| Time | Author | Lines | Revision | Filename | Comments |
| 2008/04/23 00:15:16 | jim | +2 -59 | 1.17 | src/ComputeSelfTuples.h | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +1 -10 | 1.1019 | src/ComputeImpropers.h | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +8 -7 | 1.1049 | src/ComputeHomeTuples.h | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +1 -11 | 1.1006 | src/ComputeDihedrals.inl | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +1 -18 | 1.3 | src/ComputeCrossterms.h | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +1 -7 | 1.1005 | src/ComputeBonds.inl | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/23 00:15:16 | jim | +1 -9 | 1.1008 | src/ComputeAngles.inl | Cleaning up bond code, removed UniqueList for tuples. |
| 2008/04/14 23:14:47 | dbwells2 | +1 -1 | 1.4 | src/GridForceGrid.C | Removing "DEBUGM" definition to suppress debugging output. |
| 2008/04/09 19:16:49 | jim | +2 -1 | 1.1030 | src/ProxyMgr.h | AIX compile fixes. |
| 2008/04/09 19:16:49 | jim | +1 -1 | 1.1062 | src/ProxyMgr.C | AIX compile fixes. |
| 2008/04/09 19:16:49 | jim | +1 -1 | 1.2 | src/GridForceGrid.h | AIX compile fixes. |
| 2008/04/09 19:16:48 | jim | +3 -3 | 1.114 | src/ComputePme.C | AIX compile fixes. |
| 2008/04/09 19:16:45 | jim | +1 -1 | 1.3 | arch/Linux-POWER-xlc.arch | AIX compile fixes. |
| 2008/04/09 19:16:45 | jim | +3 -3 | 1.9 | arch/AIX-POWER-xlC.arch | AIX compile fixes. |
| 2008/04/08 16:23:40 | jim | +1 -1 | 1.1232 | Makefile | Re-enable fixed extracopy parallel optimization. |
| 2008/04/08 06:29:31 | chaomei2 | +3 -2 | 1.1061 | src/ProxyMgr.C | Fixed a bug when removing the extra copy of ProxyResultMsg. The bug is caused by incorrect indexing into force arrays. |
| 2008/04/08 02:30:21 | jim | +1 -1 | 1.1231 | Makefile | Disable buggy extracopy parallel optimization that was giving bad forces. |
| 2008/04/07 21:22:24 | dbwells2 | +41 -35 | 1.3 | src/GridForceGrid.C | Gridforce update: voltage offsets between periodic images of grid fixed. |
| 2008/04/01 03:22:20 | petefred | +148 -112 | 1.2 | ug/figures/dual_top.pdf | Fix figures from chipot's additions to the alchemy docs |
| 2008/04/01 03:22:19 | petefred | +614 -449 | 1.2 | ug/figures/dual_top.eps | Fix figures from chipot's additions to the alchemy docs |
| 2008/03/30 19:36:21 | petefred | +1 -1 | 1.13 | ug/ug_alchemy.tex | Fix Jerome's name |
| 2008/03/20 19:17:22 | jim | +2 -0 | 1.1057 | src/NamdState.C | Fix crash when using constraints with amber coordinate file. |
| 2008/03/20 19:12:33 | petefred | None | 1.1 | ug/figures/overlap_dens3.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:33 | petefred | None | 1.1 | ug/figures/overlap_dens2.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap_dens1.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap3.ps | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap3.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap2.ps | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap2.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap1.ps | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:32 | petefred | None | 1.1 | ug/figures/overlap1.pdf | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:30 | petefred | +425 -213 | 1.12 | ug/ug_alchemy.tex | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:29 | petefred | +1 -1 | 1.11 | ug/ug.tex | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:29 | petefred | None | 1.1 | ug/fep.bib | Add in Chipot's changes to the fep documentation |
| 2008/03/20 19:12:29 | petefred | +1 -0 | 1.40 | ug/Makefile | Add in Chipot's changes to the fep documentation |
| 2008/03/07 01:15:56 | chaomei2 | +8 -3 | 1.1027 | src/Patch.h | Changes due to keeping the extra copy overhead for ProxyDataMsg becauseif we still want the 32-byte alignment on CompAtom list regardless theunderlying Charm layer. |
| 2008/03/07 01:15:56 | chaomei2 | +16 -3 | 1.1047 | src/Patch.C | Changes due to keeping the extra copy overhead for ProxyDataMsg becauseif we still want the 32-byte alignment on CompAtom list regardless theunderlying Charm layer. |
| 2008/03/07 00:59:34 | chaomei2 | +9 -5 | 1.1230 | Makefile | Add flags for removing the extra copy overhead related to proxy msgs. |
| 2008/03/07 00:57:41 | chaomei2 | +35 -14 | 1.1043 | src/ProxyPatch.C | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/07 00:57:41 | chaomei2 | +41 -0 | 1.1029 | src/ProxyMgr.h | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/07 00:57:40 | chaomei2 | +10 -0 | 1.1012 | src/ProxyMgr.ci | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/07 00:57:40 | chaomei2 | +63 -4 | 1.1060 | src/ProxyMgr.C | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/07 00:57:40 | chaomei2 | +5 -2 | 1.1055 | src/HomePatch.h | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/07 00:57:39 | chaomei2 | +29 -1 | 1.1152 | src/HomePatch.C | 1. Add comppile-time flags to allow users to choose whether to removethe extra copy overhead of proxy msgs (ProxyDataMsg and ProxyResultMsg).2. Add the optimization to remove the extra copy involved in the proxyresult msg.2. Add padding bytes to the varsize proxy msgs, so that the beginning ofCompAtom list in the ProxyDataMsg is 32-byte aligned if the underlyingCharm layer has ensured the beginning of a msg is 32-byte aligned;the beginning of Force list in the ProxyResultVarsizeMsg is 8-bytealigned. This is done to accord to the alignment requirement before thisoptimization since the alignment will give better performance,especially on the BG/L machine. |
| 2008/03/03 21:12:46 | chaomei2 | +14 -0 | 1.1250 | src/SimParameters.C | Added a warning for memory optimized version that the load balancing period and the first step to do load balancing should be a multiple of stepspercycle in order to avoid some msgoverheads during runs. |
| 2008/03/03 21:11:28 | chaomei2 | +9 -0 | 1.1027 | src/ComputePatchPair.C | A little change for the memory optimized version |
| 2008/03/03 21:11:28 | chaomei2 | +3 -3 | 1.1040 | src/ComputeNonbondedPair.C | A little change for the memory optimized version |
| 2008/03/03 21:10:29 | chaomei2 | +4 -0 | 1.1013 | src/PositionOwnerBox.h | Added functions to return the owner of the position box. |
