CVS time sorted logs

Time Author Lines Revision Filename Comments
2009/11/24 04:27:00 bhatele +2 -2 1.2 arch/MacOSX-x86_64-g++.archcompilation fixes for Mac
2009/11/24 04:26:59 bhatele +5 -5 1.1177 src/Molecule.Ccompilation fixes for Mac
2009/11/20 22:25:06 brunner +3 -3 1.1055 src/common.hReplaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers
2009/11/20 22:25:05 brunner +25 -25 1.1045 src/Parameters.CReplaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers
2009/11/20 22:25:05 brunner +3 -3 1.36 src/ComputeNonbondedBase2.hReplaced nearbyint() with mynearbyint macro, for compatibility with variouscompilers
2009/11/17 21:11:11 jim +7 -7 1.56 configfix missing quotes needed to handle options that are quoted lists
2009/11/13 04:50:03 jim +89 -0 1.15 ug/ug_runit.texUpdated from 2.7b2 notes.txt
2009/11/13 03:52:07 jim +4 -0 1.1054 src/common.hFix win32 build via #define nearbyint(X) floor((X)+0.5)
2009/11/13 02:54:55 jim +8 -8 1.17 src/memusage.CFix windows build.
2009/11/13 00:02:29 bhatele +3 -3 1.85 src/Rebalancer.Cthe 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.archupdate to net-aix-ppc
2009/11/12 22:51:36 jim +4 -4 1.55 configLook for charm-6.1.3 instead of charm-6.1
2009/11/12 22:33:43 jim +81 -0 1.70 notes.txtupdate for 2.7b2 release
2009/11/12 22:33:43 jim +6 -0 1.35 announce.txtupdate for 2.7b2 release
2009/11/12 20:28:16 char +5 -3 1.1294 src/SimParameters.Cadded 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.texadded 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.CDisable 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.CFix memopt builds.
2009/11/12 02:11:16 jim +4 -0 1.1176 src/Molecule.CFix memopt builds.
2009/11/12 01:54:28 jim +1 -1 1.7 src/ComputeNonbondedCUDAKernel.cuClean up CUDA output.
2009/11/12 01:54:28 jim +8 -4 1.20 src/ComputeNonbondedCUDA.CClean up CUDA output.
2009/11/12 01:54:06 jim +20 -3 1.1241 src/Controller.CWarn about bad pressure tensor and expensive energy evaluation with CUDA.
2009/11/11 23:23:59 jim +3 -2 1.19 src/ComputeNonbondedCUDA.Cremove 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.hNew 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.CNew 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.CNew 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 configmake config script work with CUDA 3.x
2009/11/11 05:19:04 jim +1 -2 1.4 arch/Linux-x86_64.cudaWorkaround 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 MakefileWorkaround 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/Makefileupdate versions to 2.7b1 and charm-6.1.3
2009/11/11 05:01:47 jim +9 -9 1.69 notes.txtupdate versions to 2.7b1 and charm-6.1.3
2009/11/11 05:01:47 jim +3 -3 1.34 announce.txtupdate versions to 2.7b1 and charm-6.1.3
2009/11/11 05:01:47 jim +1 -1 1.1260 Makefileupdate versions to 2.7b1 and charm-6.1.3
2009/11/11 04:46:22 jim +2 -1 1.3 arch/Linux-x86_64.cudaMake that libcudart.so.2 and also copy it to build directory.
2009/11/11 04:46:20 jim +4 -1 1.1259 MakefileMake 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.cudainclude libcudart.so in release
2009/11/11 04:18:34 jim +1 -1 1.1258 Makefileinclude libcudart.so in release
2009/11/11 03:37:53 jim +6 -6 1.1159 src/ComputeNonbondedBase.hFix performance bug in pairlist generation.
2009/11/11 02:35:45 jim +1 -1 1.1043 src/Parameters.Cremove debugging output
2009/11/09 21:12:02 jim +1 -0 1.1022 src/ParseOptions.CAlways initialize simulation parameters to default value.
2009/11/06 23:03:04 jim +1 -3 1.1257 MakefileDon'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.hreduce 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.Cmeaningless rearrangement to avoid Mac PPC compiler bug
2009/10/30 17:50:42 jim +4 -2 1.17 src/ComputeNonbondedCUDA.Cchanged to the new cpu topology API
2009/10/28 21:27:59 gzheng +6 -5 1.1049 src/ReductionMgr.Cchanged to the new cpu topology API
2009/10/28 01:40:05 char +3 -0 1.6 src/colvaratoms.Ccolvars dummy atom center of mass bugfix
2009/10/27 22:56:45 dhardy +19 -25 1.2 ug/ug_dynamics.texfixed the documentation for longSplitting and the new 'c2' option
2009/10/27 22:56:45 dhardy +15 -3 1.11 ug/ug.bibfixed the documentation for longSplitting and the new 'c2' option
2009/10/27 21:50:09 dhardy +5 -4 1.1157 src/SimParameters.hImproved 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.CImproved 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.CImproved 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 MakefileAdded ComputeNonbondedTabPot.[Ch]
2009/10/27 18:52:28 brunner +65 -15 1.128 Make.dependsAdded ComputeNonbondedTabPot.[Ch]
2009/10/27 18:50:05 brunner +11 -2 1.1156 src/SimParameters.hAdded 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.CAdded 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.hAdded 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.CAdded 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.hAdded 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.CAdded 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.hAdded 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.CAdded 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.CAdded 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.hAdded 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.hAdded 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.Cconfig file parameters and variable names changed for spanning trees
2009/10/09 20:09:05 bhatele +9 -9 1.1155 src/SimParameters.hconfig file parameters and variable names changed for spanning trees
2009/10/09 20:09:04 bhatele +7 -7 1.1290 src/SimParameters.Cconfig file parameters and variable names changed for spanning trees
2009/10/09 20:09:04 bhatele +2 -2 1.1096 src/Node.Cconfig file parameters and variable names changed for spanning trees
2009/10/09 16:03:02 gzheng None 1.1 arch/Cygwin-MPI-mingw.archbuild with MS MPI and Mingw
2009/10/09 16:00:51 gzheng +3 -3 1.43 src/BackEnd.Cenable mingw
2009/10/08 23:17:32 jim +1 -1 1.22 Make.charmCharm 6.1.3
2009/10/04 19:12:40 gzheng +3 -0 1.1067 src/main.Cprint info whether cputopology info is available or not.
2009/10/03 23:56:49 bhatele +11 -7 1.84 src/Rebalancer.Cerror check and minor fixes
2009/10/02 22:57:04 bohm +4 -1 1.125 src/ComputePme.Ccleanup to avoid memory leak in commOnly
2009/09/30 15:19:08 gzheng +1 -1 1.16 src/memusage.Cbackported 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.CFor windows, call CmiMmemoryUsage to get accurate numbers.
