| Time | Author | Lines | Revision | Filename | Comments |
| 2009/11/24 04:27:00 | bhatele | +2 -2 | 1.2 | arch/MacOSX-x86_64-g++.arch | compilation fixes for Mac |
| 2009/11/24 04:26:59 | bhatele | +5 -5 | 1.1177 | src/Molecule.C | compilation fixes for Mac |
| 2009/11/20 22:25:06 | brunner | +3 -3 | 1.1055 | src/common.h | Replaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers |
| 2009/11/20 22:25:05 | brunner | +25 -25 | 1.1045 | src/Parameters.C | Replaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers |
| 2009/11/20 22:25:05 | brunner | +3 -3 | 1.36 | src/ComputeNonbondedBase2.h | Replaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers |
| 2009/11/17 21:11:11 | jim | +7 -7 | 1.56 | config | fix missing quotes needed to handle options that are quoted lists |
| 2009/11/13 04:50:03 | jim | +89 -0 | 1.15 | ug/ug_runit.tex | Updated from 2.7b2 notes.txt |
| 2009/11/13 03:52:07 | jim | +4 -0 | 1.1054 | src/common.h | Fix win32 build via #define nearbyint(X) floor((X)+0.5) |
| 2009/11/13 02:54:55 | jim | +8 -8 | 1.17 | src/memusage.C | Fix windows build. |
| 2009/11/13 00:02:29 | bhatele | +3 -3 | 1.85 | src/Rebalancer.C | the new xlC compiler was complaining on using abs for double |
| 2009/11/12 23:01:01 | jim | +1 -1 | 1.12 | arch/AIX-POWER-xlC.arch | update to net-aix-ppc |
| 2009/11/12 22:51:36 | jim | +4 -4 | 1.55 | config | Look for charm-6.1.3 instead of charm-6.1 |
| 2009/11/12 22:33:43 | jim | +81 -0 | 1.70 | notes.txt | update for 2.7b2 release |
| 2009/11/12 22:33:43 | jim | +6 -0 | 1.35 | announce.txt | update for 2.7b2 release |
| 2009/11/12 20:28:16 | char | +5 -3 | 1.1294 | src/SimParameters.C | added TIP4P usage instructions to userguide and error checking for the user input: waterModel tip3 |
| 2009/11/12 20:27:51 | char | +17 -0 | 1.5 | ug/ug_forcefield.tex | added TIP4P usage instructions to userguide and error checking for the user input: waterModel tip3 |
| 2009/11/12 03:28:21 | jim | +13 -4 | 1.21 | src/ComputeNonbondedCUDA.C | Disable token-passing but don't submit local until remote finishedif shared_gpu is true, otherwise submit all work immediately. |
| 2009/11/12 02:11:16 | jim | +4 -0 | 1.1044 | src/Parameters.C | Fix memopt builds. |
| 2009/11/12 02:11:16 | jim | +4 -0 | 1.1176 | src/Molecule.C | Fix memopt builds. |
| 2009/11/12 01:54:28 | jim | +1 -1 | 1.7 | src/ComputeNonbondedCUDAKernel.cu | Clean up CUDA output. |
| 2009/11/12 01:54:28 | jim | +8 -4 | 1.20 | src/ComputeNonbondedCUDA.C | Clean up CUDA output. |
| 2009/11/12 01:54:06 | jim | +20 -3 | 1.1241 | src/Controller.C | Warn about bad pressure tensor and expensive energy evaluation with CUDA. |
| 2009/11/11 23:23:59 | jim | +3 -2 | 1.19 | src/ComputeNonbondedCUDA.C | remove old code to avoid device 0 (used to be display), add new codeto avoid weak devices with 2 or fewer multiprocessors. |
| 2009/11/11 20:36:45 | jim | +7 -4 | 1.1158 | src/SimParameters.h | New parameter outputCudaTiming, similar to outputTiming, to controlCUDA timing output (which can be verbose since it is printed byevery processor). |
| 2009/11/11 20:36:45 | jim | +15 -4 | 1.1293 | src/SimParameters.C | New parameter outputCudaTiming, similar to outputTiming, to controlCUDA timing output (which can be verbose since it is printed byevery processor). |
| 2009/11/11 20:36:44 | jim | +2 -2 | 1.18 | src/ComputeNonbondedCUDA.C | New parameter outputCudaTiming, similar to outputTiming, to controlCUDA timing output (which can be verbose since it is printed byevery processor). |
| 2009/11/11 20:11:52 | jim | +7 -0 | 1.54 | config | make config script work with CUDA 3.x |
| 2009/11/11 05:19:04 | jim | +1 -2 | 1.4 | arch/Linux-x86_64.cuda | Workaround to support both CUDA 2.2 and 2.3 (which adds lib64 directory)without modifying arch/Linux-x86_64.cuda |
| 2009/11/11 05:19:01 | jim | +5 -1 | 1.1261 | Makefile | Workaround to support both CUDA 2.2 and 2.3 (which adds lib64 directory)without modifying arch/Linux-x86_64.cuda |
| 2009/11/11 05:01:53 | jim | +1 -1 | 1.47 | ug/Makefile | update versions to 2.7b1 and charm-6.1.3 |
| 2009/11/11 05:01:47 | jim | +9 -9 | 1.69 | notes.txt | update versions to 2.7b1 and charm-6.1.3 |
| 2009/11/11 05:01:47 | jim | +3 -3 | 1.34 | announce.txt | update versions to 2.7b1 and charm-6.1.3 |
| 2009/11/11 05:01:47 | jim | +1 -1 | 1.1260 | Makefile | update versions to 2.7b1 and charm-6.1.3 |
| 2009/11/11 04:46:22 | jim | +2 -1 | 1.3 | arch/Linux-x86_64.cuda | Make that libcudart.so.2 and also copy it to build directory. |
| 2009/11/11 04:46:20 | jim | +4 -1 | 1.1259 | Makefile | Make that libcudart.so.2 and also copy it to build directory. |
| 2009/11/11 04:18:38 | jim | +3 -2 | 1.2 | arch/Linux-x86_64.cuda | include libcudart.so in release |
| 2009/11/11 04:18:34 | jim | +1 -1 | 1.1258 | Makefile | include libcudart.so in release |
| 2009/11/11 03:37:53 | jim | +6 -6 | 1.1159 | src/ComputeNonbondedBase.h | Fix performance bug in pairlist generation. |
| 2009/11/11 02:35:45 | jim | +1 -1 | 1.1043 | src/Parameters.C | remove debugging output |
| 2009/11/09 21:12:02 | jim | +1 -0 | 1.1022 | src/ParseOptions.C | Always initialize simulation parameters to default value. |
| 2009/11/06 23:03:04 | jim | +1 -3 | 1.1257 | Makefile | Don't create .cubin file, use -Xptxas -v to get register information instead. |
| 2009/11/06 22:52:51 | jim | +3 -1 | 1.5 | src/ComputeNonbondedCUDAKernel.h | reduce force table size to work on older compute 1.0 and 1.1 devices |
| 2009/11/04 22:40:09 | jim | +5 -10 | 1.1175 | src/Molecule.C | meaningless rearrangement to avoid Mac PPC compiler bug |
| 2009/10/30 17:50:42 | jim | +4 -2 | 1.17 | src/ComputeNonbondedCUDA.C | changed to the new cpu topology API |
| 2009/10/28 21:27:59 | gzheng | +6 -5 | 1.1049 | src/ReductionMgr.C | changed to the new cpu topology API |
| 2009/10/28 01:40:05 | char | +3 -0 | 1.6 | src/colvaratoms.C | colvars dummy atom center of mass bugfix |
| 2009/10/27 22:56:45 | dhardy | +19 -25 | 1.2 | ug/ug_dynamics.tex | fixed the documentation for longSplitting and the new 'c2' option |
| 2009/10/27 22:56:45 | dhardy | +15 -3 | 1.11 | ug/ug.bib | fixed the documentation for longSplitting and the new 'c2' option |
| 2009/10/27 21:50:09 | dhardy | +5 -4 | 1.1157 | src/SimParameters.h | Improved MTS splitting function for electrostatics contributed byBruce Berne, Ruhong Zhou, and Joe Morrone.Use by setting "longSplitting = C2" |
| 2009/10/27 21:50:09 | dhardy | +8 -4 | 1.1292 | src/SimParameters.C | Improved MTS splitting function for electrostatics contributed byBruce Berne, Ruhong Zhou, and Joe Morrone.Use by setting "longSplitting = C2" |
| 2009/10/27 21:50:09 | dhardy | +22 -0 | 1.1094 | src/ComputeNonbondedUtil.C | Improved MTS splitting function for electrostatics contributed byBruce Berne, Ruhong Zhou, and Joe Morrone.Use by setting "longSplitting = C2" |
| 2009/10/27 18:52:28 | brunner | +1 -0 | 1.1256 | Makefile | Added ComputeNonbondedTabPot.[Ch] |
| 2009/10/27 18:52:28 | brunner | +65 -15 | 1.128 | Make.depends | Added ComputeNonbondedTabPot.[Ch] |
| 2009/10/27 18:50:05 | brunner | +11 -2 | 1.1156 | src/SimParameters.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +8 -2 | 1.1291 | src/SimParameters.C | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +41 -0 | 1.1023 | src/Parameters.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +1381 -3 | 1.1042 | src/Parameters.C | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +1 -0 | 1.1010 | src/LJTable.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +11 -0 | 1.1022 | src/LJTable.C | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:04 | brunner | +21 -0 | 1.1067 | src/ComputeNonbondedUtil.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:03 | brunner | +27 -0 | 1.1093 | src/ComputeNonbondedUtil.C | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:03 | brunner | None | 1.1 | src/ComputeNonbondedTabEnergies.C | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:03 | brunner | +161 -10 | 1.35 | src/ComputeNonbondedBase2.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/27 18:50:03 | brunner | +22 -4 | 1.1158 | src/ComputeNonbondedBase.h | Added tabulated potential code from Peter Freddolino. Allows LJ interactionfor selected pairs of atos to be replaced by a potential interpolatedfrom tables read in at start-up |
| 2009/10/09 20:09:05 | bhatele | +5 -5 | 1.1197 | src/WorkDistrib.C | config file parameters and variable names changed for spanning trees |
| 2009/10/09 20:09:05 | bhatele | +9 -9 | 1.1155 | src/SimParameters.h | config file parameters and variable names changed for spanning trees |
| 2009/10/09 20:09:04 | bhatele | +7 -7 | 1.1290 | src/SimParameters.C | config file parameters and variable names changed for spanning trees |
| 2009/10/09 20:09:04 | bhatele | +2 -2 | 1.1096 | src/Node.C | config file parameters and variable names changed for spanning trees |
| 2009/10/09 16:03:02 | gzheng | None | 1.1 | arch/Cygwin-MPI-mingw.arch | build with MS MPI and Mingw |
| 2009/10/09 16:00:51 | gzheng | +3 -3 | 1.43 | src/BackEnd.C | enable mingw |
| 2009/10/08 23:17:32 | jim | +1 -1 | 1.22 | Make.charm | Charm 6.1.3 |
| 2009/10/04 19:12:40 | gzheng | +3 -0 | 1.1067 | src/main.C | print info whether cputopology info is available or not. |
| 2009/10/03 23:56:49 | bhatele | +11 -7 | 1.84 | src/Rebalancer.C | error check and minor fixes |
| 2009/10/02 22:57:04 | bohm | +4 -1 | 1.125 | src/ComputePme.C | cleanup to avoid memory leak in commOnly |
| 2009/09/30 15:19:08 | gzheng | +1 -1 | 1.16 | src/memusage.C | backported new memory stats for windows on 6.1.3, so lower the version checking. |
| 2009/09/30 15:10:06 | gzheng | +6 -0 | 1.15 | src/memusage.C | For windows, call CmiMmemoryUsage to get accurate numbers. |
| 2009/09/30 00:23:58 | gzheng | +4 -0 | 1.1174 | src/Molecule.C | define M_PI when needed |
| 2009/09/29 04:50:09 | gzheng | +2 -1 | 1.2 | src/colvargrid.h | round is not defined in VC++ |
| 2009/09/29 04:41:14 | gzheng | None | 1.1 | arch/Win64.tcl | arch files of fftw and tcl for win64 |
| 2009/09/29 04:41:14 | gzheng | None | 1.1 | arch/Win64.fftw | arch files of fftw and tcl for win64 |
| 2009/09/29 04:38:37 | gzheng | +5 -0 | 1.1022 | src/Parameters.h | define cbrt if it is undefined |
| 2009/09/29 04:35:26 | gzheng | +1 -1 | 1.12 | src/MStream.h | cast size_t in pup length to avoid ambiguity in overloading |
| 2009/09/21 00:36:49 | dhardy | +1 -66 | 1.1173 | src/Molecule.C | removed dead code for Drude exclusions |