| 2008/03/03 21:10:29 | chaomei2 | +4 -0 | 1.1007 | src/PositionBox.h | Added functions to return the owner of the position box. |
| 2008/03/03 21:09:31 | chaomei2 | +16 -8 | 1.1032 | src/NamdTypes.h | CompAtomExt class is now needed even for non-memory optimized version because of the change in ProxyPatch related msgs |
| 2008/03/03 21:05:52 | chaomei2 | +13 -4 | 1.1008 | src/ProxyPatch.h | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +111 -34 | 1.1042 | src/ProxyPatch.C | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +34 -27 | 1.1028 | src/ProxyMgr.h | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +9 -4 | 1.1011 | src/ProxyMgr.ci | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +8 -90 | 1.1059 | src/ProxyMgr.C | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +13 -2 | 1.1026 | src/Patch.h | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +9 -8 | 1.1046 | src/Patch.C | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +11 -0 | 1.1054 | src/HomePatch.h | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/03/03 21:05:52 | chaomei2 | +61 -38 | 1.1151 | src/HomePatch.C | 1. Declare the ProxyDataMsg and ProxyAllMsg as the same type which makes codes cleaner. The only overhead per msg added is just 4 bytes.2. Change the packed type ProxyDataMsg (including ProxyAllMsg) into varsize msg, and the position array inside the msg will be reused in the computation so that the overhead of extra copyis avoided.3. Fixed a tricky bug that is related to load balancing for the memory optimized version. |
| 2008/02/25 23:58:12 | petefred | +1 -0 | 1.1015 | src/structures.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +4 -0 | 1.1049 | src/common.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +10 -6 | 1.1177 | src/WorkDistrib.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +2 -0 | 1.1137 | src/SimParameters.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +17 -0 | 1.1249 | src/SimParameters.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +2 -3 | 1.1046 | src/Sequencer.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:12 | petefred | +99 -94 | 1.1161 | src/Sequencer.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:11 | petefred | +2 -0 | 1.1072 | src/Molecule.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:11 | petefred | +74 -10 | 1.1139 | src/Molecule.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:11 | petefred | +6 -1 | 1.1053 | src/HomePatch.h | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:11 | petefred | +254 -21 | 1.1150 | src/HomePatch.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/25 23:58:11 | petefred | +7 -3 | 1.1218 | src/Controller.C | Add initial implementation of TIP4P water.TIP4P is requested with the watModel tip4p simulation parameter. I'll be curating and distributing compatible top/par files; a couple of namd-l denizens seem interested in early access, but all of the physical properties check out ok, so I don't expect that many further changes will be needed until we move to wanting more general lone pairs. |
| 2008/02/11 19:20:16 | bhatele | +38 -38 | 1.21 | src/ComputePmeMgr.ci | fixed indentation for better readability |
| 2008/02/11 02:56:19 | jim | +4 -0 | 1.1248 | src/SimParameters.C | Catch error where energy is printed without updated full electrostatics.Didn't affect dynamics but tended to confuse the users. |
| 2008/02/11 02:14:44 | jim | +1 -0 | 1.2 | src/GlobalMasterTMD.h | Fix bug that broke targetted MD for parallel runs. Forces were calculatedcorrectly but applied to the wrong targetted atoms in random permutation. |
| 2008/02/11 02:14:44 | jim | +13 -2 | 1.3 | src/GlobalMasterTMD.C | Fix bug that broke targetted MD for parallel runs. Forces were calculatedcorrectly but applied to the wrong targetted atoms in random permutation. |
| 2008/02/10 20:29:43 | jim | +8 -0 | 1.6 | src/GlobalMasterServer.C | Catch bug. Due to a design error, GlobalMasterServer does not supportindividual atom requests from multiple global force clients on parallel runs. |
| 2008/02/09 21:45:40 | jim | +1 -0 | 1.6 | src/GlobalMasterFreeEnergy.C | Fix crash when truncating very long config for printing. |
| 2008/02/03 05:21:50 | bhatele | +1 -1 | 1.1136 | src/SimParameters.h | To use new load balancers use "ldbStrategy asb8" in the config file |
| 2008/02/03 05:21:50 | bhatele | +4 -4 | 1.1247 | src/SimParameters.C | To use new load balancers use "ldbStrategy asb8" in the config file |
| 2008/02/03 05:21:50 | bhatele | +3 -3 | 1.84 | src/NamdCentLB.C | To use new load balancers use "ldbStrategy asb8" in the config file |
| 2008/02/03 05:08:37 | bhatele | +0 -3 | 1.27 | src/Sync.C | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:37 | bhatele | +4 -4 | 1.80 | src/Rebalancer.C | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:37 | bhatele | +1 -1 | 1.1007 | src/ProxyPatch.h | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:37 | bhatele | +2 -0 | 1.1041 | src/ProxyPatch.C | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:37 | bhatele | +1 -1 | 1.1027 | src/ProxyMgr.h | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:37 | bhatele | +15 -14 | 1.1058 | src/ProxyMgr.C | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:36 | bhatele | +0 -3 | 1.1048 | src/common.h | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:36 | bhatele | +1 -1 | 1.1052 | src/HomePatch.h | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 05:08:36 | bhatele | +19 -16 | 1.1149 | src/HomePatch.C | PROXY_SPAN_DIM is no longer a #defineit is now defined in ProxyMgr.C as proxySpanDimEventually it'll become a SimParameter |
| 2008/02/03 02:26:10 | bhatele | +2 -4 | 1.11 | src/TorusLB.C | some extra statements removed |
| 2008/02/03 02:26:10 | bhatele | +19 -28 | 1.12 | src/RefineTorusLB.C | some extra statements removed |
| 2008/02/03 02:26:10 | bhatele | +2 -6 | 1.31 | src/Rebalancer.h | some extra statements removed |
| 2008/02/03 02:26:10 | bhatele | +7 -3 | 1.79 | src/Rebalancer.C | some extra statements removed |
| 2008/01/23 07:19:31 | bhatele | +3 -1 | 1.113 | src/ComputePme.C | added commonly wrappers around some work |
| 2008/01/23 07:19:31 | bhatele | +11 -17 | 1.1048 | src/ComputeHomeTuples.h | added commonly wrappers around some work |