2009/09/30 00:23:58 gzheng +4 -0 1.1174 src/Molecule.Cdefine M_PI when needed
2009/09/29 04:50:09 gzheng +2 -1 1.2 src/colvargrid.hround is not defined in VC++
2009/09/29 04:41:14 gzheng None 1.1 arch/Win64.tclarch files of fftw and tcl for win64
2009/09/29 04:41:14 gzheng None 1.1 arch/Win64.fftwarch files of fftw and tcl for win64
2009/09/29 04:38:37 gzheng +5 -0 1.1022 src/Parameters.hdefine cbrt if it is undefined
2009/09/29 04:35:26 gzheng +1 -1 1.12 src/MStream.hcast size_t in pup length to avoid ambiguity in overloading
2009/09/21 00:36:49 dhardy +1 -66 1.1173 src/Molecule.Cremoved dead code for Drude exclusions
2009/09/20 22:29:51 dhardy +13 -0 1.1172 src/Molecule.Cinitialize lphostIndexes to index lphosts array through atomid of the lone pair
2009/09/20 22:05:58 dhardy +20 -3 1.1087 src/Molecule.hRemoved 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.CRemoved 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.Cchanged 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.hchanged 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.CFixed 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.CRemove fflush calls left over from debugging.
2009/09/16 23:04:56 dhardy +32 -0 1.1018 src/structures.hPSF reader for Drude model, fix 1-3 exclusions for Drude particles
2009/09/16 23:04:56 dhardy +21 -1 1.1086 src/Molecule.hPSF reader for Drude model, fix 1-3 exclusions for Drude particles
2009/09/16 23:04:56 dhardy +208 -0 1.1169 src/Molecule.CPSF reader for Drude model, fix 1-3 exclusions for Drude particles
2009/09/08 16:21:39 jim +1 -1 1.1021 src/LJTable.CNFBIX -> NBFIX in CUDA warning
2009/09/03 21:52:25 brunner +1 -1 1.4 src/colvarparse.hCompiler workarounds for Solaris X86_64
2009/09/03 21:52:25 brunner +2 -1 1.1168 src/Molecule.CCompiler workarounds for Solaris X86_64
2009/08/31 21:06:01 brunner +28 -19 1.1048 src/ReductionMgr.CFixed error with node-local reduction code. It works on Abe now.
2009/08/28 20:57:00 jim +9 -2 1.1288 src/SimParameters.CFixed atoms need forces calculated to get correct pressure from CUDA.
2009/08/27 20:25:10 jim +5 -3 1.1287 src/SimParameters.CDon't remove patches from any pe with CUDA enabled.
2009/08/27 20:15:11 jim +38 -3 1.1196 src/WorkDistrib.CEnsure at least one patch per processor for CUDA-enabled NAMD.
2009/08/27 19:09:38 jim +4 -0 1.15 src/ComputeNonbondedCUDA.CDisable useFlexibleCell with CUDA.
2009/08/27 18:04:40 jim +12 -2 1.1175 src/Sequencer.Cadditional diagnostics
2009/08/27 18:01:23 jim +2 -2 1.4 src/ComputeNonbondedCUDAKernel.henable multiple timestepping with CUDA
2009/08/27 18:01:23 jim +39 -8 1.6 src/ComputeNonbondedCUDAKernel.cuenable multiple timestepping with CUDA
2009/08/27 18:01:23 jim +2 -1 1.3 src/ComputeNonbondedCUDAExcl.henable multiple timestepping with CUDA
2009/08/27 18:01:23 jim +47 -16 1.6 src/ComputeNonbondedCUDAExcl.Cenable multiple timestepping with CUDA
2009/08/27 18:01:23 jim +43 -18 1.14 src/ComputeNonbondedCUDA.Cenable multiple timestepping with CUDA
2009/08/26 21:04:24 jim +2 -2 1.5 src/ComputeNonbondedCUDAExcl.CPut exclusion forces in the correct array for multiple timestepping.
2009/08/26 19:55:22 jim +3 -1 1.3 src/ComputeNonbondedCUDAKernel.hIncrease size of interpolation table to improve force/pressure accuracy.
2009/08/26 19:55:21 jim +3 -1 1.13 src/ComputeNonbondedCUDA.CIncrease size of interpolation table to improve force/pressure accuracy.
2009/08/26 19:30:49 jim +4 -0 1.1020 src/LJTable.CSafety check for NBFIX parameters not supported in CUDA version.
2009/08/17 21:28:24 chaomei2 +3 -3 1.1038 src/ProxyMgr.hDisabled 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.CDisabled 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.CDisabled 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.cppupdate/bugfix for abf_integrate
2009/08/14 22:53:02 char +81 -61 1.2 lib/abf_integrate/abf_data.hupdate/bugfix for abf_integrate
2009/08/14 22:53:02 char +219 -167 1.2 lib/abf_integrate/abf_data.cppupdate/bugfix for abf_integrate
2009/08/13 06:17:55 chaomei2 +33 -0 1.1037 src/ProxyMgr.hFix 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.CFix 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.CFix 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.texNew 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.hNew 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.CNew 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.hNew 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.hNew 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.CNew 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.hNew 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.hNew 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.CNew 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.hNew 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.CNew 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.CNew 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.CNew 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.CNew 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.CNew 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.CNew 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.hNew 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.CNew 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.hNew 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.CNew 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.hNew 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.CNew 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.hNew 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.hNew 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.CNew 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.hNew 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.CNew 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 MakefileNew 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.dependsNew 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.CMake physical node code build with released versions of charm.
2009/08/12 20:45:39 jim +10 -7 1.1286 src/SimParameters.CBe sure that alchFepOn and alchThermIntOn are set to FALSE by default.
2009/08/12 20:40:51 jim +4 -3 1.1240 src/Controller.CFix trajectory output during initial stages of minimization.
2009/08/07 04:43:04 jim +5 -3 1.1285 src/SimParameters.CDon't remove patches from pe 0 when CUDA is enabled.
2009/08/06 17:23:58 brunner +25 -2 1.1047 src/ReductionMgr.hReductions 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.CReductions 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.CFix 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.CFixed 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.dependsAdded new GridForce files
2009/07/20 20:55:03 brunner +9 -1 1.1254 MakefileAdded ComputeGridForceMgr
2009/07/20 20:51:41 brunner +1 -0 1.1018 src/main.ciThis 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.CThis 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.CThis 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.hThis 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.CThis 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.hThis 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.CThis 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.CThis 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.hThis 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.CThis 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.CThis 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.hThis 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.CDon'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.texAdd 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.CMake sure that we're using pbc if LJcorrection is on
2009/07/13 00:22:30 petefred +5 -5 1.1239 src/Controller.CMake sure that we're using pbc if LJcorrection is on
2009/07/08 14:57:32 char +9 -5 1.1281 src/SimParameters.Cfixed minor bug in alchemical module faulting initialization of alchFepOn & alchThermIntOn.
