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2005-03-11 00:43 chrisfen |
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2005-09-16 18:04 chuckv |
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* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
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dump files. |
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2005-09-16 16:07 chrisfen |
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* src/: UseTheForce/doForces_interface.F90, |
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UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
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bug that ifc missed... |
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2005-09-16 15:36 chrisfen |
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* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
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fixing some summation method issues |
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2005-09-16 14:35 chrisfen |
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* src/brains/SimInfo.cpp: fixed a capitalization error |
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2005-09-16 14:34 chrisfen |
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* src/UseTheForce/: fElectrostaticSummationMethod.h, |
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DarkSide/fElectrostaticSummationMethod.h: moved a header file |
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around |
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2005-09-16 14:00 chrisfen |
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* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
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brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
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are known issues - particularly with reaction field... |
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2005-09-16 11:07 chrisfen |
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* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
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io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
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(cutting out the old way to do reaction field) |
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2005-09-15 17:05 gezelter |
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* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
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fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
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DarkSide/electrostatic_interface.F90, |
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DarkSide/electrostatic_interface.h: Working on adding WOLF |
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2005-09-15 14:17 tim |
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* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
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is called without calling getNFrames |
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2005-09-15 08:47 chrisfen |
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* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
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2005-09-14 21:48 chuckv |
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* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
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not initialized after creation. When maxval(gtypeMaxCutoff) was |
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called, the largest random garbage value was returned from the |
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array. |
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2005-09-14 19:14 chrisfen |
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* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
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io/Globals.hpp: changes to include the coulombicCorrection selector |
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2005-09-14 19:13 chrisfen |
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* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
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reactionField.F90: added in the undamped wolf, in the process of |
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doing the damped wolf |
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2005-09-14 19:13 chrisfen |
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|
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* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
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doForces_interface.h, notifyCutoffs.F90: some changes to activate |
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the coulombicCorrection selector |
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2005-09-14 19:11 chrisfen |
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* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
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2005-09-14 19:11 chrisfen |
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* samples/argon/: 500.in, 500.md: Equilibrated the sample |
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2005-09-14 19:10 chrisfen |
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* forceFields/DUFF2.frc: re-added Cl- and Na+ |
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2005-09-14 15:31 chuckv |
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* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
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eamAtypes instead of assuming a 1-1 correspondence to atypes. |
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2005-09-14 15:28 gezelter |
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* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
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do_prepair |
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2005-09-14 14:02 gezelter |
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* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
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createMixingMap routine. It should now set doShift correctly |
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2005-09-07 17:44 chuckv |
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* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
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2005-09-07 17:23 chuckv |
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* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
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logical variables |
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2005-09-07 17:08 gezelter |
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* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
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algorithm |
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2005-09-07 15:46 gezelter |
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|
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* src/: UseTheForce/doForces.F90, |
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UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
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UseTheForce/notifyCutoffs_interface.F90, |
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UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
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io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
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cutoff Policy |
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2005-09-07 14:18 gezelter |
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|
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* src/UseTheForce/doForces.F90: Some bug hunting |
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2005-09-07 14:18 gezelter |
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* samples/argon/argonNVT.md: Just a longer test |
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2005-09-06 12:32 chuckv |
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* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
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etc.. |
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2005-09-01 17:56 gezelter |
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* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
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zero |
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2005-09-01 15:17 gezelter |
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* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
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createGtypeCutoffMap |
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2005-08-30 13:23 chrisfen |
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|
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* src/: UseTheForce/doForces.F90, |
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UseTheForce/doForces_interface.F90, |
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UseTheForce/doForces_interface.h, |
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UseTheForce/DarkSide/electrostatic.F90, |
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UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
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brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
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changes for implementing the wolf potential |
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2005-08-26 17:39 chrisfen |