| 2008/01/20 21:07:53 | bhatele | +4 -4 | 1.11 | src/RefineTorusLB.C | *** empty log message *** |
| 2008/01/17 23:30:10 | bhatele | +5 -4 | 1.30 | src/Rebalancer.h | corrected some changes which shouldn't be turned on in the CVS version |
| 2008/01/17 23:30:10 | bhatele | +2 -2 | 1.84 | src/LdbCoordinator.C | corrected some changes which shouldn't be turned on in the CVS version |
| 2008/01/17 23:30:09 | bhatele | +9 -3 | 1.78 | src/Rebalancer.C | corrected some changes which shouldn't be turned on in the CVS version |
| 2008/01/17 23:21:58 | bhatele | +5 -6 | 1.1135 | src/SimParameters.h | new ldbs can be used from the config file now |
| 2008/01/17 23:21:58 | bhatele | +4 -8 | 1.1246 | src/SimParameters.C | new ldbs can be used from the config file now |
| 2008/01/17 23:21:58 | bhatele | +10 -52 | 1.83 | src/NamdCentLB.C | new ldbs can be used from the config file now |
| 2008/01/17 23:21:57 | bhatele | +4 -6 | 1.83 | src/LdbCoordinator.C | new ldbs can be used from the config file now |
| 2008/01/14 19:30:41 | bhatele | +4 -2 | 1.10 | src/RefineTorusLB.C | changes to the PROXY_CORRECTION code |
| 2008/01/14 19:30:41 | bhatele | +22 -24 | 1.29 | src/Rebalancer.h | changes to the PROXY_CORRECTION code |
| 2008/01/14 19:30:41 | bhatele | +39 -100 | 1.77 | src/Rebalancer.C | changes to the PROXY_CORRECTION code |
| 2008/01/07 22:15:20 | bhatele | +2 -3 | 1.10 | src/TorusLB.C | fixed compilation error |
| 2007/12/28 23:28:29 | bhatele | +1 -0 | 1.2 | src/TorusLB.h | added badP |
| 2007/12/28 23:27:58 | bhatele | +28 -5 | 1.9 | src/TorusLB.C | This case was not caught by the LDBs earlier (where we couldnt find a processorto place a compute). Now we place it on a overloaded processor - badP |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.9 | arch/Win32.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.6 | arch/Tru64-Alpha.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.5 | arch/T3E.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.5 | arch/Solaris-i686.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.7 | arch/Solaris-Sparc.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.8 | arch/Origin2000.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.4 | arch/MacOSX-i686.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.5 | arch/MacOSX-PPC.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.4 | arch/Linux-ia64.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.12 | arch/Linux-i686.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.2 | arch/Linux-i686-redhat9.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.2 | arch/Linux-PPC.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.2 | arch/Linux-POWER.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.5 | arch/Linux-Alpha.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.5 | arch/HPUX.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.3 | arch/HPUX-ia64.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.4 | arch/HPUX-PA2.0.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.4 | arch/Cygwin-i686.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.4 | arch/Cygwin-i686-MSVC.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.3 | arch/CRAY-XT3.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.3 | arch/CRAY-X1.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.2 | arch/BlueGeneP.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:22 | jim | +1 -1 | 1.2 | arch/BlueGeneL.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:47:21 | jim | +1 -1 | 1.2 | arch/AIX-POWER.tcl | Remove USE_NON_CONST flags, since source now has USE_COMPAT_CONST. |
| 2007/12/20 16:02:20 | bhatele | +3 -3 | 1.9 | src/RefineTorusLB.C | compilation error fixed |
| 2007/12/13 04:57:02 | bhatele | +69 -63 | 1.8 | src/TorusLB.C | made the load balancers aware of multiple nodes per processor |
| 2007/12/13 04:57:02 | bhatele | +83 -76 | 1.8 | src/RefineTorusLB.C | made the load balancers aware of multiple nodes per processor |
| 2007/12/11 05:49:58 | chaomei2 | +14 -1 | 1.1071 | src/Molecule.h | Fixed errors that multiple memory deletion operations are performed regard with some data structures in the Molecule object. This error has caused NAMD-smp version to crash. Only one Molecule object copy is kept on a node in the smp version. |
| 2007/12/11 05:49:58 | chaomei2 | +2 -0 | 1.1138 | src/Molecule.C | Fixed errors that multiple memory deletion operations are performed regard with some data structures in the Molecule object. This error has caused NAMD-smp version to crash. Only one Molecule object copy is kept on a node in the smp version. |
| 2007/12/10 23:06:17 | bhatele | +36 -4 | 1.76 | src/Rebalancer.C | adding a penalty to proxy creationthis helps on 511 procs on Abe (turned off by default) |
| 2007/12/10 23:04:48 | bhatele | +3 -3 | 1.82 | src/NamdCentLB.C | topo placement of proxies is good with the new LDBs alsoonce the spanning tree is moved to the LDBs, we wouldnt need it anymore |
| 2007/12/10 22:06:35 | bhatele | +44 -14 | 1.7 | src/TorusLB.C | bug fixes |
| 2007/12/10 21:59:57 | bhatele | +41 -7 | 1.7 | src/RefineTorusLB.C | bug fixes |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.9 | src/TclCommands.h | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.15 | src/TclCommands.C | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.28 | src/ScriptTcl.h | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +6 -5 | 1.61 | src/ScriptTcl.C | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.2 | src/Measure.h | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.7 | src/GlobalMasterTcl.h | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +5 -4 | 1.17 | src/GlobalMasterTcl.C | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +1 -0 | 1.5 | src/ComputeTclBC.h | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/12/05 22:08:37 | jim | +4 -3 | 1.5 | src/ComputeTclBC.C | Define USE_COMPAT_CONST before every include of tcl.h to allow buildingwith either Tcl 8.3 or 8.4. Treat strings returned from Tcl as const. |
| 2007/11/30 15:34:10 | kunzman | +16 -2 | 1.1047 | src/common.h | Added comments to atom sort defines. Modified merge sort to try andimprove performance. |
