| Time | Author | Lines | Revision | Filename | Comments |
| 2002/11/06 01:24:38 | justin | +54 -0 | 1.50 | ug/ug_add.tex | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:34 | justin | +9 -0 | 1.1092 | src/SimParameters.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:33 | justin | +35 -0 | 1.1128 | src/Sequencer.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:33 | justin | +46 -0 | 1.1171 | src/SimParameters.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:33 | justin | +2 -0 | 1.1039 | src/Sequencer.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | +1 -0 | 1.1047 | src/Controller.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | +26 -1 | 1.1064 | src/ComputeNonbondedUtil.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | +2 -0 | 1.1012 | src/ComputeNonbondedSelf.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | +7 -0 | 1.1044 | src/ComputeNonbondedUtil.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | +16 -0 | 1.1169 | src/Controller.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:32 | justin | None | 1.1 | src/PressureProfile.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +2 -0 | 1.1014 | src/ComputeNonbondedPair.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +41 -1 | 1.1036 | src/ComputeHomeTuples.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +22 -0 | 1.1028 | src/ComputeNonbondedPair.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +13 -0 | 1.3 | src/ComputeNonbondedBase2.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +16 -0 | 1.1023 | src/ComputeNonbondedSelf.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +5 -1 | 1.1093 | src/ComputeNonbondedBase.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +6 -1 | 1.1016 | src/ComputeImpropers.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:31 | justin | +31 -2 | 1.1022 | src/ComputeImpropers.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +6 -1 | 1.1016 | src/ComputeDihedrals.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +31 -2 | 1.1024 | src/ComputeDihedrals.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +24 -2 | 1.1023 | src/ComputeAngles.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +6 -1 | 1.1017 | src/ComputeBonds.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +19 -3 | 1.1019 | src/ComputeBonds.C | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:30 | justin | +6 -1 | 1.1019 | src/ComputeAngles.h | Added pressure profile code and associated documentation. |
| 2002/11/06 01:24:22 | justin | +10 -5 | 1.91 | Make.depends | Added pressure profile code and associated documentation. |
| 2002/09/20 15:12:03 | jim | +9 -0 | 1.1047 | src/main.C | Added build date/user/machine message on startup. |
| 2002/09/20 15:11:58 | jim | +16 -0 | 1.1187 | Makefile | Added build date/user/machine message on startup. |
| 2002/09/20 14:15:38 | jim | +0 -16 | 1.1170 | src/SimParameters.C | Eliminated unnecessary errors/warnings about useSettle. |
| 2002/09/13 02:00:18 | jim | +2 -2 | 1.1169 | src/SimParameters.C | Use Settle by default, higher tolerance for rigid bonds. |
| 2002/09/13 01:52:06 | jim | +1 -1 | 1.2 | src/Settle.C | Changed "dt > 0" to "dt != 0" to correctly handle startup. |
| 2002/09/13 01:51:30 | jim | +1 -1 | 1.2 | src/Settle.h | Fixed misleading declaration to match definition in Settle.C. |
| 2002/09/10 21:00:26 | gzheng | +5 -0 | 1.1005 | src/ProxyPatch.h | added using persistent comm for proxyPatch's recvResult(). Also instead of destorying all persistent comm at one time, allow destorying individule persistent handler at a time. (need to compile with latest Charm++) |
| 2002/09/10 21:00:26 | gzheng | +12 -15 | 1.68 | src/LdbCoordinator.C | added using persistent comm for proxyPatch's recvResult(). Also instead of destorying all persistent comm at one time, allow destorying individule persistent handler at a time. (need to compile with latest Charm++) |
| 2002/09/10 21:00:26 | gzheng | +18 -0 | 1.1035 | src/ProxyPatch.C | added using persistent comm for proxyPatch's recvResult(). Also instead of destorying all persistent comm at one time, allow destorying individule persistent handler at a time. (need to compile with latest Charm++) |
| 2002/09/10 21:00:25 | gzheng | +2 -0 | 1.1039 | src/HomePatch.h | added using persistent comm for proxyPatch's recvResult(). Also instead of destorying all persistent comm at one time, allow destorying individule persistent handler at a time. (need to compile with latest Charm++) |
| 2002/09/10 21:00:25 | gzheng | +11 -0 | 1.1103 | src/HomePatch.C | added using persistent comm for proxyPatch's recvResult(). Also instead of destorying all persistent comm at one time, allow destorying individule persistent handler at a time. (need to compile with latest Charm++) |
| 2002/09/10 16:19:41 | jim | +1 -1 | 1.23 | src/dcdlib.C | Improved backup file behavior - now checks return value of rename call. |
| 2002/09/10 16:19:41 | jim | +17 -8 | 1.1041 | src/common.C | Improved backup file behavior - now checks return value of rename call. |
| 2002/09/10 16:19:40 | jim | +4 -30 | 1.46 | src/Output.C | Improved backup file behavior - now checks return value of rename call. |
| 2002/09/10 16:19:40 | jim | +1 -8 | 1.1030 | src/CollectionMaster.C | Improved backup file behavior - now checks return value of rename call. |
| 2002/09/10 06:34:11 | jim | +3 -0 | 1.1091 | src/SimParameters.h | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:11 | jim | +9 -87 | 1.1131 | src/WorkDistrib.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:10 | jim | +1 -1 | 1.15 | src/RecBisection.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:10 | jim | +30 -30 | 1.1032 | src/PatchMap.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:10 | jim | +11 -1 | 1.1021 | src/PatchMap.h | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:10 | jim | +37 -0 | 1.7 | src/PatchMap.inl | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:10 | jim | +6 -0 | 1.1168 | src/SimParameters.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:09 | jim | +0 -2 | 1.67 | src/LdbCoordinator.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:09 | jim | +7 -3 | 1.1102 | src/HomePatch.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:09 | jim | +1 -0 | 1.1038 | src/HomePatch.h | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:08 | jim | +2 -2 | 1.1028 | src/ComputeMap.h | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/10 06:34:08 | jim | +17 -39 | 1.1024 | src/ComputeMap.C | Allow two-away neighbors on any combination of dimensions with new optionstwoAwayX, twoAwayY, twoAwayZ (all boolean). Eventually turn this on whenmore patches are needed automatically. Off by default since criteria forthis helping performance aren't well understood yet. |
