| Time | Author | Lines | Revision | Filename | Comments |
| 2012/05/22 20:53:45 | dhardy | +1 -0 | 1.1027 | src/main.ci | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:45 | dhardy | +7 -4 | 1.1244 | src/WorkDistrib.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +4 -4 | 1.1391 | src/SimParameters.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +41 -0 | 1.1132 | src/Node.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +3 -57 | 1.3 | src/ComputeMsmMgr.ci | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +8 -63 | 1.3 | src/ComputeMsm.h | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +384 -2011 | 1.3 | src/ComputeMsm.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +6 -0 | 1.1114 | src/ComputeMgr.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:44 | dhardy | +1 -0 | 1.1053 | src/ComputeMap.h | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:43 | dhardy | +1 -0 | 1.59 | src/BackEnd.C | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:53:43 | dhardy | +1 -0 | 1.1026 | src/BOCgroup.h | New MSM code, in progress. Nothing is presently calculated. |
| 2012/05/22 20:50:42 | dhardy | +3 -0 | 1.1321 | Makefile | Build files for new MSM |
| 2012/05/22 20:50:42 | dhardy | +66 -0 | 1.159 | Make.depends | Build files for new MSM |
| 2012/05/18 18:19:10 | jim | +8 -2 | 1.15 | src/PmeKSpace.C | Replace variable-size arrays with alloca macro. |
| 2012/05/18 17:45:13 | jim | +2 -0 | 1.1131 | src/Node.C | Macro-protect CmiTurnOnStats and CmiTurnOffStats. |
| 2012/05/18 17:24:56 | jim | +8 -5 | 1.158 | Make.depends | Rebuild to remove fftw3 paths, etc. |
| 2012/05/18 07:33:49 | gzheng | +22 -4 | 1.1205 | src/SimParameters.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:49 | gzheng | +7 -3 | 1.1390 | src/SimParameters.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:49 | gzheng | +17 -5 | 1.1206 | src/Sequencer.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +2 -2 | 1.96 | src/Rebalancer.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +1 -1 | 1.1051 | src/ProxyMgr.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +12 -0 | 1.1105 | src/ProxyMgr.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +3 -2 | 1.9 | src/PmeRealSpace.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +89 -0 | 1.12 | src/PmeRealSpace.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +2 -0 | 1.13 | src/PmeKSpace.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +193 -4 | 1.14 | src/PmeKSpace.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +10 -0 | 1.1130 | src/Node.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +5 -2 | 1.115 | src/NamdCentLB.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +42 -7 | 1.116 | src/LdbCoordinator.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:48 | gzheng | +1 -0 | 1.1081 | src/HomePatch.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +5 -5 | 1.1286 | src/Controller.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +2 -2 | 1.26 | src/ComputeSelfTuples.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +17 -1 | 1.29 | src/ComputePmeMgr.ci | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +2 -0 | 1.32 | src/ComputePme.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +1254 -95 | 1.156 | src/ComputePme.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +6 -1 | 1.1113 | src/ComputeMgr.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +5 -0 | 1.1061 | src/ComputeHomeTuples.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +5 -1 | 1.58 | src/BackEnd.C | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:47 | gzheng | +7 -2 | 1.1025 | src/BOCgroup.h | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/18 07:33:45 | gzheng | +32 -19 | 1.157 | Make.depends | changes from many people:1. nodehelper2. nodegroup for PME3. load balancer instrument HomePatch and bonded work separately now. |
| 2012/05/16 20:48:01 | dhardy | +26 -5 | 1.1242 | src/Molecule.C | Molecule::assignLCPOType checks for Drude or LP and resets LCPO type to 0so that particle is ignored by SASA (just like hydrogen). Print warning.Also changed a couple of other "warning" messages to use iWARN. |
| 2012/05/15 20:40:55 | dtanner | +9 -5 | 1.1241 | src/Molecule.C | LCPO types only calculated when LCPO is on |
| 2012/05/14 21:42:38 | jim | +20 -0 | 1.1107 | src/ComputeNonbondedUtil.C | Use proper Coulomb switching for MARTINI force field AGAIN since it wasblown away by the Weeks-Chandler-Anderson commit on 2011/11/17. |
| 2012/05/10 17:46:23 | dtanner | +0 -3 | 1.7 | src/ComputeLCPO.h | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:23 | dtanner | +8 -23 | 1.11 | src/ComputeLCPO.C | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:23 | dtanner | +8 -0 | 1.2 | src/ComputeGBISserMgr.ci | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:23 | dtanner | +8 -0 | 1.2 | src/ComputeGBISser.h | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:23 | dtanner | +8 -0 | 1.3 | src/ComputeGBISser.C | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:22 | dtanner | +4 -0 | 1.3 | src/ComputeGBISCUDAKernel.h | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:22 | dtanner | +5 -0 | 1.5 | src/ComputeGBIS.inl | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/05/10 17:46:22 | dtanner | +17 -0 | 1.5 | src/ComputeGBIS.C | SASA conserves energy better now by regenerating coordinate pairlists every step; comments from David T. put throughout implicit solvent code. |
| 2012/04/30 18:47:46 | dtanner | +3 -3 | 1.5 | ug/ug_gbis.tex | updating SASA syntax |
| 2012/04/30 16:53:02 | dtanner | +2 -0 | 1.72 | src/ComputeNonbondedCUDA.C | SASA evaluated at nonbonded frequency, not fullElect; energy summed into elect |
| 2012/04/30 16:53:02 | dtanner | +6 -6 | 1.10 | src/ComputeLCPO.C | SASA evaluated at nonbonded frequency, not fullElect; energy summed into elect |
| 2012/04/29 20:19:21 | jim | +17 -11 | 1.9 | src/ComputeLCPO.C | Reformulate distance tests to remove unnecessary sqrt() calls. |
| 2012/04/29 19:27:13 | jim | +0 -1 | 1.6 | src/ComputeLCPO.h | Fix LCPO SASA multiple timestepping, move energy from BOUNDARY to ELECT. |
| 2012/04/29 19:27:13 | jim | +6 -8 | 1.8 | src/ComputeLCPO.C | Fix LCPO SASA multiple timestepping, move energy from BOUNDARY to ELECT. |
| 2012/04/27 15:53:26 | jim | +1 -1 | 1.59 | ug/Makefile | Update to version 2.9. |
| 2012/04/27 15:53:24 | jim | +5 -5 | 1.98 | notes.txt | Update to version 2.9. |
| 2012/04/27 15:53:24 | jim | +3 -3 | 1.52 | announce.txt | Update to version 2.9. |
| 2012/04/27 15:53:24 | jim | +1 -1 | 1.1320 | Makefile | Update to version 2.9. |
| 2012/04/26 16:17:16 | jim | +6 -0 | 1.12 | src/colvarbias_meta.C | Patch from Li Li to print hill height during well-tempered metadynamics. |
| 2012/04/18 22:20:47 | jim | +50 -3 | 1.20 | ug/ug.bib | Updated colvars references from Giacomo Fiorin. |
| 2012/04/18 22:20:34 | jim | +24 -1 | 1.20 | ug/ug_colvars.tex | Well-temperated metadynamics docs from Jérôme Hénin and Giacomo Fiorin. |
| 2012/04/18 22:17:45 | jim | +6 -0 | 1.8 | src/colvarbias_meta.h | Well-temperated metadynamics implementation from Li Li. |
| 2012/04/18 22:17:44 | jim | +39 -7 | 1.11 | src/colvarbias_meta.C | Well-temperated metadynamics implementation from Li Li. |
| 2012/04/18 16:45:17 | dtanner | +3 -3 | 1.1389 | src/SimParameters.C | fixed CUDA GBIS 1-2-4 multiple timestepping bug |
| 2012/04/18 16:45:17 | dtanner | +2 -2 | 1.30 | src/ComputeNonbondedCUDAKernel.cu | fixed CUDA GBIS 1-2-4 multiple timestepping bug |
| 2012/04/12 18:17:44 | jim | +6 -5 | 1.10 | src/colvarbias_meta.C | Typo corrections from Giacomo Fiorin. |
| 2012/04/05 22:09:49 | jim | +1 -1 | 1.58 | ug/Makefile | Update to version 2.9b3. |
| 2012/04/05 22:09:46 | jim | +5 -5 | 1.97 | notes.txt | Update to version 2.9b3. |
| 2012/04/05 22:09:46 | jim | +3 -3 | 1.51 | announce.txt | Update to version 2.9b3. |
| 2012/04/05 22:09:46 | jim | +1 -1 | 1.1319 | Makefile | Update to version 2.9b3. |
| 2012/04/05 22:06:31 | jim | +1 -1 | 1.71 | src/ComputeNonbondedCUDA.C | If there is only one patch treat it as local rather than remote. |
| 2012/04/05 21:40:09 | dtanner | +4 -6 | 1.1388 | src/SimParameters.C | SASA 2-away warning moved to WorkDistrib |
| 2012/04/05 21:11:47 | dtanner | +7 -8 | 1.1387 | src/SimParameters.C | changed SASA tracking invalid patches to not use numAtoms = -1 |
| 2012/04/05 21:11:47 | dtanner | +2 -1 | 1.5 | src/ComputeLCPO.h | changed SASA tracking invalid patches to not use numAtoms = -1 |
| 2012/04/05 21:11:47 | dtanner | +30 -28 | 1.7 | src/ComputeLCPO.C | changed SASA tracking invalid patches to not use numAtoms = -1 |
| 2012/04/05 19:04:31 | jim | +12 -4 | 1.1243 | src/WorkDistrib.C | Disable twoAway[XYZ] in combination with LCPO SASA. |
| 2012/04/04 19:38:41 | dhardy | +3 -3 | 1.1318 | Makefile | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:41 | dhardy | +10 -10 | 1.156 | Make.depends | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:09 | dhardy | +1 -1 | 1.1026 | src/main.ci | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:09 | dhardy | +1 -1 | 1.1071 | src/main.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:09 | dhardy | +5 -5 | 1.1242 | src/WorkDistrib.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:09 | dhardy | +1 -1 | 1.1068 | src/ProxyPatch.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:09 | dhardy | +1 -1 | 1.1043 | src/PatchMgr.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:08 | dhardy | +4 -4 | 1.1129 | src/Node.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:08 | dhardy | +3 -3 | 1.1112 | src/ComputeMgr.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:08 | dhardy | +1 -1 | 1.1052 | src/ComputeMap.h | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:08 | dhardy | +2 -2 | 1.57 | src/BackEnd.C | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:38:08 | dhardy | +1 -1 | 1.1024 | src/BOCgroup.h | Changed ComputeMsm to ComputeMsmMsa along with related names. |
| 2012/04/04 19:34:24 | dhardy | None | 1.1 | src/ComputeMsmMsaMgr.ci | renamed ComputeMsmMgr.ci to ComputeMsmMsaMgr.ci |
| 2012/04/04 19:34:23 | dhardy | +0 -0 | 1.2 | src/ComputeMsmMgr.ci | renamed ComputeMsmMgr.ci to ComputeMsmMsaMgr.ci |
| 2012/04/04 19:33:56 | dhardy | None | 1.1 | src/ComputeMsmMsa.C | renamed ComputeMsm.C to ComputeMsmMsa.C |
| 2012/04/04 19:33:56 | dhardy | +0 -0 | 1.2 | src/ComputeMsm.C | renamed ComputeMsm.C to ComputeMsmMsa.C |
| 2012/04/04 19:33:15 | dhardy | None | 1.1 | src/ComputeMsmMsa.h | renamed ComputeMsm.h to ComputeMsmMsa.h |
| 2012/04/04 19:33:14 | dhardy | +0 -0 | 1.2 | src/ComputeMsm.h | renamed ComputeMsm.h to ComputeMsmMsa.h |
| 2012/04/04 15:25:18 | dtanner | +2 -0 | 1.4 | src/ComputeLCPO.h | bug fix for when there is only 1 patch in a given dimension |
| 2012/04/04 15:25:18 | dtanner | +89 -18 | 1.6 | src/ComputeLCPO.C | bug fix for when there is only 1 patch in a given dimension |
| 2012/04/03 21:09:29 | gzheng | +6 -2 | 1.31 | src/ComputePme.h | make homepatch to pme also persistent |
| 2012/04/03 21:09:29 | gzheng | +107 -3 | 1.155 | src/ComputePme.C | make homepatch to pme also persistent |
| 2012/04/02 05:58:39 | gzheng | +14 -10 | 1.1104 | src/ProxyMgr.C | debugged node-aware spanning tree |
| 2012/04/02 05:58:39 | gzheng | +11 -4 | 1.1210 | src/HomePatch.C | debugged node-aware spanning tree |
| 2012/04/02 05:58:39 | gzheng | +21 -10 | 1.154 | src/ComputePme.C | debugged node-aware spanning tree |
| 2012/03/30 15:16:24 | jim | +1 -1 | 1.25 | src/ComputeSelfTuples.h | Fix for GCC 4.7.0. |
| 2012/03/27 04:42:33 | gzheng | +5 -1 | 1.1103 | src/ProxyMgr.C | relax error checking since size of pids may be reduced to exclude same nodes. |
| 2012/03/27 03:31:34 | gzheng | +1 -1 | 1.1067 | src/ProxyPatch.C | debug the nodegroup case of spanning tree with persistent |
| 2012/03/27 03:31:34 | gzheng | +30 -23 | 1.1209 | src/HomePatch.C | debug the nodegroup case of spanning tree with persistent |
| 2012/03/26 19:51:43 | jim | +1 -1 | 1.57 | ug/Makefile | Version 2.9b2. |
| 2012/03/26 19:51:40 | jim | +5 -5 | 1.96 | notes.txt | Version 2.9b2. |
| 2012/03/26 19:51:40 | jim | +3 -3 | 1.50 | announce.txt | Version 2.9b2. |
| 2012/03/26 19:51:40 | jim | +1 -1 | 1.1317 | Makefile | Version 2.9b2. |
| 2012/03/26 14:47:08 | dtanner | +7 -4 | 1.4 | ug/ug_gbis.tex | updated GBIS to reflect that LCPO was renamed as SASA and turned off |
| 2012/03/26 14:19:28 | dtanner | +7 -10 | 1.1386 | src/SimParameters.C | LCPO now called SASA, and defaulted to off |
| 2012/03/25 23:33:54 | gzheng | +14 -16 | 1.1066 | src/ProxyPatch.C | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 23:33:54 | gzheng | +4 -0 | 1.1050 | src/ProxyMgr.h | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 23:33:54 | gzheng | +8 -8 | 1.1102 | src/ProxyMgr.C | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 23:33:53 | gzheng | +4 -16 | 1.115 | src/LdbCoordinator.C | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 23:33:53 | gzheng | +2 -3 | 1.1080 | src/HomePatch.h | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 23:33:53 | gzheng | +24 -25 | 1.1208 | src/HomePatch.C | persistent works now for non-bounded calcs if not using nodegroup. |
| 2012/03/25 02:10:33 | gzheng | +81 -107 | 1.153 | src/ComputePme.C | debugged persistent with PME. (persistent default off) |
| 2012/03/24 19:36:23 | jim | +2 -2 | 1.9 | src/colvarbias.h | Fix warnings about comparing size_t to -1. |