| 2007/11/30 15:34:10 | kunzman | +145 -0 | 1.1138 | src/ComputeNonbondedBase.h | Added comments to atom sort defines. Modified merge sort to try andimprove performance. |
| 2007/11/27 22:32:48 | kunzman | +2 -1 | 1.1046 | src/common.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +16 -0 | 1.1040 | src/ProxyPatch.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +13 -0 | 1.1026 | src/ProxyMgr.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +43 -0 | 1.1057 | src/ProxyMgr.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +14 -0 | 1.1025 | src/Patch.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +5 -0 | 1.1045 | src/Patch.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +13 -0 | 1.1031 | src/NamdTypes.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +1 -6 | 1.1051 | src/HomePatch.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +12 -0 | 1.1148 | src/HomePatch.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +6 -0 | 1.1013 | src/ComputePatchPair.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +8 -0 | 1.1026 | src/ComputePatchPair.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +6 -0 | 1.1013 | src/ComputePatch.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +5 -0 | 1.1025 | src/ComputePatch.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +21 -0 | 1.1058 | src/ComputeNonbondedUtil.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:48 | kunzman | +8 -0 | 1.5 | src/ComputeNonbondedStd.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:47 | kunzman | +7 -0 | 1.1033 | src/ComputeNonbondedSelf.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:47 | kunzman | +7 -0 | 1.1039 | src/ComputeNonbondedPair.C | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/27 22:32:47 | kunzman | +647 -40 | 1.1137 | src/ComputeNonbondedBase.h | Modified atom separation code to pass the number of water atoms on tothe compute code in ComputeNonbondedBase.h.Modified pairlist generation code to sort atoms along the line betweenthe center of masses for a pair of patches. The sort information isthen used to skip as many distance caclculations as possible to reducepairlist generation time if possible. |
| 2007/11/20 05:04:39 | bhatele | +14 -2 | 1.81 | src/NamdCentLB.C | correct the way hops are calculated |
| 2007/11/12 19:01:41 | bhatele | +349 -60 | 1.115 | Make.depends | includes the TorusLB.o and RefineTorusLB.o targets |
| 2007/11/12 17:31:29 | dbwells2 | +1 -0 | 1.1134 | src/SimParameters.h | Added new transverse force feature to SMD. The user may now optionallyspecify a second spring constant (keyword SMDk2) which will describe aforce perpendicular to the pulling direction. This second springconstant defaults to zero, which reproduces the original SMDbehavior. This feature is particularly useful for restraining thecenter of mass of atoms in all three directions simultaneously(i.e. SMDVel = 0.) |
| 2007/11/12 17:31:29 | dbwells2 | +6 -0 | 1.1245 | src/SimParameters.C | Added new transverse force feature to SMD. The user may now optionallyspecify a second spring constant (keyword SMDk2) which will describe aforce perpendicular to the pulling direction. This second springconstant defaults to zero, which reproduces the original SMDbehavior. This feature is particularly useful for restraining thecenter of mass of atoms in all three directions simultaneously(i.e. SMDVel = 0.) |
| 2007/11/12 17:31:29 | dbwells2 | +4 -1 | 1.3 | src/GlobalMasterSMD.h | Added new transverse force feature to SMD. The user may now optionallyspecify a second spring constant (keyword SMDk2) which will describe aforce perpendicular to the pulling direction. This second springconstant defaults to zero, which reproduces the original SMDbehavior. This feature is particularly useful for restraining thecenter of mass of atoms in all three directions simultaneously(i.e. SMDVel = 0.) |
| 2007/11/12 17:31:29 | dbwells2 | +6 -2 | 1.7 | src/GlobalMasterSMD.C | Added new transverse force feature to SMD. The user may now optionallyspecify a second spring constant (keyword SMDk2) which will describe aforce perpendicular to the pulling direction. This second springconstant defaults to zero, which reproduces the original SMDbehavior. This feature is particularly useful for restraining thecenter of mass of atoms in all three directions simultaneously(i.e. SMDVel = 0.) |
| 2007/11/12 17:31:29 | dbwells2 | +2 -1 | 1.1073 | src/ComputeMgr.C | Added new transverse force feature to SMD. The user may now optionallyspecify a second spring constant (keyword SMDk2) which will describe aforce perpendicular to the pulling direction. This second springconstant defaults to zero, which reproduces the original SMDbehavior. This feature is particularly useful for restraining thecenter of mass of atoms in all three directions simultaneously(i.e. SMDVel = 0.) |
| 2007/11/12 07:06:25 | bhatele | +9 -10 | 1.1176 | src/WorkDistrib.C | now uses TopoManager for RecBisection, this change should hopefullymake topology awareness work on Cray |
| 2007/11/12 07:06:25 | bhatele | +12 -11 | 1.23 | src/RecBisection.C | now uses TopoManager for RecBisection, this change should hopefullymake topology awareness work on Cray |
| 2007/11/12 02:37:25 | bhatele | +5 -5 | 1.6 | src/TorusLB.C | corrected the brick expansion logic |
| 2007/11/12 02:37:25 | bhatele | +7 -5 | 1.6 | src/RefineTorusLB.C | corrected the brick expansion logic |
| 2007/11/10 19:45:58 | bhatele | +8 -6 | 1.80 | src/NamdCentLB.C | some changes in the dump logs function |
| 2007/11/08 20:55:07 | bhatele | +7 -7 | 1.5 | src/TorusLB.C | increasing the overload factor |
| 2007/11/07 21:36:12 | bhatele | +2 -0 | 1.1229 | Makefile | added targets for TorusLB and RefineTorusLB |
| 2007/11/07 16:43:26 | jordi | +1 -1 | 1.11 | ug/ug_alchemy.tex | Docs: Mention that fepElecLambdaStart does not affect PME |
| 2007/11/07 16:42:50 | jordi | +2 -13 | 1.112 | src/ComputePme.C | *** empty log message *** |
| 2007/11/07 16:42:50 | jordi | +7 -3 | 1.27 | src/ComputeNonbondedBase2.h | *** empty log message *** |
| 2007/11/05 20:27:49 | bhatele | +3 -3 | 1.5 | src/RefineTorusLB.C | small error |
| 2007/11/05 20:23:49 | bhatele | +40 -25 | 1.4 | src/RefineTorusLB.C | more bug fixes |
| 2007/11/05 20:23:48 | bhatele | +14 -7 | 1.4 | src/TorusLB.C | more bug fixes |
