--- /src ---

Filename: AtomMap.h
Revision 1.1018jim 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 1.1034jim 2016/09/29 20:31:46+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1033 and 1.1034
Revision 1.1033jim 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 1.80jim 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 1.79jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.78 and 1.79
Revision 1.78jim 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 1.1038jim 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 1.1jim 2017/03/30 20:06:17None
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 1.1jim 2017/03/30 20:06:17None
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 1.1jim 2017/03/30 20:06:17None
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 1.1jim 2017/03/30 20:06:17None
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 1.1035jim 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 1.2jim 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 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputeCUDAMgr.ci
Revision 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputeCUDAMgr.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputeConsForce.C

Filename: ComputeDihedrals.C
Revision 1.1038jim 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 1.6jim 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 1.28ryanmcgreevy 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 1.1065jim 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 1.1035jim 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 1.14jim 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 1.1060jim 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 1.1059jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1058 and 1.1059
Revision 1.1058jim 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 1.1133jim 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 1.1132jim 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 1.1131jim 2016/09/29 20:31:47+11 -2
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1130 and 1.1131
Revision 1.1130jim 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 1.1129jim 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 1.1024jim 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 1.1023jim 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 1.1022jim 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 1.1047jim 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 1.1046jim 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 1.1045jim 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 1.73dhardy 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 1.72dhardy 2017/03/29 19:25:55+1 -0
Added another comment
Show difference between Revision 1.71 and 1.72
Revision 1.71dhardy 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 1.21dhardy 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 1.1192jim 2016/09/29 20:31:47+48 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1191 and 1.1192
Revision 1.1191jim 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 1.1190jim 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 1.1189jim 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 1.55jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.54 and 1.55
Revision 1.54jim 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 1.53jim 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 1.6jim 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 1.5jim 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 1.4jim 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 1.3jim 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 1.2jim 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 1.1jim 2016/08/23 21:29:08None
Optimized kernel for KNL.

Filename: ComputeNonbondedCUDA.C
Revision 1.102jim 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 1.101jim 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 1.100jim 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 1.25jim 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 1.24jim 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 1.39jim 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 1.38jim 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 1.16jim 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 1.1070jim 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 1.1069jim 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 1.1068jim 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 1.1064jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1063 and 1.1064
Revision 1.1063jim 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 1.1062jim 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 1.1061jim 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 1.1126jim 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 1.1125jim 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 1.1124jim 2016/09/29 20:31:47+3 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1123 and 1.1124
Revision 1.1123jim 2016/09/14 20:13:26+1 -2
Remove unused static alchLambda.
Show difference between Revision 1.1122 and 1.1123
Revision 1.1122jim 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 1.1121jim 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 1.1094jim 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 1.1093jim 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 1.1092jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1091 and 1.1092
Revision 1.1091jim 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 1.1090jim 2016/09/14 20:13:26+0 -1
Remove unused static alchLambda.
Show difference between Revision 1.1089 and 1.1090
Revision 1.1089jim 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 1.1088jim 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 1.229jim 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 1.228jim 2017/02/17 17:19:05+5 -5
Change "Bool useCkLoop" to "int useCkLoop".
Show difference between Revision 1.227 and 1.228
Revision 1.227jim 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 1.226jim 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 1.225jim 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 1.224jim 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 1.223jim 2016/09/29 20:31:47+81 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.222 and 1.223
Revision 1.222jim 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 1.221jim 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 1.220jim 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 1.37jim 2016/09/29 20:31:47+11 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.36 and 1.37
Revision 1.36jim 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 1.2jim 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 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputePmeCUDA.h
Revision 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputePmeCUDAKernel.cu

Filename: ComputePmeCUDAMgr.C
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputePmeCUDAMgr.ci
Revision 1.2jim 2017/03/28 19:45:55+2 -2
Only call ckNew() on pe 0.
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2016/09/14 15:47:31None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputePmeCUDAMgr.h
Revision 1.3jim 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 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: ComputePmeMgr.ci
Revision 1.39jim 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 1.4jim 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 1.3jim 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 1.2jim 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 1.1jim 2016/09/29 20:31:47None
QM/MM interface from Marcelo Melo.

Filename: ComputeQM.h
Revision 1.1jim 2016/09/29 20:31:47None
QM/MM interface from Marcelo Melo.

Filename: ComputeQMMgr.ci
Revision 1.1jim 2016/09/29 20:31:47None
QM/MM interface from Marcelo Melo.