| 2009/09/20 22:29:51 | dhardy | +13 -0 | 1.1172 | src/Molecule.C | initialize lphostIndexes to index lphosts array through atomid of the lone pair |
| 2009/09/20 22:05:58 | dhardy | +20 -3 | 1.1087 | src/Molecule.h | Removed earlier incorrect code to extend parent 1-3 exclusions for Drude.Added routine for Drude and lone pair particles to "inherit" the exclusionsof their parents. Works for up to 1-3 exclusions. |
| 2009/09/20 22:05:58 | dhardy | +165 -0 | 1.1171 | src/Molecule.C | Removed earlier incorrect code to extend parent 1-3 exclusions for Drude.Added routine for Drude and lone pair particles to "inherit" the exclusionsof their parents. Works for up to 1-3 exclusions. |
| 2009/09/18 21:55:14 | bhatele | +4 -4 | 1.1289 | src/SimParameters.C | changed the name of config file parameters to be the same as thevariable names to avoid confusion (sendProxySpanningTree -> enableProxySendST) |
| 2009/09/18 21:55:13 | bhatele | +11 -10 | 1.1154 | src/SimParameters.h | changed the name of config file parameters to be the same as thevariable names to avoid confusion (sendProxySpanningTree -> enableProxySendST) |
| 2009/09/17 22:07:01 | dhardy | +5 -4 | 1.1170 | src/Molecule.C | Fixed bug in Drude PSF: read in lone pair hosts first, then later verify thatthe number host sets is the same as the number lone pairs |
| 2009/09/16 23:32:18 | jim | +0 -3 | 1.16 | src/ComputeNonbondedCUDA.C | Remove fflush calls left over from debugging. |
| 2009/09/16 23:04:56 | dhardy | +32 -0 | 1.1018 | src/structures.h | PSF reader for Drude model, fix 1-3 exclusions for Drude particles |
| 2009/09/16 23:04:56 | dhardy | +21 -1 | 1.1086 | src/Molecule.h | PSF reader for Drude model, fix 1-3 exclusions for Drude particles |
| 2009/09/16 23:04:56 | dhardy | +208 -0 | 1.1169 | src/Molecule.C | PSF reader for Drude model, fix 1-3 exclusions for Drude particles |
| 2009/09/08 16:21:39 | jim | +1 -1 | 1.1021 | src/LJTable.C | NFBIX -> NBFIX in CUDA warning |
| 2009/09/03 21:52:25 | brunner | +1 -1 | 1.4 | src/colvarparse.h | Compiler workarounds for Solaris X86_64 |
| 2009/09/03 21:52:25 | brunner | +2 -1 | 1.1168 | src/Molecule.C | Compiler workarounds for Solaris X86_64 |
| 2009/08/31 21:06:01 | brunner | +28 -19 | 1.1048 | src/ReductionMgr.C | Fixed error with node-local reduction code. It works on Abe now. |
| 2009/08/28 20:57:00 | jim | +9 -2 | 1.1288 | src/SimParameters.C | Fixed atoms need forces calculated to get correct pressure from CUDA. |
| 2009/08/27 20:25:10 | jim | +5 -3 | 1.1287 | src/SimParameters.C | Don't remove patches from any pe with CUDA enabled. |
| 2009/08/27 20:15:11 | jim | +38 -3 | 1.1196 | src/WorkDistrib.C | Ensure at least one patch per processor for CUDA-enabled NAMD. |
| 2009/08/27 19:09:38 | jim | +4 -0 | 1.15 | src/ComputeNonbondedCUDA.C | Disable useFlexibleCell with CUDA. |
| 2009/08/27 18:04:40 | jim | +12 -2 | 1.1175 | src/Sequencer.C | additional diagnostics |
| 2009/08/27 18:01:23 | jim | +2 -2 | 1.4 | src/ComputeNonbondedCUDAKernel.h | enable multiple timestepping with CUDA |
| 2009/08/27 18:01:23 | jim | +39 -8 | 1.6 | src/ComputeNonbondedCUDAKernel.cu | enable multiple timestepping with CUDA |
| 2009/08/27 18:01:23 | jim | +2 -1 | 1.3 | src/ComputeNonbondedCUDAExcl.h | enable multiple timestepping with CUDA |
| 2009/08/27 18:01:23 | jim | +47 -16 | 1.6 | src/ComputeNonbondedCUDAExcl.C | enable multiple timestepping with CUDA |
| 2009/08/27 18:01:23 | jim | +43 -18 | 1.14 | src/ComputeNonbondedCUDA.C | enable multiple timestepping with CUDA |
| 2009/08/26 21:04:24 | jim | +2 -2 | 1.5 | src/ComputeNonbondedCUDAExcl.C | Put exclusion forces in the correct array for multiple timestepping. |
| 2009/08/26 19:55:22 | jim | +3 -1 | 1.3 | src/ComputeNonbondedCUDAKernel.h | Increase size of interpolation table to improve force/pressure accuracy. |
| 2009/08/26 19:55:21 | jim | +3 -1 | 1.13 | src/ComputeNonbondedCUDA.C | Increase size of interpolation table to improve force/pressure accuracy. |
| 2009/08/26 19:30:49 | jim | +4 -0 | 1.1020 | src/LJTable.C | Safety check for NBFIX parameters not supported in CUDA version. |
| 2009/08/17 21:28:24 | chaomei2 | +3 -3 | 1.1038 | src/ProxyMgr.h | Disabled the src-level hack for QD with immediate msgs in SMP layer because now the charm++ runtime takes care of the problem. |
| 2009/08/17 21:28:24 | chaomei2 | +10 -10 | 1.1074 | src/ProxyMgr.C | Disabled the src-level hack for QD with immediate msgs in SMP layer because now the charm++ runtime takes care of the problem. |
| 2009/08/17 21:28:24 | chaomei2 | +1 -1 | 1.1164 | src/HomePatch.C | Disabled the src-level hack for QD with immediate msgs in SMP layer because now the charm++ runtime takes care of the problem. |
| 2009/08/14 22:53:03 | char | +309 -197 | 1.2 | lib/abf_integrate/abf_integrate.cpp | update/bugfix for abf_integrate |
| 2009/08/14 22:53:02 | char | +81 -61 | 1.2 | lib/abf_integrate/abf_data.h | update/bugfix for abf_integrate |
| 2009/08/14 22:53:02 | char | +219 -167 | 1.2 | lib/abf_integrate/abf_data.cpp | update/bugfix for abf_integrate |
| 2009/08/13 06:17:55 | chaomei2 | +33 -0 | 1.1037 | src/ProxyMgr.h | Fix the QD in case of using the optimization (using node-aware spanning three and the node-level proxy manager) which takes advantage of immediate messages exectuing on the communication thread in the charm SMP layer. |
| 2009/08/13 06:17:55 | chaomei2 | +70 -1 | 1.1073 | src/ProxyMgr.C | Fix the QD in case of using the optimization (using node-aware spanning three and the node-level proxy manager) which takes advantage of immediate messages exectuing on the communication thread in the charm SMP layer. |
| 2009/08/13 06:17:54 | chaomei2 | +5 -1 | 1.1163 | src/HomePatch.C | Fix the QD in case of using the optimization (using node-aware spanning three and the node-level proxy manager) which takes advantage of immediate messages exectuing on the communication thread in the charm SMP layer. |
| 2009/08/12 22:53:48 | char | +810 -607 | 1.8 | ug/ug_colvars.tex | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +1 -1 | 1.3 | src/colvarvalue.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +1 -0 | 1.2 | src/colvarvalue.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +562 -380 | 1.4 | src/colvartypes.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +4 -14 | 1.3 | src/colvarproxy_namd.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +14 -3 | 1.7 | src/colvarproxy_namd.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +10 -6 | 1.3 | src/colvarproxy.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:48 | char | +35 -27 | 1.3 | src/colvarparse.h | *** empty log message *** |
| 2009/08/12 22:53:48 | char | +1 -2 | 1.2 | src/colvarparse.C | *** empty log message *** |
| 2009/08/12 22:53:48 | char | +9 -18 | 1.4 | src/colvarmodule.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +282 -184 | 1.7 | src/colvarmodule.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | None | 1.1 | src/colvargrid.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | None | 1.1 | src/colvargrid.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +54 -238 | 1.6 | src/colvarcomp_rotations.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +3 -3 | 1.2 | src/colvarcomp_protein.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +551 -60 | 1.2 | src/colvarcomp_distances.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +0 -4 | 1.2 | src/colvarcomp_coordnums.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +11 -8 | 1.2 | src/colvarcomp_angles.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +226 -106 | 1.3 | src/colvarcomp.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +4 -2 | 1.2 | src/colvarcomp.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +61 -73 | 1.4 | src/colvarbias_meta.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +642 -548 | 1.4 | src/colvarbias_meta.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +1 -4 | 1.3 | src/colvarbias_abf.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +1 -5 | 1.5 | src/colvarbias_abf.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +0 -13 | 1.2 | src/colvarbias.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +3 -0 | 1.2 | src/colvaratoms.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:47 | char | +72 -26 | 1.5 | src/colvaratoms.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:46 | char | +80 -796 | 1.4 | src/colvar.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:46 | char | +209 -335 | 1.4 | src/colvar.C | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:46 | char | +1 -0 | 1.1255 | Makefile | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 22:53:46 | char | +9 -0 | 1.127 | Make.depends | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2009/08/12 20:57:23 | jim | +6 -0 | 1.1047 | src/ReductionMgr.C | Make physical node code build with released versions of charm. |
| 2009/08/12 20:45:39 | jim | +10 -7 | 1.1286 | src/SimParameters.C | Be sure that alchFepOn and alchThermIntOn are set to FALSE by default. |
| 2009/08/12 20:40:51 | jim | +4 -3 | 1.1240 | src/Controller.C | Fix trajectory output during initial stages of minimization. |
| 2009/08/07 04:43:04 | jim | +5 -3 | 1.1285 | src/SimParameters.C | Don't remove patches from pe 0 when CUDA is enabled. |
| 2009/08/06 17:23:58 | brunner | +25 -2 | 1.1047 | src/ReductionMgr.h | Reductions now collect data from pes on the same node at the lowest level,to take advantage of faster communication within nodesNo performance affect (good or bad) observed on 16 way, 128 core run onRanger, but perhaps bigger runs will benefit |
| 2009/08/06 17:23:58 | brunner | +162 -5 | 1.1046 | src/ReductionMgr.C | Reductions now collect data from pes on the same node at the lowest level,to take advantage of faster communication within nodesNo performance affect (good or bad) observed on 16 way, 128 core run onRanger, but perhaps bigger runs will benefit |
| 2009/08/06 03:05:14 | petefred | +10 -5 | 1.1162 | src/HomePatch.C | Fix interaction of lone pairs with fixed atoms (previously, lone pair constraints wouldn't be applied if fixed atoms were on) |
| 2009/07/27 21:42:52 | char | +14 -8 | 1.1284 | src/SimParameters.C | Fixed alch/alchFepOn/alchThermIntOn error in which alchemical calculations failed to be turned on. Also fixed alchDecouple issue where if alchOn=FALSE && alchDecouple=TRUE resulted in NAMD_die event. Now this situation issues iout << iWARN to logfile and sets alchDecouple to FALSE |
| 2009/07/24 03:21:38 | brunner | None | 1.1 | src/ComputeGridForceMgr.ci | *** empty log message *** |