2009/07/01 22:08:55 dbwells2 +7 -1 1.7 src/GridForceGrid.hUpdated 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.CUpdated 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.CUpdated 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.CWrite .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.Cifdef to work with pre-2.2 cuda
2009/06/22 07:28:54 jim +1 -1 1.2 src/ComputeNonbondedCUDAKernel.hscale offset vectors at every step to allow constant pressure
2009/06/22 07:28:54 jim +21 -2 1.5 src/ComputeNonbondedCUDAKernel.cuscale offset vectors at every step to allow constant pressure
2009/06/22 07:28:54 jim +17 -10 1.11 src/ComputeNonbondedCUDA.Cscale offset vectors at every step to allow constant pressure
2009/06/22 06:52:20 jim +1 -3 1.4 src/ComputeNonbondedCUDAKernel.cuSimpler calculation for virial.
2009/06/22 06:47:57 jim +4 -0 1.1031 src/PatchMap.huse offsets relative to patch centers on GPU
2009/06/22 06:47:57 jim +3 -0 1.1048 src/PatchMap.Cuse offsets relative to patch centers on GPU
2009/06/22 06:47:57 jim +1 -1 1.4 src/ComputeNonbondedCUDA.huse offsets relative to patch centers on GPU
2009/06/22 06:47:57 jim +27 -24 1.10 src/ComputeNonbondedCUDA.Cuse offsets relative to patch centers on GPU
2009/06/22 05:36:59 jim +9 -7 1.3 src/ComputeNonbondedCUDAKernel.cuscalar pressure calculation on GPU - won't work with flexible cells
2009/06/22 05:36:59 jim +2 -2 1.2 src/ComputeNonbondedCUDAExcl.hscalar pressure calculation on GPU - won't work with flexible cells
2009/06/22 05:36:59 jim +6 -8 1.4 src/ComputeNonbondedCUDAExcl.Cscalar pressure calculation on GPU - won't work with flexible cells
2009/06/22 05:36:59 jim +14 -4 1.9 src/ComputeNonbondedCUDA.Cscalar pressure calculation on GPU - won't work with flexible cells
2009/06/22 02:06:26 char +71 -69 1.6 src/colvarproxy_namd.Cbugfixes 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.hbugfixes 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.Cbugfixes 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.Cbugfixes 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.CPunt 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.CAdd +ignoresharing flag to disable shared-GPU coordination messages.
2009/06/17 21:42:32 brunner +21 -13 1.3 ug/ug_userdef.texAdded 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.texFixed 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.CChanged 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.CChanged 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.CChanged 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.texMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +8 -12 1.1194 src/WorkDistrib.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +30 -34 1.1153 src/SimParameters.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +153 -150 1.1279 src/SimParameters.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +1 -1 1.2 src/OptPme.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +4 -4 1.6 src/OptPme.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:48 char +5 -18 1.1069 src/NamdState.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +38 -40 1.1165 src/Molecule.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +6 -7 1.6 src/DumpBenchParams.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +57 -58 1.1238 src/Controller.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +3 -3 1.27 src/ComputePme.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +48 -47 1.124 src/ComputePme.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +8 -8 1.1066 src/ComputeNonbondedUtil.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +20 -20 1.1092 src/ComputeNonbondedUtil.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:47 char +2 -2 1.4 src/ComputeNonbondedFEP.CMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:46 char +1 -1 1.34 src/ComputeNonbondedBase2.hMerged FEP and TI code into shared common interface. Updated manual accordingly.
2009/06/14 07:01:46 char +25 -25 1.1157 src/ComputeNonbondedBase.hMerged 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.CRepaired 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.texAdd documentation for LJ tail corrections
2009/06/14 01:28:16 petefred +16 -1 1.10 ug/ug.bibAdd documentation for LJ tail corrections
2009/06/14 01:27:31 petefred +8 -8 1.4 src/colvarproxy_namd.CRevert spurious commit to colvarproxy_namd
2009/06/14 01:23:50 petefred +9 -9 1.3 src/colvarproxy_namd.CImproved 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.hImproved 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.CImproved 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.hImproved 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.CImproved 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.CImproved 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.archCRAY XT pgcc build
2009/06/12 18:49:52 bhatele None 1.1 arch/MacOSX-x86_64.tclmacosx x86_64 build
2009/06/12 18:49:51 bhatele None 1.1 arch/MacOSX-x86_64.fftwmacosx x86_64 build
2009/06/12 18:49:51 bhatele None 1.1 arch/MacOSX-x86_64.basemacosx x86_64 build
2009/06/12 18:49:51 bhatele None 1.1 arch/MacOSX-x86_64-g++.archmacosx x86_64 build
2009/06/05 00:30:32 char +23 -7 1.1277 src/SimParameters.CUpdated output of FEP parameters; to clarify for user understanding
2009/06/03 17:14:45 char +37 -2 1.1068 src/NamdState.CUpdated 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.hUpdated 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.CUpdated 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.CBug fixes for loading ldb data from text file.
2009/05/29 20:54:59 jim +1 -0 1.1036 src/ProxyMgr.hMake compile with latest Charm++ that hides message envelope definition.
2009/05/27 18:16:28 jim +2 -2 1.26 ug/ug_alchemy.texRemove .pdf from images to fix latex2html.
2009/05/27 18:16:05 jim +6 -1 1.46 ug/Makefilebuild tarfile automatically
2009/05/27 02:46:17 char +1 -1 1.25 ug/ug_alchemy.texfixed typo in ug/ug_alchemy.tex
2009/05/26 21:19:09 char None 1.1 ug/figures/softcore_lambda.pngAdded 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.pdfAdded 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.texAdded 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.CCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 08:45:42 jim +0 -4 1.1046 src/ComputeNonbondedPair.CCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 08:45:42 jim +26 -14 1.3 src/ComputeNonbondedCUDAExcl.CCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 08:45:41 jim +11 -9 1.6 src/ComputeNonbondedCUDA.CCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 08:45:41 jim +6 -2 1.33 src/ComputeNonbondedBase2.hCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 08:45:41 jim +6 -0 1.1156 src/ComputeNonbondedBase.hCUDA-enabled NAMD now works with PME, but not multiple timestepping.
2009/05/22 04:16:20 jim +3 -1 1.2 src/ComputeNonbondedCUDAExcl.CFixes to exclusion calculation.
2009/05/21 23:23:55 chaomei2 +2 -1 1.1162 src/Molecule.CAdded 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.hChange 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.CFixed 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.hFixed 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.CFixed 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.archadded back the -m64 flag
2009/05/19 22:42:31 bhatele +3 -3 1.3 arch/Linux-x86_64-MPI-pathcc.archSiCortex arch files
2009/05/19 22:42:31 bhatele None 1.1 arch/Linux-mips64.tclSiCortex arch files
2009/05/19 22:42:31 bhatele None 1.1 arch/Linux-mips64.fftwSiCortex arch files
2009/05/19 22:42:31 bhatele None 1.1 arch/Linux-mips64.baseSiCortex arch files
2009/05/19 22:42:31 bhatele None 1.1 arch/Linux-mips64-MPI-pathcc.archSiCortex arch files
2009/05/19 22:42:30 bhatele None 1.1 arch/Linux-mips64-MPI-g++.archSiCortex arch files
2009/05/19 05:11:08 jim +1 -0 1.1253 MakefileImplement modified 1-4 exclusions for CUDA.