| 2012/03/23 21:48:55 | jim | +315 -239 | 1.19 | ug/ug_colvars.tex | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:51 | jim | +6 -6 | 1.3 | src/colvarvalue.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:51 | jim | +17 -10 | 1.7 | src/colvartypes.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:51 | jim | +7 -2 | 1.13 | src/colvarproxy_namd.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +4 -40 | 1.9 | src/colvarproxy.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +0 -5 | 1.4 | src/colvarparse.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +5 -1 | 1.12 | src/colvarmodule.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +8 -5 | 1.15 | src/colvarmodule.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +6 -0 | 1.7 | src/colvargrid.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +190 -10 | 1.6 | src/colvarcomp_protein.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +31 -1 | 1.14 | src/colvarcomp.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +6 -2 | 1.7 | src/colvarbias_meta.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +138 -97 | 1.9 | src/colvarbias_meta.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +2 -2 | 1.7 | src/colvarbias_abf.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:50 | jim | +7 -7 | 1.12 | src/colvarbias_abf.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:49 | jim | +6 -0 | 1.8 | src/colvarbias.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:49 | jim | +76 -23 | 1.10 | src/colvarbias.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:49 | jim | +6 -6 | 1.11 | src/colvaratoms.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:49 | jim | +2 -1 | 1.11 | src/colvar.h | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 21:48:49 | jim | +3 -0 | 1.17 | src/colvar.C | colvars update from Giacomo Fiorin and Jerome Henin:General interface:- Allowed firstTimeStep from the NAMD configuration to override thestep number in the colvars state fileCollective variables:- Added dihedralPC component, i.e. the projection of protein backbonedihedrals onto a dihedral principal componentHarmonic restraints / thermodynamic integration:- Added targetEquilSteps option to moving harmonic restraints todiscard the equilibration phase from the TI estimate- Added lambdaSchedule option to change the harmonic force constantin predefined stagesMetadynamics:- Redesigned multipleReplicas, enabling usage of grids support andrecovering full NAMD scalability (same keywords as before)- Added option dumpPartialFreeEnergyFile for multipleReplicas, tokeep track of what configuration each replica visits. |
| 2012/03/23 19:23:59 | ryanmcgreevy | +1 -0 | 1.10 | src/GlobalMasterTMD.C | fixed TMD startup printing wrong # TMD atoms |
| 2012/03/23 18:34:46 | gzheng | +129 -0 | 1.152 | src/ComputePme.C | support persistent message |
| 2012/03/23 15:35:51 | gzheng | +4 -0 | 1.1020 | src/ProxyPatch.h | setup persistent handler along the send proxy spanning tree |
| 2012/03/23 15:35:51 | gzheng | +47 -0 | 1.1065 | src/ProxyPatch.C | setup persistent handler along the send proxy spanning tree |
| 2012/03/23 15:35:51 | gzheng | +32 -1 | 1.1101 | src/ProxyMgr.C | setup persistent handler along the send proxy spanning tree |
| 2012/03/23 15:35:50 | gzheng | +1 -1 | 1.1207 | src/HomePatch.C | setup persistent handler along the send proxy spanning tree |
| 2012/03/23 02:43:05 | jim | +1 -1 | 1.70 | src/ComputeNonbondedCUDA.C | disable second stream since it doesn't overlap anyway. |
| 2012/03/21 21:05:47 | jim | +3 -3 | 1.6 | src/GoMolecule.C | Fix from Jonathan Lai for segfault when Go is only applied to certain atoms. |
| 2012/03/21 00:59:59 | jim | +1 -1 | 1.7 | arch/Win64.cuda | Build with compute_20 ptx code for forward compatibility with Kepler. |
| 2012/03/21 00:59:59 | jim | +1 -1 | 1.4 | arch/MacOSX-x86_64.cuda | Build with compute_20 ptx code for forward compatibility with Kepler. |
| 2012/03/21 00:59:59 | jim | +1 -1 | 1.10 | arch/Linux-x86_64.cuda | Build with compute_20 ptx code for forward compatibility with Kepler. |
| 2012/03/20 20:50:54 | gzheng | +4 -1 | 1.1064 | src/ProxyPatch.C | make persistent communication on HomePatch working again. (protected by macro) |
| 2012/03/20 20:50:53 | gzheng | +4 -4 | 1.1206 | src/HomePatch.C | make persistent communication on HomePatch working again. (protected by macro) |
| 2012/03/20 20:04:33 | jim | +1 -1 | 1.42 | src/Sync.C | Disable useProxySync on BlueGene/Q as on BlueGene/P. |
| 2012/03/19 16:47:18 | char | +6 -6 | 1.5 | src/ComputeMoa.C | fixing even more PEBCK errors...renaming recvBGrid and recvQGrid to recvB and recvQ |
| 2012/03/19 16:29:01 | char | +1 -1 | 1.7 | src/ComputeMoa.h | fixing more PBECK errors for fixing msa/msa.h include |
| 2012/03/19 16:26:10 | char | +1 -1 | 1.6 | src/ComputeMoa.h | restoring #include msa/msa.h b/c of PBECK and removing MSA PAGE SIZE define as it is now defined inside charm++ src |
| 2012/03/19 16:23:29 | char | +0 -1 | 1.4 | src/ComputeMoa.C | removing include of MoaMacros.h |
| 2012/03/19 14:41:55 | char | +5 -3 | 1.5 | src/ComputeMoaMgr.ci | fixing typo on recvB entry method |
| 2012/03/19 14:40:49 | char | +1 -1 | 1.5 | src/ComputeMoa.h | adding MSA_PAGE_SIZE def |
| 2012/03/19 04:24:56 | jim | +10 -1 | 1.4 | src/ComputeMoa.h | Should build without MSA now. |
| 2012/03/19 03:49:14 | jim | +1 -0 | 1.12 | src/PmeKSpace.h | Fix MOA build. |
| 2012/03/19 03:49:14 | jim | +0 -2 | 1.4 | src/ComputeMoaMgr.ci | Fix MOA build. |
| 2012/03/19 03:49:14 | jim | +2 -11 | 1.3 | src/ComputeMoa.h | Fix MOA build. |
| 2012/03/19 03:49:14 | jim | +5 -5 | 1.3 | src/ComputeMoa.C | Fix MOA build. |
| 2012/03/19 03:49:02 | jim | +1 -0 | 1.1316 | Makefile | Fix MOA build. |
| 2012/03/19 03:49:01 | jim | +104 -20 | 1.155 | Make.depends | Fix MOA build. |
| 2012/03/19 02:57:32 | char | +30 -2 | 1.3 | src/ComputeMoaMgr.ci | pushing in Moa files v0 |
| 2012/03/19 02:57:32 | char | +93 -1 | 1.2 | src/ComputeMoa.h | pushing in Moa files v0 |
| 2012/03/19 02:57:32 | char | +506 -1 | 1.2 | src/ComputeMoa.C | pushing in Moa files v0 |
| 2012/03/19 02:36:37 | jim | +1 -1 | 1.15 | ug/namd_macros.tex | Add J. Lai and D. Wells to authors. |
| 2012/03/19 02:34:20 | jim | +59 -29 | 1.15 | ug/ug_accel.tex | Update for new replica exchange implementation. |
| 2012/03/19 01:42:45 | jim | +29 -19 | 1.26 | ug/ug_runit.tex | Update CUDA docs. |
| 2012/03/19 01:42:42 | jim | +28 -18 | 1.95 | notes.txt | Update CUDA docs. |
| 2012/03/19 01:42:42 | jim | +1 -1 | 1.49 | announce.txt | Update CUDA docs. |
| 2012/03/17 02:51:10 | jim | +31 -31 | 1.1082 | src/NamdState.C | Proper fix to keep Go forces from breaking alchemical free energy calcs. |
| 2012/03/17 02:51:10 | jim | +2 -1 | 1.1240 | src/Molecule.C | Proper fix to keep Go forces from breaking alchemical free energy calcs. |
| 2012/03/17 02:51:10 | jim | +5 -26 | 1.5 | src/GoMolecule.C | Proper fix to keep Go forces from breaking alchemical free energy calcs. |
| 2012/03/17 02:24:09 | jim | +1 -1 | 1.4 | src/GoMolecule.C | Don't break other features when Go is off. |
| 2012/03/16 22:50:07 | jim | +1 -1 | 1.48 | announce.txt | Move release date back. |
| 2012/03/16 22:48:51 | jim | +1 -1 | 1.6 | arch/Win64.cuda | Remove -ftz=true option that was causing instability. |
| 2012/03/16 22:48:51 | jim | +1 -1 | 1.3 | arch/MacOSX-x86_64.cuda | Remove -ftz=true option that was causing instability. |
| 2012/03/16 22:48:51 | jim | +1 -1 | 1.9 | arch/Linux-x86_64.cuda | Remove -ftz=true option that was causing instability. |
| 2012/03/16 19:47:35 | dbwells2 | +1 -1 | 1.2 | src/GridForceGrid.inl | Fixed bug in Gridforce wrapping code |
| 2012/03/15 20:12:08 | jim | +0 -2 | 1.1315 | Makefile | Generating ptx code doesn't work with multiple device code generation. |
| 2012/03/15 20:11:16 | jim | +1 -1 | 1.5 | arch/Win64.cuda | Generate code for both 1.1 and 2.0 devices. |
| 2012/03/15 20:11:15 | jim | +1 -1 | 1.2 | arch/MacOSX-x86_64.cuda | Generate code for both 1.1 and 2.0 devices. |
| 2012/03/15 20:11:15 | jim | +1 -1 | 1.8 | arch/Linux-x86_64.cuda | Generate code for both 1.1 and 2.0 devices. |
| 2012/03/15 20:11:15 | jim | +1 -1 | 1.2 | arch/CRAY-XT.cuda | Generate code for both 1.1 and 2.0 devices. |
| 2012/03/15 16:46:26 | jim | +3 -0 | 1.151 | src/ComputePme.C | Fix bug causing "PmePencilMap multiple pencils on a pe?" error. |
| 2012/03/15 14:00:12 | jim | +12 -2 | 1.69 | src/ComputeNonbondedCUDA.C | Add CUDA error checking in progress polling functions. |
| 2012/03/14 23:06:38 | jim | +2 -1 | 1.68 | src/ComputeNonbondedCUDA.C | Fix bug for multicore with one patch per pe. |
| 2012/03/14 22:28:04 | jim | +3 -3 | 1.1241 | src/WorkDistrib.C | Remove bogus "REDUCING NUMBER OF PATCHES" message. |
| 2012/03/14 17:56:57 | jim | +23 -1 | 1.67 | src/ComputeNonbondedCUDA.C | Turn dual streams back on with timeout adding to polling functions. |
| 2012/03/14 15:44:16 | dtanner | +4 -4 | 1.1385 | src/SimParameters.C | adding Amber structure support to LCPO |
| 2012/03/14 15:44:15 | dtanner | +4 -4 | 1.114 | src/NamdCentLB.C | adding Amber structure support to LCPO |
| 2012/03/14 15:44:15 | dtanner | +127 -11 | 1.1239 | src/Molecule.C | adding Amber structure support to LCPO |
| 2012/03/14 15:44:14 | dtanner | +1 -0 | 1.3 | src/ComputeLCPO.h | adding Amber structure support to LCPO |
| 2012/03/14 15:44:14 | dtanner | +8 -3 | 1.5 | src/ComputeLCPO.C | adding Amber structure support to LCPO |
| 2012/03/13 17:02:56 | jim | +3 -3 | 1.25 | ug/ug_runit.tex | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:56 | jim | +1 -21 | 1.28 | ug/ug_intro.tex | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:56 | jim | +22 -15 | 1.12 | ug/ug_avail.tex | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:55 | jim | +2 -2 | 1.56 | ug/Makefile | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:52 | jim | +57 -36 | 1.94 | notes.txt | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:52 | jim | +17 -17 | 1.47 | announce.txt | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:52 | jim | +2 -2 | 1.13 | README.txt | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 17:02:52 | jim | +1 -1 | 1.1314 | Makefile | Update docs/notes/announcement and bump version to 2.9b1. |
| 2012/03/13 15:08:15 | jim | +1 -0 | 1.154 | Make.depends | Update dependencies. |
| 2012/03/13 12:50:59 | jim | +4 -0 | 1.66 | src/ComputeNonbondedCUDA.C | Disable multiple streams because of unexplained hangs. |
| 2012/03/13 06:22:28 | jim | +1 -1 | 1.65 | src/ComputeNonbondedCUDA.C | Check if local work is done immediately after processing remote workrather than waiting for next polling period. |
| 2012/03/12 01:17:38 | jim | +1 -0 | 1.12 | src/ComputeNonbondedCUDA.h | Disable event timers, fix GBIS timing, clean up timing output. |
| 2012/03/12 01:17:38 | jim | +28 -56 | 1.64 | src/ComputeNonbondedCUDA.C | Disable event timers, fix GBIS timing, clean up timing output. |
| 2012/03/11 23:40:51 | jim | +79 -21 | 1.1240 | src/WorkDistrib.C | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:51 | jim | +5 -0 | 1.3 | src/SortAtoms.h | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:50 | jim | +55 -0 | 1.4 | src/SortAtoms.C | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:50 | jim | +4 -3 | 1.1204 | src/SimParameters.h | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:50 | jim | +5 -3 | 1.1384 | src/SimParameters.C | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:50 | jim | +2 -2 | 1.1041 | src/PatchMap.h | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:50 | jim | +11 -3 | 1.1059 | src/PatchMap.C | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 23:40:49 | jim | +3 -2 | 1.1205 | src/HomePatch.C | Add staticAtomAssignment parameter, which places equal numbers of atomsin each patch and never migrates them, limiting the patch grid to 2in each dimension, or 3 for dimensions with twoAway... enabled. Neverenabled automatically since it can error on startup on missing bonds, etc.Provides a benefit in CUDA-accelerated GBIS by balancing block runtime. |
| 2012/03/11 05:57:18 | jim | +6 -24 | 1.63 | src/ComputeNonbondedCUDA.C | Move all box opening to noWork to simplify code and fix GBIS with multiplehost threads. Also fix nonbondedFreq > 1 with multiple host threads. |
| 2012/03/11 05:00:23 | jim | +8 -4 | 1.18 | src/ComputeNonbondedCUDAKernel.h | Split remote and local work into separate streams to allow overlap. |
| 2012/03/11 05:00:22 | jim | +16 -9 | 1.29 | src/ComputeNonbondedCUDAKernel.cu | Split remote and local work into separate streams to allow overlap. |
| 2012/03/11 05:00:22 | jim | +14 -11 | 1.62 | src/ComputeNonbondedCUDA.C | Split remote and local work into separate streams to allow overlap. |
| 2012/03/09 07:37:04 | jim | +0 -2 | 1.17 | ug/ug_forcefield.tex | Uncomment tabulated energies since implementation is fixed now. |
| 2012/03/09 07:35:02 | jim | +7 -125 | 1.40 | src/ComputeNonbondedBase2.h | Fix and simplify tabulated energies. |
| 2012/03/08 22:55:50 | jim | +1 -1 | 1.11 | src/PmeKSpace.h | Fix build with stub files includes. |
| 2012/03/08 22:55:50 | jim | +3 -3 | 1.13 | src/PmeKSpace.C | Fix build with stub files includes. |
| 2012/03/08 22:55:49 | jim | +1 -1 | 1.150 | src/ComputePme.C | Fix build with stub files includes. |
| 2012/03/08 22:55:49 | jim | +4 -0 | 1.2 | src/ComputeMoaMgr.ci | Fix build with stub files includes. |
| 2012/03/08 22:55:47 | jim | +2 -0 | 1.1313 | Makefile | Fix build with stub files includes. |