| 2009/07/20 20:57:14 | brunner | +106 -21 | 1.126 | Make.depends | Added new GridForce files |
| 2009/07/20 20:55:03 | brunner | +9 -1 | 1.1254 | Makefile | Added ComputeGridForceMgr |
| 2009/07/20 20:51:41 | brunner | +1 -0 | 1.1018 | src/main.ci | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +4 -4 | 1.1195 | src/WorkDistrib.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +1 -0 | 1.1095 | src/Node.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +1 -1 | 1.1085 | src/Molecule.h | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +29 -4 | 1.1167 | src/Molecule.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +264 -4 | 1.8 | src/GridForceGrid.h | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:40 | brunner | +772 -51 | 1.12 | src/GridForceGrid.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:39 | brunner | +1 -1 | 1.1081 | src/ComputeMgr.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:39 | brunner | +101 -4 | 1.2 | src/ComputeGridForce.h | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:39 | brunner | +530 -19 | 1.13 | src/ComputeGridForce.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:39 | brunner | +3 -0 | 1.42 | src/BackEnd.C | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:51:39 | brunner | +2 -0 | 1.1014 | src/BOCgroup.h | This code distributes the GridForce grid data among all nodes to reduce memusage for large grids. The ComputeGridForce works somewhat like the ComputePMEcode now, with 1 object per processor. Also, the force computation issplit-phase like PME, so that its calculate - communicate - finish calculation |
| 2009/07/20 20:40:01 | brunner | +4 -4 | 1.1283 | src/SimParameters.C | Don't check useOptPME unless PMEOn is true. Gets rid of valgrind error |
| 2009/07/13 00:24:34 | petefred | +2 -1 | 1.4 | ug/ug_forcefield.tex | Add a warning about the need for tail corrections to have PBC on |
| 2009/07/13 00:22:31 | petefred | +7 -3 | 1.1282 | src/SimParameters.C | Make sure that we're using pbc if LJcorrection is on |
| 2009/07/13 00:22:30 | petefred | +5 -5 | 1.1239 | src/Controller.C | Make sure that we're using pbc if LJcorrection is on |
| 2009/07/08 14:57:32 | char | +9 -5 | 1.1281 | src/SimParameters.C | fixed minor bug in alchemical module faulting initialization of alchFepOn & alchThermIntOn. |
| 2009/07/01 22:08:55 | dbwells2 | +7 -1 | 1.7 | src/GridForceGrid.h | Updated gridforce code to make sure that the grids provided don'tintersect the edge of the periodic cell (centered on the grid center.)If such an overlap occurs, the force applied isn't guaranteed to besmooth in time. The check occurs every time step (on one node only), sothis should also make gridforce fully NPT-safe. |
| 2009/07/01 22:08:55 | dbwells2 | +1 -1 | 1.11 | src/GridForceGrid.C | Updated gridforce code to make sure that the grids provided don'tintersect the edge of the periodic cell (centered on the grid center.)If such an overlap occurs, the force applied isn't guaranteed to besmooth in time. The check occurs every time step (on one node only), sothis should also make gridforce fully NPT-safe. |
| 2009/07/01 22:08:55 | dbwells2 | +29 -0 | 1.12 | src/ComputeGridForce.C | Updated gridforce code to make sure that the grids provided don'tintersect the edge of the periodic cell (centered on the grid center.)If such an overlap occurs, the force applied isn't guaranteed to besmooth in time. The check occurs every time step (on one node only), sothis should also make gridforce fully NPT-safe. |
| 2009/06/23 21:02:41 | petefred | +7 -2 | 1.6 | src/colvarmodule.C | Write .old files for the colvars restart files in case a run dies while writing them |
| 2009/06/22 21:37:48 | jim | +4 -0 | 1.12 | src/ComputeNonbondedCUDA.C | ifdef to work with pre-2.2 cuda |
| 2009/06/22 07:28:54 | jim | +1 -1 | 1.2 | src/ComputeNonbondedCUDAKernel.h | scale offset vectors at every step to allow constant pressure |
| 2009/06/22 07:28:54 | jim | +21 -2 | 1.5 | src/ComputeNonbondedCUDAKernel.cu | scale offset vectors at every step to allow constant pressure |
| 2009/06/22 07:28:54 | jim | +17 -10 | 1.11 | src/ComputeNonbondedCUDA.C | scale offset vectors at every step to allow constant pressure |
| 2009/06/22 06:52:20 | jim | +1 -3 | 1.4 | src/ComputeNonbondedCUDAKernel.cu | Simpler calculation for virial. |
| 2009/06/22 06:47:57 | jim | +4 -0 | 1.1031 | src/PatchMap.h | use offsets relative to patch centers on GPU |
| 2009/06/22 06:47:57 | jim | +3 -0 | 1.1048 | src/PatchMap.C | use offsets relative to patch centers on GPU |
| 2009/06/22 06:47:57 | jim | +1 -1 | 1.4 | src/ComputeNonbondedCUDA.h | use offsets relative to patch centers on GPU |
| 2009/06/22 06:47:57 | jim | +27 -24 | 1.10 | src/ComputeNonbondedCUDA.C | use offsets relative to patch centers on GPU |
| 2009/06/22 05:36:59 | jim | +9 -7 | 1.3 | src/ComputeNonbondedCUDAKernel.cu | scalar pressure calculation on GPU - won't work with flexible cells |
| 2009/06/22 05:36:59 | jim | +2 -2 | 1.2 | src/ComputeNonbondedCUDAExcl.h | scalar pressure calculation on GPU - won't work with flexible cells |
| 2009/06/22 05:36:59 | jim | +6 -8 | 1.4 | src/ComputeNonbondedCUDAExcl.C | scalar pressure calculation on GPU - won't work with flexible cells |
| 2009/06/22 05:36:59 | jim | +14 -4 | 1.9 | src/ComputeNonbondedCUDA.C | scalar pressure calculation on GPU - won't work with flexible cells |
| 2009/06/22 02:06:26 | char | +71 -69 | 1.6 | src/colvarproxy_namd.C | bugfixes for colvars module -- colvarcomp_rotations.C fixes RMSD Jacobian term, colvaratoms.C fixes erroneous wrapping of ref coords, colvarmodule.h + colvaratoms.C + colvarproxy_namd.C fix colvar atom definition from columns of PDB file. |
| 2009/06/22 02:06:26 | char | +4 -2 | 1.3 | src/colvarmodule.h | bugfixes for colvars module -- colvarcomp_rotations.C fixes RMSD Jacobian term, colvaratoms.C fixes erroneous wrapping of ref coords, colvarmodule.h + colvaratoms.C + colvarproxy_namd.C fix colvar atom definition from columns of PDB file. |
| 2009/06/22 02:06:26 | char | +45 -1 | 1.5 | src/colvarcomp_rotations.C | bugfixes for colvars module -- colvarcomp_rotations.C fixes RMSD Jacobian term, colvaratoms.C fixes erroneous wrapping of ref coords, colvarmodule.h + colvaratoms.C + colvarproxy_namd.C fix colvar atom definition from columns of PDB file. |
| 2009/06/22 02:06:26 | char | +8 -8 | 1.4 | src/colvaratoms.C | bugfixes for colvars module -- colvarcomp_rotations.C fixes RMSD Jacobian term, colvaratoms.C fixes erroneous wrapping of ref coords, colvarmodule.h + colvaratoms.C + colvarproxy_namd.C fix colvar atom definition from columns of PDB file. |
| 2009/06/19 19:48:58 | jim | +21 -4 | 1.8 | src/ComputeNonbondedCUDA.C | Punt on picking a device if there are not enough for all processes on thenode and any of them are in exclusive mode. |
| 2009/06/17 22:40:11 | jim | +5 -1 | 1.7 | src/ComputeNonbondedCUDA.C | Add +ignoresharing flag to disable shared-GPU coordination messages. |
| 2009/06/17 21:42:32 | brunner | +21 -13 | 1.3 | ug/ug_userdef.tex | Added most of David W.'s comments about the gridforce docs, changed parameternames for potfile and chargecol |
| 2009/06/17 21:41:48 | brunner | +2 -2 | 1.28 | ug/ug_alchemy.tex | Fixed an open brace and removed a newline that were making LaTeX complain |
| 2009/06/17 21:09:12 | brunner | +18 -18 | 1.1280 | src/SimParameters.C | Changed conf file keywords [m]gridforceqcol to [m]gridforcechargecol and[m]gridforcevfile to [m]gridforcepotfile |
| 2009/06/17 21:09:12 | brunner | +2 -2 | 1.1070 | src/NamdState.C | Changed conf file keywords [m]gridforceqcol to [m]gridforcechargecol and[m]gridforcevfile to [m]gridforcepotfile |
| 2009/06/17 21:09:12 | brunner | +4 -4 | 1.1166 | src/Molecule.C | Changed conf file keywords [m]gridforceqcol to [m]gridforcechargecol and[m]gridforcevfile to [m]gridforcepotfile |
| 2009/06/14 07:01:49 | char | +88 -83 | 1.27 | ug/ug_alchemy.tex | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +8 -12 | 1.1194 | src/WorkDistrib.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +30 -34 | 1.1153 | src/SimParameters.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +153 -150 | 1.1279 | src/SimParameters.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +1 -1 | 1.2 | src/OptPme.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +4 -4 | 1.6 | src/OptPme.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:48 | char | +5 -18 | 1.1069 | src/NamdState.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +38 -40 | 1.1165 | src/Molecule.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +6 -7 | 1.6 | src/DumpBenchParams.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +57 -58 | 1.1238 | src/Controller.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +3 -3 | 1.27 | src/ComputePme.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +48 -47 | 1.124 | src/ComputePme.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +8 -8 | 1.1066 | src/ComputeNonbondedUtil.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +20 -20 | 1.1092 | src/ComputeNonbondedUtil.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:47 | char | +2 -2 | 1.4 | src/ComputeNonbondedFEP.C | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:46 | char | +1 -1 | 1.34 | src/ComputeNonbondedBase2.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 07:01:46 | char | +25 -25 | 1.1157 | src/ComputeNonbondedBase.h | Merged FEP and TI code into shared common interface. Updated manual accordingly. |
| 2009/06/14 06:58:42 | char | +1 -1 | 1.5 | src/colvarproxy_namd.C | Repaired prior commit accidental comment-induced-destruction of colvar module object deallocation |
| 2009/06/14 01:28:16 | petefred | +13 -0 | 1.3 | ug/ug_forcefield.tex | Add documentation for LJ tail corrections |
| 2009/06/14 01:28:16 | petefred | +16 -1 | 1.10 | ug/ug.bib | Add documentation for LJ tail corrections |
| 2009/06/14 01:27:31 | petefred | +8 -8 | 1.4 | src/colvarproxy_namd.C | Revert spurious commit to colvarproxy_namd |
| 2009/06/14 01:23:50 | petefred | +9 -9 | 1.3 | src/colvarproxy_namd.C | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/14 01:23:50 | petefred | +9 -5 | 1.1152 | src/SimParameters.h | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/14 01:23:49 | petefred | +24 -5 | 1.1278 | src/SimParameters.C | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/14 01:23:49 | petefred | +30 -15 | 1.1021 | src/Parameters.h | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/14 01:23:49 | petefred | +142 -0 | 1.1164 | src/Molecule.C | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/14 01:23:48 | petefred | +32 -4 | 1.1237 | src/Controller.C | Improved version of tail corrections (thanks for Floris Buelens) that will work for heterogeneous systems |