2009/05/19 05:10:29 jim +1 -0 1.1041 src/WorkDistrib.hImplement 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.ciImplement 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.CImplement 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.hImplement 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.CImplement 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.hImplement 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.inlImplement 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.hImplement 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.CImplement 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.hImplement 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.CImplement 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.hImplement 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.dependsImplement modified 1-4 exclusions for CUDA.
2009/05/13 21:05:17 jim +1 -1 1.41 src/BackEnd.COnly require +idlepoll for net version.
2009/05/13 16:10:43 jim +11 -0 1.68 notes.txtnotes on CUDA builds
2009/05/13 16:10:43 jim +2 -1 1.53 confignotes on CUDA builds
2009/05/12 18:21:21 brunner +8 -9 1.1276 src/SimParameters.CFixed 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.CFixed 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.CFixed 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.txtchange --no-shared to --no-build-shared (which matches charm docs)
2009/05/08 21:21:32 char +1 -1 1.23 ug/ug_alchemy.texinitial updates to alchemy
2009/05/07 19:47:22 jim +2 -1 1.2 src/ComputeNonbondedCUDAKernel.cuAttach events to non-zero stream in case this effects overlap.
2009/05/07 19:47:22 jim +16 -12 1.5 src/ComputeNonbondedCUDA.CAttach events to non-zero stream in case this effects overlap.
2009/05/07 19:11:58 jim +1 -1 1.1252 MakefileWhen making projections also enable summary because it's useful.
2009/05/07 18:00:14 jim +5 -1 1.3 src/ComputeNonbondedCUDA.hUse 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.CUse 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.hUse 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.ciUse 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.CUse 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.hAdded 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.hAdded 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.CAdded 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.CSwitched 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.hSwitched 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.CAdded /proc/self/stat as first alternative after CmiMemoryUsage (GNU).
2009/04/12 11:57:16 char +4 -4 1.1274 src/SimParameters.Cswitched 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.texfixed typo in ug_alchemy. switched fepOn to fep
2009/04/09 19:24:57 char +4 -4 1.1273 src/SimParameters.CAlchemical decouple default switched from FALSE to TRUE
2009/04/07 20:50:01 brunner None 1.1 ug/figures/gridshift.pdfFigures for grid force docs
2009/04/07 20:50:01 brunner None 1.1 ug/figures/gridshift.epsFigures for grid force docs
2009/04/07 20:49:36 brunner +126 -1 1.2 ug/ug_userdef.texAdded first draft of docs for grid forces
2009/04/07 20:49:36 brunner +14 -0 1.15 ug/ug_macros.texAdded first draft of docs for grid forces
2009/04/07 19:31:00 jim +1 -1 1.2 arch/Solaris-x86_64-CC.archSwitch to SMP.
2009/04/07 19:30:49 jim +5 -0 1.1066 src/main.CWarn about experimental memory optimized builds.
2009/04/03 18:48:54 jim +1 -1 1.1094 src/Node.CAdd ", see error messages above" to "Exiting prematurely".
2009/04/02 03:17:48 jim +87 -16 1.3 src/ComputeNonbondedCUDA.CUse new Charm++ PhysicalNode interface to find shared CUDA devices.
2009/04/02 03:17:48 jim +7 -2 1.40 src/BackEnd.CUse new Charm++ PhysicalNode interface to find shared CUDA devices.
2009/03/31 20:14:41 jim +2 -2 1.3 src/colvarbias_meta.hFix to build on IBM xlc 08.00.0000.0013.
2009/03/26 21:43:55 jim +8 -0 1.1066 src/NamdState.CPrint 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.CMake minimizer more robust and informative at startup.
2009/03/26 19:44:02 jim +6 -6 1.39 src/BackEnd.CFix CUDA build.
2009/03/25 21:58:22 jim +3 -2 1.1174 src/Sequencer.CMinimizer should not slowly move *fixed* atoms downhill.
2009/03/25 19:43:56 chaomei2 +1 -1 1.7 src/CompressPsf.hChanged 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.CChanged 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.CChanged 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-initwhite background for figures works again
2009/03/25 05:00:50 jim +1 -1 1.45 ug/Makefileonly build pdf before html since dvi build fails
2009/03/24 03:01:55 char +3 -3 1.21 ug/ug_alchemy.texChanged default keyword values to match those in SimParameters
2009/03/23 22:44:08 jim +1 -0 1.2 ug/ug_forcefield.texFix references.
2009/03/23 22:44:08 jim +1 -1 1.7 ug/ug_colvars.texFix references.
2009/03/23 21:06:58 char +141 -107 1.2 ug/figures/TI.pdfupdated refs for alchemical section
2009/03/23 21:06:58 char +1 -2 1.26 ug/ug_intro.texupdated refs for alchemical section
2009/03/23 21:06:58 char +120 -153 1.20 ug/ug_alchemy.texupdated refs for alchemical section
2009/03/23 21:06:57 char +66 -15 1.9 ug/ug.bibupdated refs for alchemical section
2009/03/23 07:11:57 jim +1 -1 1.66 notes.txtx86_64
2009/03/23 07:06:40 jim +64 -41 1.65 notes.txtmany updates to compile process.
2009/03/23 06:07:03 jim +4 -13 1.64 notes.txtperformance updates
2009/03/23 06:06:46 jim +2 -4 1.14 ug/ug_runit.texupdates
2009/03/23 06:05:04 jim +1 -1 1.11 ug/namd_macros.texupdate macros
2009/03/23 06:01:11 jim +10 -18 1.33 announce.txtUpdated
2009/03/23 05:44:32 jim +247 -411 1.63 notes.txtrearrange and update building
2009/03/23 05:20:16 jim +3 -10 1.12 README.txtcleaned up
2009/03/23 05:18:55 jim +19 -115 1.13 ug/ug_runit.texupdate docs
2009/03/23 05:18:55 jim +1 -66 1.25 ug/ug_intro.texupdate docs
2009/03/23 05:18:55 jim +3 -0 1.16 ug/ug.texupdate docs
2009/03/23 04:36:38 jim +17 -11 1.11 ug/ug_avail.texupdate
2009/03/23 03:59:49 jim +7 -1 1.6 ug/ug_colvars.texComment on replacing freeEnergy module.
2009/03/23 03:59:17 jim +5 -8 1.44 ug/MakefileBuild pdf by default (used to be ps).