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* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
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2005-08-26 16:30 chrisfen |
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|
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* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
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DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
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some probably nonfunctional get*cut routines |
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|
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2005-08-26 15:34 chuckv |
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|
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* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
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2005-08-26 11:36 gezelter |
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* src/UseTheForce/doForces.F90: fixing some of the problems in the |
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interactionHash and gtypeCutoff routines |
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2005-08-17 10:26 gezelter |
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* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
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DarkSide/simulation.F90: added fCutoffPolicy.h |
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2005-08-11 16:04 gezelter |
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* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
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progress |
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2005-08-10 14:17 gezelter |
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* src/primitives/StuntDouble.hpp: putting spaceballs back where |
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they belong |
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2005-08-09 17:33 gezelter |
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* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
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Jones module |
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2005-08-09 17:33 gezelter |
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* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
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2005-08-09 14:40 chuckv |
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* src/UseTheForce/doForces.F90: In process of re-write for group |
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based cutoff.... |
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2005-07-29 14:38 gezelter |
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* src/UseTheForce/doForces.F90: fixes in progress |
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2005-07-29 12:34 tim |
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* src/UseTheForce/doForces.F90: fix a bug which does not update |
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me_i and me_j correctly |
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2005-07-28 17:12 chuckv |
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* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
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cutoffs... Segfaults nicely now... |
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2005-07-20 12:04 gezelter |
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* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
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error messages from pathscale compiler |
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2005-07-13 11:48 tim |
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|
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* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
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<functional> |
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2005-07-13 10:54 tim |
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|
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* src/: UseTheForce/fSwitchingFunction.h, |
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UseTheForce/mpiComponentPlan.h, |
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UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
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io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
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io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
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io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
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io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
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utils/simError.c, utils/simError.h: replace c++ style comment in c |
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files |
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2005-07-03 15:53 chuckv |
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* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
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UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
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subroutine to set cuttoff for Interaction map and function in |
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simulation.F90 to determine if a particular atype is present in a |
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simulation. |
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2005-06-28 08:58 gezelter |
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* src/UseTheForce/doForces.F90: [no log message] |
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2005-06-27 17:21 chuckv |
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* src/UseTheForce/doForces.F90: More breaking and destruction of |
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force code. Does not build at this point... |
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2005-06-27 16:01 gezelter |
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|
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* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
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UseTheForce/DarkSide/fInteractionMap.h, |
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UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
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Breaky breaky! |
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2005-06-20 11:03 gezelter |
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* samples/water/ssd/ssd.md, |
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src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
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simulation |
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|
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2005-06-13 13:25 tim |
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|
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* src/: applications/staticProps/DensityPlot.cpp, |
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applications/staticProps/DensityPlot.hpp, |
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applications/staticProps/SCDOrderParameter.cpp, |
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applications/staticProps/StaticProps.cpp, |
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io/AtomTypesSectionParser.cpp: working version of DensityPlot |
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2005-05-31 17:31 chuckv |
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|
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* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
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remove angular momentum. |
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2005-05-31 12:34 chuckv |
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|
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* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
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typo in nanorodBuilder. |
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|
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2005-05-30 09:01 chuckv |
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|
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* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
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brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
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brains/Stats.hpp, integrators/Velocitizer.cpp, |
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integrators/Velocitizer.hpp: Added method to remove system angular |
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momentum to velocitizer and added method to calculate system |
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angular momentum to siminfo. |
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|
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2005-05-29 16:16 chrisfen |
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|
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* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
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balance from the Darkside (files) |
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|
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2005-05-29 16:15 chrisfen |
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|
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* src/UseTheForce/doForces.F90: Removed balance from doForces |
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2005-05-29 16:15 chrisfen |