| 2002/09/09 15:45:46 | jim | +5 -2 | 1.7 | ug/namd_macros.tex | Version updates - now 2.5b2 |
| 2002/09/09 15:45:45 | jim | +1 -1 | 1.28 | ug/Makefile | Version updates - now 2.5b2 |
| 2002/09/09 15:45:38 | jim | +1 -1 | 1.37 | notes.txt | Version updates - now 2.5b2 |
| 2002/09/09 15:45:38 | jim | +3 -3 | 1.22 | announce.txt | Version updates - now 2.5b2 |
| 2002/09/09 15:45:37 | jim | +1 -1 | 1.1186 | Makefile | Version updates - now 2.5b2 |
| 2002/09/09 15:24:44 | jim | +79 -17 | 1.4 | psfgen/src/topo_mol.c | Imported psfgen 1.3 changes. |
| 2002/09/09 15:24:44 | jim | +3 -0 | 1.4 | psfgen/src/topo_mol.h | Imported psfgen 1.3 changes. |
| 2002/09/09 15:24:43 | jim | +48 -1 | 1.6 | psfgen/src/tcl_psfgen.c | Imported psfgen 1.3 changes. |
| 2002/09/09 15:24:39 | jim | +10 -0 | 1.4 | psfgen/doc/ug_psfgen.tex | Imported psfgen 1.3 changes. |
| 2002/09/09 15:24:38 | jim | +1 -1 | 1.2 | psfgen/doc/ug_macros.tex | Imported psfgen 1.3 changes. |
| 2002/09/08 21:44:46 | jim | +8 -2 | 1.1101 | src/HomePatch.C | Fixed stupid bug. Pressure with rigid bonds should be correct now. |
| 2002/09/07 20:47:41 | jim | +6 -3 | 1.1079 | src/Molecule.C | Fixed bad algorithm in cluster finding code. |
| 2002/09/04 19:06:10 | jim | +6 -2 | 1.1092 | src/ComputeNonbondedBase.h | Whoops! Fixed new exclusion code for fixed atoms and interaction energies. |
| 2002/09/03 21:22:51 | jim | +1 -0 | 1.1168 | src/Controller.C | Protect against initstep underflow in minimizer. |
| 2002/08/30 20:17:24 | jim | +13 -3 | 1.1127 | src/Sequencer.C | Fixed periodic velocity reassignment to use half-step velocities properly. |
| 2002/08/30 20:17:23 | jim | +0 -1 | 1.1167 | src/Controller.C | Fixed periodic velocity reassignment to use half-step velocities properly. |
| 2002/08/30 15:39:56 | jim | +5 -5 | 1.1063 | src/ComputeNonbondedUtil.C | Reordered to possibly avoid cache line overlap. |
| 2002/08/29 00:21:19 | gzheng | +10 -12 | 1.66 | src/LdbCoordinator.C | fixed trace projection broken with CMK_OPTIMIZE=1. |
| 2002/08/27 23:15:28 | jim | +57 -36 | 1.1166 | src/Controller.C | Added TEMPAVG, TOTAL2, TOTAL3, and improved formatting on 80-column screens. |
| 2002/08/27 23:15:28 | jim | +4 -1 | 1.1046 | src/Controller.h | Added TEMPAVG, TOTAL2, TOTAL3, and improved formatting on 80-column screens. |
| 2002/08/27 20:34:28 | jim | +10 -8 | 1.43 | src/NamdCentLB.C | Eliminating unecessarily verbose load balancing output. |
| 2002/08/27 20:34:28 | jim | +2 -2 | 1.14 | src/RefineOnly.C | Eliminating unecessarily verbose load balancing output. |
| 2002/08/27 20:34:28 | jim | +21 -16 | 1.47 | src/Rebalancer.C | Eliminating unecessarily verbose load balancing output. |
| 2002/08/27 20:34:27 | jim | +2 -2 | 1.39 | src/AlgSeven.C | Eliminating unecessarily verbose load balancing output. |
| 2002/08/27 20:34:27 | jim | +2 -0 | 1.67 | src/ComputePme.C | Eliminating unecessarily verbose load balancing output. |
| 2002/08/27 18:45:39 | jim | +7 -6 | 1.1185 | Makefile | Added CMK_OPTIMIZE=1 to all builds, which should eliminate verbose"tracing not available" warnings. |
| 2002/08/27 06:25:41 | gzheng | +13 -1 | 1.42 | src/NamdCentLB.C | fixed a bug in namdcentralLB when unload PME and all processors are PME processors which makes available pes is 0. |
| 2002/08/27 06:25:41 | gzheng | +7 -2 | 1.46 | src/Rebalancer.C | fixed a bug in namdcentralLB when unload PME and all processors are PME processors which makes available pes is 0. |
| 2002/08/26 14:09:08 | jim | +1 -1 | 1.1046 | src/main.C | Fix for Win32. |
| 2002/08/25 22:25:40 | jim | +2 -0 | 1.1043 | src/ComputeNonbondedUtil.h | Improved cache performance by reordering table. |
| 2002/08/25 22:25:40 | jim | +17 -13 | 1.2 | src/ComputeNonbondedBase2.h | Improved cache performance by reordering table. |
| 2002/08/25 22:25:40 | jim | +24 -9 | 1.1062 | src/ComputeNonbondedUtil.C | Improved cache performance by reordering table. |
| 2002/08/25 22:25:39 | jim | +2 -9 | 1.1091 | src/ComputeNonbondedBase.h | Improved cache performance by reordering table. |
| 2002/08/25 20:44:37 | jim | +8 -0 | 1.1126 | src/Sequencer.C | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:37 | jim | +1 -0 | 1.15 | src/PatchTypes.h | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:36 | jim | +135 -17 | 1.1061 | src/ComputeNonbondedUtil.C | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:36 | jim | +23 -50 | 1.1027 | src/ComputeNonbondedPair.C | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:36 | jim | +11 -5 | 1.1022 | src/ComputeNonbondedSelf.C | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:36 | jim | +36 -10 | 1.1042 | src/ComputeNonbondedUtil.h | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:35 | jim | +111 -207 | 1.1090 | src/ComputeNonbondedBase.h | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:44:35 | jim | None | 1.1 | src/ComputeNonbondedBase2.h | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/25 20:43:58 | jim | +63 -16 | 1.90 | Make.depends | Eliminated unnecessary energy calculations, use lookup table for VDW. |
| 2002/08/20 21:25:19 | jim | +0 -6 | 1.1167 | src/SimParameters.C | fixedAtomsForces not required for constant pressure. |
| 2002/08/20 17:52:54 | jim | +14 -7 | 1.1089 | src/ComputeNonbondedBase.h | Major IA64 speedup, adding second loop to group-based distance check. |
| 2002/08/20 14:12:31 | jim | +29 -42 | 1.1088 | src/ComputeNonbondedBase.h | Added lambda_table and code to pipeline most loops on IA64. |
| 2002/08/20 14:12:31 | jim | +42 -0 | 1.1060 | src/ComputeNonbondedUtil.C | Added lambda_table and code to pipeline most loops on IA64. |
| 2002/08/20 14:12:31 | jim | +2 -0 | 1.1041 | src/ComputeNonbondedUtil.h | Added lambda_table and code to pipeline most loops on IA64. |
| 2002/08/19 20:43:43 | jim | +45 -21 | 1.1087 | src/ComputeNonbondedBase.h | Improved speed on non-IA64 and cleaned up compile warnings. |
| 2002/08/19 18:45:48 | jim | +2 -0 | 1.1059 | src/ComputeNonbondedUtil.C | Added missing #undef NBTYPE lines. |
| 2002/08/19 16:36:56 | jim | +27 -7 | 1.1078 | src/Molecule.C | Split FEP, LES, and pairwise interaction code to eliminate if statements. |
| 2002/08/19 16:36:56 | jim | +14 -0 | 1.1040 | src/ComputeNonbondedUtil.h | Split FEP, LES, and pairwise interaction code to eliminate if statements. |
| 2002/08/19 16:36:55 | jim | +89 -43 | 1.1086 | src/ComputeNonbondedBase.h | Split FEP, LES, and pairwise interaction code to eliminate if statements. |
| 2002/08/19 16:36:55 | jim | +57 -5 | 1.1058 | src/ComputeNonbondedUtil.C | Split FEP, LES, and pairwise interaction code to eliminate if statements. |