| 2012/03/08 22:55:46 | jim | +20 -2 | 1.153 | Make.depends | Fix build with stub files includes. |
| 2012/03/08 22:29:06 | char | +3 -0 | 1.1025 | src/main.ci | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:06 | char | +10 -3 | 1.1203 | src/SimParameters.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +26 -3 | 1.1383 | src/SimParameters.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +10 -2 | 1.10 | src/PmeKSpace.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +50 -4 | 1.12 | src/PmeKSpace.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +6 -2 | 1.1048 | src/Node.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +4 -0 | 1.1032 | src/Node.ci | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +49 -0 | 1.1128 | src/Node.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +11 -4 | 1.1081 | src/NamdState.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:05 | char | +1 -1 | 1.1112 | src/Molecule.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:04 | char | +44 -6 | 1.1238 | src/Molecule.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:04 | char | +1 -1 | 1.28 | src/ComputePmeMgr.ci | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:04 | char | +62 -0 | 1.149 | src/ComputePme.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:04 | char | +4 -0 | 1.56 | src/BackEnd.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:29:04 | char | +3 -0 | 1.1023 | src/BOCgroup.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:12:40 | char | None | 1.1 | src/ComputeMoaMgr.ci | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:12:40 | char | None | 1.1 | src/ComputeMoa.h | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 22:12:40 | char | None | 1.1 | src/ComputeMoa.C | Beginning initial integration of NAMD-OPENATOM QM/MM module |
| 2012/03/08 18:16:50 | jim | +2 -0 | 1.16 | ug/ug_forcefield.tex | Comment out tabulated energies until implementation is fixed. |
| 2012/03/07 20:36:15 | jim | +2 -4 | 1.1063 | src/ProxyPatch.C | Eliminate extra copy of CUDA atom data. |
| 2012/03/07 20:36:15 | jim | +3 -2 | 1.1042 | src/Patch.h | Eliminate extra copy of CUDA atom data. |
| 2012/03/07 20:36:15 | jim | +1 -0 | 1.1079 | src/HomePatch.h | Eliminate extra copy of CUDA atom data. |
| 2012/03/07 20:36:15 | jim | +3 -3 | 1.1204 | src/HomePatch.C | Eliminate extra copy of CUDA atom data. |
| 2012/03/07 07:07:06 | jim | +10 -0 | 1.1062 | src/ProxyPatch.C | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:06 | jim | +1 -0 | 1.1049 | src/ProxyMgr.h | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:06 | jim | +1 -0 | 1.1025 | src/ProxyMgr.ci | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:06 | jim | +2 -0 | 1.1041 | src/Patch.h | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:06 | jim | +5 -0 | 1.1051 | src/NamdTypes.h | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:05 | jim | +31 -1 | 1.1203 | src/HomePatch.C | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/07 07:07:05 | jim | +6 -0 | 1.61 | src/ComputeNonbondedCUDA.C | Move formatting of position data for GPU to HomePatch to eliminateredundant work and serial bottleneck at cost of larger messages. |
| 2012/03/06 19:46:13 | jim | +5 -5 | 1.1239 | src/WorkDistrib.C | Patch from Phil Miller for g++ 3.3 on ancient PPC Mac OS X cluster. |
| 2012/03/06 06:22:57 | jim | +1 -0 | 1.11 | src/ComputeNonbondedCUDA.h | Multiple CUDA devices use home patches rather than proxies for patcheson the same node. Should help single-node multi-GPU runs. |
| 2012/03/06 06:22:57 | jim | +34 -10 | 1.60 | src/ComputeNonbondedCUDA.C | Multiple CUDA devices use home patches rather than proxies for patcheson the same node. Should help single-node multi-GPU runs. |
| 2012/03/06 06:22:57 | jim | +1 -8 | 1.1111 | src/ComputeMgr.C | Multiple CUDA devices use home patches rather than proxies for patcheson the same node. Should help single-node multi-GPU runs. |
| 2012/03/05 17:56:44 | jim | +6 -4 | 1.81 | src/ScriptTcl.C | replicaRecv source required to avoid race condition when receiving multiplemessages. This could be avoided by adding tags to CmiReplica arguments todistinguish size messages and including source in size message. |
| 2012/03/03 23:48:49 | jim | +1 -1 | 1.14 | ug/ug_accel.tex | Change < and > to $<$ and $>$. |
| 2012/03/03 23:40:27 | jim | +0 -1 | 1.13 | ug/ug_accel.tex | remove extra \item tag. |
| 2012/03/03 23:38:23 | jim | None | 1.1 | ug/ug_go.tex | Document Go forces module. |
| 2012/03/03 23:38:22 | jim | +4 -0 | 1.19 | ug/ug.tex | Document Go forces module. |
| 2012/03/03 23:38:04 | jim | +15 -15 | 1.17 | ug/ug_macros.tex | Add braces around arguments to limit font changes. |
| 2012/03/02 19:50:41 | jim | +88 -45 | 1.4 | plugins/molfile_plugin/src/psfplugin.c | Merge from VMD plugin tree. Handle long type names and large atom counts. |
| 2012/03/02 19:33:36 | jim | +1 -1 | 1.11 | psfgen/src/topo_mol.c | Pull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,prepends "psfgen)" to most messages on stdout, increases version to 1.6. |
| 2012/03/02 19:33:36 | jim | +44 -7 | 1.17 | psfgen/src/tcl_psfgen.c | Pull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,prepends "psfgen)" to most messages on stdout, increases version to 1.6. |
| 2012/03/02 19:33:35 | jim | +1 -1 | 1.6 | psfgen/src/pdb_file_extract.c | Pull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,prepends "psfgen)" to most messages on stdout, increases version to 1.6. |
| 2012/03/02 19:33:35 | jim | +1 -1 | 1.6 | psfgen/src/charmm_parse_topo_defs.c | Pull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,prepends "psfgen)" to most messages on stdout, increases version to 1.6. |
| 2012/03/02 19:33:30 | jim | +2 -2 | 1.6 | psfgen/doc/ug_macros.tex | Pull changes from VMD plugin tree. Tests _MSC_VER instead of WIN32,prepends "psfgen)" to most messages on stdout, increases version to 1.6. |
| 2012/03/02 07:13:19 | jim | None | 1.1 | lib/replica/charm_replica.patch | Include Charm++ patch to enable replica exchange in MPI builds. |
| 2012/03/02 07:13:19 | jim | +4 -0 | 1.7 | lib/replica/README.txt | Include Charm++ patch to enable replica exchange in MPI builds. |
| 2012/03/02 07:00:08 | jim | +3 -3 | 1.9 | src/Sync.h | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:07 | jim | +3 -5 | 1.41 | src/Sync.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:07 | jim | +31 -31 | 1.1040 | src/Patch.h | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:07 | jim | +53 -56 | 1.1062 | src/Patch.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:07 | jim | +4 -4 | 1.24 | src/ComputeSelfTuples.h | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:07 | jim | +4 -4 | 1.1037 | src/ComputePatchPair.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:06 | jim | +4 -4 | 1.1034 | src/ComputePatch.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:06 | jim | +14 -14 | 1.1054 | src/ComputeNonbondedSelf.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:06 | jim | +14 -14 | 1.1061 | src/ComputeNonbondedPair.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:06 | jim | +9 -9 | 1.59 | src/ComputeNonbondedCUDA.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:05 | jim | +6 -6 | 1.4 | src/ComputeLCPO.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:05 | jim | +3 -3 | 1.1060 | src/ComputeHomeTuples.h | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:05 | jim | +1 -1 | 1.1014 | src/ComputeHomePatches.h | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:05 | jim | +1 -1 | 1.1017 | src/ComputeHomePatches.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/02 07:00:05 | jim | +4 -4 | 1.9 | src/ComputeHomePatch.C | Switch from storing a ComputeID and looking up the object in ComputeMapto do anything with it to storing the Compute* itself. |
| 2012/03/01 02:12:11 | jim | +5 -5 | 1.93 | notes.txt | Update to charm-6.4.0. |
| 2012/03/01 02:12:11 | jim | +5 -5 | 1.76 | config | Update to charm-6.4.0. |
| 2012/03/01 02:12:11 | jim | +2 -2 | 1.27 | Make.charm | Update to charm-6.4.0. |
| 2012/03/01 01:58:56 | jim | +1 -1 | 1.5 | arch/Linux-x86_64-icc.arch | Make multicore default charm arch. |
| 2012/03/01 01:58:56 | jim | +1 -1 | 1.5 | arch/Linux-x86_64-g++.arch | Make multicore default charm arch. |
| 2012/02/29 23:22:23 | jim | +8 -0 | 1.8 | src/sortreplicas.c | Fix Windows by using _ftelli64() instead of ftello(), etc. |
| 2012/02/29 21:57:04 | jim | +1 -1 | 1.2 | lib/colvars/colvarproxy_standalone.h | Fix position_distance sign error to be consistent with code in NAMD. |
| 2012/02/29 08:05:24 | jim | +1 -1 | 1.7 | src/sortreplicas.c | Fix printf format. |
| 2012/02/29 07:59:01 | jim | +30 -0 | 1.3 | lib/replica/umbrella.namd | Add internal consistency check for replica_neighbors proc. |
| 2012/02/29 07:15:36 | jim | +2 -2 | 1.3 | lib/replica/umbrella2d/stretch_alanin.conf | Tweak documentation. |
| 2012/02/29 07:15:35 | jim | +2 -2 | 1.2 | lib/replica/umbrella/stretch_alanin.conf | Tweak documentation. |
| 2012/02/29 07:15:34 | jim | +5 -2 | 1.6 | lib/replica/README.txt | Tweak documentation. |
| 2012/02/29 07:09:38 | jim | +3 -1 | 1.6 | src/sortreplicas.c | Skip first entry in colvars.traj file since it just repeats input state. |
| 2012/02/29 06:57:46 | jim | +23 -2 | 1.5 | src/sortreplicas.c | Add final_step argument to trim trajectory back to restart point. |
| 2012/02/29 05:58:01 | jim | +6 -1 | 1.2 | lib/replica/umbrella.namd | Rename colvars state file to save as part of restart files. |
| 2012/02/29 04:53:47 | jim | +1 -1 | 1.2 | lib/replica/umbrella2d/colvars.conf | Write colvars trajectory more often to test sortreplicas. |
| 2012/02/29 04:53:46 | jim | +1 -1 | 1.2 | lib/replica/umbrella/colvars.conf | Write colvars trajectory more often to test sortreplicas. |
| 2012/02/29 04:48:39 | jim | +3 -0 | 1.2 | lib/replica/example/alanin_base.namd | Move Langevin params other than langevinTemperature to alanin_base.namd. |
| 2012/02/29 04:48:38 | jim | +0 -2 | 1.3 | lib/replica/replica.namd | Move Langevin params other than langevinTemperature to alanin_base.namd. |
| 2012/02/29 04:36:32 | jim | +11 -1 | 1.4 | src/sortreplicas.c | Filter out repeated timesteps in colvar trajectory file. |
| 2012/02/29 04:07:19 | jim | +92 -3 | 1.3 | src/sortreplicas.c | Process colvar trajectory files if they are present. |
| 2012/02/28 21:48:33 | jim | +9 -10 | 1.2 | lib/replica/umbrella2d/stretch_alanin.conf | Expand to 64 replicas. |
| 2012/02/28 21:48:05 | jim | None | 1.1 | lib/replica/make_output_dirs.sh | Add script for creating multiple output directories. |
| 2012/02/28 18:42:22 | jim | None | 1.1 | lib/replica/umbrella2d/stretch_alanin.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:22 | jim | None | 1.1 | lib/replica/umbrella2d/job1.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:22 | jim | None | 1.1 | lib/replica/umbrella2d/job0.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:22 | jim | None | 1.1 | lib/replica/umbrella2d/colvars.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:22 | jim | None | 1.1 | lib/replica/umbrella2d/alanin_base.namd | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:21 | jim | None | 1.1 | lib/replica/umbrella2d/alanin.psf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:21 | jim | None | 1.1 | lib/replica/umbrella2d/alanin.pdb | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:21 | jim | None | 1.1 | lib/replica/umbrella2d/alanin.params | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.9.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.9.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.9.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.8.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.8.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.8.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.7.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:18 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.7.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.7.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.6.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.6.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.6.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.5.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.5.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.5.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:17 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.4.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.4.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.4.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.3.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.3.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.3.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.2.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:16 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.2.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.2.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.15.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.15.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.15.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.14.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.14.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.14.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.13.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:15 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.13.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.13.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.12.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.12.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.12.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.11.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.11.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.11.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:14 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.10.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.10.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.10.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.1.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.1.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.1.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.0.xsc | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.0.vel | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:13 | jim | None | 1.1 | lib/replica/umbrella/input/alanin.initial.0.coor | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:12 | jim | None | 1.1 | lib/replica/umbrella/stretch_alanin.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/job1.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/job0.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/colvars.conf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/alanin_base.namd | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/alanin.psf | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/alanin.pdb | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:11 | jim | None | 1.1 | lib/replica/umbrella/alanin.params | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:42:10 | jim | None | 1.1 | lib/replica/umbrella.namd | Implement umbrella sampling using colvars in arbitrary dimensions. |