Filename: ComputeRestraints.C

Filename: ComputeSelfTuples.h
Revision 1.27jim 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 1.9jim 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 1.1011jim 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 1.1326jim 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 1.1325jim 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 1.1324jim 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 1.1323jim 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 1.1322jim 2016/09/29 20:31:47+6 -4
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1321 and 1.1322
Revision 1.1321jim 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 1.1320jim 2016/09/05 18:25:42+2 -3
Alchemical cleanup from Brian Radak.
Show difference between Revision 1.1319 and 1.1320
Revision 1.1319jim 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 1.1093jim 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 1.1092jim 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 1.1091jim 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 1.1090jim 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 1.1089jim 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 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaComputeGBISKernel.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaComputeNonbonded.C
Revision 1.3jim 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 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaComputeNonbonded.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaComputeNonbondedKernel.cu
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaComputeNonbondedKernel.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaNonbondedTables.C
Revision 1.1jim 2017/03/30 20:06:17None
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 1.1jim 2017/03/30 20:06:17None
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 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolver.ci
Revision 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolver.h
Revision 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolverUtil.C
Revision 1.3jim 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 1.2jim 2016/10/27 22:04:05+4 -4
Fix spelling of "orthorhombic".
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolverUtil.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolverUtilKernel.cu
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaPmeSolverUtilKernel.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaTileListKernel.cu
Revision 1.3jim 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 1.2jim 2016/12/05 22:20:43+2 -2
Remove unnecessary safety check.
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaTileListKernel.h
Revision 1.2jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: CudaUtils.C
Revision 1.2jim 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 1.4jim 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 1.3jim 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 1.6jim 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 1.5jim 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 1.4jim 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 1.5jim 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 1.4jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: DumpBench.C

Filename: GlobalMasterIMD.C
Revision 1.10jim 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 1.6jim 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 1.24jim 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 1.24ryanmcgreevy 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 1.17ryanmcgreevy 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 1.1238jim 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 1.1237jim 2016/09/29 20:31:47+64 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1236 and 1.1237
Revision 1.1236jim 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 1.1235jim 2016/09/06 18:17:54+1 -3
Tweak rattle list regeneration flag.
Show difference between Revision 1.1234 and 1.1235
Revision 1.1234jim 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 1.1090jim 2016/09/29 20:31:47+4 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1089 and 1.1090
Revision 1.1089jim 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 1.15jim 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 1.1020jim 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 1.1021jim 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 1.1012jim 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 1.1036jim 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 1.128jim 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 1.5ryanmcgreevy 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 1.5ryanmcgreevy 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 1.1266jim 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 1.1265jim 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 1.1264jim 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 1.1263jim 2016/09/29 20:31:47+227 -15
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1262 and 1.1263
Revision 1.1262jim 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 1.1261jim 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 1.1121jim 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 1.1120jim 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 1.5jim 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 1.4jim 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 1.3jim 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 1.2jim 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 1.1jim 2016/09/29 20:31:47None
QM/MM interface from Marcelo Melo.

Filename: MsmMacros.h

Filename: NamdCentLB.C
Revision 1.125jim 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 1.40jim 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 1.1092jim 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 1.1091jim 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 1.1090jim 2016/09/29 20:31:47+21 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1089 and 1.1090
Revision 1.1089jim 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 1.1055jim 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 1.1054jim 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 1.1053jim 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 1.1159dhardy 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 1.1158dhardy 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 1.1157jim 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 1.1156jim 2017/03/28 19:45:55+2 -1
Only call ckNew() on pe 0.
Show difference between Revision 1.1155 and 1.1156
Revision 1.1155dhardy 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 1.1154jim 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 1.1153jim 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 1.1152ryanmcgreevy 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 1.1151jim 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 1.1150jim 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 1.1035ryanmcgreevy 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 1.1054ryanmcgreevy 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 1.1058jim 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 1.1071jim 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 1.1070jim 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 1.1069jim 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 1.1068jim 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 1.1067jim 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 1.1047jim 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 1.1046jim 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 1.25jim 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 1.24jim 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 1.23jim 2016/11/05 15:42:09+2 -0
Limit CkLoop minimum grainsize.
Show difference between Revision 1.22 and 1.23
Revision 1.22jim 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 1.21jim 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 1.20jim 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 1.14jim 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 1.1jim 2016/09/14 15:47:32None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: PmeSolver.ci
Revision 1.1jim 2016/09/14 15:47:33None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: PmeSolver.h
Revision 1.1jim 2016/09/14 15:47:33None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: PmeSolverUtil.h
Revision 1.1jim 2016/09/14 15:47:33None
New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes".