| 2002/08/16 19:55:47 | jim | +4 -3 | 1.1038 | src/Sequencer.h | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:46 | jim | +111 -41 | 1.1125 | src/Sequencer.C | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:46 | jim | +1 -1 | 1.1031 | src/ReductionMgr.h | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:46 | jim | +1 -1 | 1.1037 | src/HomePatch.h | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:46 | jim | +11 -3 | 1.1100 | src/HomePatch.C | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:45 | jim | +1 -0 | 1.1045 | src/Controller.h | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/16 19:55:45 | jim | +11 -7 | 1.1165 | src/Controller.C | Switched to half-step pressure, temperature, and kinetic energy. Fixedstartup and velocity reassignment to get SHAKE pressure right (but grouppressure is still required when using SHAKE). Add SMOOTH total energyoutput, which adds twice the difference between centered and half-stepkinetic energy to eliminate short-time oscillations (but long-time willlikely not be conserved as well. |
| 2002/08/12 21:50:01 | jim | +26 -28 | 1.1052 | src/ComputeMgr.C | Moved global forces initialization to ensure it always runs. |
| 2002/08/06 14:37:10 | jim | +2 -2 | 1.11 | src/FreeEnergyParse.C | Hacked to handle ', ", and * in atom names (DNA uses these). |
| 2002/08/05 23:22:12 | jim | +1 -0 | 1.1164 | src/Controller.C | Manually null-terminate strings for callback function. |
| 2002/08/02 21:58:36 | justin | +11 -0 | 1.1166 | src/SimParameters.C | Tell the user that Settle doesn't implement atom-based pressure yet, whichmeans that the PRESSURE output is wrong. |
| 2002/08/02 21:46:26 | justin | +2 -0 | 1.1090 | src/SimParameters.h | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:25 | justin | None | 1.1 | src/Settle.C | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:25 | justin | +9 -0 | 1.1165 | src/SimParameters.C | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:25 | justin | +22 -0 | 1.1099 | src/HomePatch.C | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:25 | justin | None | 1.1 | src/Settle.h | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:20 | justin | +1 -0 | 1.1184 | Makefile | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:46:20 | justin | +8 -0 | 1.89 | Make.depends | Added Settle, an analytical form of Shake/Rattle for waters. |
| 2002/08/02 21:03:58 | jim | +9 -28 | 1.45 | src/Output.C | Fixed bug and replaced stupid dual implementation with template! |
| 2002/08/02 18:46:46 | gzheng | +4 -0 | 1.1098 | src/HomePatch.C | missed a couple places for #if CMK_PERSISTENT_COMM |
| 2002/08/02 15:53:30 | gzheng | +2 -0 | 1.65 | src/LdbCoordinator.C | put CMK_PERSISTENT_COMM around new calls. |
| 2002/08/02 15:53:29 | gzheng | +4 -0 | 1.1097 | src/HomePatch.C | put CMK_PERSISTENT_COMM around new calls. |
| 2002/08/02 15:32:47 | jim | None | 1.1 | arch/Linux-ia64.plugins | Added plugins for LINUXIA64. |
| 2002/08/02 14:19:52 | gzheng | +15 -0 | 1.64 | src/LdbCoordinator.C | checked in persistent comm for elan version.default is not turned on. uncomment CmiUsePersistentHandle() in HomePatch.C to activate it. |
| 2002/08/02 14:19:52 | gzheng | +6 -0 | 1.1036 | src/HomePatch.h | checked in persistent comm for elan version.default is not turned on. uncomment CmiUsePersistentHandle() in HomePatch.C to activate it. |
| 2002/08/02 14:19:51 | gzheng | +19 -0 | 1.1096 | src/HomePatch.C | checked in persistent comm for elan version.default is not turned on. uncomment CmiUsePersistentHandle() in HomePatch.C to activate it. |
| 2002/08/01 23:26:40 | jim | +1 -1 | 1.2 | arch/AIX-RS6000.plugins | AIX -> AIX4 |
| 2002/08/01 22:41:55 | jim | +1 -1 | 1.63 | src/LdbCoordinator.C | Eliminate compiler crash on Scyld. |
| 2002/08/01 22:21:44 | jim | +1 -1 | 1.2 | arch/IBM-SP.plugins | AIX -> AIX4 |
| 2002/08/01 21:49:26 | jim | +1 -1 | 1.6 | arch/AIX-RS6000.fftw | Use same fftw directory as IBM-SP. |
| 2002/08/01 19:58:06 | jim | +17 -11 | 1.44 | src/Output.C | New cluster code to handle structures with waters between bonded segments. |
| 2002/08/01 19:58:05 | jim | +4 -2 | 1.1047 | src/Molecule.h | New cluster code to handle structures with waters between bonded segments. |
| 2002/08/01 19:58:04 | jim | +31 -13 | 1.1077 | src/Molecule.C | New cluster code to handle structures with waters between bonded segments. |
| 2002/08/01 15:28:22 | jim | None | 1.1 | arch/HPUX-ia64.tcl | HPUX-ia64 port |
| 2002/08/01 15:28:22 | jim | None | 1.1 | arch/HPUX-ia64.fftw | HPUX-ia64 port |
| 2002/08/01 15:28:21 | jim | None | 1.1 | arch/HPUX-ia64-aCC.arch | HPUX-ia64 port |
| 2002/08/01 15:28:21 | jim | None | 1.1 | arch/HPUX-ia64.base | HPUX-ia64 port |
| 2002/07/30 21:50:28 | jim | +31 -0 | 1.1076 | src/Molecule.C | Remove spurious exclusions generated due to FEP or LES. |
| 2002/07/30 21:50:28 | jim | +1 -0 | 1.1046 | src/Molecule.h | Remove spurious exclusions generated due to FEP or LES. |
| 2002/07/30 17:45:11 | jim | +5 -3 | 1.14 | src/RecBisection.C | New x-dim splitting criteria. |
| 2002/07/29 04:18:10 | justin | +6 -10 | 1.37 | src/ScriptTcl.C | Bring the Tcl interface up to date with the new plugins API. |
| 2002/07/29 03:52:00 | justin | +2 -0 | 1.1027 | src/Parameters.C | Fixed some UMR's uncovered by Valgrind. |
| 2002/07/29 03:51:59 | justin | +2 -1 | 1.1075 | src/Molecule.C | Fixed some UMR's uncovered by Valgrind. |
| 2002/07/27 22:07:13 | gzheng | +6 -4 | 1.62 | src/LdbCoordinator.C | fix partial projection log according to ldbCycleNum change recently. |
| 2002/07/27 21:27:28 | jim | +2 -1 | 1.41 | src/NamdCentLB.C | Actually run Alg7. |
| 2002/07/27 21:26:37 | jim | +2 -0 | 1.61 | src/LdbCoordinator.C | Remove warnings. |
| 2002/07/26 22:47:42 | jim | +6 -14 | 1.1163 | src/Controller.C | Wait, alg7, refine, refine, then run for a long time. |
| 2002/07/26 22:47:42 | jim | +7 -1 | 1.60 | src/LdbCoordinator.C | Wait, alg7, refine, refine, then run for a long time. |
| 2002/07/26 21:59:18 | jim | +14 -15 | 1.45 | src/Rebalancer.C | Better behaviour when extra proxies are needed to balance load. |
| 2002/07/26 21:59:18 | jim | +8 -19 | 1.38 | src/AlgSeven.C | Better behaviour when extra proxies are needed to balance load. |
| 2002/07/26 21:57:46 | jim | +10 -0 | 1.1164 | src/SimParameters.C | Added ldbHomeBackgroundScaling and unloadZero options. |
| 2002/07/26 21:57:46 | jim | +6 -0 | 1.40 | src/NamdCentLB.C | Added ldbHomeBackgroundScaling and unloadZero options. |
| 2002/07/26 21:57:46 | jim | +2 -0 | 1.1089 | src/SimParameters.h | Added ldbHomeBackgroundScaling and unloadZero options. |
| 2002/07/26 19:30:59 | jim | +8 -1 | 1.13 | src/RecBisection.C | Tune bisection to match load distribution. |
| 2002/07/26 14:04:40 | jim | +47 -9 | 1.39 | src/NamdCentLB.C | New smarter algorithm for locating initial proxies on vacant nodes. |