| 2007/11/05 19:49:16 | kunzman | +8 -0 | 1.1045 | src/common.h | Modified HomePatch to separate hydrogen groups (waters vs.non-waters). To enable this separation, set NAMD_SeparateWaters (incommon.h) to a non-zero value. |
| 2007/11/05 19:49:16 | kunzman | +22 -0 | 1.1050 | src/HomePatch.h | Modified HomePatch to separate hydrogen groups (waters vs.non-waters). To enable this separation, set NAMD_SeparateWaters (incommon.h) to a non-zero value. |
| 2007/11/05 19:49:16 | kunzman | +433 -18 | 1.1147 | src/HomePatch.C | Modified HomePatch to separate hydrogen groups (waters vs.non-waters). To enable this separation, set NAMD_SeparateWaters (incommon.h) to a non-zero value. |
| 2007/11/04 20:22:52 | johns | +52 -46 | 1.10 | src/Settle.C | Converted all of the SSE code to intrinsics, as they are availablein new versions of GNU gcc, and Microsoft's compilers, whereas theIntel SIMD vector classes are not. The intrinsics are also more portablethan inline assembly, since there are several dialects of inlineasm blocks which differ between Intel, GNU, and Microsoft.The new intrinsics-based code should generate identical assemblylanguage to the previous class-based code. There may be a coupleof places where we can eliminate some redundant conversion instructionssince the intrinsics expose a few more details than the classes didand map more directly to the actual machine instructions. |
| 2007/11/04 20:22:52 | johns | +34 -34 | 1.1136 | src/ComputeNonbondedBase.h | Converted all of the SSE code to intrinsics, as they are availablein new versions of GNU gcc, and Microsoft's compilers, whereas theIntel SIMD vector classes are not. The intrinsics are also more portablethan inline assembly, since there are several dialects of inlineasm blocks which differ between Intel, GNU, and Microsoft.The new intrinsics-based code should generate identical assemblylanguage to the previous class-based code. There may be a coupleof places where we can eliminate some redundant conversion instructionssince the intrinsics expose a few more details than the classes didand map more directly to the actual machine instructions. |
| 2007/11/02 22:26:38 | jim | +1 -1 | 1.1039 | src/WorkDistrib.h | Ensure that basednodes and PME nodes do not overlap if possible. Onlyworks with bit-reversal assignment (i.e., not with Blue Gene torus mapper). |
| 2007/11/02 22:26:38 | jim | +1 -0 | 1.1029 | src/PatchMap.h | Ensure that basednodes and PME nodes do not overlap if possible. Onlyworks with bit-reversal assignment (i.e., not with Blue Gene torus mapper). |
| 2007/11/02 22:26:38 | jim | +4 -0 | 1.1045 | src/PatchMap.C | Ensure that basednodes and PME nodes do not overlap if possible. Onlyworks with bit-reversal assignment (i.e., not with Blue Gene torus mapper). |
| 2007/11/02 22:26:37 | jim | +12 -11 | 1.1175 | src/WorkDistrib.C | Ensure that basednodes and PME nodes do not overlap if possible. Onlyworks with bit-reversal assignment (i.e., not with Blue Gene torus mapper). |
| 2007/11/02 22:24:17 | jordi | +2 -2 | 1.1244 | src/SimParameters.C | FEP: Responded to feedback suggesting that it's worth breaking with thepast and set the default parameters to something that will work, ratherthan trying to maintain compatibility with the old behavior (which didn'twork well anyways). fepElecLambdaStart and fepVdwLambdaEnd now bothdefault to 0.5. This is not always optimal, but at least it's neverterrible! |
| 2007/11/02 22:24:14 | jordi | +2 -2 | 1.10 | ug/ug_alchemy.tex | FEP: Responded to feedback suggesting that it's worth breaking with thepast and set the default parameters to something that will work, ratherthan trying to maintain compatibility with the old behavior (which didn'twork well anyways). fepElecLambdaStart and fepVdwLambdaEnd now bothdefault to 0.5. This is not always optimal, but at least it's neverterrible! |
| 2007/11/02 18:36:32 | jordi | +13 -2 | 1.111 | src/ComputePme.C | FEP: FEP electrostatics clamping (through the fepElecLambdaStartoption) now supports PME. |
| 2007/11/02 04:19:01 | johns | +4 -4 | 1.1135 | src/ComputeNonbondedBase.h | Made the SSE pairlist code use 16-byte-aligned stores, which areslightly faster. |
| 2007/11/01 21:40:35 | bhatele | +53 -27 | 1.3 | src/TorusLB.C | 1. more bug fixes2. additions so that the code can run on non-topo machines |
| 2007/11/01 21:40:35 | bhatele | +70 -51 | 1.3 | src/RefineTorusLB.C | 1. more bug fixes2. additions so that the code can run on non-topo machines |
| 2007/11/01 21:39:41 | bhatele | +4 -4 | 1.79 | src/NamdCentLB.C | we dont need to use the topomap requiredProxiesOnGrid for the new ldbs |
| 2007/11/01 21:37:53 | bhatele | +4 -2 | 1.28 | src/Rebalancer.h | added a new function withinBrick |
| 2007/11/01 21:37:53 | bhatele | +25 -3 | 1.75 | src/Rebalancer.C | added a new function withinBrick |
| 2007/11/01 18:41:40 | bhatele | +32 -0 | 1.11 | src/NamdCentLB.h | comments |
| 2007/11/01 18:38:59 | bhatele | +15 -4 | 1.27 | src/Rebalancer.h | 1. changed the way how LDB_DEBUG is used2. added a new flag USE_NEW_LDBS3. added comments and headers |
| 2007/11/01 18:38:59 | bhatele | +14 -7 | 1.74 | src/Rebalancer.C | 1. changed the way how LDB_DEBUG is used2. added a new flag USE_NEW_LDBS3. added comments and headers |
| 2007/11/01 18:38:59 | bhatele | +43 -17 | 1.78 | src/NamdCentLB.C | 1. changed the way how LDB_DEBUG is used2. added a new flag USE_NEW_LDBS3. added comments and headers |
| 2007/11/01 17:42:35 | bhatele | +14 -7 | 1.1174 | src/WorkDistrib.C | fixed the usage of USE_TOPOMAP flag |
| 2007/11/01 17:42:35 | bhatele | +8 -4 | 1.26 | src/Rebalancer.h | fixed the usage of USE_TOPOMAP flag |
| 2007/11/01 17:42:35 | bhatele | +8 -1 | 1.1024 | src/PatchMgr.h | fixed the usage of USE_TOPOMAP flag |
| 2007/11/01 17:39:53 | bhatele | +8 -1 | 1.55 | src/AlgSeven.C | fixed the USE_TOPOMAP flag usage |
| 2007/11/01 06:36:25 | johns | +74 -11 | 1.9 | src/Settle.C | Added more SSE to the Settle implementation, speeding it up by another10 percent or more. Impact on the full NAMD folding run is minor butbeneficial. |
| 2007/10/31 17:46:28 | jordi | +4 -4 | 1.1134 | src/ComputeNonbondedBase.h | FEP: Fixed a small mismatch when using fepVdwLambdaEnd that would causevdw scaling to not be completely confined in its stated range of lambda. |