| 2012/02/28 18:29:29 | jim | +6 -6 | 1.5 | lib/replica/README.txt | Move "source ../replica.namd" from command line to jobX.conf files. |
| 2012/02/28 18:23:48 | jim | +1 -1 | 1.2 | lib/replica/example/load_all.vmd | Move "source ../replica.namd" from command line to jobX.conf files. |
| 2012/02/28 18:23:48 | jim | None | 1.1 | lib/replica/example/job1.conf | Move "source ../replica.namd" from command line to jobX.conf files. |
| 2012/02/28 18:23:48 | jim | None | 1.1 | lib/replica/example/job0.conf | Move "source ../replica.namd" from command line to jobX.conf files. |
| 2012/02/28 18:23:48 | jim | +4 -4 | 1.7 | lib/replica/example/fold_alanin.conf | Move "source ../replica.namd" from command line to jobX.conf files. |
| 2012/02/27 17:11:57 | chaomei2 | +10 -1 | 1.1100 | src/ProxyMgr.C | Fixed the bug in creating spanning tree for home patches in the case thata node doesn't have any home patches. |
| 2012/02/27 17:03:05 | dtanner | +2 -2 | 1.3 | src/ComputeLCPO.C | correct LCPO pairlist update frequency |
| 2012/02/27 04:03:04 | jim | +2 -0 | 1.12 | src/colvarproxy_namd.C | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:04 | jim | +6 -0 | 1.11 | src/colvarmodule.h | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:04 | jim | +39 -0 | 1.14 | src/colvarmodule.C | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:04 | jim | +12 -0 | 1.7 | src/colvarbias.h | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:04 | jim | +52 -0 | 1.9 | src/colvarbias.C | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:04 | jim | +1 -0 | 1.35 | src/ScriptTcl.h | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:03 | jim | +42 -0 | 1.80 | src/ScriptTcl.C | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:03 | jim | +2 -0 | 1.1047 | src/Node.h | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/27 04:03:03 | jim | +1 -0 | 1.1127 | src/Node.C | Add colvarbias Tcl command with changeconfig and energydiff sub-commandsto enable combining replica exchange with umbrella sampling. |
| 2012/02/25 02:33:37 | jim | +7 -7 | 1.1238 | src/WorkDistrib.C | Switch recursive bisection fallback from lowest-load node to space-filling curve. |
| 2012/02/24 22:19:36 | jim | +1 -1 | 1.148 | src/ComputePme.C | Only allocate as much memory as needed for X pencil. (Was safe before.) |
| 2012/02/24 22:04:13 | jim | +3 -3 | 1.1382 | src/SimParameters.C | Do not use GlobalMasterServer for IDM if IMDignore is on. |
| 2012/02/24 22:04:13 | jim | +1 -0 | 1.12 | src/IMDOutput.h | Do not use GlobalMasterServer for IDM if IMDignore is on. |
| 2012/02/24 22:04:13 | jim | +6 -0 | 1.14 | src/IMDOutput.C | Do not use GlobalMasterServer for IDM if IMDignore is on. |
| 2012/02/24 22:04:13 | jim | +2 -0 | 1.5 | src/GlobalMasterIMD.h | Do not use GlobalMasterServer for IDM if IMDignore is on. |
| 2012/02/24 22:04:13 | jim | +6 -1 | 1.1110 | src/ComputeMgr.C | Do not use GlobalMasterServer for IDM if IMDignore is on. |
| 2012/02/24 22:01:57 | jim | +5 -1 | 1.9 | src/GlobalMasterIMD.C | Reduce number of "Ignoring IMD forces due to IMDignore" messages. |
| 2012/02/24 01:25:01 | jim | +17 -8 | 1.1285 | src/Controller.C | Don't die (but still warn) about low exclusion count if full electrostatics is off. |
| 2012/02/23 19:39:49 | dtanner | +20 -16 | 1.1381 | src/SimParameters.C | LCPO improved initial parameters |
| 2012/02/23 19:26:01 | dtanner | +5 -0 | 1.3 | ug/ug_gbis.tex | adding documentation for LCPO |
| 2012/02/23 19:26:01 | dtanner | +13 -2 | 1.19 | ug/ug.bib | adding documentation for LCPO |
| 2012/02/23 16:46:29 | dtanner | +12 -4 | 1.1380 | src/SimParameters.C | made LCPO a little faster and more robust |
| 2012/02/23 16:46:28 | dtanner | +0 -2 | 1.1237 | src/Molecule.C | made LCPO a little faster and more robust |
| 2012/02/23 16:46:28 | dtanner | +78 -7 | 1.2 | src/ComputeLCPO.h | made LCPO a little faster and more robust |
| 2012/02/23 16:46:28 | dtanner | +226 -302 | 1.2 | src/ComputeLCPO.C | made LCPO a little faster and more robust |
| 2012/02/23 03:54:30 | jim | +1 -0 | 1.75 | config | Add -ugni arch suffix. |
| 2012/02/23 02:45:31 | jim | +1 -1 | 1.7 | src/ParallelIOMgr.h | Turn off "Num fixedAtom lookup" messages. |
| 2012/02/22 21:56:25 | jim | +3 -0 | 1.1071 | src/Controller.h | Fix uninitialized go energies when go not active. |
| 2012/02/22 21:56:25 | jim | +8 -27 | 1.1284 | src/Controller.C | Fix uninitialized go energies when go not active. |
| 2012/02/22 21:15:24 | jim | +3 -1 | 1.1236 | src/Molecule.C | Eliminate variable-size array. |
| 2012/02/22 20:40:14 | jim | +14 -6 | 1.1283 | src/Controller.C | More information on bad exclusion count errors. |
| 2012/02/22 03:32:49 | chaomei2 | +18 -18 | 1.27 | src/ComputePmeMgr.ci | Added note for PmePencil atomic blocks so that it is clear to know the meaningof each atomic block in Projection |
| 2012/02/21 20:48:42 | chaomei2 | +5 -3 | 1.1099 | src/ProxyMgr.C | Disable the debugging output for proxy lists of patches |
| 2012/02/21 19:35:51 | jim | +1 -0 | 1.152 | Make.depends | Rebuild dependencies. |
| 2012/02/21 18:51:05 | jim | +9 -5 | 1.1282 | src/Controller.C | Add additional information to bad global atom count error. |
| 2012/02/21 18:48:13 | jim | +14 -2 | 1.21 | src/ResizeArrayRaw.h | Fix implementation of clear() plus other minor cleanups. |
| 2012/02/21 18:48:13 | jim | +5 -14 | 1.17 | src/ResizeArray.h | Fix implementation of clear() plus other minor cleanups. |
| 2012/02/21 18:30:38 | jim | +1 -0 | 1.14 | src/MigrateAtomsMsg.C | Add internal consistency check for combined migration message. |
| 2012/02/21 18:29:35 | jim | +8 -0 | 1.1024 | src/AtomMap.C | Add internal consistency check. |
| 2012/02/21 17:48:21 | dtanner | +4 -5 | 1.1109 | src/ComputeMgr.C | set num LCPO patches to 8 instead of non c++ expression |
| 2012/02/21 17:14:36 | chaomei2 | +8 -6 | 1.1235 | src/Molecule.C | Fixed compilation errors regarding function assignLCPOTypes by allowing itonly in non-memopt version. |
| 2012/02/21 14:43:50 | dtanner | +2 -0 | 1.1050 | src/WorkDistrib.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:50 | dtanner | +1 -0 | 1.1028 | src/WorkDistrib.ci | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:49 | dtanner | +58 -2 | 1.1237 | src/WorkDistrib.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:49 | dtanner | +4 -2 | 1.1202 | src/SimParameters.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +21 -7 | 1.1379 | src/SimParameters.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +9 -3 | 1.1205 | src/Sequencer.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +12 -0 | 1.1061 | src/ProxyPatch.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +2 -0 | 1.1048 | src/ProxyMgr.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +2 -0 | 1.1024 | src/ProxyMgr.ci | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +1 -0 | 1.22 | src/PatchTypes.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +3 -0 | 1.1040 | src/PatchMap.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +39 -0 | 1.1058 | src/PatchMap.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:48 | dtanner | +14 -0 | 1.1039 | src/Patch.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:47 | dtanner | +22 -0 | 1.1061 | src/Patch.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:47 | dtanner | +1 -0 | 1.1050 | src/NamdTypes.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:47 | dtanner | +9 -3 | 1.113 | src/NamdCentLB.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:47 | dtanner | +15 -0 | 1.1111 | src/Molecule.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:46 | dtanner | +216 -3 | 1.1234 | src/Molecule.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:46 | dtanner | +4 -2 | 1.114 | src/LdbCoordinator.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:46 | dtanner | +3 -0 | 1.1078 | src/HomePatch.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:45 | dtanner | +32 -1 | 1.1202 | src/HomePatch.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:45 | dtanner | +21 -0 | 1.1108 | src/ComputeMgr.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:45 | dtanner | +2 -1 | 1.1051 | src/ComputeMap.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:45 | dtanner | None | 1.1 | src/ComputeLCPO.h | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:45 | dtanner | None | 1.1 | src/ComputeLCPO.C | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:44 | dtanner | +2 -2 | 1.7 | arch/Linux-x86_64.cuda | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:44 | dtanner | +1 -0 | 1.1312 | Makefile | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/21 14:43:43 | dtanner | +62 -1 | 1.151 | Make.depends | linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent |
| 2012/02/20 23:00:41 | jim | +1 -2 | 1.12 | src/ParallelIOMgr.C | Fix bug where if all home patches on a node start out empty they share the same atom array. |
| 2012/02/19 22:22:00 | jim | +1 -1 | 1.1201 | src/HomePatch.C | Avoid dynamically adjusting pairlist distance if patch is empty. |
| 2012/02/19 22:17:07 | jim | +5 -4 | 1.1027 | src/PatchMgr.h | Eliminate order-numPes loop to find messages in migration message array. |
| 2012/02/19 22:17:07 | jim | +6 -5 | 1.1042 | src/PatchMgr.C | Eliminate order-numPes loop to find messages in migration message array. |
| 2012/02/18 23:13:55 | jim | +11 -5 | 1.1204 | src/Sequencer.C | Add debugging info to "Atoms moving too fast" messages. |
| 2012/02/18 23:12:28 | jim | +3 -2 | 1.1041 | src/PatchMgr.C | Eliminate order-numPes loop to null-out migration message array. |
| 2012/02/17 22:29:49 | jim | +4 -0 | 1.1080 | src/NamdState.C | Fix memory-optimized builds by disabling Go forces. |
| 2012/02/17 22:29:49 | jim | +8 -0 | 1.3 | src/GoMolecule.C | Fix memory-optimized builds by disabling Go forces. |
| 2012/02/17 22:07:04 | jim | +9 -9 | 1.2 | src/GoMolecule.C | Pass string buffer to sscanf properly. |
| 2012/02/17 02:13:15 | jim | +20 -4 | 1.1201 | src/SimParameters.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:14 | jim | +54 -4 | 1.1378 | src/SimParameters.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:14 | jim | +5 -0 | 1.1052 | src/ReductionMgr.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:14 | jim | +13 -1 | 1.1126 | src/Node.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:14 | jim | +28 -0 | 1.1079 | src/NamdState.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:14 | jim | +105 -1 | 1.1110 | src/Molecule.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:13 | jim | +2 -2 | 1.1233 | src/Molecule.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:13 | jim | None | 1.1 | src/GoMolecule.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:13 | jim | +53 -4 | 1.1281 | src/Controller.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:13 | jim | +25 -0 | 1.1079 | src/ComputeNonbondedUtil.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:13 | jim | +35 -1 | 1.1106 | src/ComputeNonbondedUtil.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:12 | jim | None | 1.1 | src/ComputeNonbondedGo.C | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:12 | jim | +45 -0 | 1.39 | src/ComputeNonbondedBase2.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:12 | jim | +16 -2 | 1.1178 | src/ComputeNonbondedBase.h | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:06 | jim | +2 -0 | 1.1311 | Makefile | Go forces implementation from Jonathan Lai. |
| 2012/02/17 02:13:06 | jim | +107 -0 | 1.150 | Make.depends | Go forces implementation from Jonathan Lai. |
| 2012/02/16 20:08:08 | jim | +42 -22 | 1.149 | Make.depends | Rebuild dependencies. |