2009/03/23 03:58:47 jim +2 -2 1.15 ug/ug.texRemove ancient freeEnergy module from docs.
2009/03/23 03:58:08 jim +1 -1 1.19 ug/ug_alchemy.texFix one easy ref (case error).
2009/03/19 19:36:05 chaomei2 +8 -1 1.18 src/mainfunc.CTweaked 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.CTweaked 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.Cswitched 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 MakefileFix winrelease target.
2009/03/13 18:25:21 jim +39 -1 1.124 Make.dependsRebuild to add Molecule2.o dependencies.
2009/03/13 18:19:51 jim None 1.1 src/Molecule2.CDeal 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.CDeal 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 MakefileDeal 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 configPattern for MacOSX.
2009/03/12 22:21:00 jim +1 -1 1.8 arch/MacOSX-PPC-xlC.archnet-ppc-darwin -> net-darwin-ppc
2009/03/12 22:21:00 jim +1 -1 1.4 arch/MacOSX-PPC-c++.archnet-ppc-darwin -> net-darwin-ppc
2009/03/12 21:54:23 jim +1 -1 1.43 ug/MakefileUpdate versions to NAMD 2.7b1 and Charm++ 6.1.
2009/03/12 21:54:20 jim +1 -4 1.51 configUpdate versions to NAMD 2.7b1 and Charm++ 6.1.
2009/03/12 21:54:20 jim +1 -1 1.1249 MakefileUpdate versions to NAMD 2.7b1 and Charm++ 6.1.
2009/03/12 21:54:20 jim +2 -2 1.21 Make.charmUpdate versions to NAMD 2.7b1 and Charm++ 6.1.
2009/03/12 02:18:46 petefred +3 -0 1.4 src/colvarbias_abf.CRemove 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.archAdd -qnohot to bypass xlC compiler bug.
2009/03/07 22:45:01 jim +1 -1 1.2 arch/Linux-PPC-MX64-xlc64.archAdd -qnohot to avoid xlC compiler bug.
2009/03/07 22:45:01 jim +1 -1 1.2 arch/Linux-PPC-MX-xlc.archAdd -qnohot to avoid xlC compiler bug.
2009/03/07 22:39:30 jim +24 -20 1.50 configMore help on building, don't search home dir for charm.
2009/03/07 22:39:30 jim +2 -0 1.20 Make.charmMore help on building, don't search home dir for charm.
2009/03/07 21:52:07 jim +1 -1 1.2 arch/Win32-MSVC.archSwitch Win32 to multicore.
2009/03/07 21:52:06 jim +2 -1 1.1248 MakefileSwitch Win32 to multicore.
2009/03/07 21:37:42 jim +1 -1 1.5 arch/CRAY-XT3.archRemove -I/usr/include that was breaking compiler.
2009/03/07 21:37:42 jim +1 -1 1.2 arch/CRAY-XT3-g++.archRemove -I/usr/include that was breaking compiler.
2009/03/07 21:37:42 jim +1 -1 1.2 arch/CRAY-XT.archRemove -I/usr/include that was breaking compiler.
2009/03/07 21:37:42 jim +1 -1 1.2 arch/CRAY-XT-g++.archRemove -I/usr/include that was breaking compiler.
2009/03/05 21:07:09 jim +1 -1 1.19 Make.charmUpdate to 6.0.1
2009/03/05 05:21:47 jim +8 -8 1.1235 src/Controller.CRearrange 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.CRemove 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.CMake iout thread-safe.
2009/03/04 21:20:59 jim +4 -1 1.1018 src/InfoStream.hMake iout thread-safe.
2009/03/04 21:20:59 jim +0 -1 1.1017 src/InfoStream.CMake iout thread-safe.
2009/03/03 18:57:35 chaomei2 +1 -0 1.1157 src/Molecule.CAdd 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 configChange i686/amd64 to x86/x86_64
2009/02/26 23:57:50 jim None 1.1 arch/Linux-Itanium.tclRename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64.
2009/02/26 23:57:50 jim None 1.1 arch/Linux-Itanium.fftwRename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64.
2009/02/26 23:57:50 jim None 1.1 arch/Linux-Itanium.baseRename 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.archRename Linux-ia64 to Linux-Itanium to avoid confusion with x86_64.
2009/02/26 23:39:41 jim None 1.1 arch/Linux-x86.tclRename Linux-i686 Linux-x86
2009/02/26 23:39:41 jim None 1.1 arch/Linux-x86.fftwRename Linux-i686 Linux-x86
2009/02/26 23:39:41 jim None 1.1 arch/Linux-x86.cudaRename Linux-i686 Linux-x86
2009/02/26 23:39:41 jim None 1.1 arch/Linux-x86.baseRename Linux-i686 Linux-x86
2009/02/26 23:39:40 jim None 1.1 arch/Linux-x86-icc.archRename Linux-i686 Linux-x86
2009/02/26 23:39:40 jim None 1.1 arch/Linux-x86-g++.archRename Linux-i686 Linux-x86
2009/02/26 22:59:56 jim None 1.1 arch/MacOSX-x86.tclRename MacOSX-i686 to MacOSX-x86.
2009/02/26 22:59:56 jim None 1.1 arch/MacOSX-x86.fftwRename MacOSX-i686 to MacOSX-x86.
2009/02/26 22:59:56 jim None 1.1 arch/MacOSX-x86.baseRename MacOSX-i686 to MacOSX-x86.
2009/02/26 22:59:56 jim None 1.1 arch/MacOSX-x86-g++.archRename MacOSX-i686 to MacOSX-x86.
2009/02/26 22:57:40 jim None 1.1 arch/Cygwin.tclRename Cygwin-i686 to Cygwin.
2009/02/26 22:57:39 jim None 1.1 arch/Cygwin.fftwRename Cygwin-i686 to Cygwin.
2009/02/26 22:57:39 jim None 1.1 arch/Cygwin.baseRename Cygwin-i686 to Cygwin.
2009/02/26 22:57:39 jim None 1.1 arch/Cygwin.archRename Cygwin-i686 to Cygwin.
2009/02/26 22:49:41 jim None 1.1 arch/Solaris-x86_64.tclRenaming Solaris-amd64 to Solaris-x86_64.
2009/02/26 22:49:41 jim None 1.1 arch/Solaris-x86_64.fftwRenaming Solaris-amd64 to Solaris-x86_64.
2009/02/26 22:49:41 jim None 1.1 arch/Solaris-x86_64.cudaRenaming Solaris-amd64 to Solaris-x86_64.
2009/02/26 22:49:41 jim None 1.1 arch/Solaris-x86_64.baseRenaming Solaris-amd64 to Solaris-x86_64.
2009/02/26 22:49:41 jim None 1.1 arch/Solaris-x86_64-CC.archRenaming Solaris-amd64 to Solaris-x86_64.