| 2007/10/30 17:46:23 | dbwells2 | +3 -1 | 1.114 | Make.depends | Fixed Make.depends for dependence on GridForceGrid.h. |
| 2007/10/30 17:44:40 | dbwells2 | +3 -1 | 1.1137 | src/Molecule.C | Fixed missing header includes. |
| 2007/10/30 17:44:40 | dbwells2 | +2 -1 | 1.8 | src/ComputeGridForce.C | Fixed missing header includes. |
| 2007/10/30 17:00:23 | jordi | +20 -13 | 1.9 | ug/ug_alchemy.tex | Docs: Added docs for fepVdwLambdaEnd and fepElecLambdaStart |
| 2007/10/30 16:59:21 | jordi | +2 -2 | 1.1133 | src/SimParameters.h | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:21 | jordi | +11 -4 | 1.1243 | src/SimParameters.C | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:21 | jordi | +0 -1 | 1.5 | src/DumpBenchParams.h | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:20 | jordi | +2 -1 | 1.1057 | src/ComputeNonbondedUtil.h | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:20 | jordi | +12 -10 | 1.1089 | src/ComputeNonbondedUtil.C | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:20 | jordi | +39 -31 | 1.26 | src/ComputeNonbondedBase2.h | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 16:59:20 | jordi | +20 -5 | 1.1133 | src/ComputeNonbondedBase.h | FEP: Added fepVdwLambdaEnd and fepElecLambdaStart to control when toscale vdw and electrostatics. This very significantly improves theresults of FEP calcuclations when charges are involved. Also, removedfepVdwScaleExp (which was not that useful in retrospect) |
| 2007/10/30 05:51:36 | dbwells2 | +14 -8 | 1.1136 | src/Molecule.C | Had deleted calls to distribute Gridforce parameters to nodes... oops. Now repaired. |
| 2007/10/30 05:51:36 | dbwells2 | +19 -1 | 1.2 | src/GridForceGrid.C | Had deleted calls to distribute Gridforce parameters to nodes... oops. Now repaired. |
| 2007/10/30 05:51:36 | dbwells2 | +1 -1 | 1.7 | src/ComputeGridForce.C | Had deleted calls to distribute Gridforce parameters to nodes... oops. Now repaired. |
| 2007/10/30 04:24:01 | johns | +3 -2 | 1.1132 | src/ComputeNonbondedBase.h | prettied up the code a tad |
| 2007/10/30 04:17:14 | johns | +64 -1 | 1.1131 | src/ComputeNonbondedBase.h | Added another SSE accelerated pairlist loop where we already had anexisting optimized loop. The remaining loops do not appear to beviewed as performance-critical based on their appearance, so furtherSSE pairlist acceleration will require consultation with Jim andmore profiling. |
| 2007/10/30 03:56:53 | johns | +61 -2 | 1.1130 | src/ComputeNonbondedBase.h | Added an Intel SSE pairlist loop directly based on the existingpairlist loop that was already made to be friendly to the IBM double-hummer.This initial implementation gives a nice little speed boost, but candefinitely be improved by using SSE conditionals and other niceties thatthe present code doesn't bother with. |
| 2007/10/30 02:25:57 | dbwells2 | +1 -0 | 1.1228 | Makefile | Updated Makefile and Make.depends for the addition ofGridForceGrid.[Ch] |
| 2007/10/30 02:25:57 | dbwells2 | +11 -0 | 1.113 | Make.depends | Updated Makefile and Make.depends for the addition ofGridForceGrid.[Ch] |
| 2007/10/30 02:24:47 | dbwells2 | +1 -1 | 1.1242 | src/SimParameters.C | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/30 02:24:47 | dbwells2 | +4 -44 | 1.1070 | src/Molecule.h | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/30 02:24:47 | dbwells2 | +14 -515 | 1.1135 | src/Molecule.C | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/30 02:24:47 | dbwells2 | None | 1.1 | src/GridForceGrid.h | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/30 02:24:47 | dbwells2 | None | 1.1 | src/GridForceGrid.C | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/30 02:24:46 | dbwells2 | +159 -163 | 1.6 | src/ComputeGridForce.C | * Drastic structural changes to Gridforce code. There is now a'GridforceGrid' object which includes essentially all the informationthat was previously a 'gridfrc...' variable in the Molecule object.This cleans up Molecule a lot, and more importantly paves the wayfor multiple grids.* Also fixed a fairly major Gridforce bug in which the grid wasshifted slightly from the correct position. This is because the gridorigin was not corrected when adding border grid points. |
| 2007/10/29 20:41:27 | johns | +66 -9 | 1.8 | src/Settle.C | Added an SSE2-accelerated version of some of the costlier components ofthe settle algorithm. The new code is currently only enabled when compiledwith the macros NAMD_SSE, __INTEL_COMPILER, __SSE2__ all defined.If any of these are not defined, the plain C code path is used.The current code uses the Intel Class library, but could be convertedto intrinsics or even inline assembler, though the existing class-basedcode is likely the most readable. |
| 2007/10/29 05:01:49 | johns | +10 -6 | 1.7 | src/Settle.C | Eliminated another redundant multiply, and identified three areas wherewe're doing math that ends up getting thrown away. This was previouslyobscured by the fact that we used the vector classes that make the codeeasy to write, but also obscure when you're using vector elements or not.A subsequent patch should eliminate 15 FLOPS of wasted arithmetic per water. |
| 2007/10/29 04:11:26 | bhatele | +31 -110 | 1.2 | src/TorusLB.C | some bug fixes for the new ldb's |
| 2007/10/29 04:11:26 | bhatele | +51 -117 | 1.2 | src/RefineTorusLB.C | some bug fixes for the new ldb's |
| 2007/10/29 04:11:26 | bhatele | +1 -0 | 1.25 | src/Rebalancer.h | some bug fixes for the new ldb's |
| 2007/10/29 04:11:25 | bhatele | +17 -0 | 1.73 | src/Rebalancer.C | some bug fixes for the new ldb's |
| 2007/10/26 21:50:54 | johns | +9 -4 | 1.4 | src/Settle.h | Split the initialization logic for cached water atom properties into a newsettle1init() function, added a settle1isinitted() query, and eliminatedruntime initialization tests from settle1().Eliminated redundant arithmetic in settlec() and inlined the wholefunction into settle1() since it is not used elsewhere.The new code avoids expensive divisions where possible, precalculatesa couple of additional quantities, but makes no assumptions that theoriginal code wasn't already making. The settle1init() routine iscurrently called on entry into rattle1() if it has not already beeninitialized. The initialization will move to Molecule::build_atom_statusonce that version is debugged. |