| 2012/02/13 23:07:36 | jim | +12 -9 | 1.5 | src/DumpBench.C | Revert to work with SPEC benchmark. |
| 2012/02/11 23:14:45 | jim | +5 -4 | 1.1098 | src/ProxyMgr.C | Handle variable node sizes. |
| 2012/02/11 22:50:36 | jim | +2 -2 | 1.1097 | src/ProxyMgr.C | Avoid some race conditions. |
| 2012/02/11 22:45:46 | jim | +1 -2 | 1.1125 | src/Node.C | Use proxyMgr->getSendSpanning() to determine if spanning tree is in useinstead of simParameters->isSendSpanningTreeOn(), which only tells if theconfig file has explicitly enabled it. |
| 2012/02/11 01:14:13 | chaomei2 | +54 -0 | 1.1047 | src/ProxyMgr.h | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:13 | chaomei2 | +9 -0 | 1.1023 | src/ProxyMgr.ci | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:13 | chaomei2 | +201 -2 | 1.1096 | src/ProxyMgr.C | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:13 | chaomei2 | +15 -1 | 1.1124 | src/Node.C | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:12 | chaomei2 | +7 -1 | 1.1200 | src/HomePatch.C | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:12 | chaomei2 | +1 -1 | 1.55 | src/BackEnd.C | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/11 01:14:12 | chaomei2 | +1 -1 | 1.1022 | src/BOCgroup.h | Created a node-aware spanning tree for home patches, and used it for sending proxy info from each home patch to PE 0. |
| 2012/02/10 21:45:53 | jim | None | 1.1 | arch/CRAY-XT.cuda | CUDA for Cray XK. |
| 2012/02/10 21:03:08 | jim | +6 -5 | 1.1236 | src/WorkDistrib.C | Use recursive bisection if PME is disabled. |
| 2012/02/06 23:03:51 | jim | +5 -4 | 1.1200 | src/SimParameters.h | Add alchEnsembleAvg from Wei Jiang, on by default, to allow replicas to disable ensemble averaging. |
| 2012/02/06 23:03:50 | jim | +18 -4 | 1.1377 | src/SimParameters.C | Add alchEnsembleAvg from Wei Jiang, on by default, to allow replicas to disable ensemble averaging. |
| 2012/02/06 23:03:50 | jim | +34 -12 | 1.1280 | src/Controller.C | Add alchEnsembleAvg from Wei Jiang, on by default, to allow replicas to disable ensemble averaging. |
| 2012/02/01 03:48:17 | jim | +2 -2 | 1.3 | arch/BlueGeneP.tcl | Updates to work on Intrepid. |
| 2012/02/01 03:48:17 | jim | +3 -3 | 1.2 | arch/BlueGeneP.fftw | Updates to work on Intrepid. |
| 2012/02/01 03:48:17 | jim | +4 -5 | 1.7 | arch/BlueGeneP-xlC.arch | Updates to work on Intrepid. |
| 2012/02/01 03:48:17 | jim | +1 -12 | 1.5 | arch/BlueGeneP-MPI-xlC.arch | Updates to work on Intrepid. |
| 2012/01/31 21:45:48 | jim | +2 -5 | 1.40 | src/Sync.C | No proxy sync if at least four patches per pe. |
| 2012/01/31 21:41:34 | dhardy | +5 -3 | 1.2 | src/MsmNotes.txt | fixed instructions to rebuild file dependencies for parallel MSM |
| 2012/01/31 19:15:31 | jim | +2 -2 | 1.2 | lib/replica/replica.namd | Increase temperature precision from 1 to .01 K. |
| 2012/01/30 23:28:08 | ryanmcgreevy | +2 -2 | 1.9 | src/GlobalMasterTMD.C | fixed to allow initialRMSD/finalrmsd to be equal |
| 2012/01/30 19:36:11 | jim | +2 -2 | 1.1095 | src/ProxyMgr.C | Remove useless "sheer evil" messages. |
| 2012/01/29 23:32:34 | jim | +5 -6 | 1.1235 | src/WorkDistrib.C | Print diagnostic information for "Incorrect atom count in WorkDistrib::assignNodeToPatch" error. |
| 2012/01/29 23:23:19 | jim | +7 -3 | 1.1279 | src/Controller.C | Flush stdout once per minute after timing output. |
| 2012/01/29 23:20:59 | jim | +4 -0 | 1.6 | src/ParallelIOMgr.h | Distribute input procs across machine and add flow control to atom sends. |
| 2012/01/29 23:20:59 | jim | +1 -0 | 1.6 | src/ParallelIOMgr.ci | Distribute input procs across machine and add flow control to atom sends. |
| 2012/01/29 23:20:59 | jim | +58 -8 | 1.11 | src/ParallelIOMgr.C | Distribute input procs across machine and add flow control to atom sends. |
| 2012/01/28 22:08:17 | jim | +44 -22 | 1.10 | src/ParallelIOMgr.C | Use fseeko instead of repeating fseek and add return value checking. |
| 2012/01/28 22:08:17 | jim | +28 -10 | 1.68 | src/Output.C | Use fseeko instead of repeating fseek and add return value checking. |
| 2012/01/28 22:08:17 | jim | +27 -11 | 1.1232 | src/Molecule.C | Use fseeko instead of repeating fseek and add return value checking. |
| 2012/01/28 22:05:55 | jim | +8 -4 | 1.3 | src/largefiles.h | Make more robust on AIX and complain if included before stdio.h. |
| 2012/01/28 22:04:28 | jim | +1 -1 | 1.11 | src/dcdlib.h | Comment that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:04:27 | jim | +1 -1 | 1.1048 | src/CollectionMaster.C | Comment that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:31 | jim | +1 -1 | 1.4 | src/loaddcd.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:31 | jim | +1 -1 | 1.8 | src/flipdcd.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:31 | jim | +1 -1 | 1.5 | src/flipbinpdb.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:31 | jim | +1 -1 | 1.4 | src/fixdcd.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:30 | jim | +1 -1 | 1.5 | src/dumpdcd.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 22:02:29 | jim | +1 -1 | 1.6 | src/diffbinpdb.c | Commend that largefiles.h must be included first, before system headers. |
| 2012/01/28 19:11:28 | jim | +2 -2 | 1.1039 | src/PatchMap.h | Add error checking on maximum number of atoms per patch. |
| 2012/01/28 19:11:28 | jim | +2 -2 | 1.5 | src/ParallelIOMgr.h | Add error checking on maximum number of atoms per patch. |
| 2012/01/28 19:11:28 | jim | +2 -2 | 1.5 | src/ParallelIOMgr.ci | Add error checking on maximum number of atoms per patch. |
| 2012/01/28 19:11:27 | jim | +17 -0 | 1.9 | src/ParallelIOMgr.C | Add error checking on maximum number of atoms per patch. |
| 2012/01/27 01:41:54 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/readpdb.h | Update from plugins tree. |
| 2012/01/27 01:41:54 | jim | +79 -20 | 1.3 | plugins/molfile_plugin/src/psfplugin.c | Update from plugins tree. |
| 2012/01/27 01:41:54 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/periodic_table.h | Update from plugins tree. |
| 2012/01/27 01:41:54 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/pdbplugin.c | Update from plugins tree. |
| 2012/01/27 01:41:54 | jim | +0 -0 | 1.2 | plugins/molfile_plugin/src/namdbinplugin.c | Update from plugins tree. |
| 2012/01/27 01:41:54 | jim | +0 -0 | 1.4 | plugins/molfile_plugin/src/largefiles.h | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +608 -65 | 1.3 | plugins/molfile_plugin/src/jsplugin.c | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/hash.h | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/hash.c | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/fortread.h | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +40 -18 | 1.5 | plugins/molfile_plugin/src/fastio.h | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +0 -0 | 1.5 | plugins/molfile_plugin/src/endianswap.h | Update from plugins tree. |
| 2012/01/27 01:41:53 | jim | +23 -4 | 1.5 | plugins/molfile_plugin/src/dcdplugin.c | Update from plugins tree. |
| 2012/01/27 01:41:43 | jim | +0 -0 | 1.6 | plugins/include/vmdplugin.h | Update from plugins tree. |
| 2012/01/27 01:41:43 | jim | +41 -2 | 1.5 | plugins/include/molfile_plugin.h | Update from plugins tree. |
| 2012/01/26 03:55:51 | chaomei2 | +1 -4 | 1.1019 | src/ProxyPatch.h | Fixed bug using NodeProxyMgr when node-aware spanning tree is enabled. Whenusing NodeProxyMgr, we assumed that all PEs attached to a node are on thesame tree level (i.e. a simple 2-level tree). However, when creating thenode-aware spanning tree, this assumption is broken as the PEs could beorganized into a multi-level tree depending on the branch factor. |
| 2012/01/26 03:55:51 | chaomei2 | +32 -26 | 1.1094 | src/ProxyMgr.C | Fixed bug using NodeProxyMgr when node-aware spanning tree is enabled. Whenusing NodeProxyMgr, we assumed that all PEs attached to a node are on thesame tree level (i.e. a simple 2-level tree). However, when creating thenode-aware spanning tree, this assumption is broken as the PEs could beorganized into a multi-level tree depending on the branch factor. |
| 2012/01/25 19:08:43 | dbwells2 | +32 -3 | 1.10 | ug/ug_userdef.tex | Added documentation for Gridforce LiteAdded documentation for 'SMDk2' keyword (which was added a long, long time ago...) |
| 2012/01/21 21:42:14 | jim | +7 -5 | 1.1093 | src/ProxyMgr.C | Use alloca for variable-size local arrays. |
| 2012/01/21 21:24:52 | jim | +2 -2 | 1.1310 | Makefile | Change -e to -f in file existence test to support sh on Solaris. |
| 2012/01/21 07:54:24 | gzheng | +2 -0 | 1.79 | src/ScriptTcl.C | fix compilation error when TCL is disabled |
| 2012/01/19 21:50:09 | dbwells2 | None | 1.1 | src/GridForceGrid.inl | Optimizations of gridforce code |
| 2012/01/19 21:50:09 | dbwells2 | +19 -24 | 1.14 | src/GridForceGrid.h | Optimizations of gridforce code |
| 2012/01/19 21:50:08 | dbwells2 | +41 -441 | 1.19 | src/GridForceGrid.C | Optimizations of gridforce code |
| 2012/01/19 21:50:08 | dbwells2 | +5 -0 | 1.7 | src/ComputeGridForce.h | Optimizations of gridforce code |
| 2012/01/19 21:50:08 | dbwells2 | +73 -86 | 1.24 | src/ComputeGridForce.C | Optimizations of gridforce code |
| 2012/01/19 21:50:05 | dbwells2 | +2 -0 | 1.148 | Make.depends | Optimizations of gridforce code |
| 2012/01/18 22:20:36 | jim | +5 -1 | 1.14 | src/parm.C | Skip (and warn about) unexpected sections in AMBER prmtop files. |
| 2012/01/18 16:11:54 | jim | +1 -1 | 1.1199 | src/HomePatch.C | Fix bug (typo) for massless particles in rigid bond code. |
| 2012/01/17 06:51:14 | jim | +6 -4 | 1.1123 | src/Node.C | Move sync and spanning tree build to startup phase after compute creation. |
| 2012/01/16 17:30:49 | dtanner | +3 -2 | 1.2 | src/ComputeGBISCUDAKernel.h | fixed energy reduction; bug had been brought on by twoAway |
| 2012/01/15 02:22:40 | jim | +4 -2 | 1.1234 | src/WorkDistrib.C | Do not build node-aware spanning tree with only one node. |
| 2012/01/14 22:06:43 | jim | +3 -3 | 1.1022 | src/ProxyMgr.ci | Change immediate messages to expedited. |
| 2012/01/14 22:06:43 | jim | +2 -2 | 1.26 | src/ComputePmeMgr.ci | Change immediate messages to expedited. |
| 2012/01/14 21:55:45 | jim | +1 -2 | 1.1309 | Makefile | Add -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR |
| 2012/01/14 21:02:00 | jim | +12 -4 | 1.1233 | src/WorkDistrib.C | Enable spanning tree for CkNumPes() > CkNumNodes() whenNODEAWARE_PROXY_SPANNINGTREE is defined. |
| 2012/01/13 19:48:57 | jim | +4 -0 | 1.39 | src/Sync.C | Disable proxy sync with USE_NODEPATCHMGR and node size > 2. |
| 2012/01/13 17:08:14 | jim | +24 -22 | 1.1308 | Makefile | Eliminate spurious re-linking by depending on obj/.exists instead of obj. |
| 2012/01/13 16:23:00 | jim | +6 -2 | 1.1092 | src/ProxyMgr.C | Fix USE_NODEPATCHMGR compile and bug. |
| 2012/01/13 02:50:43 | jim | +3 -3 | 1.1091 | src/ProxyMgr.C | Fix assertions in node-aware proxy spanning tree creation. |
| 2012/01/12 21:55:32 | jim | +33 -31 | 1.1232 | src/WorkDistrib.C | Trace calls to machine progress layer. |
| 2012/01/12 21:54:45 | jim | +0 -1 | 1.8 | src/Sync.h | Make events static again since they must be the same for all pes. |
| 2012/01/12 21:54:45 | jim | +3 -0 | 1.38 | src/Sync.C | Make events static again since they must be the same for all pes. |
| 2012/01/12 21:14:50 | jim | +12 -9 | 1.37 | src/Sync.C | Fix proxy sync, which is used with proxy tree. |
| 2012/01/08 21:30:02 | jim | +4 -3 | 1.7 | src/Sync.h | Fix Sync system which holds computes on a pe until all home patches areready or, optionally, until all home patches and proxies are ready. |
| 2012/01/08 21:30:01 | jim | +28 -12 | 1.36 | src/Sync.C | Fix Sync system which holds computes on a pe until all home patches areready or, optionally, until all home patches and proxies are ready. |
| 2012/01/08 21:30:01 | jim | +2 -4 | 1.1060 | src/Patch.C | Fix Sync system which holds computes on a pe until all home patches areready or, optionally, until all home patches and proxies are ready. |
| 2012/01/08 21:30:01 | jim | +5 -2 | 1.113 | src/LdbCoordinator.C | Fix Sync system which holds computes on a pe until all home patches areready or, optionally, until all home patches and proxies are ready. |
| 2012/01/08 21:30:01 | jim | +1 -1 | 1.1198 | src/HomePatch.C | Fix Sync system which holds computes on a pe until all home patches areready or, optionally, until all home patches and proxies are ready. |
| 2012/01/04 17:50:34 | jim | +32 -32 | 1.1231 | src/WorkDistrib.C | Change CmiNetworkProgressAfter(0) to CmiMachineProgressImpl(). |
| 2012/01/04 15:47:55 | jim | +32 -32 | 1.1230 | src/WorkDistrib.C | Call CmiNetworkProgressAfter(0) at end of every compute object doWork()to ensure that high-priority incoming messages are received promptly. |
| 2011/12/30 16:46:11 | jim | +25 -25 | 1.4 | src/ComputeGBIS.inl | inline -> static inline |
| 2011/12/22 22:53:12 | jim | +5 -1 | 1.1057 | src/Sequencer.h | Use priorities with Sequencer thread resumes. |
| 2011/12/22 22:53:12 | jim | +16 -5 | 1.1203 | src/Sequencer.C | Use priorities with Sequencer thread resumes. |
| 2011/12/22 20:12:40 | jim | +1 -5 | 1.1036 | src/ComputePatchPair.C | Implement noWork() to skip work for GBIS and fix non-GBIS priorities. |
| 2011/12/22 20:12:40 | jim | +1 -5 | 1.1033 | src/ComputePatch.C | Implement noWork() to skip work for GBIS and fix non-GBIS priorities. |
| 2011/12/22 20:12:40 | jim | +28 -10 | 1.1053 | src/ComputeNonbondedSelf.C | Implement noWork() to skip work for GBIS and fix non-GBIS priorities. |