| 2009/06/12 18:53:44 | bhatele | None | 1.1 | arch/CRAY-XT-pgcc.arch | CRAY XT pgcc build |
| 2009/06/12 18:49:52 | bhatele | None | 1.1 | arch/MacOSX-x86_64.tcl | macosx x86_64 build |
| 2009/06/12 18:49:51 | bhatele | None | 1.1 | arch/MacOSX-x86_64.fftw | macosx x86_64 build |
| 2009/06/12 18:49:51 | bhatele | None | 1.1 | arch/MacOSX-x86_64.base | macosx x86_64 build |
| 2009/06/12 18:49:51 | bhatele | None | 1.1 | arch/MacOSX-x86_64-g++.arch | macosx x86_64 build |
| 2009/06/05 00:30:32 | char | +23 -7 | 1.1277 | src/SimParameters.C | Updated output of FEP parameters; to clarify for user understanding |
| 2009/06/03 17:14:45 | char | +37 -2 | 1.1068 | src/NamdState.C | Updated src/Molecule.C, src/Molecule.h and src/NamdState.C with new auto-alchemify code for FEP simulations to automatically remove bonds, angles, dihedrals and impropers containing atoms in both partitions. Automatic removal of these terms is not supported in the MEM_OPT_VERSION. |
| 2009/06/03 17:14:45 | char | +5 -0 | 1.1084 | src/Molecule.h | Updated src/Molecule.C, src/Molecule.h and src/NamdState.C with new auto-alchemify code for FEP simulations to automatically remove bonds, angles, dihedrals and impropers containing atoms in both partitions. Automatic removal of these terms is not supported in the MEM_OPT_VERSION. |
| 2009/06/03 17:14:45 | char | +108 -0 | 1.1163 | src/Molecule.C | Updated src/Molecule.C, src/Molecule.h and src/NamdState.C with new auto-alchemify code for FEP simulations to automatically remove bonds, angles, dihedrals and impropers containing atoms in both partitions. Automatic removal of these terms is not supported in the MEM_OPT_VERSION. |
| 2009/06/02 16:39:58 | chaomei2 | +11 -7 | 1.89 | src/NamdCentLB.C | Bug fixes for loading ldb data from text file. |
| 2009/05/29 20:54:59 | jim | +1 -0 | 1.1036 | src/ProxyMgr.h | Make compile with latest Charm++ that hides message envelope definition. |
| 2009/05/27 18:16:28 | jim | +2 -2 | 1.26 | ug/ug_alchemy.tex | Remove .pdf from images to fix latex2html. |
| 2009/05/27 18:16:05 | jim | +6 -1 | 1.46 | ug/Makefile | build tarfile automatically |
| 2009/05/27 02:46:17 | char | +1 -1 | 1.25 | ug/ug_alchemy.tex | fixed typo in ug/ug_alchemy.tex |
| 2009/05/26 21:19:09 | char | None | 1.1 | ug/figures/softcore_lambda.png | Added softcore-potential-coupling equation and updated softcore-potential descrip in ug_alchemy.tex to clarify usage. Added figures/softcore_lambda.png/.pdf |
| 2009/05/26 21:19:09 | char | None | 1.1 | ug/figures/softcore_lambda.pdf | Added softcore-potential-coupling equation and updated softcore-potential descrip in ug_alchemy.tex to clarify usage. Added figures/softcore_lambda.png/.pdf |
| 2009/05/26 21:19:09 | char | +35 -15 | 1.24 | ug/ug_alchemy.tex | Added softcore-potential-coupling equation and updated softcore-potential descrip in ug_alchemy.tex to clarify usage. Added figures/softcore_lambda.png/.pdf |
| 2009/05/22 08:45:42 | jim | +0 -4 | 1.1038 | src/ComputeNonbondedSelf.C | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 08:45:42 | jim | +0 -4 | 1.1046 | src/ComputeNonbondedPair.C | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 08:45:42 | jim | +26 -14 | 1.3 | src/ComputeNonbondedCUDAExcl.C | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 08:45:41 | jim | +11 -9 | 1.6 | src/ComputeNonbondedCUDA.C | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 08:45:41 | jim | +6 -2 | 1.33 | src/ComputeNonbondedBase2.h | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 08:45:41 | jim | +6 -0 | 1.1156 | src/ComputeNonbondedBase.h | CUDA-enabled NAMD now works with PME, but not multiple timestepping. |
| 2009/05/22 04:16:20 | jim | +3 -1 | 1.2 | src/ComputeNonbondedCUDAExcl.C | Fixes to exclusion calculation. |
| 2009/05/21 23:23:55 | chaomei2 | +2 -1 | 1.1162 | src/Molecule.C | Added the if condition when calling build_extra_bonds when extraBonds is off in read_compressed_psf for memory optimized version. |
| 2009/05/21 22:40:22 | chaomei2 | +2 -2 | 1.1038 | src/NamdTypes.h | Change the type of signature index from short to unsigned short to allow more signatures in the case of extra bonds/angles/dihedrals/impropers. |
| 2009/05/21 22:38:14 | chaomei2 | +5 -1 | 1.1067 | src/NamdState.C | Fixed the bug for memory optimized version when extraBonds feature is turned on.The bug is that I forgot to re-load the extra bonds information when reading the compressed molecule object. |
| 2009/05/21 22:38:14 | chaomei2 | +1 -1 | 1.1083 | src/Molecule.h | Fixed the bug for memory optimized version when extraBonds feature is turned on.The bug is that I forgot to re-load the extra bonds information when reading the compressed molecule object. |
| 2009/05/21 22:38:14 | chaomei2 | +7 -2 | 1.1161 | src/Molecule.C | Fixed the bug for memory optimized version when extraBonds feature is turned on.The bug is that I forgot to re-load the extra bonds information when reading the compressed molecule object. |
| 2009/05/19 22:51:22 | bhatele | +3 -3 | 1.4 | arch/Linux-x86_64-MPI-pathcc.arch | added back the -m64 flag |
| 2009/05/19 22:42:31 | bhatele | +3 -3 | 1.3 | arch/Linux-x86_64-MPI-pathcc.arch | SiCortex arch files |
| 2009/05/19 22:42:31 | bhatele | None | 1.1 | arch/Linux-mips64.tcl | SiCortex arch files |
| 2009/05/19 22:42:31 | bhatele | None | 1.1 | arch/Linux-mips64.fftw | SiCortex arch files |
| 2009/05/19 22:42:31 | bhatele | None | 1.1 | arch/Linux-mips64.base | SiCortex arch files |
| 2009/05/19 22:42:31 | bhatele | None | 1.1 | arch/Linux-mips64-MPI-pathcc.arch | SiCortex arch files |
| 2009/05/19 22:42:30 | bhatele | None | 1.1 | arch/Linux-mips64-MPI-g++.arch | SiCortex arch files |
| 2009/05/19 05:11:08 | jim | +1 -0 | 1.1253 | Makefile | Implement modified 1-4 exclusions for CUDA. |
| 2009/05/19 05:10:29 | jim | +1 -0 | 1.1041 | src/WorkDistrib.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:29 | jim | +1 -0 | 1.1020 | src/WorkDistrib.ci | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:29 | jim | +14 -2 | 1.1193 | src/WorkDistrib.C | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:29 | jim | +2 -0 | 1.1082 | src/Molecule.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | +5 -3 | 1.91 | src/LdbCoordinator.C | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | +1 -1 | 1.1065 | src/ComputeNonbondedUtil.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | None | 1.1 | src/ComputeNonbondedCUDAExcl.inl | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | None | 1.1 | src/ComputeNonbondedCUDAExcl.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | None | 1.1 | src/ComputeNonbondedCUDAExcl.C | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | +2 -0 | 1.1155 | src/ComputeNonbondedBase.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:28 | jim | +18 -0 | 1.1080 | src/ComputeMgr.C | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:10:27 | jim | +2 -0 | 1.1041 | src/ComputeMap.h | Implement modified 1-4 exclusions for CUDA. Only works for cutoffand pressure is still not reported correctly for CUDA calculation. |
| 2009/05/19 05:09:35 | jim | +71 -0 | 1.125 | Make.depends | Implement modified 1-4 exclusions for CUDA. |
| 2009/05/13 21:05:17 | jim | +1 -1 | 1.41 | src/BackEnd.C | Only require +idlepoll for net version. |
| 2009/05/13 16:10:43 | jim | +11 -0 | 1.68 | notes.txt | notes on CUDA builds |
| 2009/05/13 16:10:43 | jim | +2 -1 | 1.53 | config | notes on CUDA builds |
| 2009/05/12 18:21:21 | brunner | +8 -9 | 1.1276 | src/SimParameters.C | Fixed bug where leaving gridforceQcol blank did not default to using theatom charge. Instead it switched to using column K of the PDB |
| 2009/05/12 18:21:21 | brunner | +1 -1 | 1.1160 | src/Molecule.C | Fixed bug where leaving gridforceQcol blank did not default to using theatom charge. Instead it switched to using column K of the PDB |
| 2009/05/12 18:21:21 | brunner | +18 -7 | 1.2 | src/MGridforceParams.C | Fixed bug where leaving gridforceQcol blank did not default to using theatom charge. Instead it switched to using column K of the PDB |
| 2009/05/11 15:58:55 | jim | +4 -4 | 1.67 | notes.txt | change --no-shared to --no-build-shared (which matches charm docs) |
| 2009/05/08 21:21:32 | char | +1 -1 | 1.23 | ug/ug_alchemy.tex | initial updates to alchemy |
| 2009/05/07 19:47:22 | jim | +2 -1 | 1.2 | src/ComputeNonbondedCUDAKernel.cu | Attach events to non-zero stream in case this effects overlap. |
| 2009/05/07 19:47:22 | jim | +16 -12 | 1.5 | src/ComputeNonbondedCUDA.C | Attach events to non-zero stream in case this effects overlap. |
| 2009/05/07 19:11:58 | jim | +1 -1 | 1.1252 | Makefile | When making projections also enable summary because it's useful. |
| 2009/05/07 18:00:14 | jim | +5 -1 | 1.3 | src/ComputeNonbondedCUDA.h | Use Charm++ physical node detection to identify which pes are sharing aGPU and then use explicit messages to coordinate sharing. Sharing is ina fixed ring order. First pass is for remote work, second is for local. |
| 2009/05/07 18:00:14 | jim | +113 -12 | 1.4 | src/ComputeNonbondedCUDA.C | Use Charm++ physical node detection to identify which pes are sharing aGPU and then use explicit messages to coordinate sharing. Sharing is ina fixed ring order. First pass is for remote work, second is for local. |
| 2009/05/07 18:00:14 | jim | +7 -0 | 1.1030 | src/ComputeMgr.h | Use Charm++ physical node detection to identify which pes are sharing aGPU and then use explicit messages to coordinate sharing. Sharing is ina fixed ring order. First pass is for remote work, second is for local. |
| 2009/05/07 18:00:14 | jim | +2 -0 | 1.1014 | src/ComputeMgr.ci | Use Charm++ physical node detection to identify which pes are sharing aGPU and then use explicit messages to coordinate sharing. Sharing is ina fixed ring order. First pass is for remote work, second is for local. |
| 2009/05/07 18:00:13 | jim | +13 -1 | 1.1079 | src/ComputeMgr.C | Use Charm++ physical node detection to identify which pes are sharing aGPU and then use explicit messages to coordinate sharing. Sharing is ina fixed ring order. First pass is for remote work, second is for local. |