| 2007/10/26 21:50:54 | johns | +48 -53 | 1.6 | src/Settle.C | Split the initialization logic for cached water atom properties into a newsettle1init() function, added a settle1isinitted() query, and eliminatedruntime initialization tests from settle1().Eliminated redundant arithmetic in settlec() and inlined the wholefunction into settle1() since it is not used elsewhere.The new code avoids expensive divisions where possible, precalculatesa couple of additional quantities, but makes no assumptions that theoriginal code wasn't already making. The settle1init() routine iscurrently called on entry into rattle1() if it has not already beeninitialized. The initialization will move to Molecule::build_atom_statusonce that version is debugged. |
| 2007/10/26 21:50:54 | johns | +20 -3 | 1.1146 | src/HomePatch.C | Split the initialization logic for cached water atom properties into a newsettle1init() function, added a settle1isinitted() query, and eliminatedruntime initialization tests from settle1().Eliminated redundant arithmetic in settlec() and inlined the wholefunction into settle1() since it is not used elsewhere.The new code avoids expensive divisions where possible, precalculatesa couple of additional quantities, but makes no assumptions that theoriginal code wasn't already making. The settle1init() routine iscurrently called on entry into rattle1() if it has not already beeninitialized. The initialization will move to Molecule::build_atom_statusonce that version is debugged. |
| 2007/10/26 15:45:06 | johns | +1 -1 | 1.3 | src/Settle.h | Replaced floating point divides in settle1() with multiplies with invdt |
| 2007/10/26 15:45:06 | johns | +6 -5 | 1.5 | src/Settle.C | Replaced floating point divides in settle1() with multiplies with invdt |
| 2007/10/26 15:45:06 | johns | +1 -1 | 1.1145 | src/HomePatch.C | Replaced floating point divides in settle1() with multiplies with invdt |
| 2007/10/26 15:32:17 | johns | +13 -10 | 1.1144 | src/HomePatch.C | Replaced slow floating point divides by dt with multiplies by precalculatedinvdt. Changed the per-water-atom fixed atom checks with a single test ofgroupFixed. |
| 2007/10/25 21:20:49 | johns | +5 -0 | 1.16 | src/vmdsock.C | Added comments warning about SMP-unsafe global and static variables. |
| 2007/10/25 21:17:57 | johns | +4 -0 | 1.1217 | src/Controller.C | Added comments warning about SMP-unsafe global and static variables.Signal handlers are also potentially thread-unsafe, though this isextremely platform dependent. |
| 2007/10/25 21:14:10 | johns | +4 -0 | 1.8 | src/GlobalMasterIMD.C | Added comments warning about SMP-unsafe global and static variables. |
| 2007/10/25 21:12:47 | johns | +2 -2 | 1.82 | src/LdbCoordinator.C | Added comments warning about SMP-unsafe global and static variables. |
| 2007/10/25 21:06:42 | johns | +5 -0 | 1.5 | src/pub3dfft.C | Added comments warning about SMP-unsafe global and static variables.The pub3dfft routines cannot be safely used for multithreaded NAMD builds. |
| 2007/10/25 21:05:12 | johns | +4 -0 | 1.60 | src/ScriptTcl.C | Added comments warning about SMP-unsafe global and static variables. |
| 2007/10/25 21:02:57 | johns | +7 -0 | 1.4 | src/Settle.C | Added comments warning about SMP-unsafe global and static variables. |
| 2007/10/25 20:57:27 | johns | +6 -1 | 1.1056 | src/ProxyMgr.C | Added comments warning about the global and static variablesreferenced in the proxy manager code. |
| 2007/10/25 20:41:20 | chaomei2 | +1 -0 | 1.12 | src/CompressPsf.C | Added an output showing the number of crossterm signatures. |
| 2007/10/25 20:04:47 | chaomei2 | +36 -1 | 1.1134 | src/Molecule.C | Added the implementation of compressing crossterms and reading crossterms from the compressed psf file.Now the crossterm calculation is supported in the memory optimized version. |
| 2007/10/25 20:04:47 | chaomei2 | +153 -5 | 1.11 | src/CompressPsf.C | Added the implementation of compressing crossterms and reading crossterms from the compressed psf file.Now the crossterm calculation is supported in the memory optimized version. |
| 2007/10/25 20:03:13 | chaomei2 | +0 -4 | 1.1014 | src/structures.h | Removed the comments about signatures about crossterms and exclusions since they are no longer true. Crossterms are now supported in the memory optimized version |
| 2007/10/25 18:31:45 | chaomei2 | +11 -1 | 1.10 | src/CompressPsf.C | Do abortion if explicit exclusions and crossterms are encountered in the psf file.The support will be implemented later. |
| 2007/10/18 21:29:09 | chaomei2 | +5 -5 | 1.1227 | Makefile | Changed the way to compile for tracing compute objects |
| 2007/10/16 01:13:25 | jim | +92 -70 | 1.110 | src/ComputePme.C | Reworked pencil placement to use bit reversal and patch locationsfollowed by round-robin to avoid sending and receiving in the samephase as much as possible. Only uses node 0 if it has a patch oris very likely to improve performance. |
| 2007/10/15 20:40:14 | jim | +34 -2 | 1.20 | src/ComputePmeMgr.ci | Eliminate replies to empty pencil PME messages. |
| 2007/10/15 20:40:14 | jim | +86 -12 | 1.109 | src/ComputePme.C | Eliminate replies to empty pencil PME messages. |
| 2007/10/15 19:26:03 | chaomei2 | +25 -3 | 1.1226 | Makefile | Added compiling target for tracing compute objects |
| 2007/10/15 19:23:58 | chaomei2 | +5 -0 | 1.1083 | src/Node.C | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +8 -0 | 1.16 | src/ComputeSelfTuples.h | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +8 -0 | 1.108 | src/ComputePme.C | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +8 -0 | 1.1032 | src/ComputeNonbondedSelf.C | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +8 -0 | 1.1038 | src/ComputeNonbondedPair.C | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +567 -408 | 1.1072 | src/ComputeMgr.C | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/15 19:23:58 | chaomei2 | +7 -0 | 1.1018 | src/Compute.h | Added user events for every compute object's work. The user event name of every compute object is "type_computeId". This is useful in two aspects:1. Track the execution time of every compute object.2. In the timeline view in projections (the performance analysis tool), a timeline event will be associated with such a user event which shows the compute object that is directly related with this timeline event.To enable tracing compute objects, one has to type "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)" to generate the namd binary. |