Filename: Pointer.h

Filename: ProxyMgr.C
Revision 1.1114jim 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 1.26jim 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 1.123jim 2017/03/21 20:15:50+20 -17
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.122 and 1.123
Revision 1.122jim 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 1.121ryanmcgreevy 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 1.120jim 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 1.119jim 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 1.118jim 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 1.117jim 2016/09/15 20:56:12+1 -1
Return bools to Python from Tcl.
Show difference between Revision 1.116 and 1.117
Revision 1.116jim 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 1.115jim 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 1.114jim 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 1.113jim 2016/09/05 18:25:42+1 -1
Alchemical cleanup from Brian Radak.
Show difference between Revision 1.112 and 1.113
Revision 1.112jim 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 1.111jim 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 1.110jim 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 1.109jim 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 1.51jim 2017/03/21 20:15:50+1 -1
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.50 and 1.51
Revision 1.50ryanmcgreevy 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 1.49jim 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 1.1230jim 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 1.1063jim 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 1.1478jim 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 1.1477jim 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 1.1476jim 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 1.1475jim 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 1.1474jim 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 1.1473jim 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 1.1472jim 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 1.1471jim 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 1.1470jim 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 1.1469jim 2016/09/29 20:31:47+395 -5
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1468 and 1.1469
Revision 1.1468ryanmcgreevy 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 1.1467jim 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 1.1466jim 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 1.1465jim 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 1.1464jim 2016/09/05 18:25:43+126 -166
Alchemical cleanup from Brian Radak.
Show difference between Revision 1.1463 and 1.1464
Revision 1.1463jim 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 1.1248jim 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 1.1247jim 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 1.1246jim 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 1.1245jim 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 1.1244jim 2016/09/29 20:31:47+48 -2
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1243 and 1.1244
Revision 1.1243jim 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 1.1242jim 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 1.1jim 2017/03/30 20:06:17None
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 1.1291jim 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 1.1290jim 2016/09/29 20:31:47+5 -2
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1289 and 1.1290
Revision 1.1289jim 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 1.1288jim 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 1.35jim 2017/05/16 21:14:20+66 -45
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.34 and 1.35
Revision 1.34jim 2017/03/21 20:15:50+7 -20
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.33 and 1.34
Revision 1.33jim 2017/03/08 18:57:23+5 -5
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.32 and 1.33
Revision 1.32jim 2017/03/01 14:34:00+19 -19
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098
Show difference between Revision 1.31 and 1.32
Revision 1.31jim 2017/02/08 16:58:30+248 -175
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.30 and 1.31
Revision 1.30jim 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 1.29jim 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 1.28jim 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 1.27jim 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 1.26jim 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 1.19jim 2017/05/16 21:14:20+8 -14
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.18 and 1.19
Revision 1.18jim 2017/02/08 16:58:30+44 -6
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.17 and 1.18
Revision 1.17jim 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 1.27jim 2017/05/16 21:14:20+99 -24
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.26 and 1.27
Revision 1.26jim 2017/03/21 20:15:50+23 -57
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.25 and 1.26
Revision 1.25jim 2017/03/08 18:57:23+1 -1
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.24 and 1.25
Revision 1.24jim 2017/02/08 16:58:30+14 -5
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.23 and 1.24
Revision 1.23jim 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 1.22jim 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 1.21jim 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 1.20jim 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 1.17jim 2017/05/16 21:14:20+8 -4
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/03/21 20:15:50+12 -15
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 2017/02/08 16:58:30+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.14 and 1.15
Revision 1.14jim 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 1.13jim 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 1.12jim 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 1.20jim 2017/05/16 21:14:20+15 -5
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.19 and 1.20
Revision 1.19jim 2017/02/08 16:58:30+161 -31
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.18 and 1.19
Revision 1.18jim 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 1.17jim 2017/05/16 21:14:20+1 -1
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/02/08 16:58:30+93 -20
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 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 1.24jim 2017/05/16 21:14:20+10 -8
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.23 and 1.24
Revision 1.23jim 2017/03/21 20:15:50+6 -6
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.22 and 1.23
Revision 1.22jim 2017/02/08 16:58:30+25 -91
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.21 and 1.22
Revision 1.21jim 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 1.20jim 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 1.14jim 2017/02/08 16:58:30+9 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.13 and 1.14
Revision 1.13jim 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 1.7jim 2017/03/21 20:15:50+0 -3
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.6 and 1.7
Revision 1.6jim 2017/02/08 16:58:30+15 -49
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 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 1.4jim 2017/02/08 16:58:30+11 -3
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.3 and 1.4
Revision 1.3jim 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 1.4jim 2017/03/21 20:15:50+2 -4
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.3 and 1.4
Revision 1.3jim 2017/02/08 16:58:30+16 -62
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.2 and 1.3
Revision 1.2jim 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 1.3jim 2017/02/08 16:58:30+9 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.2 and 1.3
Revision 1.2jim 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 1.23jim 2017/03/21 20:15:50+1 -5
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.22 and 1.23
Revision 1.22jim 2017/02/08 16:58:30+358 -320
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.21 and 1.22
Revision 1.21jim 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 1.20jim 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 1.19jim 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 1.16jim 2017/02/08 16:58:30+35 -17
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 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 1.14jim 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 1.8jim 2017/05/16 21:14:20+7 -6