| 2002/07/26 13:41:31 | jim | +2 -0 | 1.37 | src/AlgSeven.C | Balance number of proxies for each patch. |
| 2002/07/26 13:41:31 | jim | +16 -12 | 1.44 | src/Rebalancer.C | Balance number of proxies for each patch. |
| 2002/07/26 13:32:54 | jim | +2 -0 | 1.13 | src/Rebalancer.h | Balance proxy counts, both per home patch and per remote processor. |
| 2002/07/26 13:32:54 | jim | +36 -9 | 1.43 | src/Rebalancer.C | Balance proxy counts, both per home patch and per remote processor. |
| 2002/07/26 13:32:53 | jim | +23 -17 | 1.36 | src/AlgSeven.C | Balance proxy counts, both per home patch and per remote processor. |
| 2002/07/25 15:49:31 | jim | +1 -0 | 1.38 | src/NamdCentLB.C | Fixed bug - initialize available to true! |
| 2002/07/24 05:19:35 | gzheng | +3 -0 | 1.1088 | src/SimParameters.h | unload one rank of pe on a SMP node. added these in SimParameter:e.g.ldbUnloadSMP yes // turn this lb onprocsPerNode 4 // 4 procs per nodeldbUnloadRank 3 // the 3rd rank pe is unloaded.fix computeAverage to exclude the unavailable pes, otherwise computeAverage won;t work correct for RefineLB, this also applys unloadPME. |
| 2002/07/24 05:19:34 | gzheng | +9 -0 | 1.37 | src/NamdCentLB.C | unload one rank of pe on a SMP node. added these in SimParameter:e.g.ldbUnloadSMP yes // turn this lb onprocsPerNode 4 // 4 procs per nodeldbUnloadRank 3 // the 3rd rank pe is unloaded.fix computeAverage to exclude the unavailable pes, otherwise computeAverage won;t work correct for RefineLB, this also applys unloadPME. |
| 2002/07/24 05:19:34 | gzheng | +8 -3 | 1.42 | src/Rebalancer.C | unload one rank of pe on a SMP node. added these in SimParameter:e.g.ldbUnloadSMP yes // turn this lb onprocsPerNode 4 // 4 procs per nodeldbUnloadRank 3 // the 3rd rank pe is unloaded.fix computeAverage to exclude the unavailable pes, otherwise computeAverage won;t work correct for RefineLB, this also applys unloadPME. |
| 2002/07/24 05:19:34 | gzheng | +19 -0 | 1.1163 | src/SimParameters.C | unload one rank of pe on a SMP node. added these in SimParameter:e.g.ldbUnloadSMP yes // turn this lb onprocsPerNode 4 // 4 procs per nodeldbUnloadRank 3 // the 3rd rank pe is unloaded.fix computeAverage to exclude the unavailable pes, otherwise computeAverage won;t work correct for RefineLB, this also applys unloadPME. |
| 2002/07/23 21:05:44 | gzheng | +27 -32 | 1.41 | src/Rebalancer.C | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:44 | gzheng | +9 -0 | 1.36 | src/NamdCentLB.C | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:44 | gzheng | +3 -1 | 1.8 | src/elements.h | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:44 | gzheng | +4 -4 | 1.14 | src/NamdNborLB.C | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:44 | gzheng | +3 -3 | 1.14 | src/Broadcasts.h | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:44 | gzheng | +1 -7 | 1.35 | src/AlgSeven.C | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 21:05:43 | gzheng | +1 -1 | 1.5 | src/AlgNbor.C | processorInfo has a flag(changed to available) for each processor. Use this availaibity flag to determine if compute will be assigned to that processor. |
| 2002/07/23 20:55:39 | gzheng | +5 -0 | 1.1037 | src/common.h | added PME_BARRIER: barrier before and after PME step. set PME_BARRIER in common.h to turn this on. |
| 2002/07/23 20:55:39 | gzheng | +13 -2 | 1.1162 | src/Controller.C | added PME_BARRIER: barrier before and after PME step. set PME_BARRIER in common.h to turn this on. |
| 2002/07/23 20:55:39 | gzheng | +13 -2 | 1.1124 | src/Sequencer.C | added PME_BARRIER: barrier before and after PME step. set PME_BARRIER in common.h to turn this on. |
| 2002/07/23 20:50:01 | jim | +2 -2 | 1.20 | src/ScriptTcl.h | With Tcl can now parse multiple config files. This is useful if you wantto switch options using the command line only. |
| 2002/07/23 20:50:01 | jim | +26 -4 | 1.13 | src/mainfunc.C | With Tcl can now parse multiple config files. This is useful if you wantto switch options using the command line only. |
| 2002/07/23 20:50:00 | jim | +34 -22 | 1.36 | src/ScriptTcl.C | With Tcl can now parse multiple config files. This is useful if you wantto switch options using the command line only. |
| 2002/07/23 20:28:54 | jim | +9 -6 | 1.66 | src/ComputePme.C | Made to compile on broken compilers. |
| 2002/07/23 19:54:09 | jim | +1 -1 | 1.1162 | src/SimParameters.C | Output formatting fix. |
| 2002/07/23 19:08:32 | jim | +4 -0 | 1.1087 | src/SimParameters.h | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/23 19:08:30 | jim | +15 -2 | 1.35 | src/NamdCentLB.C | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/23 19:08:30 | jim | +29 -2 | 1.1161 | src/SimParameters.C | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/23 19:08:30 | jim | +3 -2 | 1.40 | src/Rebalancer.C | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/23 19:08:29 | jim | +7 -8 | 1.65 | src/ComputePme.C | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/23 19:08:29 | jim | +5 -2 | 1.34 | src/AlgSeven.C | Added options to turn on various load balancing test features: ldbBackgroundScaling <double> ldbPMEBackgroundScaling <double> ldbUnloadPME <bool> PMEBarrier <bool> |
| 2002/07/22 23:03:24 | jim | +4 -2 | 1.64 | src/ComputePme.C | Turned off barrier. |
| 2002/07/22 22:19:40 | jim | +9 -0 | 1.39 | src/Rebalancer.C | Don't load PME processors if > 1000 processors. |
| 2002/07/22 22:19:40 | jim | +8 -0 | 1.33 | src/AlgSeven.C | Don't load PME processors if > 1000 processors. |
| 2002/07/22 21:58:50 | jim | +2 -2 | 1.63 | src/ComputePme.C | Fix for isComputePme. |
| 2002/07/22 21:05:24 | jim | +12 -7 | 1.62 | src/ComputePme.C | Reimplemented isComputePme() efficiently. |
| 2002/07/22 20:55:17 | jim | +4 -4 | 1.61 | src/ComputePme.C | Fixed bugs in barrier code. |
| 2002/07/22 19:17:23 | gzheng | +9 -0 | 1.34 | src/NamdCentLB.C | added QueryDumpData interface for dumping load data into disk file. |
| 2002/07/22 16:34:39 | jim | +1 -0 | 1.12 | src/ComputePmeMgr.ci | Added direct calls to ComputePme doWork and sendData.Added barrier before sendTrans to ensure all sendGrids are complete. |
| 2002/07/22 16:34:39 | jim | +4 -0 | 1.1130 | src/WorkDistrib.C | Added direct calls to ComputePme doWork and sendData.Added barrier before sendTrans to ensure all sendGrids are complete. |
| 2002/07/22 16:34:39 | jim | +12 -1 | 1.33 | src/NamdCentLB.C | Added direct calls to ComputePme doWork and sendData.Added barrier before sendTrans to ensure all sendGrids are complete. |
| 2002/07/22 16:34:39 | jim | +3 -0 | 1.20 | src/ComputePme.h | Added direct calls to ComputePme doWork and sendData.Added barrier before sendTrans to ensure all sendGrids are complete. |