| 2011/12/22 20:12:40 | jim | +35 -11 | 1.1060 | src/ComputeNonbondedPair.C | Implement noWork() to skip work for GBIS and fix non-GBIS priorities. |
| 2011/12/22 16:31:52 | jim | +5 -5 | 1.1202 | src/Sequencer.C | Allow firstTimestep to not be a multiple of stepsPerCycle for "run 0". |
| 2011/12/22 16:31:52 | jim | +8 -0 | 1.78 | src/ScriptTcl.C | Allow firstTimestep to not be a multiple of stepsPerCycle for "run 0". |
| 2011/12/22 16:31:52 | jim | +5 -5 | 1.1278 | src/Controller.C | Allow firstTimestep to not be a multiple of stepsPerCycle for "run 0". |
| 2011/12/22 15:31:09 | dtanner | +4 -5 | 1.1201 | src/Sequencer.C | fixing gbisPhase |
| 2011/12/22 15:31:09 | dtanner | +0 -1 | 1.1017 | src/ComputePatchPair.h | fixing gbisPhase |
| 2011/12/22 15:31:09 | dtanner | +0 -1 | 1.1018 | src/ComputePatch.h | fixing gbisPhase |
| 2011/12/22 15:31:09 | dtanner | +1 -1 | 1.1022 | src/Compute.h | fixing gbisPhase |
| 2011/12/16 22:40:14 | dbwells2 | +1 -0 | 1.1059 | src/common.h | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:14 | dbwells2 | +2 -2 | 1.77 | src/ScriptTcl.C | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:13 | dbwells2 | +1 -1 | 1.1046 | src/Node.h | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:13 | dbwells2 | +1 -1 | 1.1031 | src/Node.ci | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:13 | dbwells2 | +30 -13 | 1.1122 | src/Node.C | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:13 | dbwells2 | +10 -0 | 1.1109 | src/Molecule.h | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:40:13 | dbwells2 | +4 -1 | 1.23 | src/ComputeGridForce.C | Changed grid reload code so that it broadcasts complete grid objects,rather than just grid values. This way, the code supports grid objectsthat change size and shape when reloaded. |
| 2011/12/16 22:28:46 | dtanner | +2 -0 | 1.1049 | src/WorkDistrib.h | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:46 | dtanner | +2 -0 | 1.1027 | src/WorkDistrib.ci | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:46 | dtanner | +22 -5 | 1.1229 | src/WorkDistrib.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +0 -4 | 1.1197 | src/HomePatch.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +2 -6 | 1.1035 | src/ComputePatchPair.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +3 -6 | 1.1032 | src/ComputePatch.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +1 -0 | 1.28 | src/ComputeNonbondedCUDAKernel.cu | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +45 -11 | 1.58 | src/ComputeNonbondedCUDA.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 22:28:45 | dtanner | +6 -3 | 1.1034 | src/Compute.C | GBIS changes for multicore w/ CUDA |
| 2011/12/16 21:45:42 | dbwells2 | +9 -1 | 1.13 | src/GridForceGrid.h | Gridforce now checks for grid self-overlap over periodic boundaryconditions at startup and, if pressure control is used, every 100steps. |
| 2011/12/16 21:45:42 | dbwells2 | +70 -5 | 1.18 | src/GridForceGrid.C | Gridforce now checks for grid self-overlap over periodic boundaryconditions at startup and, if pressure control is used, every 100steps. |
| 2011/12/16 21:45:42 | dbwells2 | +19 -8 | 1.22 | src/ComputeGridForce.C | Gridforce now checks for grid self-overlap over periodic boundaryconditions at startup and, if pressure control is used, every 100steps. |
| 2011/12/16 06:50:16 | jim | +11 -4 | 1.147 | src/ComputePme.C | Make pencil PME obey PMEProcessors limit. |
| 2011/12/13 00:11:35 | jim | +7 -4 | 1.1307 | Makefile | Fix Windows builds of sortreplicas. |
| 2011/12/13 00:08:33 | jim | +1 -0 | 1.2 | src/sortreplicas.c | Fix compiler warning. |
| 2011/12/12 23:15:52 | jim | +4 -0 | 1.6 | lib/replica/example/fold_alanin.conf | Add basic documentation for sortreplicas. |
| 2011/12/12 23:15:49 | jim | +8 -0 | 1.4 | lib/replica/README.txt | Add basic documentation for sortreplicas. |
| 2011/12/12 23:00:03 | jim | None | 1.1 | src/sortreplicas.c | Add new sortreplicas program to un-shuffle replica-exchange trajectories. |
| 2011/12/12 22:59:50 | jim | +9 -3 | 1.1306 | Makefile | Add new sortreplicas program to un-shuffle replica-exchange trajectories. |
| 2011/12/11 09:03:43 | johanstr | +10 -4 | 1.1200 | src/Sequencer.C | modified adaptive tempering to take initial temperature from thermostat |
| 2011/12/11 09:03:43 | johanstr | +8 -4 | 1.1277 | src/Controller.C | modified adaptive tempering to take initial temperature from thermostat |
| 2011/12/07 20:26:41 | johanstr | +8 -18 | 1.1276 | src/Controller.C | Cleaned up adaptive tempering code and modified debug output |
| 2011/12/06 21:37:57 | dtanner | +6 -4 | 1.1199 | src/SimParameters.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:57 | dtanner | +12 -7 | 1.1376 | src/SimParameters.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:57 | dtanner | +7 -6 | 1.1199 | src/Sequencer.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +4 -4 | 1.1060 | src/ProxyPatch.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +4 -4 | 1.1046 | src/ProxyMgr.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +4 -4 | 1.1021 | src/ProxyMgr.ci | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +18 -18 | 1.1038 | src/Patch.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +13 -10 | 1.1059 | src/Patch.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +1 -2 | 1.9 | src/OwnerBox.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:56 | dtanner | +2 -0 | 1.1049 | src/NamdTypes.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:55 | dtanner | +4 -3 | 1.1196 | src/HomePatch.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:55 | dtanner | +5 -5 | 1.1275 | src/Controller.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:55 | dtanner | +5 -4 | 1.1078 | src/ComputeNonbondedUtil.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:55 | dtanner | +4 -4 | 1.1023 | src/ComputeNonbondedSelf.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:55 | dtanner | +0 -1 | 1.1052 | src/ComputeNonbondedSelf.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +4 -4 | 1.1024 | src/ComputeNonbondedPair.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +0 -1 | 1.1059 | src/ComputeNonbondedPair.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +54 -1 | 1.17 | src/ComputeNonbondedCUDAKernel.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +236 -2 | 1.27 | src/ComputeNonbondedCUDAKernel.cu | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +13 -1 | 1.10 | src/ComputeNonbondedCUDA.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +331 -37 | 1.57 | src/ComputeNonbondedCUDA.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | +53 -127 | 1.2 | src/ComputeGBISser.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:54 | dtanner | None | 1.1 | src/ComputeGBISCUDAKernel.h | adding CUDA support for GBIS |
| 2011/12/06 21:37:53 | dtanner | +374 -293 | 1.3 | src/ComputeGBIS.inl | adding CUDA support for GBIS |
| 2011/12/06 21:37:53 | dtanner | +237 -129 | 1.4 | src/ComputeGBIS.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:53 | dtanner | +0 -2 | 1.1033 | src/Compute.C | adding CUDA support for GBIS |
| 2011/12/06 21:37:52 | dtanner | +2 -1 | 1.1305 | Makefile | adding CUDA support for GBIS |
| 2011/12/06 21:37:52 | dtanner | +23 -74 | 1.147 | Make.depends | adding CUDA support for GBIS |
| 2011/12/06 01:59:04 | jim | +8 -4 | 1.1375 | src/SimParameters.C | Allow script modification of accelMDE, accelMDalpha, accelMDTE, and accelMDTalpha. |
| 2011/12/05 23:21:35 | jim | +13 -45 | 1.5 | lib/replica/example/fold_alanin.conf | Update example for new replica exchange scripts. |
| 2011/12/05 23:20:58 | jim | +16 -31 | 1.2 | lib/replica/show_replicas.vmd | New replica exchange scripts based on patched MPI build of Charm++. |
| 2011/12/05 23:20:58 | jim | None | 1.1 | lib/replica/replica.namd | New replica exchange scripts based on patched MPI build of Charm++. |
| 2011/12/05 23:20:58 | jim | +19 -13 | 1.3 | lib/replica/README.txt | New replica exchange scripts based on patched MPI build of Charm++. |
| 2011/12/05 21:00:33 | jim | +4 -0 | 1.76 | src/ScriptTcl.C | Work around new "out of stack space (infinite loop?)" error from Tcl byonly calling reduction callback on last step, outside controller loop. |
| 2011/12/05 21:00:33 | jim | +1 -0 | 1.1020 | src/NamdState.h | Work around new "out of stack space (infinite loop?)" error from Tcl byonly calling reduction callback on last step, outside controller loop. |
| 2011/12/05 21:00:32 | jim | +8 -8 | 1.1274 | src/Controller.C | Work around new "out of stack space (infinite loop?)" error from Tcl byonly calling reduction callback on last step, outside controller loop. |
| 2011/12/05 20:44:57 | jim | +6 -0 | 1.34 | src/ScriptTcl.h | Add procs to access replica capabilities in modified mpi Charm++ port:numReplicas, myReplica, replicaSendrecv, replicaSend, replicaRecv, replicaBarrier |
| 2011/12/05 20:44:56 | jim | +116 -0 | 1.75 | src/ScriptTcl.C | Add procs to access replica capabilities in modified mpi Charm++ port:numReplicas, myReplica, replicaSendrecv, replicaSend, replicaRecv, replicaBarrier |
| 2011/12/02 22:49:51 | dbwells2 | +4 -3 | 1.1198 | src/SimParameters.h | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:51 | dbwells2 | +48 -3 | 1.1374 | src/SimParameters.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:51 | dbwells2 | +2 -2 | 1.1121 | src/Node.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:51 | dbwells2 | +3 -3 | 1.1108 | src/Molecule.h | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +20 -22 | 1.1231 | src/Molecule.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +2 -0 | 1.4 | src/MGridforceParams.h | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +6 -4 | 1.4 | src/MGridforceParams.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +183 -39 | 1.12 | src/GridForceGrid.h | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +472 -145 | 1.17 | src/GridForceGrid.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/12/02 22:49:50 | dbwells2 | +15 -13 | 1.21 | src/ComputeGridForce.C | Added Gridforce Lite feature, which uses a linear interpolation scheme which is easily portable to GPUs. |
| 2011/11/28 22:52:12 | johanstr | +4 -3 | 1.1197 | src/SimParameters.h | Fixed initialization+restart bugs in adaptive tempering calculations |
| 2011/11/28 22:52:11 | johanstr | +10 -12 | 1.1373 | src/SimParameters.C | Fixed initialization+restart bugs in adaptive tempering calculations |
| 2011/11/28 22:52:11 | johanstr | +5 -0 | 1.1070 | src/Controller.h | Fixed initialization+restart bugs in adaptive tempering calculations |
| 2011/11/28 22:52:11 | johanstr | +87 -9 | 1.1273 | src/Controller.C | Fixed initialization+restart bugs in adaptive tempering calculations |
| 2011/11/18 06:06:55 | char | +26 -16 | 1.7 | src/ComputeNonbondedFEP.C | typo fixes |
| 2011/11/17 06:00:14 | jim | +2 -0 | 1.4 | src/ComputeNonbondedCUDAKernelBase.h | Workaround for CUDA 4.0 compiler bug giving bad pressure on timesteps whenenergies are calculated. Also follow __threadfence() with __syncthreads()to ensure all threads have written data to global. |
| 2011/11/17 04:31:30 | char | +6 -2 | 1.1196 | src/SimParameters.h | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:30 | char | +31 -4 | 1.1372 | src/SimParameters.C | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:30 | char | +4 -0 | 1.1077 | src/ComputeNonbondedUtil.h | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:30 | char | +8 -20 | 1.1105 | src/ComputeNonbondedUtil.C | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:30 | char | +49 -13 | 1.6 | src/ComputeNonbondedFEP.C | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:30 | char | +2 -1 | 1.38 | src/ComputeNonbondedBase2.h | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/17 04:31:29 | char | +4 -0 | 1.1177 | src/ComputeNonbondedBase.h | addition of Weeks-Chandler-Anderson decomposition of intermolecular pair potential as option for FEP simulations. |
| 2011/11/16 21:21:08 | jim | +65 -13 | 1.146 | src/ComputePme.C | Consolidate slab PME untranspose messages sent to pes on the same node. |
| 2011/11/16 19:08:56 | jim | +9 -0 | 1.25 | src/ComputePmeMgr.ci | Consolidate slab PME transpose messages sent to pes on the same node. |
| 2011/11/16 19:08:56 | jim | +252 -36 | 1.145 | src/ComputePme.C | Consolidate slab PME transpose messages sent to pes on the same node. |
| 2011/11/16 19:08:55 | jim | +1 -0 | 1.54 | src/BackEnd.C | Consolidate slab PME transpose messages sent to pes on the same node. |
| 2011/11/16 19:08:55 | jim | +1 -0 | 1.1021 | src/BOCgroup.h | Consolidate slab PME transpose messages sent to pes on the same node. |
| 2011/11/15 02:34:29 | dbwells2 | +2 -0 | 1.16 | src/GridForceGrid.C | Fixed memory leak. |
| 2011/11/12 01:08:07 | dbwells2 | +4 -4 | 1.1371 | src/SimParameters.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:07 | dbwells2 | +1 -0 | 1.33 | src/ScriptTcl.h | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:07 | dbwells2 | +30 -0 | 1.74 | src/ScriptTcl.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:07 | dbwells2 | +3 -0 | 1.1045 | src/Node.h | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:07 | dbwells2 | +2 -0 | 1.1030 | src/Node.ci | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +47 -0 | 1.1120 | src/Node.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +5 -1 | 1.1107 | src/Molecule.h | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +3 -0 | 1.3 | src/MGridforceParams.h | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +21 -0 | 1.3 | src/MGridforceParams.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +6 -1 | 1.11 | src/GridForceGrid.h | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +91 -22 | 1.15 | src/GridForceGrid.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/12 01:08:06 | dbwells2 | +13 -2 | 1.20 | src/ComputeGridForce.C | Added 'reloadGridforceGrid' Tcl command. |
