.12 | |||
Revision 1.11 | jim | 2017/03/21 20:15:50 | +275 -0 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.10 and 1.11 | |||
Revision 1.10 | jim | 2017/02/08 16:58:31 | +10 -52 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.9 and 1.10 | |||
Revision 1.9 | jim | 2016/11/28 17:30:57 | +33 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.8 and 1.9 | |||
Revision 1.8 | jim | 2016/10/07 16:14:08 | +1 -1 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.7 and 1.8 |
Filename: colvarvalue.h | |||
Revision 1.17 | jim | 2017/05/16 21:14:20 | +48 -20 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
Show difference between Revision 1.16 and 1.17 | |||
Revision 1.16 | jim | 2017/03/21 20:15:50 | +4 -272 |
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 | |||
Show difference between Revision 1.15 and 1.16 | |||
Revision 1.15 | jim | 2017/02/08 16:58:31 | +31 -24 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
Show difference between Revision 1.14 and 1.15 | |||
Revision 1.14 | jim | 2016/11/28 17:30:57 | +3 -0 |
Colvars fixes from Giacomo Fiorin and Jerome Henin. | |||
Show difference between Revision 1.13 and 1.14 | |||
Revision 1.13 | jim | 2016/10/07 16:14:08 | +1 -1 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
Show difference between Revision 1.12 and 1.13 |
Filename: common.C | |||
Revision 1.1060 | jim | 2016/08/09 21:51:30 | +4 -0 |
Print "(unknown error)" rather than segfault if null is passed to NAMD_die variants. | |||
Show difference between Revision 1.1059 and 1.1060 |
Filename: dc.pl | |||
Revision 1.1006 | jim | 2016/07/21 20:33:30 | +1 -0 |
Add obj/.exists dependencies to all targets in obj directory. | |||
Show difference between Revision 1.1005 and 1.1006 |
Filename: eabf.h | |||
Revision 1.1 | jim | 2016/09/27 15:40:41 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabf1D.C | |||
Revision 1.2 | jim | 2016/12/18 21:19:04 | +9 -0 |
From Chris Chipot, eABF count files are now properly outputted. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/27 15:40:41 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabf1D.h | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabf2D.C | |||
Revision 1.2 | jim | 2016/12/18 21:19:05 | +14 -3 |
From Chris Chipot, eABF count files are now properly outputted. | |||
Show difference between Revision 1.1 and 1.2 | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabf2D.h | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabfTcl.C | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabffunc.C | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: eabffunc.h | |||
Revision 1.1 | jim | 2016/09/27 15:40:42 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: elements.h | |||
Filename: fftlib.C | |||
Revision 1.8 | jim | 2016/10/30 22:50:03 | +1 -1 |
Auto-enable useCkLoop for thread-parallel PME when it makes sense. | |||
Show difference between Revision 1.7 and 1.8 |
Filename: fstream_namd.C | |||
Revision 1.4 | jim | 2016/09/27 15:33:10 | +6 -0 |
Add option to create backup file by passing extension to constructor or open(). | |||
Show difference between Revision 1.3 and 1.4 |
Filename: fstream_namd.h | |||
Revision 1.4 | jim | 2016/09/27 15:33:10 | +6 -0 |
Add option to create backup file by passing extension to constructor or open(). | |||
Show difference between Revision 1.3 and 1.4 |
Filename: main.ci | |||
Revision 1.1031 | jim | 2016/09/29 20:31:47 | +1 -0 |
QM/MM interface from Marcelo Melo. | |||
Show difference between Revision 1.1030 and 1.1031 | |||
Revision 1.1030 | jim | 2016/09/14 15:47:33 | +4 -0 |
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". | |||
Show difference between Revision 1.1029 and 1.1030 |
Filename: mainfunc.C | |||
Revision 1.25 | jim | 2016/09/18 22:28:32 | +2 -0 |
Fix non-Tcl builds. | |||
Show difference between Revision 1.24 and 1.25 | |||
Revision 1.24 | jim | 2016/09/18 22:24:34 | +13 -0 |
Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". | |||
Show difference between Revision 1.23 and 1.24 |
Filename: sortreplicas.c | |||
Revision 1.9 | jim | 2016/09/19 21:39:24 | +1 -1 |
Fix bug where trajectory frames were sorted based on index of previous frame (caught by Wen Ma). | |||
Show difference between Revision 1.8 and 1.9 |
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