| 2002/07/22 16:34:38 | jim | +32 -1 | 1.60 | src/ComputePme.C | Added direct calls to ComputePme doWork and sendData.Added barrier before sendTrans to ensure all sendGrids are complete. |
| 2002/07/21 21:59:40 | jim | +2 -2 | 1.32 | src/NamdCentLB.C | Fixed to match new (or any newer) patch distribution. |
| 2002/07/21 21:22:10 | jim | +6 -6 | 1.31 | src/NamdCentLB.C | Maximum background load multiplier is now 2.0. |
| 2002/07/21 21:06:43 | jim | +3 -9 | 1.30 | src/NamdCentLB.C | Fixed crasher. |
| 2002/07/21 20:21:02 | jim | +11 -3 | 1.29 | src/NamdCentLB.C | Adjusted and turned on PME node background load adjustment. |
| 2002/07/21 19:27:33 | sameer | +21 -6 | 1.59 | src/ComputePme.C | Adding code to computePme.C to detect if a particular processor is a PME processor or not |
| 2002/07/21 18:21:43 | jim | +1 -0 | 1.11 | src/LdbCoordinator.ci | Fixed load balancer so that barrier is triggered by controller only. |
| 2002/07/21 18:21:43 | jim | +1 -1 | 1.34 | src/LdbCoordinator.h | Fixed load balancer so that barrier is triggered by controller only. |
| 2002/07/21 18:21:43 | jim | +8 -35 | 1.59 | src/LdbCoordinator.C | Fixed load balancer so that barrier is triggered by controller only. |
| 2002/07/21 16:10:04 | jim | +16 -0 | 1.1031 | src/PatchMap.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:04 | jim | +15 -11 | 1.1129 | src/WorkDistrib.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:04 | jim | +4 -0 | 1.1020 | src/PatchMap.h | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:03 | jim | +0 -9 | 1.1031 | src/Node.h | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:03 | jim | +1 -6 | 1.1029 | src/ComputeFullDirect.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:03 | jim | +0 -13 | 1.1069 | src/Node.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:03 | jim | +2 -4 | 1.1095 | src/HomePatch.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:02 | jim | +1 -3 | 1.1026 | src/CollectionMaster.h | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:02 | jim | +1 -5 | 1.23 | src/ComputeDPME.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:02 | jim | +1 -5 | 1.1067 | src/ComputeDPMTA.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 16:10:02 | jim | +1 -3 | 1.4 | src/ComputeExt.C | Removed patches from node 0 when more procesors than 64 or number of patches. |
| 2002/07/21 00:36:35 | sameer | +19 -10 | 1.28 | src/NamdCentLB.C | adding code to reduce load on pme processors |
| 2002/07/20 21:46:39 | gzheng | +10 -0 | 1.27 | src/NamdCentLB.C | add QueryDumpData() to interface with load balancer to dump load data into disk file. |
| 2002/07/20 21:46:39 | gzheng | +1 -0 | 1.5 | src/NamdCentLB.h | add QueryDumpData() to interface with load balancer to dump load data into disk file. |
| 2002/07/20 17:00:13 | jim | +1 -1 | 1.12 | src/RecBisection.C | Subdivide along x dimension if possible to reduces PME message count. |
| 2002/07/20 16:47:16 | jim | +16 -3 | 1.1128 | src/WorkDistrib.C | Now sorting by all three dimensions. |
| 2002/07/19 22:57:50 | jim | +1 -0 | 1.1030 | src/WorkDistrib.h | Reordered patches to align with PME and increase grid communication locality,possibly at the expense of patch locality, but that is fixable with someadditional reordering. |
| 2002/07/19 22:57:50 | jim | +8 -0 | 1.58 | src/ComputePme.C | Reordered patches to align with PME and increase grid communication locality,possibly at the expense of patch locality, but that is fixable with someadditional reordering. |
| 2002/07/19 22:57:50 | jim | +68 -16 | 1.1127 | src/WorkDistrib.C | Reordered patches to align with PME and increase grid communication locality,possibly at the expense of patch locality, but that is fixable with someadditional reordering. |
| 2002/07/19 05:01:08 | jim | +77 -49 | 1.32 | src/AlgSeven.C | Added short cut search. |
| 2002/07/19 05:01:08 | jim | +2 -1 | 1.3 | src/Alg7.h | Added short cut search. |
| 2002/07/19 04:11:39 | jim | +10 -0 | 1.12 | src/Rebalancer.h | Faster "short cut" method for finding destination processors. |
| 2002/07/19 04:11:38 | jim | +103 -72 | 1.38 | src/Rebalancer.C | Faster "short cut" method for finding destination processors. |
| 2002/07/19 01:29:47 | jim | +0 -10 | 1.37 | src/Rebalancer.C | Removed do-nothing, O(N^2) loop! |
| 2002/07/18 23:51:28 | jim | +1 -1 | 1.1012 | src/InfoStream.h | Fixed extra semicolons. |
| 2002/07/18 23:51:28 | jim | +13 -13 | 1.1008 | src/InfoStream.C | Fixed extra semicolons. |
| 2002/07/18 21:28:53 | jim | +11 -2 | 1.4 | arch/Linux-ia64-ecc.arch | IA64 options. |
| 2002/07/18 21:28:53 | jim | +2 -2 | 1.2 | arch/Linux-ia64.tcl | IA64 options. |
| 2002/07/18 21:26:25 | jim | +75 -69 | 1.1085 | src/ComputeNonbondedBase.h | Rewrote several loops to software pipeline on IA64. Test fixed atoms! |
| 2002/07/18 21:24:53 | jim | +10 -13 | 1.1011 | src/InfoStream.h | Moved things to non-inline to avoid breaking the Intel IA64 compiler. |
| 2002/07/18 21:24:53 | jim | +41 -0 | 1.1007 | src/InfoStream.C | Moved things to non-inline to avoid breaking the Intel IA64 compiler. |
| 2002/07/12 00:51:40 | sameer | +4 -0 | 1.1034 | src/ProxyPatch.C | Adding ifdefs to not include the communications library by default |
| 2002/07/12 00:51:40 | sameer | +4 -0 | 1.1126 | src/WorkDistrib.C | Adding ifdefs to not include the communications library by default |
| 2002/07/12 00:51:39 | sameer | +3 -0 | 1.1028 | src/PatchMgr.C | Adding ifdefs to not include the communications library by default |
| 2002/07/12 00:40:13 | sameer | +1 -1 | 1.1013 | src/main.ci | Commiting change to main.ci that disables the library by default |
| 2002/07/12 00:38:19 | sameer | +1 -1 | 1.1033 | src/ProxyPatch.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:19 | sameer | +11 -1 | 1.1045 | src/main.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:19 | sameer | +1 -1 | 1.1125 | src/WorkDistrib.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:19 | sameer | +1 -0 | 1.1027 | src/PatchMgr.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:19 | sameer | +3 -0 | 1.1012 | src/main.ci | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:18 | sameer | +7 -1 | 1.58 | src/LdbCoordinator.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:18 | sameer | +5 -0 | 1.1068 | src/Node.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:18 | sameer | +0 -1 | 1.11 | src/ComputePmeMgr.ci | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:18 | sameer | +177 -67 | 1.57 | src/ComputePme.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:17 | sameer | +5 -0 | 1.19 | src/BackEnd.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:17 | sameer | +2 -0 | 1.1051 | src/ComputeMgr.C | commiting version of namd that works with the communication library |