| 2009/05/06 20:40:00 | brunner | +41 -1 | 1.1017 | src/structures.h | Added hash tables to speed up PSF compression. I'm using the CkHashtableimplementation built into Charm++. On my not-so-rigorous tests on STMV,I'm getting about 70% speedup. I expect that the speedup should be prettyindependent of number of atoms (but would vary with the number ofatom/bond/etc. signatures). I'd love to hear next time someone runs thebig system what speed improvement they see. |
| 2009/05/06 20:40:00 | brunner | +108 -0 | 1.8 | src/CompressPsf.h | Added hash tables to speed up PSF compression. I'm using the CkHashtableimplementation built into Charm++. On my not-so-rigorous tests on STMV,I'm getting about 70% speedup. I expect that the speedup should be prettyindependent of number of atoms (but would vary with the number ofatom/bond/etc. signatures). I'd love to hear next time someone runs thebig system what speed improvement they see. |
| 2009/05/06 20:40:00 | brunner | +161 -46 | 1.17 | src/CompressPsf.C | Added hash tables to speed up PSF compression. I'm using the CkHashtableimplementation built into Charm++. On my not-so-rigorous tests on STMV,I'm getting about 70% speedup. I expect that the speedup should be prettyindependent of number of atoms (but would vary with the number ofatom/bond/etc. signatures). I'd love to hear next time someone runs thebig system what speed improvement they see. |
| 2009/04/23 17:07:49 | char | +3 -3 | 1.1275 | src/SimParameters.C | Switched fepVdwLambdaEnd to default of 1.0. This value found to be more optimal. |
| 2009/04/23 17:07:49 | char | +1 -1 | 1.1154 | src/ComputeNonbondedBase.h | Switched fepVdwLambdaEnd to default of 1.0. This value found to be more optimal. |
| 2009/04/15 05:20:34 | jim | +25 -2 | 1.14 | src/memusage.C | Added /proc/self/stat as first alternative after CmiMemoryUsage (GNU). |
| 2009/04/12 11:57:16 | char | +4 -4 | 1.1274 | src/SimParameters.C | switched alchemical decouple default to FALSE as default TRUE interferes with initial startup. Need to later add a check in order to set default to true |
| 2009/04/10 20:42:31 | char | +2 -2 | 1.22 | ug/ug_alchemy.tex | fixed typo in ug_alchemy. switched fepOn to fep |
| 2009/04/09 19:24:57 | char | +4 -4 | 1.1273 | src/SimParameters.C | Alchemical decouple default switched from FALSE to TRUE |
| 2009/04/07 20:50:01 | brunner | None | 1.1 | ug/figures/gridshift.pdf | Figures for grid force docs |
| 2009/04/07 20:50:01 | brunner | None | 1.1 | ug/figures/gridshift.eps | Figures for grid force docs |
| 2009/04/07 20:49:36 | brunner | +126 -1 | 1.2 | ug/ug_userdef.tex | Added first draft of docs for grid forces |
| 2009/04/07 20:49:36 | brunner | +14 -0 | 1.15 | ug/ug_macros.tex | Added first draft of docs for grid forces |
| 2009/04/07 19:31:00 | jim | +1 -1 | 1.2 | arch/Solaris-x86_64-CC.arch | Switch to SMP. |
| 2009/04/07 19:30:49 | jim | +5 -0 | 1.1066 | src/main.C | Warn about experimental memory optimized builds. |
| 2009/04/03 18:48:54 | jim | +1 -1 | 1.1094 | src/Node.C | Add ", see error messages above" to "Exiting prematurely". |
| 2009/04/02 03:17:48 | jim | +87 -16 | 1.3 | src/ComputeNonbondedCUDA.C | Use new Charm++ PhysicalNode interface to find shared CUDA devices. |
| 2009/04/02 03:17:48 | jim | +7 -2 | 1.40 | src/BackEnd.C | Use new Charm++ PhysicalNode interface to find shared CUDA devices. |
| 2009/03/31 20:14:41 | jim | +2 -2 | 1.3 | src/colvarbias_meta.h | Fix to build on IBM xlc 08.00.0000.0013. |
| 2009/03/26 21:43:55 | jim | +8 -0 | 1.1066 | src/NamdState.C | Print atom and mass density during structure summary at startup.If this isn't close to 1 g/cm^3 and 0.1 atoms/A^3 something is wrong. |
| 2009/03/26 21:05:21 | jim | +17 -5 | 1.1236 | src/Controller.C | Make minimizer more robust and informative at startup. |
| 2009/03/26 19:44:02 | jim | +6 -6 | 1.39 | src/BackEnd.C | Fix CUDA build. |
| 2009/03/25 21:58:22 | jim | +3 -2 | 1.1174 | src/Sequencer.C | Minimizer should not slowly move *fixed* atoms downhill. |
| 2009/03/25 19:43:56 | chaomei2 | +1 -1 | 1.7 | src/CompressPsf.h | Changed the ordering of hydrogenGroup lists in the per-atom file.Now the hydrogenGroup is not sorted (ordered according to the atom's ID) in theper-atom input file. It is re-sorted after being loaded. |
| 2009/03/25 19:43:56 | chaomei2 | +22 -21 | 1.16 | src/CompressPsf.C | Changed the ordering of hydrogenGroup lists in the per-atom file.Now the hydrogenGroup is not sorted (ordered according to the atom's ID) in theper-atom input file. It is re-sorted after being loaded. |
| 2009/03/25 19:43:55 | chaomei2 | +35 -22 | 1.1159 | src/Molecule.C | Changed the ordering of hydrogenGroup lists in the per-atom file.Now the hydrogenGroup is not sorted (ordered according to the atom's ID) in theper-atom input file. It is re-sorted after being loaded. |
| 2009/03/25 05:01:07 | jim | +2 -0 | 1.5 | ug/.latex2html-init | white background for figures works again |
| 2009/03/25 05:00:50 | jim | +1 -1 | 1.45 | ug/Makefile | only build pdf before html since dvi build fails |
| 2009/03/24 03:01:55 | char | +3 -3 | 1.21 | ug/ug_alchemy.tex | Changed default keyword values to match those in SimParameters |
| 2009/03/23 22:44:08 | jim | +1 -0 | 1.2 | ug/ug_forcefield.tex | Fix references. |
| 2009/03/23 22:44:08 | jim | +1 -1 | 1.7 | ug/ug_colvars.tex | Fix references. |
| 2009/03/23 21:06:58 | char | +141 -107 | 1.2 | ug/figures/TI.pdf | updated refs for alchemical section |
| 2009/03/23 21:06:58 | char | +1 -2 | 1.26 | ug/ug_intro.tex | updated refs for alchemical section |
| 2009/03/23 21:06:58 | char | +120 -153 | 1.20 | ug/ug_alchemy.tex | updated refs for alchemical section |
| 2009/03/23 21:06:57 | char | +66 -15 | 1.9 | ug/ug.bib | updated refs for alchemical section |
| 2009/03/23 07:11:57 | jim | +1 -1 | 1.66 | notes.txt | x86_64 |
| 2009/03/23 07:06:40 | jim | +64 -41 | 1.65 | notes.txt | many updates to compile process. |
| 2009/03/23 06:07:03 | jim | +4 -13 | 1.64 | notes.txt | performance updates |
| 2009/03/23 06:06:46 | jim | +2 -4 | 1.14 | ug/ug_runit.tex | updates |
| 2009/03/23 06:05:04 | jim | +1 -1 | 1.11 | ug/namd_macros.tex | update macros |
| 2009/03/23 06:01:11 | jim | +10 -18 | 1.33 | announce.txt | Updated |
| 2009/03/23 05:44:32 | jim | +247 -411 | 1.63 | notes.txt | rearrange and update building |
| 2009/03/23 05:20:16 | jim | +3 -10 | 1.12 | README.txt | cleaned up |
| 2009/03/23 05:18:55 | jim | +19 -115 | 1.13 | ug/ug_runit.tex | update docs |
| 2009/03/23 05:18:55 | jim | +1 -66 | 1.25 | ug/ug_intro.tex | update docs |
| 2009/03/23 05:18:55 | jim | +3 -0 | 1.16 | ug/ug.tex | update docs |
| 2009/03/23 04:36:38 | jim | +17 -11 | 1.11 | ug/ug_avail.tex | update |
| 2009/03/23 03:59:49 | jim | +7 -1 | 1.6 | ug/ug_colvars.tex | Comment on replacing freeEnergy module. |
| 2009/03/23 03:59:17 | jim | +5 -8 | 1.44 | ug/Makefile | Build pdf by default (used to be ps). |
| 2009/03/23 03:58:47 | jim | +2 -2 | 1.15 | ug/ug.tex | Remove ancient freeEnergy module from docs. |
| 2009/03/23 03:58:08 | jim | +1 -1 | 1.19 | ug/ug_alchemy.tex | Fix one easy ref (case error). |
| 2009/03/19 19:36:05 | chaomei2 | +8 -1 | 1.18 | src/mainfunc.C | Tweaked the namd initialization part (especially for the sake of converse/charm++ runtime) for the SMP layer on MPI. This is required because now for MPI-SMP layer,the main thread now becomes the communication thread (for the safety of MPI calls). The original main thread code has to be moved to be executed by he origianl slavethread. |
| 2009/03/19 19:36:05 | chaomei2 | +41 -16 | 1.38 | src/BackEnd.C | Tweaked the namd initialization part (especially for the sake of converse/charm++ runtime) for the SMP layer on MPI. This is required because now for MPI-SMP layer,the main thread now becomes the communication thread (for the safety of MPI calls). The original main thread code has to be moved to be executed by he origianl slavethread. |
| 2009/03/13 22:19:23 | char | +1 -1 | 1.4 | src/colvarcomp_rotations.C | switched line188 from [b_Jacobian_derivative = true;] to [b_Jacobian_derivative = false;]. Switches off jacobian in rmsd colvar to prevent breakage of RMSD colvar gradients/orientation. -cbh |
| 2009/03/13 20:30:00 | jim | +6 -4 | 1.1251 | Makefile | Fix winrelease target. |
| 2009/03/13 18:25:21 | jim | +39 -1 | 1.124 | Make.depends | Rebuild to add Molecule2.o dependencies. |
| 2009/03/13 18:19:51 | jim | None | 1.1 | src/Molecule2.C | Deal with compiler limitations by compiling second half of Molecule.Cas Molecule2.C. Quick and dirty solution that can be refactored later. |
| 2009/03/13 18:19:50 | jim | +11 -0 | 1.1158 | src/Molecule.C | Deal with compiler limitations by compiling second half of Molecule.Cas Molecule2.C. Quick and dirty solution that can be refactored later. |
| 2009/03/13 18:19:45 | jim | +1 -0 | 1.1250 | Makefile | Deal with compiler limitations by compiling second half of Molecule.Cas Molecule2.C. Quick and dirty solution that can be refactored later. |
| 2009/03/13 15:40:27 | jim | +3 -0 | 1.52 | config | Pattern for MacOSX. |
| 2009/03/12 22:21:00 | jim | +1 -1 | 1.8 | arch/MacOSX-PPC-xlC.arch | net-ppc-darwin -> net-darwin-ppc |
| 2009/03/12 22:21:00 | jim | +1 -1 | 1.4 | arch/MacOSX-PPC-c++.arch | net-ppc-darwin -> net-darwin-ppc |
| 2009/03/12 21:54:23 | jim | +1 -1 | 1.43 | ug/Makefile | Update versions to NAMD 2.7b1 and Charm++ 6.1. |
| 2009/03/12 21:54:20 | jim | +1 -4 | 1.51 | config | Update versions to NAMD 2.7b1 and Charm++ 6.1. |
| 2009/03/12 21:54:20 | jim | +1 -1 | 1.1249 | Makefile | Update versions to NAMD 2.7b1 and Charm++ 6.1. |
| 2009/03/12 21:54:20 | jim | +2 -2 | 1.21 | Make.charm | Update versions to NAMD 2.7b1 and Charm++ 6.1. |
| 2009/03/12 02:18:46 | petefred | +3 -0 | 1.4 | src/colvarbias_abf.C | Remove problem where reading multiple input .grad files can crash due to failure to clear fstream status flags |
| 2009/03/07 22:45:36 | jim | +1 -1 | 1.11 | arch/AIX-POWER-xlC.arch | Add -qnohot to bypass xlC compiler bug. |
| 2009/03/07 22:45:01 | jim | +1 -1 | 1.2 | arch/Linux-PPC-MX64-xlc64.arch | Add -qnohot to avoid xlC compiler bug. |
| 2009/03/07 22:45:01 | jim | +1 -1 | 1.2 | arch/Linux-PPC-MX-xlc.arch | Add -qnohot to avoid xlC compiler bug. |
| 2009/03/07 22:39:30 | jim | +24 -20 | 1.50 | config | More help on building, don't search home dir for charm. |
| 2009/03/07 22:39:30 | jim | +2 -0 | 1.20 | Make.charm | More help on building, don't search home dir for charm. |
| 2009/03/07 21:52:07 | jim | +1 -1 | 1.2 | arch/Win32-MSVC.arch | Switch Win32 to multicore. |
| 2009/03/07 21:52:06 | jim | +2 -1 | 1.1248 | Makefile | Switch Win32 to multicore. |