2009/02/26 14:38:48 bhatele +3 -3 1.6 arch/BlueGeneP-xlC.archfixed some configs
2009/02/26 14:38:48 bhatele +2 -2 1.3 arch/BlueGeneP-g++.archfixed some configs
2009/02/26 14:38:48 bhatele +3 -3 1.4 arch/BlueGeneP-MPI-xlC.archfixed some configs
2009/02/24 23:01:38 chaomei2 +39 -23 1.1065 src/NamdState.C1. 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.h1. 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.h1. 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.C1. 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.C1. 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.tclXT4 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++.archXT4 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.fftwXT4 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.baseXT4 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.archXT4 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.tclchanged amd64 to x86_64 in the files
2009/02/22 04:16:04 bhatele +1 -1 1.2 arch/Linux-x86_64.fftwchanged amd64 to x86_64 in the files
2009/02/22 04:16:04 bhatele +2 -2 1.2 arch/Linux-x86_64-icc.archchanged amd64 to x86_64 in the files
2009/02/22 04:16:04 bhatele +2 -2 1.2 arch/Linux-x86_64-g++.archchanged amd64 to x86_64 in the files
2009/02/22 04:16:03 bhatele +1 -1 1.2 arch/Linux-x86_64-MPI-pathcc.archchanged amd64 to x86_64 in the files
2009/02/22 04:10:51 bhatele None 1.1 arch/Linux-x86_64.tclcopied over from amd64 files
2009/02/22 04:10:51 bhatele None 1.1 arch/Linux-x86_64-MPI-pathcc.archcopied over from amd64 files
2009/02/22 04:10:50 bhatele None 1.1 arch/Linux-x86_64.fftwcopied over from amd64 files
2009/02/22 04:10:50 bhatele None 1.1 arch/Linux-x86_64.cudacopied over from amd64 files
2009/02/22 04:10:50 bhatele None 1.1 arch/Linux-x86_64.basecopied over from amd64 files
2009/02/22 04:10:50 bhatele None 1.1 arch/Linux-x86_64-icc.archcopied over from amd64 files
2009/02/22 04:10:50 bhatele None 1.1 arch/Linux-x86_64-g++.archcopied over from amd64 files
2009/02/20 18:01:04 jim +0 -1 1.1155 src/Molecule.Cremove debugging message
2009/02/20 17:28:39 jim +4 -3 1.1151 src/SimParameters.hClean up minimizer output, add minVerbose config option.
2009/02/20 17:28:39 jim +5 -3 1.1272 src/SimParameters.CClean up minimizer output, add minVerbose config option.
2009/02/20 17:28:39 jim +37 -22 1.1233 src/Controller.CClean up minimizer output, add minVerbose config option.
2009/02/18 22:53:15 jim +26 -26 1.11 src/MStream.hChange int to size_t where appropriate.
2009/02/18 22:53:15 jim +8 -8 1.16 src/MStream.CChange int to size_t where appropriate.
2009/02/18 17:58:56 petefred +13 -13 1.1154 src/Molecule.CMake tail corrections work properly when switching is off
2009/02/18 16:48:08 petefred +5 -4 1.1150 src/SimParameters.hAdd 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.CAdd 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.hAdd 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.CAdd 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.CAdd 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.CAdd 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.hStart 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.CStart 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.CStart 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.CTweaks 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.CTweaks 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 Makefilethere 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.Ccommented a printf
2009/02/11 21:07:23 chaomei2 +5 -5 1.1149 src/SimParameters.hInterface 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.CInterface 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.hInterface 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.CInterface 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.CInterface 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.hInterface 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.CInterface 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.Copen pe 0 prints "useProxySync is turned on."
2009/02/07 01:33:13 jim +1 -1 1.1246 Makefiletypo
2009/02/07 01:25:29 jim +4 -0 1.2 psfgen/src/topo_mol_pluginio.cfix _snprintf for WIN32
2009/02/06 23:13:15 jim +0 -1 1.6 psfgen/src/topo_mol_struct.hUpdate psfgen to use plugins
2009/02/06 23:13:15 jim None 1.1 psfgen/src/topo_mol_pluginio.hUpdate psfgen to use plugins
2009/02/06 23:13:15 jim None 1.1 psfgen/src/topo_mol_pluginio.cUpdate psfgen to use plugins
2009/02/06 23:13:15 jim +30 -9 1.7 psfgen/src/topo_mol_output.cUpdate psfgen to use plugins
2009/02/06 23:13:15 jim +1 -5 1.9 psfgen/src/topo_mol.cUpdate psfgen to use plugins
2009/02/06 23:13:15 jim +109 -3 1.13 psfgen/src/tcl_psfgen.cUpdate psfgen to use plugins
2009/02/06 23:13:15 jim +12 -13 1.6 psfgen/src/psf_file_extract.cUpdate psfgen to use plugins
2009/02/06 23:13:15 jim +1 -6 1.3 psfgen/src/psf_file.hUpdate psfgen to use plugins
2009/02/06 23:13:14 jim +24 -92 1.3 psfgen/src/psf_file.cUpdate psfgen to use plugins
2009/02/06 23:13:09 jim +7 -6 1.1245 MakefileUpdate psfgen to use plugins
2009/02/06 23:13:09 jim +75 -12 1.123 Make.dependsUpdate psfgen to use plugins
2009/02/06 22:59:49 jim +28 -9 1.3 plugins/include/libmolfile_plugin.huse script in plugins tree to create static header
2009/02/06 22:59:44 jim +4 -0 1.4 plugins/import_treeuse script in plugins tree to create static header
2009/02/06 19:29:58 jim +20 -30 1.48 configClean 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.hCleanup Win32 build system.
2009/02/06 19:06:59 jim +4 -4 1.2 arch/Win64.baseCleanup Win32 build system.
2009/02/06 19:06:59 jim +5 -11 1.3 arch/Win64-MSVC.archCleanup Win32 build system.
2009/02/06 19:06:59 jim +5 -6 1.10 arch/Win32.tclCleanup Win32 build system.
2009/02/06 19:06:59 jim +3 -3 1.6 arch/Win32.fftwCleanup Win32 build system.
2009/02/06 19:06:59 jim +4 -4 1.5 arch/Win32.baseCleanup Win32 build system.
2009/02/06 19:06:59 jim None 1.1 arch/Win32-MSVC.archCleanup Win32 build system.
2009/02/06 19:06:58 jim +6 -5 1.47 configCleanup Win32 build system.
2009/02/06 19:06:58 jim +8 -7 1.1244 MakefileCleanup Win32 build system.
2009/02/06 19:06:58 jim +0 -1 1.18 Make.charmCleanup Win32 build system.
2009/02/06 16:40:17 jim +6 -0 1.3 src/colvartypes.hSmall fixes to build on Win32.
2009/02/06 16:40:17 jim +5 -0 1.5 src/colvarmodule.CSmall fixes to build on Win32.