| 2002/07/12 00:38:17 | sameer | +1 -0 | 1.1012 | src/BOCgroup.h | commiting version of namd that works with the communication library |
| 2002/07/11 14:53:37 | jim | +16 -0 | 1.8 | src/GlobalMasterTcl.C | Check for out-of-range atomids. |
| 2002/07/11 01:44:25 | jim | +18 -5 | 1.31 | src/AlgSeven.C | Reduced or eliminated additional proxies by preferingone home and one proxy to two homes. |
| 2002/07/11 01:41:35 | jim | +3 -2 | 1.13 | src/RefineOnly.C | Added non-per-processor load balanced diagnostics. |
| 2002/07/11 01:41:34 | jim | +5 -1 | 1.36 | src/Rebalancer.C | Added non-per-processor load balanced diagnostics. |
| 2002/07/10 22:19:29 | jim | +28 -3 | 1.30 | src/AlgSeven.C | Fixed load balancer bug that was overloading final processor. |
| 2002/07/10 22:19:29 | jim | +26 -9 | 1.35 | src/Rebalancer.C | Fixed load balancer bug that was overloading final processor. |
| 2002/07/09 21:57:06 | jim | +4 -4 | 1.1160 | src/SimParameters.C | Fixed fftw.h -> sfftw.h, double -> float, etc., following PME code. |
| 2002/07/09 05:37:36 | gzheng | +2 -0 | 1.57 | src/LdbCoordinator.C | use CHARM_VERSION to disable code for old version of charm. |
| 2002/07/09 01:46:52 | jim | +1 -1 | 1.1057 | src/ComputeNonbondedUtil.C | Removed stupid debugging code that was causing crashes. |
| 2002/07/05 21:38:52 | jim | +2 -0 | 1.10 | src/ComputePmeMgr.ci | Eliminated lots of excess reduction data in messages. |
| 2002/07/05 21:38:52 | jim | +41 -32 | 1.56 | src/ComputePme.C | Eliminated lots of excess reduction data in messages. |
| 2002/07/05 21:38:52 | jim | +2 -2 | 1.19 | src/ComputePme.h | Eliminated lots of excess reduction data in messages. |
| 2002/07/05 20:28:30 | jim | +1 -1 | 1.5 | arch/Win32.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:30 | jim | +1 -1 | 1.5 | arch/Tru64-Alpha.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:29 | jim | +1 -1 | 1.2 | arch/Linux-ia64.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:29 | jim | +1 -1 | 1.5 | arch/T3E.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:29 | jim | +1 -1 | 1.4 | arch/Solaris-Sparc.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:29 | jim | +1 -1 | 1.6 | arch/Origin2000.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:28 | jim | +1 -1 | 1.4 | arch/IBM-SP.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:28 | jim | +1 -1 | 1.4 | arch/HPUX.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:28 | jim | +1 -1 | 1.5 | arch/Linux-i686.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:28 | jim | +1 -1 | 1.3 | arch/Linux-Alpha.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:27 | jim | +1 -1 | 1.2 | arch/Cygwin-i686-MSVC.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:27 | jim | +1 -1 | 1.3 | arch/ASCI-Red.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:27 | jim | +1 -1 | 1.3 | arch/HPUX-PA2.0.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:27 | jim | +1 -1 | 1.2 | arch/Darwin-PPC.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:27 | jim | +1 -1 | 1.3 | arch/Cygwin-i686.fftw | Using single precision for FFT. |
| 2002/07/05 20:28:26 | jim | +1 -1 | 1.5 | arch/AIX-RS6000.fftw | Using single precision for FFT. |
| 2002/07/05 20:24:56 | jim | +1 -1 | 1.6 | src/PmeKSpace.h | Use float rather than double for FFT. |
| 2002/07/05 20:24:55 | jim | +1 -1 | 1.7 | src/PmeKSpace.C | Use float rather than double for FFT. |
| 2002/07/05 20:24:55 | jim | +21 -21 | 1.55 | src/ComputePme.C | Use float rather than double for FFT. |
| 2002/07/05 20:24:55 | jim | +2 -2 | 1.9 | src/ComputePmeMgr.ci | Use float rather than double for FFT. |
| 2002/07/03 15:53:43 | jim | +18 -52 | 1.54 | src/ComputePme.C | Eliminated buffered messages by using second charge grid. |
| 2002/07/03 00:31:48 | jim | +3 -0 | 1.1159 | src/SimParameters.C | Fixed uninitialized pairInteractionSelf. |
| 2002/07/02 23:43:29 | jim | +115 -83 | 1.53 | src/ComputePme.C | Separated sending and receiving processors on transpose for large-enough runs. |
| 2002/07/02 16:35:25 | gzheng | +12 -0 | 1.56 | src/LdbCoordinator.C | in the case when trace is off at the beginning(+traceoff in the command line), only turn trace on from the first LB to the firstLdbStep after the second LB.i.e. from ldbCycleNum=2 to 4. This will reduce the trace for the uninteresting part of the execution. |
| 2002/07/02 02:03:15 | jim | +1 -0 | 1.1039 | src/ComputeNonbondedUtil.h | Faster, more accurate nonbonded interpolation table. |
| 2002/07/02 02:03:15 | jim | +15 -6 | 1.1084 | src/ComputeNonbondedBase.h | Faster, more accurate nonbonded interpolation table. |
| 2002/07/02 02:03:15 | jim | +29 -15 | 1.1056 | src/ComputeNonbondedUtil.C | Faster, more accurate nonbonded interpolation table. |
| 2002/06/28 06:08:38 | jim | +4 -0 | 1.1026 | src/ComputeNonbondedPair.C | Added special code for single timestepping cases, now 25-40% faster! |
| 2002/06/28 06:08:38 | jim | +2 -0 | 1.1021 | src/ComputeNonbondedSelf.C | Added special code for single timestepping cases, now 25-40% faster! |
| 2002/06/28 06:08:38 | jim | +33 -1 | 1.1055 | src/ComputeNonbondedUtil.C | Added special code for single timestepping cases, now 25-40% faster! |
| 2002/06/28 06:08:38 | jim | +9 -0 | 1.1038 | src/ComputeNonbondedUtil.h | Added special code for single timestepping cases, now 25-40% faster! |
| 2002/06/28 06:08:37 | jim | +54 -8 | 1.1083 | src/ComputeNonbondedBase.h | Added special code for single timestepping cases, now 25-40% faster! |
| 2002/06/28 02:28:01 | jim | +2 -0 | 1.1158 | src/SimParameters.C | Fixed missing FFTW ifdef. |
| 2002/06/26 18:51:30 | pgrayson | +18 -8 | 1.2 | src/GlobalMasterIMD.C | In IMD, a zero force now causes NAMD to delete the atom from the forcelist so that we don't get a bunch of (0,0,0) vectors sitting aroundafter a while. |
| 2002/06/21 21:38:27 | jim | +1 -1 | 1.1082 | src/ComputeNonbondedBase.h | Moved high-latenty floating point divide forward. (from Justin) |
| 2002/06/21 21:06:34 | jim | +7 -1 | 1.1081 | src/ComputeNonbondedBase.h | Avoid inner loop in for pair computes when outer loop found no pairs. |
| 2002/06/21 00:55:50 | justin | +55 -0 | 1.3 | ug/ug_sample.tex | Added documentation and example scripts for using the "coorfile" trajectoryreading command. |
| 2002/06/21 00:55:50 | justin | +12 -0 | 1.12 | ug/ug_start.tex | Added documentation and example scripts for using the "coorfile" trajectoryreading command. |
| 2002/06/21 00:55:50 | justin | +1 -0 | 1.49 | ug/ug_add.tex | Added documentation and example scripts for using the "coorfile" trajectoryreading command. |
| 2002/06/20 20:55:11 | gzheng | +8 -0 | 1.1161 | src/Controller.C | in Controller::outputExtendedSystem(), add checking for xscFile to see if opened successfully. |