| 2009/03/07 21:37:42 | jim | +1 -1 | 1.5 | arch/CRAY-XT3.arch | Remove -I/usr/include that was breaking compiler. |
| 2009/03/07 21:37:42 | jim | +1 -1 | 1.2 | arch/CRAY-XT3-g++.arch | Remove -I/usr/include that was breaking compiler. |
| 2009/03/07 21:37:42 | jim | +1 -1 | 1.2 | arch/CRAY-XT.arch | Remove -I/usr/include that was breaking compiler. |
| 2009/03/07 21:37:42 | jim | +1 -1 | 1.2 | arch/CRAY-XT-g++.arch | Remove -I/usr/include that was breaking compiler. |
| 2009/03/05 21:07:09 | jim | +1 -1 | 1.19 | Make.charm | Update to 6.0.1 |
| 2009/03/05 05:21:47 | jim | +8 -8 | 1.1235 | src/Controller.C | Rearrange output to be same as 2.6 but with TOTAL2 replaced with POTENTIAL.This should allow old and new log files to be awked/catted together withoutbreaking any analysis scripts (unless they used TOTAL2, that is). |
| 2009/03/04 22:55:00 | jim | +9 -9 | 1.1234 | src/Controller.C | Remove TOTAL2 and shift fields around to preserve formatting due toadded POTENTIAL field. |
| 2009/03/04 21:20:59 | jim | +3 -0 | 1.9 | src/ProcessorPrivate.C | Make iout thread-safe. |
| 2009/03/04 21:20:59 | jim | +4 -1 | 1.1018 | src/InfoStream.h | Make iout thread-safe. |
| 2009/03/04 21:20:59 | jim | +0 -1 | 1.1017 | src/InfoStream.C | Make iout thread-safe. |
| 2009/03/03 18:57:35 | chaomei2 | +1 -0 | 1.1157 | src/Molecule.C | Add a line of message explaining the fatal error "Currently not supporting building exclusion check on the fly for memory optimized version" in the memory optimized version. |
| 2009/02/27 23:03:01 | jim | +4 -2 | 1.49 | config | Change i686/amd64 to x86/x86_64 |
| 2009/02/26 23:57:50 | jim | None | 1.1 | arch/Linux-Itanium.tcl | Rename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64. |
| 2009/02/26 23:57:50 | jim | None | 1.1 | arch/Linux-Itanium.fftw | Rename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64. |
| 2009/02/26 23:57:50 | jim | None | 1.1 | arch/Linux-Itanium.base | Rename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64. |
| 2009/02/26 23:57:49 | jim | None | 1.1 | arch/Linux-Itanium-icc.arch | Rename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64. |
| 2009/02/26 23:39:41 | jim | None | 1.1 | arch/Linux-x86.tcl | Rename Linux-i686 Linux-x86 |
| 2009/02/26 23:39:41 | jim | None | 1.1 | arch/Linux-x86.fftw | Rename Linux-i686 Linux-x86 |
| 2009/02/26 23:39:41 | jim | None | 1.1 | arch/Linux-x86.cuda | Rename Linux-i686 Linux-x86 |
| 2009/02/26 23:39:41 | jim | None | 1.1 | arch/Linux-x86.base | Rename Linux-i686 Linux-x86 |
| 2009/02/26 23:39:40 | jim | None | 1.1 | arch/Linux-x86-icc.arch | Rename Linux-i686 Linux-x86 |
| 2009/02/26 23:39:40 | jim | None | 1.1 | arch/Linux-x86-g++.arch | Rename Linux-i686 Linux-x86 |
| 2009/02/26 22:59:56 | jim | None | 1.1 | arch/MacOSX-x86.tcl | Rename MacOSX-i686 to MacOSX-x86. |
| 2009/02/26 22:59:56 | jim | None | 1.1 | arch/MacOSX-x86.fftw | Rename MacOSX-i686 to MacOSX-x86. |
| 2009/02/26 22:59:56 | jim | None | 1.1 | arch/MacOSX-x86.base | Rename MacOSX-i686 to MacOSX-x86. |
| 2009/02/26 22:59:56 | jim | None | 1.1 | arch/MacOSX-x86-g++.arch | Rename MacOSX-i686 to MacOSX-x86. |
| 2009/02/26 22:57:40 | jim | None | 1.1 | arch/Cygwin.tcl | Rename Cygwin-i686 to Cygwin. |
| 2009/02/26 22:57:39 | jim | None | 1.1 | arch/Cygwin.fftw | Rename Cygwin-i686 to Cygwin. |
| 2009/02/26 22:57:39 | jim | None | 1.1 | arch/Cygwin.base | Rename Cygwin-i686 to Cygwin. |
| 2009/02/26 22:57:39 | jim | None | 1.1 | arch/Cygwin.arch | Rename Cygwin-i686 to Cygwin. |
| 2009/02/26 22:49:41 | jim | None | 1.1 | arch/Solaris-x86_64.tcl | Renaming Solaris-amd64 to Solaris-x86_64. |
| 2009/02/26 22:49:41 | jim | None | 1.1 | arch/Solaris-x86_64.fftw | Renaming Solaris-amd64 to Solaris-x86_64. |
| 2009/02/26 22:49:41 | jim | None | 1.1 | arch/Solaris-x86_64.cuda | Renaming Solaris-amd64 to Solaris-x86_64. |
| 2009/02/26 22:49:41 | jim | None | 1.1 | arch/Solaris-x86_64.base | Renaming Solaris-amd64 to Solaris-x86_64. |
| 2009/02/26 22:49:41 | jim | None | 1.1 | arch/Solaris-x86_64-CC.arch | Renaming Solaris-amd64 to Solaris-x86_64. |
| 2009/02/26 14:38:48 | bhatele | +3 -3 | 1.6 | arch/BlueGeneP-xlC.arch | fixed some configs |
| 2009/02/26 14:38:48 | bhatele | +2 -2 | 1.3 | arch/BlueGeneP-g++.arch | fixed some configs |
| 2009/02/26 14:38:48 | bhatele | +3 -3 | 1.4 | arch/BlueGeneP-MPI-xlC.arch | fixed some configs |
| 2009/02/24 23:01:38 | chaomei2 | +39 -23 | 1.1065 | src/NamdState.C | 1. rewrite the module for compressing the psf file (or the Molecule information). Now, only the non-memory optimized version generates the compressed file2. Now there's a binary file for per-atom information including the hydrogen group information.In short, this change is to help the implementation of parallel input in namd |
| 2009/02/24 23:01:38 | chaomei2 | +32 -5 | 1.1081 | src/Molecule.h | 1. rewrite the module for compressing the psf file (or the Molecule information). Now, only the non-memory optimized version generates the compressed file2. Now there's a binary file for per-atom information including the hydrogen group information.In short, this change is to help the implementation of parallel input in namd |
| 2009/02/24 23:01:38 | chaomei2 | +11 -1 | 1.6 | src/CompressPsf.h | 1. rewrite the module for compressing the psf file (or the Molecule information). Now, only the non-memory optimized version generates the compressed file2. Now there's a binary file for per-atom information including the hydrogen group information.In short, this change is to help the implementation of parallel input in namd |
| 2009/02/24 23:01:38 | chaomei2 | +758 -13 | 1.15 | src/CompressPsf.C | 1. rewrite the module for compressing the psf file (or the Molecule information). Now, only the non-memory optimized version generates the compressed file2. Now there's a binary file for per-atom information including the hydrogen group information.In short, this change is to help the implementation of parallel input in namd |
| 2009/02/24 23:01:37 | chaomei2 | +304 -164 | 1.1156 | src/Molecule.C | 1. rewrite the module for compressing the psf file (or the Molecule information). Now, only the non-memory optimized version generates the compressed file2. Now there's a binary file for per-atom information including the hydrogen group information.In short, this change is to help the implementation of parallel input in namd |
| 2009/02/22 04:21:41 | bhatele | None | 1.1 | arch/CRAY-XT.tcl | XT4 files moved to XT which should work for both XT4 and XT5 |
| 2009/02/22 04:21:41 | bhatele | None | 1.1 | arch/CRAY-XT-g++.arch | XT4 files moved to XT which should work for both XT4 and XT5 |
| 2009/02/22 04:21:40 | bhatele | None | 1.1 | arch/CRAY-XT.fftw | XT4 files moved to XT which should work for both XT4 and XT5 |
| 2009/02/22 04:21:40 | bhatele | None | 1.1 | arch/CRAY-XT.base | XT4 files moved to XT which should work for both XT4 and XT5 |
| 2009/02/22 04:21:40 | bhatele | None | 1.1 | arch/CRAY-XT.arch | XT4 files moved to XT which should work for both XT4 and XT5 |
| 2009/02/22 04:16:04 | bhatele | +1 -1 | 1.2 | arch/Linux-x86_64.tcl | changed amd64 to x86_64 in the files |
| 2009/02/22 04:16:04 | bhatele | +1 -1 | 1.2 | arch/Linux-x86_64.fftw | changed amd64 to x86_64 in the files |
| 2009/02/22 04:16:04 | bhatele | +2 -2 | 1.2 | arch/Linux-x86_64-icc.arch | changed amd64 to x86_64 in the files |
| 2009/02/22 04:16:04 | bhatele | +2 -2 | 1.2 | arch/Linux-x86_64-g++.arch | changed amd64 to x86_64 in the files |
| 2009/02/22 04:16:03 | bhatele | +1 -1 | 1.2 | arch/Linux-x86_64-MPI-pathcc.arch | changed amd64 to x86_64 in the files |
| 2009/02/22 04:10:51 | bhatele | None | 1.1 | arch/Linux-x86_64.tcl | copied over from amd64 files |
| 2009/02/22 04:10:51 | bhatele | None | 1.1 | arch/Linux-x86_64-MPI-pathcc.arch | copied over from amd64 files |
| 2009/02/22 04:10:50 | bhatele | None | 1.1 | arch/Linux-x86_64.fftw | copied over from amd64 files |
| 2009/02/22 04:10:50 | bhatele | None | 1.1 | arch/Linux-x86_64.cuda | copied over from amd64 files |
| 2009/02/22 04:10:50 | bhatele | None | 1.1 | arch/Linux-x86_64.base | copied over from amd64 files |
| 2009/02/22 04:10:50 | bhatele | None | 1.1 | arch/Linux-x86_64-icc.arch | copied over from amd64 files |
| 2009/02/22 04:10:50 | bhatele | None | 1.1 | arch/Linux-x86_64-g++.arch | copied over from amd64 files |
| 2009/02/20 18:01:04 | jim | +0 -1 | 1.1155 | src/Molecule.C | remove debugging message |
| 2009/02/20 17:28:39 | jim | +4 -3 | 1.1151 | src/SimParameters.h | Clean up minimizer output, add minVerbose config option. |
| 2009/02/20 17:28:39 | jim | +5 -3 | 1.1272 | src/SimParameters.C | Clean up minimizer output, add minVerbose config option. |
| 2009/02/20 17:28:39 | jim | +37 -22 | 1.1233 | src/Controller.C | Clean up minimizer output, add minVerbose config option. |
| 2009/02/18 22:53:15 | jim | +26 -26 | 1.11 | src/MStream.h | Change int to size_t where appropriate. |
| 2009/02/18 22:53:15 | jim | +8 -8 | 1.16 | src/MStream.C | Change int to size_t where appropriate. |
| 2009/02/18 17:58:56 | petefred | +13 -13 | 1.1154 | src/Molecule.C | Make tail corrections work properly when switching is off |
| 2009/02/18 16:48:08 | petefred | +5 -4 | 1.1150 | src/SimParameters.h | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/18 16:48:08 | petefred | +5 -3 | 1.1271 | src/SimParameters.C | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/18 16:48:08 | petefred | +4 -0 | 1.1080 | src/Molecule.h | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/18 16:48:07 | petefred | +83 -1 | 1.1153 | src/Molecule.C | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/18 16:48:07 | petefred | +1 -0 | 1.1019 | src/LJTable.C | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/18 16:48:07 | petefred | +21 -2 | 1.1232 | src/Controller.C | Add tail corrections for water (necessary to get good agreement for cheq, tip4, etc.) |
| 2009/02/13 22:39:18 | jim | +1 -0 | 1.1049 | src/Sequencer.h | Start minimization by moving atoms with bad contacts 0.1A downhill everystep until bad contacts are gone, then continue with conjugate gradient. |
| 2009/02/13 22:39:18 | jim | +35 -8 | 1.1173 | src/Sequencer.C | Start minimization by moving atoms with bad contacts 0.1A downhill everystep until bad contacts are gone, then continue with conjugate gradient. |
| 2009/02/13 22:39:17 | jim | +10 -2 | 1.1231 | src/Controller.C | Start minimization by moving atoms with bad contacts 0.1A downhill everystep until bad contacts are gone, then continue with conjugate gradient. |