| 2011/11/06 23:02:27 | jim | +15 -7 | 1.1034 | src/CollectionMaster.h | Allocate output array to full size immediately. |
| 2011/11/06 23:02:27 | jim | +3 -3 | 1.1047 | src/CollectionMaster.C | Allocate output array to full size immediately. |
| 2011/11/06 21:55:45 | jim | +2 -3 | 1.1272 | src/Controller.C | Remove extra timer call. |
| 2011/11/06 21:33:30 | jim | +4 -3 | 1.56 | src/ComputeNonbondedCUDA.C | Don't make CUDA timer calls unless they will be used, as they appear tooccasionally take significant time to return. |
| 2011/11/03 22:22:32 | jim | +7 -2 | 1.20 | src/memusage.C | Use resident set size from /proc/self/stat for CUDA builds. |
| 2011/10/25 20:46:30 | jim | +6 -1 | 1.1058 | src/common.h | Use __tanint PowerPC intrinsic for safe rounding without redefining floor. |
| 2011/10/25 20:46:30 | jim | +25 -23 | 1.1034 | src/Lattice.h | Use __tanint PowerPC intrinsic for safe rounding without redefining floor. |
| 2011/10/20 19:50:10 | jim | +2 -0 | 1.1007 | src/Communicate.h | Add flow control to streaming messages in startup phase 1. |
| 2011/10/20 19:50:10 | jim | +39 -7 | 1.1014 | src/Communicate.C | Add flow control to streaming messages in startup phase 1. |
| 2011/10/19 20:18:31 | jim | +12 -0 | 1.1053 | src/Parameters.C | Ignore new ATOMS section in CHARMM parameter files. |
| 2011/10/13 19:34:22 | bohm | +11 -8 | 1.1370 | src/SimParameters.C | Use FFTW_MALLOC to ensure proper alignment for SIMD FFTW3 |
| 2011/10/13 19:34:22 | bohm | +7 -5 | 1.144 | src/ComputePme.C | Use FFTW_MALLOC to ensure proper alignment for SIMD FFTW3 |
| 2011/10/11 21:02:27 | bohm | None | 1.1 | arch/CRAY-XT.fftw3 | fftw3 config for XT5 (jaguar) |
| 2011/10/10 02:26:38 | gzheng | +2 -2 | 1.1059 | src/ProxyPatch.C | fix persistent communication |
| 2011/10/10 02:26:38 | gzheng | +5 -1 | 1.1195 | src/HomePatch.C | fix persistent communication |
| 2011/09/30 15:03:03 | jim | +1 -1 | 1.16 | src/colvar.C | sqrt() -> std::sqrt() |
| 2011/09/30 14:36:34 | jim | +1 -0 | 1.8 | src/colvarproxy.h | Fix missing return statement warning. |
| 2011/09/30 14:28:15 | jim | +8 -0 | 1.7 | src/colvarproxy_namd.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +12 -11 | 1.11 | src/colvarproxy_namd.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +9 -0 | 1.7 | src/colvarproxy.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +28 -4 | 1.10 | src/colvarmodule.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +7 -5 | 1.13 | src/colvarmodule.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +217 -161 | 1.6 | src/colvargrid.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +0 -2 | 1.2 | src/colvargrid.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +1 -1 | 1.10 | src/colvarcomp_rotations.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:15 | jim | +2 -171 | 1.5 | src/colvarcomp_protein.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +90 -12 | 1.7 | src/colvarcomp_distances.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +6 -0 | 1.6 | src/colvarcomp_coordnums.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +17 -8 | 1.8 | src/colvarcomp_angles.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +5 -1 | 1.13 | src/colvarcomp.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +78 -102 | 1.6 | src/colvarbias_meta.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +896 -445 | 1.8 | src/colvarbias_meta.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +19 -5 | 1.11 | src/colvarbias_abf.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +9 -2 | 1.6 | src/colvarbias.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +12 -6 | 1.8 | src/colvarbias.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +3 -3 | 1.5 | src/colvaratoms.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:14 | jim | +12 -16 | 1.10 | src/colvaratoms.C | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:13 | jim | +7 -4 | 1.10 | src/colvar.h | Colvar update from Jerome Henin. |
| 2011/09/30 14:28:13 | jim | +29 -11 | 1.15 | src/colvar.C | Colvar update from Jerome Henin. |
| 2011/09/29 15:10:00 | char | +1 -1 | 1.9 | src/colvaratoms.C | bug fix to alpha colvar |
| 2011/09/28 22:17:37 | dhardy | +199 -3 | 1.15 | ug/ug_forcefield.tex | added Drude model to user guide, with references in bib file |
| 2011/09/28 22:17:37 | dhardy | +96 -2 | 1.18 | ug/ug.bib | added Drude model to user guide, with references in bib file |
| 2011/09/28 16:41:11 | jim | +45 -3 | 1.55 | src/ComputeNonbondedCUDA.C | Add Projections user events to trace GPU execution. |
| 2011/09/27 19:44:22 | jim | +1 -1 | 1.1104 | src/ComputeNonbondedUtil.C | Fix missing type. |
| 2011/09/23 22:52:45 | char | +4 -4 | 1.1369 | src/SimParameters.C | fixed typo (alchOn -> alchFepOn) |
| 2011/09/23 22:51:56 | char | +1 -1 | 1.30 | ug/ug_alchemy.tex | fixed typo (alchOn -> alch) |
| 2011/09/23 20:34:24 | jim | +12 -16 | 1.54 | src/ComputeNonbondedCUDA.C | Replace CcdCallOnCondition with CcdCallFnAfter to get 0.1ms polling latency. |
| 2011/09/22 21:34:29 | jim | +20 -0 | 1.1103 | src/ComputeNonbondedUtil.C | Use proper Coulomb switching for MARTINI force field. |
| 2011/09/07 20:44:46 | bohm | +4 -1 | 1.1057 | src/PatchMap.C | fix allocation problem for fftw3 plans in slab case |
| 2011/09/07 20:44:45 | bohm | +9 -6 | 1.143 | src/ComputePme.C | fix allocation problem for fftw3 plans in slab case |
| 2011/08/31 02:58:48 | jim | +1 -2 | 1.53 | src/ComputeNonbondedCUDA.C | Move cuda_init into constructor to avoid "setting the device when a process is active is not allowed" errors. |
| 2011/08/30 14:54:24 | jim | +6 -5 | 1.1228 | src/WorkDistrib.C | Treat all work and patches on same node (process) as GPU as lower-priority"local" work. This allows smp to be used without reducing the amount ofwork in the second CUDA grid. +mergegrids can still be used to mergethe two grids into one for maximum GPU usage without network overlap. |
| 2011/08/30 14:54:24 | jim | +3 -1 | 1.9 | src/ComputeNonbondedCUDA.h | Treat all work and patches on same node (process) as GPU as lower-priority"local" work. This allows smp to be used without reducing the amount ofwork in the second CUDA grid. +mergegrids can still be used to mergethe two grids into one for maximum GPU usage without network overlap. |
| 2011/08/30 14:54:24 | jim | +33 -19 | 1.52 | src/ComputeNonbondedCUDA.C | Treat all work and patches on same node (process) as GPU as lower-priority"local" work. This allows smp to be used without reducing the amount ofwork in the second CUDA grid. +mergegrids can still be used to mergethe two grids into one for maximum GPU usage without network overlap. |
| 2011/08/30 14:54:24 | jim | +1 -1 | 1.1038 | src/ComputeMgr.h | Treat all work and patches on same node (process) as GPU as lower-priority"local" work. This allows smp to be used without reducing the amount ofwork in the second CUDA grid. +mergegrids can still be used to mergethe two grids into one for maximum GPU usage without network overlap. |
| 2011/08/30 14:54:24 | jim | +3 -2 | 1.1107 | src/ComputeMgr.C | Treat all work and patches on same node (process) as GPU as lower-priority"local" work. This allows smp to be used without reducing the amount ofwork in the second CUDA grid. +mergegrids can still be used to mergethe two grids into one for maximum GPU usage without network overlap. |
| 2011/08/29 20:37:04 | jim | +2 -0 | 1.8 | src/ComputeNonbondedCUDA.h | Add +mergegrids option to treat all patches/computes as remote and onlysubmit a single grid to the GPU. Should help when few local patches. |
| 2011/08/29 20:37:04 | jim | +19 -22 | 1.51 | src/ComputeNonbondedCUDA.C | Add +mergegrids option to treat all patches/computes as remote and onlysubmit a single grid to the GPU. Should help when few local patches. |
| 2011/08/28 22:46:55 | jim | +3 -0 | 1.1038 | src/PatchMap.h | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/28 22:46:55 | jim | +17 -1 | 1.7 | src/ComputeNonbondedCUDA.h | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/28 22:46:55 | jim | +234 -38 | 1.50 | src/ComputeNonbondedCUDA.C | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/28 22:46:55 | jim | +6 -0 | 1.1037 | src/ComputeMgr.h | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/28 22:46:55 | jim | +4 -0 | 1.1018 | src/ComputeMgr.ci | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/28 22:46:54 | jim | +54 -0 | 1.1106 | src/ComputeMgr.C | Optimize CUDA for smp/multicore builds by using shared memory to distributeGPU-related proxy communication load across cores in the same processsharing the same GPU. Not optimized for multiple GPUs per process. |
| 2011/08/27 15:51:17 | jim | +2 -2 | 1.1102 | src/ComputeNonbondedUtil.C | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:16 | jim | +42 -37 | 1.26 | src/ComputeNonbondedCUDAKernel.cu | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:16 | jim | +63 -48 | 1.49 | src/ComputeNonbondedCUDA.C | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:16 | jim | +2 -0 | 1.1036 | src/ComputeMgr.h | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:15 | jim | +1 -0 | 1.1017 | src/ComputeMgr.ci | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:15 | jim | +19 -0 | 1.1105 | src/ComputeMgr.C | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:51:14 | jim | +1 -1 | 1.53 | src/BackEnd.C | Make CUDA compatible with smp and multicore builds. |
| 2011/08/27 15:50:02 | jim | +1 -1 | 1.4 | arch/Win64.cuda | Pass -DWIN32 -DWIN64 to nvcc. |
| 2011/08/26 01:40:55 | jim | +1 -0 | 1.48 | src/ComputeNonbondedCUDA.C | Don't try to build tables if you don't control the GPU. |
| 2011/08/26 01:17:50 | jim | +5 -9 | 1.47 | src/ComputeNonbondedCUDA.C | Fix GPU-sharing code. |
| 2011/08/23 20:26:28 | jim | +12 -2 | 1.46 | src/ComputeNonbondedCUDA.C | Use bit-reversal ordering to avoid placing PME and GPU on same pe. |
| 2011/08/22 23:09:51 | jim | +5 -0 | 1.1090 | src/ProxyMgr.C | Don't create proxies based on nonbonded computes in compute map inCUDA builds since those computes aren't created and the CUDA workis moved to another PE on the same physical node. |
| 2011/08/19 21:57:36 | jim | +2 -2 | 1.2 | src/SortAtoms.h | Move atom sorting for gpu to HomePatch to avoid duplicate work. |
| 2011/08/19 21:57:36 | jim | +7 -7 | 1.3 | src/SortAtoms.C | Move atom sorting for gpu to HomePatch to avoid duplicate work. |
| 2011/08/19 21:57:35 | jim | +3 -0 | 1.1048 | src/NamdTypes.h | Move atom sorting for gpu to HomePatch to avoid duplicate work. |
| 2011/08/19 21:57:35 | jim | +34 -0 | 1.1194 | src/HomePatch.C | Move atom sorting for gpu to HomePatch to avoid duplicate work. |
| 2011/08/19 21:57:35 | jim | +8 -6 | 1.45 | src/ComputeNonbondedCUDA.C | Move atom sorting for gpu to HomePatch to avoid duplicate work. |
| 2011/08/19 19:36:09 | jim | +4 -0 | 1.6 | src/ComputeNonbondedCUDA.h | Only one pe drives each gpu unless it is repeated in +devices argument. |
| 2011/08/19 19:36:09 | jim | +36 -10 | 1.44 | src/ComputeNonbondedCUDA.C | Only one pe drives each gpu unless it is repeated in +devices argument. |
| 2011/08/19 19:36:09 | jim | +19 -0 | 1.1104 | src/ComputeMgr.C | Only one pe drives each gpu unless it is repeated in +devices argument. |
| 2011/08/19 16:19:38 | jim | +8 -0 | 1.1103 | src/ComputeMgr.C | Don't create nonbonded compute objects in CUDA build. |
| 2011/08/19 15:56:15 | jim | +6 -1 | 1.3 | src/ComputeNonbondedCUDAKernelBase.h | Fix CUDA energy calculation when fixed atoms are present. |
| 2011/08/19 15:56:15 | jim | +2 -2 | 1.16 | src/ComputeNonbondedCUDAKernel.h | Fix CUDA energy calculation when fixed atoms are present. |
| 2011/08/19 15:56:14 | jim | +1 -0 | 1.43 | src/ComputeNonbondedCUDA.C | Fix CUDA energy calculation when fixed atoms are present. |
| 2011/08/19 07:06:21 | jim | +4 -4 | 1.1271 | src/Controller.C | Add energy evaluation on GPU. |
| 2011/08/19 07:06:21 | jim | +4 -7 | 1.1051 | src/ComputeNonbondedSelf.C | Add energy evaluation on GPU. |
| 2011/08/19 07:06:21 | jim | +4 -7 | 1.1058 | src/ComputeNonbondedPair.C | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +78 -19 | 1.2 | src/ComputeNonbondedCUDAKernelBase.h | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +2 -2 | 1.15 | src/ComputeNonbondedCUDAKernel.h | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +23 -3 | 1.25 | src/ComputeNonbondedCUDAKernel.cu | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +1 -1 | 1.6 | src/ComputeNonbondedCUDAExcl.h | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +32 -5 | 1.11 | src/ComputeNonbondedCUDAExcl.C | Add energy evaluation on GPU. |
| 2011/08/19 07:06:20 | jim | +41 -7 | 1.42 | src/ComputeNonbondedCUDA.C | Add energy evaluation on GPU. |
| 2011/08/19 07:05:35 | jim | +1 -0 | 1.1304 | Makefile | Include new file ComputeNonbondedCUDAKernelBase.h as dependency forComputeNonbondedCUDAKernel.o. |
| 2011/08/19 02:58:57 | jim | None | 1.1 | src/ComputeNonbondedCUDAKernelBase.h | Move kernels to ComputeNonbondedCUDAKernelBase.h and specialize viapreprocessor macros and repeated includes. |