| 2002/06/20 20:39:59 | gzheng | +1 -1 | 1.2 | arch/Cygwin-i686.fftw | set the fftw path as on malta. |
| 2002/06/17 21:47:00 | jim | +81 -4 | 1.5 | psfgen/src/tcl_psfgen.c | Safety feature - after fatal error all other commands fail until resetpsf. |
| 2002/06/17 21:47:00 | jim | +4 -0 | 1.3 | psfgen/src/topo_mol_output.c | Safety feature - after fatal error all other commands fail until resetpsf. |
| 2002/06/17 21:46:59 | jim | +1 -0 | 1.2 | psfgen/src/tcl_main.c | Safety feature - after fatal error all other commands fail until resetpsf. |
| 2002/06/14 00:30:11 | justin | +4 -5 | 1.48 | ug/ug_add.tex | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:08 | justin | +2 -2 | 1.1030 | src/ReductionMgr.h | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:08 | justin | +0 -1 | 1.1044 | src/Controller.h | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:07 | justin | +14 -15 | 1.1080 | src/ComputeNonbondedBase.h | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:07 | justin | +11 -20 | 1.1160 | src/Controller.C | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:07 | justin | +1 -1 | 1.1037 | src/ComputeNonbondedUtil.h | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/14 00:30:07 | justin | +2 -1 | 1.1054 | src/ComputeNonbondedUtil.C | Removed pair virial calculation; replaced with interaction forces broken downinto electrostatic and vdw contributions. |
| 2002/06/13 21:52:00 | jim | +9 -4 | 1.1183 | Makefile | Added PLUGINLIB to all targets. |
| 2002/06/13 20:32:26 | jim | +1 -1 | 1.2 | arch/Win32.plugins | Moved default Win32 plugins directory to ~/jim/plugins. |
| 2002/06/11 22:27:26 | jim | None | 1.1 | arch/Win32.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:26 | jim | None | 1.1 | arch/Tru64-Alpha.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:26 | jim | None | 1.1 | arch/T3E.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:25 | jim | None | 1.1 | arch/Origin2000.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:25 | jim | None | 1.1 | arch/Solaris-Sparc.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:24 | jim | None | 1.1 | arch/IBM-SP.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:24 | jim | None | 1.1 | arch/Linux-Alpha.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:24 | jim | None | 1.1 | arch/Linux-i686.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:23 | jim | None | 1.1 | arch/HPUX-PA2.0.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:23 | jim | None | 1.1 | arch/HPUX.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:23 | jim | None | 1.1 | arch/Darwin-PPC.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:22 | jim | None | 1.1 | arch/AIX-RS6000.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:22 | jim | None | 1.1 | arch/All-Unix.plugins | Added support for building with plugins. |
| 2002/06/11 22:27:17 | jim | +11 -1 | 1.29 | config | Added support for building with plugins. |
| 2002/06/11 22:27:16 | jim | +0 -7 | 1.1182 | Makefile | Added support for building with plugins. |
| 2002/06/04 17:58:58 | jim | +2 -3 | 1.1040 | src/common.C | Fixed nonexistent ssize_t on Win32. |
| 2002/06/04 17:58:58 | jim | +2 -3 | 1.22 | src/dcdlib.C | Fixed nonexistent ssize_t on Win32. |
| 2002/06/04 16:16:23 | jim | +1 -0 | 1.1181 | Makefile | Added file command to release target, to check for dynamic executables. |
| 2002/06/03 23:01:01 | jim | +16 -0 | 1.17 | ug/ug_basic.tex | Added ability to save FFTW wisdom to a file, on by default. |
| 2002/06/03 23:00:57 | jim | +130 -0 | 1.1157 | src/SimParameters.C | Added ability to save FFTW wisdom to a file, on by default. |
| 2002/06/03 23:00:57 | jim | +5 -0 | 1.1086 | src/SimParameters.h | Added ability to save FFTW wisdom to a file, on by default. |
| 2002/06/03 20:30:47 | jim | +10 -10 | 1.7 | src/GlobalMasterTcl.C | Changed bogus "const foo::iterator" return type to "foo::const_iterator". |
| 2002/06/03 20:30:47 | jim | +3 -3 | 1.2 | src/GlobalMasterFreeEnergy.C | Changed bogus "const foo::iterator" return type to "foo::const_iterator". |
| 2002/06/03 20:30:46 | jim | +10 -10 | 1.3 | src/GlobalMaster.C | Changed bogus "const foo::iterator" return type to "foo::const_iterator". |
| 2002/06/03 20:30:46 | jim | +3 -3 | 1.2 | src/GlobalMasterEasy.C | Changed bogus "const foo::iterator" return type to "foo::const_iterator". |
| 2002/06/03 20:30:46 | jim | +10 -10 | 1.3 | src/GlobalMaster.h | Changed bogus "const foo::iterator" return type to "foo::const_iterator". |
| 2002/06/03 20:28:54 | jim | +1 -1 | 1.1039 | src/common.C | fixed testing unsigned < 0 warning in NAMD_write |
| 2002/06/03 20:17:53 | jim | +1 -1 | 1.21 | src/dcdlib.C | fixed warning about testing for unsigned < 0 |
| 2002/05/30 18:13:59 | jim | +10 -8 | 1.1038 | src/common.C | Fixed NAMD_write to handle interrupts gracefully. |
| 2002/05/30 18:13:59 | jim | +12 -10 | 1.20 | src/dcdlib.C | Fixed NAMD_write to handle interrupts gracefully. |
| 2002/05/24 03:09:22 | ilya | +3 -6 | 1.1123 | src/Sequencer.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:22 | ilya | +44 -0 | 1.1156 | src/SimParameters.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:22 | ilya | +2 -0 | 1.1124 | src/WorkDistrib.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:22 | ilya | +12 -1 | 1.1085 | src/SimParameters.h | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:22 | ilya | +12 -0 | 1.1042 | src/NamdState.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:21 | ilya | +5 -0 | 1.1050 | src/ComputeMgr.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:21 | ilya | +14 -0 | 1.2 | src/ComputeConsForce.h | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:21 | ilya | +1 -0 | 1.1027 | src/ComputeMap.h | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:21 | ilya | +361 -1 | 1.1074 | src/Molecule.C | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:21 | ilya | +43 -1 | 1.1045 | src/Molecule.h | added local torqueing for atoms -- Ilya |
| 2002/05/24 03:09:20 | ilya | +38 -1 | 1.2 | src/ComputeConsForce.C | added local torqueing for atoms -- Ilya |
| 2002/05/22 18:24:08 | jim | +1 -1 | 1.1155 | src/SimParameters.C | Small fix, actually runs now. |
| 2002/05/21 04:57:46 | justin | +23 -23 | 1.47 | ug/ug_add.tex | Updated docs for pair interaction calculations. |