| 2009/02/13 18:40:06 | jim | +5 -5 | 1.1270 | src/SimParameters.C | Tweaks to minimizer. Should get stuck less for large systems whereenergy and gradient are inconsistent due to limited numerical precision. |
| 2009/02/13 18:40:06 | jim | +24 -13 | 1.1230 | src/Controller.C | Tweaks to minimizer. Should get stuck less for large systems whereenergy and gradient are inconsistent due to limited numerical precision. |
| 2009/02/13 15:12:54 | bhatele | +7 -5 | 1.1247 | Makefile | there is no reason to get summary logs with projections logs. It is annoyingwhen you do large processor runs. |
| 2009/02/13 15:10:23 | bhatele | +2 -2 | 1.5 | src/OptPme.C | commented a printf |
| 2009/02/11 21:07:23 | chaomei2 | +5 -5 | 1.1149 | src/SimParameters.h | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:22 | chaomei2 | +7 -7 | 1.1269 | src/SimParameters.C | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:22 | chaomei2 | +1 -1 | 1.1020 | src/Parameters.h | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:22 | chaomei2 | +3 -3 | 1.1041 | src/Parameters.C | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:22 | chaomei2 | +12 -4 | 1.1093 | src/Node.C | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:22 | chaomei2 | +1 -1 | 1.1079 | src/Molecule.h | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/11 21:07:21 | chaomei2 | +3 -3 | 1.1152 | src/Molecule.C | Interface changes for send_SimParameters/Parameters/Molecule to make them consistent with their receiving counterpart. |
| 2009/02/09 20:11:45 | gzheng | +3 -0 | 1.35 | src/Sync.C | open pe 0 prints "useProxySync is turned on." |
| 2009/02/07 01:33:13 | jim | +1 -1 | 1.1246 | Makefile | typo |
| 2009/02/07 01:25:29 | jim | +4 -0 | 1.2 | psfgen/src/topo_mol_pluginio.c | fix _snprintf for WIN32 |
| 2009/02/06 23:13:15 | jim | +0 -1 | 1.6 | psfgen/src/topo_mol_struct.h | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | None | 1.1 | psfgen/src/topo_mol_pluginio.h | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | None | 1.1 | psfgen/src/topo_mol_pluginio.c | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | +30 -9 | 1.7 | psfgen/src/topo_mol_output.c | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | +1 -5 | 1.9 | psfgen/src/topo_mol.c | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | +109 -3 | 1.13 | psfgen/src/tcl_psfgen.c | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | +12 -13 | 1.6 | psfgen/src/psf_file_extract.c | Update psfgen to use plugins |
| 2009/02/06 23:13:15 | jim | +1 -6 | 1.3 | psfgen/src/psf_file.h | Update psfgen to use plugins |
| 2009/02/06 23:13:14 | jim | +24 -92 | 1.3 | psfgen/src/psf_file.c | Update psfgen to use plugins |
| 2009/02/06 23:13:09 | jim | +7 -6 | 1.1245 | Makefile | Update psfgen to use plugins |
| 2009/02/06 23:13:09 | jim | +75 -12 | 1.123 | Make.depends | Update psfgen to use plugins |
| 2009/02/06 22:59:49 | jim | +28 -9 | 1.3 | plugins/include/libmolfile_plugin.h | use script in plugins tree to create static header |
| 2009/02/06 22:59:44 | jim | +4 -0 | 1.4 | plugins/import_tree | use script in plugins tree to create static header |
| 2009/02/06 19:29:58 | jim | +20 -30 | 1.48 | config | Clean up config script, remove Win32 cruft, and look harder for charm. |
| 2009/02/06 19:07:00 | jim | +7 -5 | 1.4 | plugins/include/vmdplugin.h | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | +4 -4 | 1.2 | arch/Win64.base | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | +5 -11 | 1.3 | arch/Win64-MSVC.arch | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | +5 -6 | 1.10 | arch/Win32.tcl | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | +3 -3 | 1.6 | arch/Win32.fftw | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | +4 -4 | 1.5 | arch/Win32.base | Cleanup Win32 build system. |
| 2009/02/06 19:06:59 | jim | None | 1.1 | arch/Win32-MSVC.arch | Cleanup Win32 build system. |
| 2009/02/06 19:06:58 | jim | +6 -5 | 1.47 | config | Cleanup Win32 build system. |
| 2009/02/06 19:06:58 | jim | +8 -7 | 1.1244 | Makefile | Cleanup Win32 build system. |
| 2009/02/06 19:06:58 | jim | +0 -1 | 1.18 | Make.charm | Cleanup Win32 build system. |
| 2009/02/06 16:40:17 | jim | +6 -0 | 1.3 | src/colvartypes.h | Small fixes to build on Win32. |
| 2009/02/06 16:40:17 | jim | +5 -0 | 1.5 | src/colvarmodule.C | Small fixes to build on Win32. |
| 2009/02/06 16:40:17 | jim | +1 -1 | 1.3 | src/colvarbias_abf.C | Small fixes to build on Win32. |
| 2009/02/06 16:40:17 | jim | +6 -0 | 1.1072 | src/ProxyMgr.C | Small fixes to build on Win32. |
| 2009/02/06 16:40:17 | jim | +12 -12 | 1.2 | src/OptPmeRealSpace.C | Small fixes to build on Win32. |
| 2009/02/06 16:40:17 | jim | +1 -0 | 1.2 | src/MGridforceParams.h | Small fixes to build on Win32. |
| 2009/02/06 16:40:16 | jim | +2 -2 | 1.6 | src/GridForceGrid.h | Small fixes to build on Win32. |
| 2009/01/30 23:27:14 | jim | +4 -3 | 1.1192 | src/WorkDistrib.C | Removed small memory leak. |
| 2009/01/30 23:25:28 | jim | +4 -3 | 1.10 | arch/AIX-POWER-xlC.arch | Reduced optimization to eliminate crashes. |
| 2009/01/26 18:05:04 | jim | +1 -0 | 1.2 | src/ComputeNonbondedCUDA.h | Fixed to work with CompAtomExt changes. |
| 2009/01/26 18:05:04 | jim | +23 -19 | 1.2 | src/ComputeNonbondedCUDA.C | Fixed to work with CompAtomExt changes. |
| 2009/01/08 03:48:08 | jim | +1 -1 | 1.34 | src/Sync.C | Eliminate stupid Sync buffer overflow message. |
| 2008/12/31 00:14:19 | jim | +6 -1 | 1.13 | src/Settle.C | Make SSE work with Portland Group compilers (pgcc). |
| 2008/12/31 00:14:19 | jim | +3 -1 | 1.1153 | src/ComputeNonbondedBase.h | Make SSE work with Portland Group compilers (pgcc). |
| 2008/12/22 20:15:34 | sameer | +1 -1 | 1.26 | src/RecBisection.C | Assigning patches to processor 0 in each node. |
| 2008/12/19 20:40:23 | jim | +14 -0 | 1.46 | config | Add --with-memopt option to config. |
| 2008/12/19 20:40:23 | jim | +3 -3 | 1.1243 | Makefile | Add --with-memopt option to config. |
| 2008/12/19 20:38:23 | jim | +4 -0 | 1.1025 | src/PDB.C | Fixes to compile memory optimized version. |
| 2008/12/19 20:38:23 | jim | +15 -0 | 1.1151 | src/Molecule.C | Fixes to compile memory optimized version. |
| 2008/12/19 20:35:11 | jim | +5 -5 | 1.1229 | src/Controller.C | Extend maximum field width to allow 100M-atom systems. |
| 2008/12/19 19:06:39 | jim | +7 -7 | 1.4 | src/GlobalMasterTMD.C | Rename local Matrix4 class in case it is not inlined. This version isalmost the same as Matrix4.h but not quite. |
| 2008/12/18 23:32:40 | jim | +3 -2 | 1.4 | src/colvarmodule.C | Fix a couple of portability issues. |
| 2008/12/18 23:32:40 | jim | +4 -3 | 1.1071 | src/ProxyMgr.C | Fix a couple of portability issues. |
| 2008/12/18 23:32:40 | jim | +1 -1 | 1.4 | src/OptPme.C | Fix a couple of portability issues. |
| 2008/12/18 22:57:18 | jim | +2 -0 | 1.3 | src/fftlib.C | fixing compile errors on Solaris-x86 |
| 2008/12/18 22:57:18 | jim | +2 -2 | 1.2 | src/colvarparse.h | New files added: 1. colvargrid.C, 2. colvargrid.h. New features: 1) In the colvars components: added eigenvector. Computes the projection of the coordinates on the NMA modes or some other vector field. 2) In metadynamics: can now change the size and resolution of the PMF grid. Two options to do that are available: a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or b) let the code itself expand the boundaries as needed (keyword: expandBoundaries). 3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run. 4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed). 5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent). 6) Cross time-correlation functions between two colvars (in addition to the ACFs). 7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning. |
| 2008/12/18 22:57:17 | jim | +2 -0 | 1.3 | src/OptPme.C | fixing compile errors on Solaris-x86 |
| 2008/12/18 22:19:43 | jim | +15 -8 | 1.1268 | src/SimParameters.C | Prevent specifying separate coordinates file with plugin IO. |
| 2008/12/18 22:19:42 | jim | +2 -0 | 1.29 | src/NamdOneTools.C | Prevent specifying separate coordinates file with plugin IO. |
| 2008/12/18 20:38:13 | jim | +10 -10 | 1.1048 | src/ProxyPatch.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +5 -5 | 1.1051 | src/Patch.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +5 -55 | 1.1037 | src/NamdTypes.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +1 -1 | 1.1161 | src/HomePatch.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +3 -3 | 1.7 | src/ComputeTclBC.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +3 -3 | 1.19 | src/ComputeSelfTuples.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +2 -2 | 1.17 | src/ComputeRestraints.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +2 -2 | 1.123 | src/ComputePme.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:13 | jim | +5 -5 | 1.32 | src/ComputeNonbondedBase2.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +33 -33 | 1.1152 | src/ComputeNonbondedBase.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +4 -4 | 1.1030 | src/ComputeImpropers.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +3 -3 | 1.1053 | src/ComputeHomeTuples.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +1 -1 | 1.3 | src/ComputeExtMgr.ci | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +1 -0 | 1.2 | src/ComputeExt.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +14 -5 | 1.9 | src/ComputeExt.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +2 -2 | 1.4 | src/ComputeEwald.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +4 -4 | 1.1032 | src/ComputeDihedrals.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +8 -8 | 1.6 | src/ComputeCrossterms.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +2 -2 | 1.1027 | src/ComputeBonds.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +3 -3 | 1.1033 | src/ComputeAngles.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:12 | jim | +2 -2 | 1.1012 | src/AtomMap.h | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 20:38:11 | jim | +4 -4 | 1.1018 | src/AtomMap.C | Slightly more efficient splitting between CompAtom and CompAtomExt.Atom id now lives in CompAtomExt. |