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.7 and 1.8
Revision 1.7jim 2017/03/21 20:15:50+0 -1
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.6 and 1.7
Revision 1.6jim 2017/03/01 14:34:00+33 -11
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 2017/02/08 16:58:30+907 -356
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 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 1.6jim 2017/03/01 14:34:00+6 -0
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 2017/02/08 16:58:30+192 -66
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 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 1.14jim 2017/05/16 21:14:20+106 -91
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.13 and 1.14
Revision 1.13jim 2017/03/21 20:15:50+22 -11
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.12 and 1.13
Revision 1.12jim 2017/02/08 16:58:30+22 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.11 and 1.12
Revision 1.11jim 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 1.10jim 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 1.9jim 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 1.26jim 2017/05/16 21:14:20+67 -2
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.25 and 1.26
Revision 1.25jim 2017/03/08 18:57:23+9 -0
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.24 and 1.25
Revision 1.24jim 2017/02/08 16:58:30+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.23 and 1.24
Revision 1.23jim 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 1.22jim 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 1.17jim 2017/05/16 21:14:20+145 -0
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/03/21 20:15:50+4 -4
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 2017/02/08 16:58:30+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.14 and 1.15
Revision 1.14jim 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 1.13jim 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 1.14jim 2017/02/08 16:58:31+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.13 and 1.14
Revision 1.13jim 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 1.12jim 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 1.21jim 2017/05/16 21:14:20+14 -6
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.20 and 1.21
Revision 1.20jim 2017/03/21 20:15:50+10 -10
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.19 and 1.20
Revision 1.19jim 2017/03/08 18:57:23+21 -0
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.18 and 1.19
Revision 1.18jim 2017/02/08 16:58:31+8 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.17 and 1.18
Revision 1.17jim 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 1.16jim 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 1.15jim 2017/03/21 20:15:50+2 -2
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.14 and 1.15
Revision 1.14jim 2017/02/08 16:58:31+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.13 and 1.14
Revision 1.13jim 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 1.12jim 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 1.18jim 2017/02/08 16:58:31+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.17 and 1.18
Revision 1.17jim 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 1.16jim 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 1.7jim 2017/05/16 21:14:20+207 -39
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.6 and 1.7
Revision 1.6jim 2017/03/21 20:15:50+112 -96
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 2017/03/08 18:57:23+21 -24
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 2017/02/08 16:58:31+46 -21
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.3 and 1.4
Revision 1.3jim 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 1.2jim 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 1.1jim 2016/10/07 16:14:08None
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 1.5jim 2017/05/16 21:14:20+79 -28
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 2017/03/21 20:15:50+39 -24
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.3 and 1.4
Revision 1.3jim 2017/03/08 18:57:23+14 -5
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.2 and 1.3
Revision 1.2jim 2017/02/08 16:58:31+16 -6
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2016/10/07 16:14:08None
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 1.10jim 2017/02/08 16:58:31+10 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.9 and 1.10
Revision 1.9jim 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 1.8jim 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 1.19jim 2017/05/16 21:14:20+1 -1
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.18 and 1.19
Revision 1.18jim 2017/03/21 20:15:50+0 -4
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.17 and 1.18
Revision 1.17jim 2017/02/08 16:58:31+35 -24
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 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 1.15jim 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 1.32jim 2017/05/16 21:14:20+52 -21
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.31 and 1.32
Revision 1.31jim 2017/03/21 20:15:50+4 -2
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.30 and 1.31
Revision 1.30jim 2017/03/08 18:57:23+11 -6
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.29 and 1.30
Revision 1.29jim 2017/02/08 16:58:31+229 -94
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.28 and 1.29
Revision 1.28jim 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 1.27jim 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 1.26jim 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 1.30jim 2017/05/16 21:14:20+11 -2
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.29 and 1.30
Revision 1.29jim 2017/03/21 20:15:50+1 -3
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.28 and 1.29
Revision 1.28jim 2017/03/08 18:57:23+4 -1
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.27 and 1.28
Revision 1.27jim 2017/03/01 14:34:00+1 -1
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098
Show difference between Revision 1.26 and 1.27
Revision 1.26jim 2017/02/08 16:58:31+87 -30
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.25 and 1.26
Revision 1.25jim 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 1.24jim 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 1.23jim 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 1.22jim 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 1.21jim 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 1.13jim 2017/03/21 20:15:50+26 -27
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.12 and 1.13
Revision 1.12jim 2017/02/08 16:58:31+11 -4
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.11 and 1.12
Revision 1.11jim 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 1.10jim 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 1.11jim 2017/03/21 20:15:50+4 -21
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.10 and 1.11
Revision 1.10jim 2017/02/08 16:58:31+8 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.9 and 1.10
Revision 1.9jim 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 1.18jim 2017/03/21 20:15:50+5 -0
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.17 and 1.18
Revision 1.17jim 2017/02/08 16:58:31+31 -6
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 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 1.15jim 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 1.14jim 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 1.29jim 2017/05/16 21:14:20+2 -2
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.28 and 1.29
Revision 1.28jim 2017/03/21 20:15:50+10 -0
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.27 and 1.28
Revision 1.27jim 2017/02/08 16:58:31+32 -12
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.26 and 1.27
Revision 1.26jim 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 1.25jim 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 1.24jim 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 1.23jim 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 1.17jim 2017/03/21 20:15:50+14 -4
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/02/08 16:58:31+9 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 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 1.14jim 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 1.13jim 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 1.12jim 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 1.1jim 2017/03/21 20:17:09None
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707