| 2002/05/21 04:38:18 | justin | +4 -2 | 1.1041 | src/NamdState.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:18 | justin | +16 -17 | 1.1154 | src/SimParameters.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:18 | justin | +5 -4 | 1.1123 | src/WorkDistrib.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:18 | justin | +3 -3 | 1.1084 | src/SimParameters.h | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +1 -0 | 1.1043 | src/Controller.h | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +2 -7 | 1.1053 | src/ComputeNonbondedUtil.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +7 -4 | 1.1159 | src/Controller.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +15 -30 | 1.1079 | src/ComputeNonbondedBase.h | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +1 -4 | 1.1036 | src/ComputeNonbondedUtil.h | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/21 04:38:17 | justin | +22 -2 | 1.1073 | src/Molecule.C | Pair interaction changes. Can no longer compute pair interactions at the sametime as everything else. Added facility for calculating within-groupenergies and virials. Added options that allow one to specify which value inthe B column to use for the groups, so that you can use the same PDB file fordifferent sets of interactions. |
| 2002/05/20 04:29:23 | justin | +15 -0 | 1.46 | ug/ug_add.tex | Added docs for within-group pair interaction analysis, and corrected earliertypos. |
| 2002/05/20 04:29:01 | justin | +2 -0 | 1.1083 | src/SimParameters.h | Added within-group pair interaction analysis. |
| 2002/05/20 04:29:00 | justin | +4 -0 | 1.1052 | src/ComputeNonbondedUtil.C | Added within-group pair interaction analysis. |
| 2002/05/20 04:29:00 | justin | +2 -0 | 1.1035 | src/ComputeNonbondedUtil.h | Added within-group pair interaction analysis. |
| 2002/05/20 04:29:00 | justin | +10 -5 | 1.1078 | src/ComputeNonbondedBase.h | Added within-group pair interaction analysis. |
| 2002/05/20 04:29:00 | justin | +12 -0 | 1.1153 | src/SimParameters.C | Added within-group pair interaction analysis. |
| 2002/05/19 22:08:52 | justin | +1 -1 | 1.1152 | src/SimParameters.C | Remove a single ' to make gcc 2.96 happy. |
| 2002/05/18 20:25:45 | ilya | +4 -4 | 1.1122 | src/Sequencer.C | made dragging the last operation in the integrator -- Ilya |
| 2002/05/17 19:42:28 | justin | +4 -2 | 1.45 | ug/ug_add.tex | Updated docs for pair interaction to include virial. |
| 2002/05/17 19:42:06 | justin | +1 -0 | 1.1029 | src/ReductionMgr.h | Added virial calculation to pair interaction. |
| 2002/05/17 19:42:05 | justin | +12 -5 | 1.1158 | src/Controller.C | Added virial calculation to pair interaction. |
| 2002/05/17 19:42:05 | justin | +1 -0 | 1.1034 | src/ComputeNonbondedUtil.h | Added virial calculation to pair interaction. |
| 2002/05/17 19:42:04 | justin | +1 -0 | 1.1051 | src/ComputeNonbondedUtil.C | Added virial calculation to pair interaction. |
| 2002/05/17 19:42:04 | justin | +30 -6 | 1.1077 | src/ComputeNonbondedBase.h | Added virial calculation to pair interaction. |
| 2002/05/17 18:30:28 | justin | +7 -3 | 1.44 | ug/ug_add.tex | Updates for forces and new format in pair interaction calculations. |
| 2002/05/17 18:30:07 | justin | +2 -0 | 1.1028 | src/ReductionMgr.h | Added force output to pair interaction calculations, and reformatted thepair interaction output so that it appears in its own line in stdout. |
| 2002/05/17 18:30:06 | justin | +1 -0 | 1.1033 | src/ComputeNonbondedUtil.h | Added force output to pair interaction calculations, and reformatted thepair interaction output so that it appears in its own line in stdout. |
| 2002/05/17 18:30:06 | justin | +17 -7 | 1.1157 | src/Controller.C | Added force output to pair interaction calculations, and reformatted thepair interaction output so that it appears in its own line in stdout. |
| 2002/05/17 18:30:05 | justin | +1 -0 | 1.1050 | src/ComputeNonbondedUtil.C | Added force output to pair interaction calculations, and reformatted thepair interaction output so that it appears in its own line in stdout. |
| 2002/05/17 18:30:04 | justin | +14 -0 | 1.1076 | src/ComputeNonbondedBase.h | Added force output to pair interaction calculations, and reformatted thepair interaction output so that it appears in its own line in stdout. |
| 2002/05/15 23:46:15 | ilya | +4 -6 | 1.1121 | src/Sequencer.C | tested the dragging code, minor improvements -- Ilya |
| 2002/05/15 22:55:00 | ilya | +11 -1 | 1.1151 | src/SimParameters.C | added global velocity parameter to moving and rotating drag. values readfrom PDB files are now scaling factors. |
| 2002/05/15 22:55:00 | ilya | +8 -4 | 1.1120 | src/Sequencer.C | added global velocity parameter to moving and rotating drag. values readfrom PDB files are now scaling factors. |
| 2002/05/15 22:55:00 | ilya | +6 -4 | 1.1082 | src/SimParameters.h | added global velocity parameter to moving and rotating drag. values readfrom PDB files are now scaling factors. |
| 2002/05/14 22:36:18 | ilya | +53 -58 | 1.1150 | src/SimParameters.C | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/14 22:36:18 | ilya | +18 -11 | 1.1081 | src/SimParameters.h | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/14 22:36:17 | ilya | +16 -45 | 1.1119 | src/Sequencer.C | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/14 22:36:17 | ilya | +561 -212 | 1.1072 | src/Molecule.C | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/14 22:36:17 | ilya | +62 -19 | 1.1044 | src/Molecule.h | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/14 22:36:17 | ilya | +19 -6 | 1.1040 | src/NamdState.C | Changed atom dragging protocol and interface -- Ilya |
| 2002/05/13 20:39:54 | jim | +18 -21 | 1.1022 | src/Lattice.h | Fixed wrapNearest to work for more general cells. |
| 2002/05/11 23:39:28 | justin | +10 -3 | 1.43 | ug/ug_add.tex | Added docs for new pair interaction features. |
| 2002/05/11 23:39:10 | justin | +1 -0 | 1.1080 | src/SimParameters.h | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:10 | justin | +3 -2 | 1.1122 | src/WorkDistrib.C | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:09 | justin | +2 -0 | 1.1049 | src/ComputeNonbondedUtil.C | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:09 | justin | +6 -0 | 1.1149 | src/SimParameters.C | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:09 | justin | +1 -0 | 1.1032 | src/ComputeNonbondedUtil.h | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:09 | justin | +7 -0 | 1.1156 | src/Controller.C | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 23:39:08 | justin | +9 -1 | 1.1075 | src/ComputeNonbondedBase.h | When enabled, pair interaction energy calculation now take place alongsideregular calculations by default. The optional parameter pairInteractionOnlyswitches off non-pair interactions. Pair interaction energies are nowreported in a new column, PAIR_VDW and PAIR_ELECT. |
| 2002/05/11 01:09:25 | justin | +16 -0 | 1.35 | src/ScriptTcl.C | Added a "coorfile skip" command, which is much faster than distributingall the atoms to the rest of the system and then not doing anything withthem. |