| 2008/12/18 17:27:39 | jim | +6 -6 | 1.1191 | src/WorkDistrib.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:39 | jim | +21 -20 | 1.1036 | src/NamdTypes.h | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +3 -3 | 1.1160 | src/HomePatch.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +2 -2 | 1.4 | src/DumpBench.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +2 -1 | 1.122 | src/ComputePme.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +5 -4 | 1.31 | src/ComputeNonbondedBase2.h | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +36 -45 | 1.1151 | src/ComputeNonbondedBase.h | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +4 -4 | 1.1029 | src/ComputeImpropers.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:38 | jim | +2 -1 | 1.3 | src/ComputeEwald.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:37 | jim | +4 -4 | 1.1031 | src/ComputeDihedrals.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:37 | jim | +8 -8 | 1.5 | src/ComputeCrossterms.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:37 | jim | +2 -2 | 1.1026 | src/ComputeBonds.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 17:27:37 | jim | +3 -3 | 1.1032 | src/ComputeAngles.C | Rearrange CompAtom and CompAtomExt fields to support 2^28 atoms. |
| 2008/12/18 01:17:35 | sameer | +10 -20 | 1.3 | src/fftmap.h | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/18 01:17:35 | sameer | +4 -1 | 1.2 | src/fftlib.h | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/18 01:17:35 | sameer | +2 -2 | 1.2 | src/fftlib.ci | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/18 01:17:35 | sameer | +27 -5 | 1.2 | src/fftlib.C | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/18 01:17:34 | sameer | +1 -1 | 1.1267 | src/SimParameters.C | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/18 01:17:34 | sameer | +25 -6 | 1.2 | src/OptPme.C | Enabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams. |
| 2008/12/17 23:18:36 | sameer | +20 -10 | 1.2 | src/fftmap.h | Adding assertions to guard currently unsupported cases. |
| 2008/12/17 22:27:48 | sameer | +166 -28 | 1.122 | Make.depends | New optimized pme header and source files. |
| 2008/12/17 22:27:47 | sameer | +21 -0 | 1.1242 | Makefile | New optimized pme header and source files. |
| 2008/12/17 22:27:03 | sameer | None | 1.1 | src/OptPmeRealSpace.h | Adding new optimized PME. |
| 2008/12/17 22:27:03 | sameer | None | 1.1 | src/OptPmeRealSpace.C | Adding new optimized PME. |
| 2008/12/17 22:26:22 | sameer | +1 -0 | 1.1017 | src/main.ci | Adding files for the new optimized PME. |
| 2008/12/17 22:26:22 | sameer | +1 -0 | 1.1065 | src/main.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:22 | sameer | None | 1.1 | src/fftmap.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:21 | sameer | None | 1.1 | src/fftlib.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:21 | sameer | None | 1.1 | src/fftlib.ci | Adding files for the new optimized PME. |
| 2008/12/17 22:26:21 | sameer | None | 1.1 | src/fftlib.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:21 | sameer | +40 -14 | 1.1190 | src/WorkDistrib.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:21 | sameer | +7 -4 | 1.1148 | src/SimParameters.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | +9 -4 | 1.1266 | src/SimParameters.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | +1 -0 | 1.1047 | src/ProxyPatch.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | +77 -0 | 1.7 | src/PmeBase.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | None | 1.1 | src/OptPme.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | None | 1.1 | src/OptPme.ci | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | None | 1.1 | src/OptPme.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:20 | sameer | +37 -9 | 1.1092 | src/Node.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:19 | sameer | +3 -0 | 1.1032 | src/Lattice.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:19 | sameer | +0 -3 | 1.26 | src/ComputePme.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:19 | sameer | +12 -72 | 1.121 | src/ComputePme.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:19 | sameer | +6 -0 | 1.1078 | src/ComputeMgr.C | Adding files for the new optimized PME. |
| 2008/12/17 22:26:19 | sameer | +1 -0 | 1.1040 | src/ComputeMap.h | Adding files for the new optimized PME. |
| 2008/12/17 22:26:18 | sameer | +4 -2 | 1.37 | src/BackEnd.C | Adding files for the new optimized PME. |
| 2008/12/17 21:32:08 | jim | +5 -5 | 1.1189 | src/WorkDistrib.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -7 | 1.1046 | src/ProxyPatch.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.1030 | src/Patch.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +8 -8 | 1.1035 | src/NamdTypes.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -2 | 1.1061 | src/HomePatch.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -16 | 1.1159 | src/HomePatch.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.6 | src/ComputeSphericalBC.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.8 | src/ComputeSphericalBC.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -2 | 1.18 | src/ComputeSelfTuples.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.10 | src/ComputeRestraints.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.16 | src/ComputeRestraints.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:08 | jim | +0 -4 | 1.1015 | src/ComputePatchPair.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -8 | 1.1029 | src/ComputePatchPair.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -4 | 1.1016 | src/ComputePatch.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -4 | 1.1027 | src/ComputePatch.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -2 | 1.1064 | src/ComputeNonbondedUtil.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -4 | 1.1018 | src/ComputeNonbondedSelf.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -6 | 1.1037 | src/ComputeNonbondedSelf.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -4 | 1.1020 | src/ComputeNonbondedPair.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -6 | 1.1045 | src/ComputeNonbondedPair.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +1 -1 | 1.30 | src/ComputeNonbondedBase2.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -29 | 1.1150 | src/ComputeNonbondedBase.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -10 | 1.1052 | src/ComputeHomeTuples.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:07 | jim | +0 -4 | 1.11 | src/ComputeCylindricalBC.h | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/17 21:32:06 | jim | +0 -4 | 1.14 | src/ComputeCylindricalBC.C | Make CompAtomExt from MEM_OPT_VERSION part of regular build. |
| 2008/12/16 21:19:16 | jim | +2 -0 | 1.1024 | src/PDB.C | Fixed bugs in plugin-based file reader, now handles js files correctly. |
| 2008/12/16 21:19:16 | jim | +6 -5 | 1.1064 | src/NamdState.C | Fixed bugs in plugin-based file reader, now handles js files correctly. |
| 2008/12/16 21:19:15 | jim | +38 -42 | 1.1150 | src/Molecule.C | Fixed bugs in plugin-based file reader, now handles js files correctly. |
| 2008/12/16 21:17:07 | jim | +7 -4 | 1.1188 | src/WorkDistrib.C | no need for find_extremes with periodic cell |
| 2008/12/16 03:15:37 | dbwells2 | +5 -1 | 1.10 | src/GridForceGrid.C | Fixed continuity issue with gridforce. |
| 2008/12/15 17:02:23 | chaomei2 | +6 -4 | 1.1147 | src/SimParameters.h | Added options to use plugin-IO library to load molecule structure. |
| 2008/12/15 17:02:23 | chaomei2 | +5 -3 | 1.1265 | src/SimParameters.C | Added options to use plugin-IO library to load molecule structure. |
| 2008/12/15 17:01:12 | chaomei2 | +2 -1 | 1.1013 | src/PDBData.h | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:12 | chaomei2 | +5 -1 | 1.1014 | src/PDB.h | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:12 | chaomei2 | +51 -0 | 1.1023 | src/PDB.C | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:12 | chaomei2 | +71 -14 | 1.1063 | src/NamdState.C | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:12 | chaomei2 | +24 -0 | 1.1078 | src/Molecule.h | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:12 | chaomei2 | +383 -1 | 1.1149 | src/Molecule.C | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:11 | chaomei2 | None | 1.1 | src/PluginIOMgr.h | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 17:01:11 | chaomei2 | None | 1.1 | src/PluginIOMgr.C | Added support for initializing Molecule and PDB object by using plugi-IO library. |
| 2008/12/15 16:58:29 | chaomei2 | +1 -0 | 1.1241 | Makefile | Add rules for PluginIOMgr class |
| 2008/12/15 16:58:29 | chaomei2 | +109 -10 | 1.121 | Make.depends | Add rules for PluginIOMgr class |
| 2008/12/09 20:11:29 | jim | +5 -2 | 1.1240 | Makefile | update dependencies for new plugins |
| 2008/12/09 20:11:29 | jim | +32 -1 | 1.120 | Make.depends | update dependencies for new plugins |
| 2008/12/09 20:10:36 | jim | +11 -3 | 1.2 | plugins/include/libmolfile_plugin.h | add plugin declarations |
| 2008/12/09 19:46:24 | jim | None | 1.1 | plugins/molfile_plugin/src/readpdb.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:24 | jim | None | 1.1 | plugins/molfile_plugin/src/psfplugin.c | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | None | 1.1 | plugins/molfile_plugin/src/periodic_table.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | None | 1.1 | plugins/molfile_plugin/src/pdbplugin.c | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | +0 -0 | 1.2 | plugins/molfile_plugin/src/largefiles.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | None | 1.1 | plugins/molfile_plugin/src/jsplugin.c | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | None | 1.1 | plugins/molfile_plugin/src/hash.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:23 | jim | None | 1.1 | plugins/molfile_plugin/src/hash.c | importing new plugins, updating old ones |
| 2008/12/09 19:46:22 | jim | None | 1.1 | plugins/molfile_plugin/src/fortread.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:22 | jim | +215 -3 | 1.3 | plugins/molfile_plugin/src/fastio.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:22 | jim | +0 -0 | 1.3 | plugins/molfile_plugin/src/endianswap.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:22 | jim | +301 -145 | 1.3 | plugins/molfile_plugin/src/dcdplugin.c | importing new plugins, updating old ones |
| 2008/12/09 19:46:17 | jim | +12 -10 | 1.3 | plugins/include/vmdplugin.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:17 | jim | +273 -34 | 1.3 | plugins/include/molfile_plugin.h | importing new plugins, updating old ones |
| 2008/12/09 19:46:14 | jim | +3 -1 | 1.3 | plugins/import_tree | importing new plugins, updating old ones |
| 2008/12/05 02:45:01 | petefred | +5 -1 | 1.1040 | src/Parameters.C | Fix initialization of cosangles flag when using amber or gromacs files |