Filename: colvars_version.h
Revision 1.2jim 2017/05/16 21:14:20+1 -3
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2017/03/21 20:17:09None
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707

Filename: colvarscript.C
Revision 1.11jim 2017/05/16 21:14:20+2 -5
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.10 and 1.11
Revision 1.10jim 2017/03/21 20:15:50+71 -68
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.9 and 1.10
Revision 1.9jim 2017/03/08 18:57:23+12 -1
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.8 and 1.9
Revision 1.8jim 2017/02/08 16:58:31+101 -12
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.7 and 1.8
Revision 1.7jim 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 1.6jim 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 1.7jim 2017/05/16 21:14:20+1 -1
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.6 and 1.7
Revision 1.6jim 2017/03/21 20:15:50+13 -5
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 2017/02/08 16:58:31+11 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 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 1.6jim 2017/02/08 16:58:31+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 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 1.17jim 2017/05/16 21:14:20+5 -0
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/02/08 16:58:31+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 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 1.12jim 2017/05/16 21:14:20+2 -2
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.11 and 1.12
Revision 1.11jim 2017/03/21 20:15:50+275 -0
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.10 and 1.11
Revision 1.10jim 2017/02/08 16:58:31+10 -52
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.9 and 1.10
Revision 1.9jim 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 1.8jim 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 1.17jim 2017/05/16 21:14:20+48 -20
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.16 and 1.17
Revision 1.16jim 2017/03/21 20:15:50+4 -272
Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707
Show difference between Revision 1.15 and 1.16
Revision 1.15jim 2017/02/08 16:58:31+31 -24
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.14 and 1.15
Revision 1.14jim 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 1.13jim 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 1.1060jim 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 1.1006jim 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 1.1jim 2016/09/27 15:40:41None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabf1D.C
Revision 1.2jim 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 1.1jim 2016/09/27 15:40:41None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabf1D.h
Revision 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabf2D.C
Revision 1.2jim 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 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabf2D.h
Revision 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabfTcl.C
Revision 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabffunc.C
Revision 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: eabffunc.h
Revision 1.1jim 2016/09/27 15:40:42None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: elements.h

Filename: fftlib.C
Revision 1.8jim 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 1.4jim 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 1.4jim 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 1.1031jim 2016/09/29 20:31:47+1 -0
QM/MM interface from Marcelo Melo.
Show difference between Revision 1.1030 and 1.1031
Revision 1.1030jim 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 1.25jim 2016/09/18 22:28:32+2 -0
Fix non-Tcl builds.
Show difference between Revision 1.24 and 1.25
Revision 1.24jim 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 1.9jim 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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