2009/02/06 16:40:17 jim +1 -1 1.3 src/colvarbias_abf.CSmall fixes to build on Win32.
2009/02/06 16:40:17 jim +6 -0 1.1072 src/ProxyMgr.CSmall fixes to build on Win32.
2009/02/06 16:40:17 jim +12 -12 1.2 src/OptPmeRealSpace.CSmall fixes to build on Win32.
2009/02/06 16:40:17 jim +1 -0 1.2 src/MGridforceParams.hSmall fixes to build on Win32.
2009/02/06 16:40:16 jim +2 -2 1.6 src/GridForceGrid.hSmall fixes to build on Win32.
2009/01/30 23:27:14 jim +4 -3 1.1192 src/WorkDistrib.CRemoved small memory leak.
2009/01/30 23:25:28 jim +4 -3 1.10 arch/AIX-POWER-xlC.archReduced optimization to eliminate crashes.
2009/01/26 18:05:04 jim +1 -0 1.2 src/ComputeNonbondedCUDA.hFixed to work with CompAtomExt changes.
2009/01/26 18:05:04 jim +23 -19 1.2 src/ComputeNonbondedCUDA.CFixed to work with CompAtomExt changes.
2009/01/08 03:48:08 jim +1 -1 1.34 src/Sync.CEliminate stupid Sync buffer overflow message.
2008/12/31 00:14:19 jim +6 -1 1.13 src/Settle.CMake SSE work with Portland Group compilers (pgcc).
2008/12/31 00:14:19 jim +3 -1 1.1153 src/ComputeNonbondedBase.hMake SSE work with Portland Group compilers (pgcc).
2008/12/22 20:15:34 sameer +1 -1 1.26 src/RecBisection.CAssigning patches to processor 0 in each node.
2008/12/19 20:40:23 jim +14 -0 1.46 configAdd --with-memopt option to config.
2008/12/19 20:40:23 jim +3 -3 1.1243 MakefileAdd --with-memopt option to config.
2008/12/19 20:38:23 jim +4 -0 1.1025 src/PDB.CFixes to compile memory optimized version.
2008/12/19 20:38:23 jim +15 -0 1.1151 src/Molecule.CFixes to compile memory optimized version.
2008/12/19 20:35:11 jim +5 -5 1.1229 src/Controller.CExtend maximum field width to allow 100M-atom systems.
2008/12/19 19:06:39 jim +7 -7 1.4 src/GlobalMasterTMD.CRename 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.CFix a couple of portability issues.
2008/12/18 23:32:40 jim +4 -3 1.1071 src/ProxyMgr.CFix a couple of portability issues.
2008/12/18 23:32:40 jim +1 -1 1.4 src/OptPme.CFix a couple of portability issues.
2008/12/18 22:57:18 jim +2 -0 1.3 src/fftlib.Cfixing compile errors on Solaris-x86
2008/12/18 22:57:18 jim +2 -2 1.2 src/colvarparse.hNew 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.Cfixing compile errors on Solaris-x86
2008/12/18 22:19:43 jim +15 -8 1.1268 src/SimParameters.CPrevent specifying separate coordinates file with plugin IO.
2008/12/18 22:19:42 jim +2 -0 1.29 src/NamdOneTools.CPrevent specifying separate coordinates file with plugin IO.
2008/12/18 20:38:13 jim +10 -10 1.1048 src/ProxyPatch.CSlightly 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.CSlightly 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.hSlightly 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.CSlightly 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.CSlightly 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.hSlightly 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.CSlightly 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.CSlightly 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.hSlightly 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.hSlightly 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.CSlightly 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.hSlightly 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.ciSlightly 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.hSlightly 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.CSlightly 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.CSlightly 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.CSlightly 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.CSlightly 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.CSlightly 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.CSlightly 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.hSlightly 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.CSlightly 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.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:39 jim +21 -20 1.1036 src/NamdTypes.hRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +3 -3 1.1160 src/HomePatch.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +2 -2 1.4 src/DumpBench.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +2 -1 1.122 src/ComputePme.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +5 -4 1.31 src/ComputeNonbondedBase2.hRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +36 -45 1.1151 src/ComputeNonbondedBase.hRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +4 -4 1.1029 src/ComputeImpropers.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:38 jim +2 -1 1.3 src/ComputeEwald.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:37 jim +4 -4 1.1031 src/ComputeDihedrals.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:37 jim +8 -8 1.5 src/ComputeCrossterms.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:37 jim +2 -2 1.1026 src/ComputeBonds.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 17:27:37 jim +3 -3 1.1032 src/ComputeAngles.CRearrange CompAtom and CompAtomExt fields to support 2^28 atoms.
2008/12/18 01:17:35 sameer +10 -20 1.3 src/fftmap.hEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/18 01:17:35 sameer +4 -1 1.2 src/fftlib.hEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/18 01:17:35 sameer +2 -2 1.2 src/fftlib.ciEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/18 01:17:35 sameer +27 -5 1.2 src/fftlib.CEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/18 01:17:34 sameer +1 -1 1.1267 src/SimParameters.CEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/18 01:17:34 sameer +25 -6 1.2 src/OptPme.CEnabling compatibility with Charm 6.0 and enabling manytomany correctly in simparams.
2008/12/17 23:18:36 sameer +20 -10 1.2 src/fftmap.hAdding assertions to guard currently unsupported cases.
2008/12/17 22:27:48 sameer +166 -28 1.122 Make.dependsNew optimized pme header and source files.
2008/12/17 22:27:47 sameer +21 -0 1.1242 MakefileNew optimized pme header and source files.
2008/12/17 22:27:03 sameer None 1.1 src/OptPmeRealSpace.hAdding new optimized PME.
2008/12/17 22:27:03 sameer None 1.1 src/OptPmeRealSpace.CAdding new optimized PME.
2008/12/17 22:26:22 sameer +1 -0 1.1017 src/main.ciAdding files for the new optimized PME.
2008/12/17 22:26:22 sameer +1 -0 1.1065 src/main.CAdding files for the new optimized PME.
2008/12/17 22:26:22 sameer None 1.1 src/fftmap.hAdding files for the new optimized PME.
2008/12/17 22:26:21 sameer None 1.1 src/fftlib.hAdding files for the new optimized PME.
2008/12/17 22:26:21 sameer None 1.1 src/fftlib.ciAdding files for the new optimized PME.
2008/12/17 22:26:21 sameer None 1.1 src/fftlib.CAdding files for the new optimized PME.
2008/12/17 22:26:21 sameer +40 -14 1.1190 src/WorkDistrib.CAdding files for the new optimized PME.
2008/12/17 22:26:21 sameer +7 -4 1.1148 src/SimParameters.hAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer +9 -4 1.1266 src/SimParameters.CAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer +1 -0 1.1047 src/ProxyPatch.CAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer +77 -0 1.7 src/PmeBase.hAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer None 1.1 src/OptPme.hAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer None 1.1 src/OptPme.ciAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer None 1.1 src/OptPme.CAdding files for the new optimized PME.