| 2011/08/19 02:58:57 | jim | +52 -508 | 1.24 | src/ComputeNonbondedCUDAKernel.cu | Move kernels to ComputeNonbondedCUDAKernelBase.h and specialize viapreprocessor macros and repeated includes. |
| 2011/08/16 21:24:59 | dhardy | +8 -2 | 1.1303 | Makefile | build parallel MSM using Charm MSA module |
| 2011/08/16 21:24:59 | dhardy | +65 -0 | 1.146 | Make.depends | build parallel MSM using Charm MSA module |
| 2011/08/16 21:23:45 | dhardy | +1 -0 | 1.1024 | src/main.ci | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:45 | dhardy | +1 -0 | 1.1070 | src/main.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:45 | dhardy | +8 -3 | 1.1227 | src/WorkDistrib.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:45 | dhardy | None | 1.1 | src/ComputeMsmMgr.ci | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:45 | dhardy | None | 1.1 | src/ComputeMsm.h | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:45 | dhardy | None | 1.1 | src/ComputeMsm.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +6 -3 | 1.1195 | src/SimParameters.h | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +15 -4 | 1.1368 | src/SimParameters.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +1 -0 | 1.1058 | src/ProxyPatch.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +1 -0 | 1.1040 | src/PatchMgr.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +20 -0 | 1.1119 | src/Node.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +73 -63 | 1.2 | src/MsmMacros.h | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:44 | dhardy | +8 -0 | 1.1102 | src/ComputeMgr.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:43 | dhardy | +1 -0 | 1.1050 | src/ComputeMap.h | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:43 | dhardy | +6 -0 | 1.52 | src/BackEnd.C | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:23:43 | dhardy | +1 -0 | 1.1020 | src/BOCgroup.h | Parallel MSM using Charm MSA for long-range part. |
| 2011/08/16 21:19:42 | dhardy | None | 1.1 | src/MsmTouch.txt | Notes on how to build parallel MSM with MSA and list of files that needto be touched before recompiling NAMD. |
| 2011/08/16 21:19:42 | dhardy | None | 1.1 | src/MsmNotes.txt | Notes on how to build parallel MSM with MSA and list of files that needto be touched before recompiling NAMD. |
| 2011/08/16 16:27:20 | jim | +1 -4 | 1.51 | src/BackEnd.C | ComputePmeMgr group is created during startup, don't need to do it here. |
| 2011/08/14 18:37:30 | jim | +8 -0 | 1.2 | src/msm_defn.h | Fix missing strcasecmp() on Windows. |
| 2011/08/14 14:18:22 | dhardy | +1 -1 | 1.1302 | Makefile | had to take out msa module, not yet included in Jim's charm++ builds |
| 2011/08/14 13:49:14 | dhardy | None | 1.1 | src/wkfutils.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:14 | dhardy | None | 1.1 | src/wkfutils.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:14 | dhardy | None | 1.1 | src/msm_shortrng_sprec.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:14 | dhardy | None | 1.1 | src/msm_shortrng.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm_setup.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm_longrng_sprec.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm_longrng.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm_defn.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | None | 1.1 | src/msm.c | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:13 | dhardy | +1 -0 | 1.1023 | src/main.ci | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:12 | dhardy | +28 -8 | 1.1226 | src/WorkDistrib.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:12 | dhardy | +11 -3 | 1.1194 | src/SimParameters.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:12 | dhardy | +44 -4 | 1.1367 | src/SimParameters.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | +19 -1 | 1.1015 | src/PDB.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | +64 -5 | 1.1026 | src/PDB.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | None | 1.1 | src/MsmMacros.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | +11 -1 | 1.1101 | src/ComputeNonbondedUtil.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | None | 1.1 | src/ComputeMsmSerialMgr.ci | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | None | 1.1 | src/ComputeMsmSerial.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | None | 1.1 | src/ComputeMsmSerial.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:11 | dhardy | +6 -0 | 1.1101 | src/ComputeMgr.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:10 | dhardy | +1 -0 | 1.1049 | src/ComputeMap.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:10 | dhardy | +1 -0 | 1.50 | src/BackEnd.C | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:49:10 | dhardy | +1 -0 | 1.1019 | src/BOCgroup.h | Initial version of MSM having parallel nonbonded short-range evaluationand serial long-range grid solver. Long-range part is computed throughComputeMsmSerial* that imitates design of ComputeExt*.The serial part includes NAMD-Lite msm* files and VMD timers.Also modified PDB interface to find and get the extreme coordinatesof the space domain. This will be needed for fully parallel MSM. |
| 2011/08/14 13:38:43 | dhardy | +14 -1 | 1.1301 | Makefile | Building serial version of MSM long-range calculation. |
| 2011/08/14 13:38:43 | dhardy | +113 -1 | 1.145 | Make.depends | Building serial version of MSM long-range calculation. |
| 2011/08/11 15:13:28 | jim | +17 -18 | 1.2 | src/SortAtoms.C | Use std::nth_element instead of std::sort for recursive spatial bisection. |
| 2011/08/09 17:56:26 | bohm | +6 -3 | 1.1366 | src/SimParameters.C | Fix bug in fftw3 Y pencil backward FFT.Use slightly different filename for FFTW3 Wisdom. |
| 2011/08/09 17:56:26 | bohm | +55 -6 | 1.142 | src/ComputePme.C | Fix bug in fftw3 Y pencil backward FFT.Use slightly different filename for FFTW3 Wisdom. |
| 2011/08/02 20:02:19 | dhardy | +1 -1 | 1.1230 | src/Molecule.C | Fixed bug: create support arrays for Thole and aniso needed for Drudesimulation even when not reading in a "correct" PSF. |
| 2011/07/26 16:55:54 | jim | +1 -1 | 1.4 | arch/CRAY-XT-pgcc.arch | Also add -DNO_GETPWUID to fix DCD file writing crashes on Cray XE6. |
| 2011/07/26 16:55:54 | jim | +1 -1 | 1.7 | arch/CRAY-XT-g++.arch | Also add -DNO_GETPWUID to fix DCD file writing crashes on Cray XE6. |
| 2011/07/22 19:32:45 | jim | +1 -1 | 1.3 | arch/CRAY-XT-pgcc.arch | Add back -DNOHOSTNAME to avoid XE6 issue. |
| 2011/07/22 19:32:44 | jim | +1 -1 | 1.6 | arch/CRAY-XT-g++.arch | Add back -DNOHOSTNAME to avoid XE6 issue. |
| 2011/07/19 22:39:49 | jim | +6 -4 | 1.1270 | src/Controller.C | Maintain TOTAL3 across run commands. |
| 2011/07/19 22:25:19 | jim | +1 -0 | 1.1069 | src/Controller.h | Maintain TOTAL3 across CHECKPOINT/REVERT. |
| 2011/07/19 22:25:18 | jim | +5 -3 | 1.1269 | src/Controller.C | Maintain TOTAL3 across CHECKPOINT/REVERT. |
| 2011/07/19 22:07:03 | jim | +2 -0 | 1.1193 | src/HomePatch.C | Clear atom map when loading new coordinates from file. |
| 2011/07/19 21:08:30 | jim | +1 -0 | 1.1033 | src/CollectionMaster.h | Limit position/velocity/force output timings. |
| 2011/07/19 21:08:30 | jim | +26 -6 | 1.1046 | src/CollectionMaster.C | Limit position/velocity/force output timings. |
| 2011/07/19 19:52:40 | jim | +9 -3 | 1.1056 | src/PatchMap.C | Handle very large cutoffs for non-periodic systems better by generatingup to 3x3x3 patch grid using 2-away in all dimensions. Since all patchesinteract patch dimensions can be based on initial coordinates rather thanon the cutoff distance. |
| 2011/07/19 19:52:40 | jim | +1 -1 | 1.1077 | src/HomePatch.h | Handle very large cutoffs for non-periodic systems better by generatingup to 3x3x3 patch grid using 2-away in all dimensions. Since all patchesinteract patch dimensions can be based on initial coordinates rather thanon the cutoff distance. |
| 2011/07/19 19:52:40 | jim | +48 -12 | 1.1192 | src/HomePatch.C | Handle very large cutoffs for non-periodic systems better by generatingup to 3x3x3 patch grid using 2-away in all dimensions. Since all patchesinteract patch dimensions can be based on initial coordinates rather thanon the cutoff distance. |
| 2011/07/18 20:33:43 | jim | +3 -3 | 1.1059 | src/ComputeHomeTuples.h | Do not die if patch needed for tuple is missing. Print a warning, skipthe tuple, and let the checksum code catch it so that the error can beignored during minimization. |
| 2011/07/13 18:00:50 | bohm | +0 -4 | 1.141 | src/ComputePme.C | remove stray prints from slab case |
| 2011/07/12 20:48:15 | jim | +1 -1 | 1.140 | src/ComputePme.C | Eliminate "myGrid values" debugging output. |
| 2011/07/12 18:23:11 | bohm | +12 -0 | 1.3 | src/fftlib.h | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:11 | bohm | +85 -2 | 1.4 | src/fftlib.C | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:10 | bohm | +5 -4 | 1.1193 | src/SimParameters.h | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:10 | bohm | +112 -10 | 1.1365 | src/SimParameters.C | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:10 | bohm | +4 -0 | 1.11 | src/OptPme.C | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:10 | bohm | +273 -13 | 1.139 | src/ComputePme.C | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:09 | bohm | None | 1.1 | arch/Linux-x86_64.fftw3 | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:09 | bohm | +4 -4 | 1.4 | arch/Linux-x86_64-g++.arch | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/07/12 18:23:08 | bohm | +11 -2 | 1.74 | config | Add support for building against FFTW-3.2 instead of FFTW-2.1.5 |
| 2011/06/21 14:21:36 | jim | +1 -1 | 1.3 | arch/Win64.cuda | Update dll version to final CUDA 4.0 release. |
| 2011/06/19 20:45:58 | jim | +1 -1 | 1.12 | arch/Win32.tcl | Copy dll from bin rather than lib directory. |
| 2011/06/19 20:15:47 | jim | +3 -3 | 1.2 | arch/Win64.tcl | Use new thread-safe Tcl libs. |
| 2011/06/19 20:15:47 | jim | +3 -3 | 1.11 | arch/Win32.tcl | Use new thread-safe Tcl libs. |
| 2011/06/17 21:55:09 | jim | +10 -0 | 1.73 | config | Look for ./tcl-threaded or ~/tcl-threaded first for smp or multicore builds |
| 2011/06/17 20:38:44 | jim | +2 -2 | 1.2 | arch/Solaris-x86_64.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +2 -2 | 1.3 | arch/MacOSX-x86_64.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +2 -2 | 1.2 | arch/MacOSX-x86.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +2 -2 | 1.7 | arch/MacOSX-PPC.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +4 -2 | 1.3 | arch/Linux-x86_64.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +2 -2 | 1.2 | arch/Linux-x86.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 20:38:43 | jim | +1 -1 | 1.3 | arch/CRAY-XT.tcl | Update to Tcl 8.5.9 with threads enabled. |
| 2011/06/17 19:03:55 | jim | +1 -1 | 1.3 | arch/MacOSX-x86-g++.arch | Remove flag for missing sse instruction that is now generally available. |
| 2011/06/16 19:17:23 | jim | +18 -6 | 1.1229 | src/Molecule.C | Modify extraBonds to allow sinusoidal dihedrals and impropers. |
| 2011/06/16 19:17:20 | jim | +12 -4 | 1.14 | ug/ug_forcefield.tex | Modify extraBonds to allow sinusoidal dihedrals and impropers. |
| 2011/06/15 03:30:56 | chaomei2 | +14 -0 | 1.19 | src/memusage.C | updated the memory usage report on BG/P according to the method mentioned on the BG/P wiki page at ANL. |
| 2011/06/11 21:42:04 | jim | +7 -4 | 1.1192 | src/SimParameters.h | Prevent trying to run tclBC with non-threaded Tcl library on multiplethreads per process. |
| 2011/06/11 21:42:04 | jim | +5 -0 | 1.73 | src/ScriptTcl.C | Prevent trying to run tclBC with non-threaded Tcl library on multiplethreads per process. |
| 2011/06/11 21:42:04 | jim | +4 -0 | 1.8 | src/ComputeTclBC.C | Prevent trying to run tclBC with non-threaded Tcl library on multiplethreads per process. |
| 2011/06/10 21:20:30 | jim | +1 -1 | 1.5 | arch/Win64-MSVC.arch | Fix Win64 CUDA autobuild. |
| 2011/05/28 16:07:53 | jim | +1 -1 | 1.46 | announce.txt | Move release date to May 31. |
| 2011/05/28 15:46:14 | jim | +2 -6 | 1.44 | src/dcdlib.C | Eliminate O_EXCL and O_TRUNC flags and use O_WRONLY on parallel slave open. |
| 2011/05/28 15:45:06 | jim | +1 -1 | 1.5 | arch/CRAY-XT-g++.arch | Eliminate defines for features that were missing from Catamount on XT3. |
| 2011/05/27 21:28:04 | johanstr | +16 -5 | 1.1364 | src/SimParameters.C | Added correct checks for required adaptive tempering parameters if adaptTempMD is on |
| 2011/05/27 21:27:10 | johanstr | +113 -0 | 1.12 | ug/ug_accel.tex | Added entry for adaptive tempering to accelerated sampling methods |
| 2011/05/27 07:22:07 | chaomei2 | +2 -0 | 1.10 | src/dcdlib.h | Fixed the issue of using SEEK_END for parallel IO on slave procs that the filesize updated on master proc may not be available on slave procs when such infois needed. Using SEEK_CUR instead is the appropriate approach. |
| 2011/05/27 07:22:07 | chaomei2 | +16 -0 | 1.43 | src/dcdlib.C | Fixed the issue of using SEEK_END for parallel IO on slave procs that the filesize updated on master proc may not be available on slave procs when such infois needed. Using SEEK_CUR instead is the appropriate approach. |
| 2011/05/27 07:22:07 | chaomei2 | +45 -6 | 1.67 | src/Output.C | Fixed the issue of using SEEK_END for parallel IO on slave procs that the filesize updated on master proc may not be available on slave procs when such infois needed. Using SEEK_CUR instead is the appropriate approach. |