| 2007/10/14 16:42:24 | jim | +4 -12 | 1.19 | src/ComputePmeMgr.ci | simple cleanups |
| 2007/10/14 16:42:24 | jim | +10 -8 | 1.107 | src/ComputePme.C | simple cleanups |
| 2007/10/11 20:59:31 | jim | +3 -3 | 1.1173 | src/WorkDistrib.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +7 -8 | 1.1039 | src/ProxyPatch.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +3 -2 | 1.1055 | src/ProxyMgr.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +43 -63 | 1.5 | src/Priorities.h | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +6 -7 | 1.1143 | src/HomePatch.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +2 -2 | 1.15 | src/ComputeSelfTuples.h | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +39 -34 | 1.106 | src/ComputePme.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +14 -14 | 1.1025 | src/ComputePatchPair.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +3 -2 | 1.1024 | src/ComputePatch.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +2 -1 | 1.1047 | src/ComputeHomeTuples.h | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +1 -1 | 1.1015 | src/ComputeHomePatches.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +3 -2 | 1.6 | src/ComputeHomePatch.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/11 20:59:31 | jim | +3 -2 | 1.1029 | src/Compute.C | Completely revamped message priority system. New file Priorities.hcontains high-level priorities and macros for prioritizing messages. |
| 2007/10/10 23:30:50 | jim | +20 -20 | 1.18 | src/ComputePmeMgr.ci | removed [expedited] to allow prioritization of messages |
| 2007/10/10 23:29:41 | jim | +17 -7 | 1.105 | src/ComputePme.C | prioritize pencil pme messages |
| 2007/10/09 22:36:53 | dbwells2 | +3 -1 | 1.1069 | src/Molecule.h | Updated Gridforces:* Fixed way in which continuous grids are handled.* Fixed handling of grids whose unit vectors are not mutuallyorthogonal and/or not parallel to those of the periodic cell. |
| 2007/10/09 22:36:53 | dbwells2 | +73 -64 | 1.1133 | src/Molecule.C | Updated Gridforces:* Fixed way in which continuous grids are handled.* Fixed handling of grids whose unit vectors are not mutuallyorthogonal and/or not parallel to those of the periodic cell. |
| 2007/10/09 22:36:53 | dbwells2 | +5 -3 | 1.5 | src/ComputeGridForce.C | Updated Gridforces:* Fixed way in which continuous grids are handled.* Fixed handling of grids whose unit vectors are not mutuallyorthogonal and/or not parallel to those of the periodic cell. |
| 2007/10/08 03:38:55 | jim | +11 -6 | 1.104 | src/ComputePme.C | Put PME grid and transpose slabs on different processors. |
| 2007/10/07 21:12:20 | jim | +19 -3 | 1.103 | src/ComputePme.C | Prioritize slab-based PME messages. |
| 2007/10/07 20:05:31 | jordi | +3 -3 | 1.8 | ug/ug_alchemy.tex | typos |
| 2007/10/07 20:03:31 | jordi | +26 -0 | 1.7 | ug/ug_alchemy.tex | FEP docs: Added docs for the new fepVdWShiftCoeff and fepVdwScaleExpparameters |
| 2007/10/07 01:03:34 | jordi | +17 -11 | 1.1132 | src/SimParameters.h | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significant).Also added two new NAMD config file options: fepVdwShiftCoeff: sets value "shift" [default 5, range >= 0] fepVdwScaleExp: sets the exponent "n" [default 0]Values one can use: shift = 0, n=0: old NAMD way (crashes a lot and bad convergence) shift = 5, n=0: used in CHARMM shift = 1, n=2: this scales quite nicely as well |
| 2007/10/07 01:03:34 | jordi | +12 -2 | 1.1241 | src/SimParameters.C | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significant).Also added two new NAMD config file options: fepVdwShiftCoeff: sets value "shift" [default 5, range >= 0] fepVdwScaleExp: sets the exponent "n" [default 0]Values one can use: shift = 0, n=0: old NAMD way (crashes a lot and bad convergence) shift = 5, n=0: used in CHARMM shift = 1, n=2: this scales quite nicely as well |
| 2007/10/07 01:03:34 | jordi | +3 -1 | 1.4 | src/DumpBenchParams.h | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significant).Also added two new NAMD config file options: fepVdwShiftCoeff: sets value "shift" [default 5, range >= 0] fepVdwScaleExp: sets the exponent "n" [default 0]Values one can use: shift = 0, n=0: old NAMD way (crashes a lot and bad convergence) shift = 5, n=0: used in CHARMM shift = 1, n=2: this scales quite nicely as well |
| 2007/10/07 01:03:34 | jordi | +2 -0 | 1.1056 | src/ComputeNonbondedUtil.h | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significant).Also added two new NAMD config file options: fepVdwShiftCoeff: sets value "shift" [default 5, range >= 0] fepVdwScaleExp: sets the exponent "n" [default 0]Values one can use: shift = 0, n=0: old NAMD way (crashes a lot and bad convergence) shift = 5, n=0: used in CHARMM shift = 1, n=2: this scales quite nicely as well |
| 2007/10/07 01:03:34 | jordi | +5 -1 | 1.1088 | src/ComputeNonbondedUtil.C | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significant).Also added two new NAMD config file options: fepVdwShiftCoeff: sets value "shift" [default 5, range >= 0] fepVdwScaleExp: sets the exponent "n" [default 0]Values one can use: shift = 0, n=0: old NAMD way (crashes a lot and bad convergence) shift = 5, n=0: used in CHARMM shift = 1, n=2: this scales quite nicely as well |
| 2007/10/07 01:03:34 | jordi | +11 -11 | 1.25 | src/ComputeNonbondedBase2.h | Towards a working FEP...Implemented a new FEP vdW scaling function that removes the end-pointcatastrophe that used to happen a lot in NAMD. The vdw potential hasthe form: V(r) = A/r^12 - B/r^6The new scaled V looks like this: V'(r) = lambda A'/r'^12 - B'/r'^6where: A' = lambda^2n * A B' = lambda^n * B r'^2 = r^2 + shift * (1.-lambda)This form scales well and gives accurate and reproducibleresults for tested FEP calculations. Velocity crashes are now almostnon-existent (if Coulomb forces are not significan |