2008/12/17 22:26:20 sameer +37 -9 1.1092 src/Node.CAdding files for the new optimized PME.
2008/12/17 22:26:19 sameer +3 -0 1.1032 src/Lattice.hAdding files for the new optimized PME.
2008/12/17 22:26:19 sameer +0 -3 1.26 src/ComputePme.hAdding files for the new optimized PME.
2008/12/17 22:26:19 sameer +12 -72 1.121 src/ComputePme.CAdding files for the new optimized PME.
2008/12/17 22:26:19 sameer +6 -0 1.1078 src/ComputeMgr.CAdding files for the new optimized PME.
2008/12/17 22:26:19 sameer +1 -0 1.1040 src/ComputeMap.hAdding files for the new optimized PME.
2008/12/17 22:26:18 sameer +4 -2 1.37 src/BackEnd.CAdding files for the new optimized PME.
2008/12/17 21:32:08 jim +5 -5 1.1189 src/WorkDistrib.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -7 1.1046 src/ProxyPatch.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.1030 src/Patch.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +8 -8 1.1035 src/NamdTypes.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -2 1.1061 src/HomePatch.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -16 1.1159 src/HomePatch.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.6 src/ComputeSphericalBC.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.8 src/ComputeSphericalBC.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -2 1.18 src/ComputeSelfTuples.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.10 src/ComputeRestraints.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.16 src/ComputeRestraints.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:08 jim +0 -4 1.1015 src/ComputePatchPair.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -8 1.1029 src/ComputePatchPair.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -4 1.1016 src/ComputePatch.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -4 1.1027 src/ComputePatch.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -2 1.1064 src/ComputeNonbondedUtil.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -4 1.1018 src/ComputeNonbondedSelf.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -6 1.1037 src/ComputeNonbondedSelf.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -4 1.1020 src/ComputeNonbondedPair.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -6 1.1045 src/ComputeNonbondedPair.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +1 -1 1.30 src/ComputeNonbondedBase2.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -29 1.1150 src/ComputeNonbondedBase.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -10 1.1052 src/ComputeHomeTuples.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:07 jim +0 -4 1.11 src/ComputeCylindricalBC.hMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/17 21:32:06 jim +0 -4 1.14 src/ComputeCylindricalBC.CMake CompAtomExt from MEM_OPT_VERSION part of regular build.
2008/12/16 21:19:16 jim +2 -0 1.1024 src/PDB.CFixed bugs in plugin-based file reader, now handles js files correctly.
2008/12/16 21:19:16 jim +6 -5 1.1064 src/NamdState.CFixed bugs in plugin-based file reader, now handles js files correctly.
2008/12/16 21:19:15 jim +38 -42 1.1150 src/Molecule.CFixed bugs in plugin-based file reader, now handles js files correctly.
2008/12/16 21:17:07 jim +7 -4 1.1188 src/WorkDistrib.Cno need for find_extremes with periodic cell
2008/12/16 03:15:37 dbwells2 +5 -1 1.10 src/GridForceGrid.CFixed continuity issue with gridforce.
2008/12/15 17:02:23 chaomei2 +6 -4 1.1147 src/SimParameters.hAdded options to use plugin-IO library to load molecule structure.
2008/12/15 17:02:23 chaomei2 +5 -3 1.1265 src/SimParameters.CAdded options to use plugin-IO library to load molecule structure.
2008/12/15 17:01:12 chaomei2 +2 -1 1.1013 src/PDBData.hAdded 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.hAdded 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.CAdded 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.CAdded 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.hAdded 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.CAdded support for initializing Molecule and PDB object by using plugi-IO library.
2008/12/15 17:01:11 chaomei2 None 1.1 src/PluginIOMgr.hAdded support for initializing Molecule and PDB object by using plugi-IO library.
2008/12/15 17:01:11 chaomei2 None 1.1 src/PluginIOMgr.CAdded support for initializing Molecule and PDB object by using plugi-IO library.
2008/12/15 16:58:29 chaomei2 +1 -0 1.1241 MakefileAdd rules for PluginIOMgr class
2008/12/15 16:58:29 chaomei2 +109 -10 1.121 Make.dependsAdd rules for PluginIOMgr class
2008/12/09 20:11:29 jim +5 -2 1.1240 Makefileupdate dependencies for new plugins
2008/12/09 20:11:29 jim +32 -1 1.120 Make.dependsupdate dependencies for new plugins
2008/12/09 20:10:36 jim +11 -3 1.2 plugins/include/libmolfile_plugin.hadd plugin declarations
2008/12/09 19:46:24 jim None 1.1 plugins/molfile_plugin/src/readpdb.himporting new plugins, updating old ones
2008/12/09 19:46:24 jim None 1.1 plugins/molfile_plugin/src/psfplugin.cimporting new plugins, updating old ones
2008/12/09 19:46:23 jim None 1.1 plugins/molfile_plugin/src/periodic_table.himporting new plugins, updating old ones
2008/12/09 19:46:23 jim None 1.1 plugins/molfile_plugin/src/pdbplugin.cimporting new plugins, updating old ones
2008/12/09 19:46:23 jim +0 -0 1.2 plugins/molfile_plugin/src/largefiles.himporting new plugins, updating old ones
2008/12/09 19:46:23 jim None 1.1 plugins/molfile_plugin/src/jsplugin.cimporting new plugins, updating old ones
2008/12/09 19:46:23 jim None 1.1 plugins/molfile_plugin/src/hash.himporting new plugins, updating old ones
2008/12/09 19:46:23 jim None 1.1 plugins/molfile_plugin/src/hash.cimporting new plugins, updating old ones
2008/12/09 19:46:22 jim None 1.1 plugins/molfile_plugin/src/fortread.himporting new plugins, updating old ones
2008/12/09 19:46:22 jim +215 -3 1.3 plugins/molfile_plugin/src/fastio.himporting new plugins, updating old ones
2008/12/09 19:46:22 jim +0 -0 1.3 plugins/molfile_plugin/src/endianswap.himporting new plugins, updating old ones
2008/12/09 19:46:22 jim +301 -145 1.3 plugins/molfile_plugin/src/dcdplugin.cimporting new plugins, updating old ones
2008/12/09 19:46:17 jim +12 -10 1.3 plugins/include/vmdplugin.himporting new plugins, updating old ones
2008/12/09 19:46:17 jim +273 -34 1.3 plugins/include/molfile_plugin.himporting new plugins, updating old ones
2008/12/09 19:46:14 jim +3 -1 1.3 plugins/import_treeimporting new plugins, updating old ones
2008/12/05 02:45:01 petefred +5 -1 1.1040 src/Parameters.CFix initialization of cosangles flag when using amber or gromacs files


File made using version 1.53 of cvs2html by at 109-11-24 4:07 leaving out any log message prior to Nov 24 2008