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|
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* samples/water/tap/: tap.in, tap.md: Updated tap sample |
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2005-05-29 16:15 chrisfen |
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* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
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dimer for testing purposes |
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2005-05-29 16:14 chrisfen |
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|
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* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
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was apparently wiped earlier this month... |
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2005-05-29 16:13 chrisfen |
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|
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* ChangeLog: ran make cvslog |
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2005-05-28 19:16 tim |
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|
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* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
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AtomNameVisitor |
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|
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2005-05-28 19:09 tim |
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|
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* src/integrators/Integrator.cpp: dding resetIntegrator |
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|
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2005-05-28 19:06 tim |
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|
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* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
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NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
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VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
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resetIntegrator |
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|
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2005-05-27 16:11 tim |
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|
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* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
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Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
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SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
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StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
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StaticProps |
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2005-05-26 23:41 tim |
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|
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* src/: applications/staticProps/Makefile, |
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applications/staticProps/P2OrderParameter.cpp, |
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applications/staticProps/P2OrderParameter.hpp, |
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applications/staticProps/StaticProps.cpp, |
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applications/staticProps/StaticProps.ggo, |
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applications/staticProps/StaticPropsCmd.c, |
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applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
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utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
364 |
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2005-05-26 17:45 tim |
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|
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
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applications/dump2Xyz/Dump2XYZCmd.c, |
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applications/dump2Xyz/Dump2XYZCmd.h, |
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applications/staticProps/Makefile, |
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applications/staticProps/P2OrderParameter.cpp, |
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applications/staticProps/P2OrderParameter.hpp, |
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applications/staticProps/RadialDistrFunc.cpp, |
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applications/staticProps/RadialDistrFunc.hpp, |
375 |
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applications/staticProps/StaticAnalyser.hpp, |
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applications/staticProps/StaticProps.cpp, |
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applications/staticProps/StaticProps.ggo, |
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applications/staticProps/StaticPropsCmd.c, |
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applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
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visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
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AtomNameVisitor to convert atom name to its base name; |
382 |
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wrappingvisitor now wrap back to the center of the mass; adding |
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P2OrderParameter into StaticProps |
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|
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2005-05-22 16:36 chuckv |
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|
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* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
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src/applications/nanoRodBuilder/Geometry.cpp, |
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src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
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src/applications/nanoRodBuilder/GeometryFactory.cpp, |
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src/applications/nanoRodBuilder/GeometryFactory.hpp, |
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src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
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src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
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tensor. |
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|
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2005-05-22 16:05 tim |
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|
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* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
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integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
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io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
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printPressureTensor |
402 |
> |
|
403 |
> |
2005-05-20 14:27 tim |
404 |
> |
|
405 |
> |
* src/integrators/NPrT.cpp: NPrT in progress |
406 |
> |
|
407 |
> |
2005-05-20 11:01 tim |
408 |
> |
|
409 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
410 |
> |
utils/OOPSEConstant.hpp: NPrT in progress |
411 |
> |
|
412 |
> |
2005-05-19 16:31 tim |
413 |
> |
|
414 |
> |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
415 |
> |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
416 |
> |
io/Globals.hpp: NPAT is working |
417 |
> |
|
418 |
> |
2005-05-19 10:49 tim |
419 |
> |
|
420 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
421 |
> |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
422 |
> |
|
423 |
> |
2005-05-18 23:28 tim |
424 |
> |
|
425 |
> |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
426 |
> |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
427 |
> |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
428 |
> |
|
429 |
> |
2005-05-18 14:06 chrisfen |
430 |
> |
|
431 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
432 |
> |
some tap changes |
433 |
> |
|
434 |
> |
2005-05-18 13:31 chrisfen |
435 |
> |
|
436 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
437 |
> |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
438 |
> |
in the first solvation shell for tap |
439 |
> |
|
440 |
> |
2005-05-18 07:35 chrisfen |
441 |
> |
|
442 |
> |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
443 |
> |
for testing purposes |
444 |
> |
|
445 |
> |
2005-05-17 17:35 chrisfen |
446 |
> |
|
447 |
> |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
448 |
> |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
449 |
> |
src/UseTheForce/doForces.F90, |
450 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
451 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
452 |
> |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
453 |
> |
correcting changes to the previous merge that were not caught |
454 |
> |
|
455 |
> |
2005-05-16 23:20 chuckv |
456 |
> |
|
457 |
> |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
458 |
> |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
459 |
> |
build. |
460 |
> |
|
461 |
> |
2005-05-16 22:46 kdaily |
462 |
> |
|
463 |
> |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
464 |
> |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
465 |
> |
|
466 |
> |
2005-05-16 21:08 kdaily |
467 |
> |
|
468 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
469 |
> |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
470 |
> |
src/types/DirectionalAtomType.cpp, |
471 |
> |
src/types/DirectionalAtomType.hpp: added gb |
472 |
> |
|
473 |
> |
2005-05-13 15:36 chrisfen |
474 |
> |
|
475 |
> |
* forceFields/DUFF2.frc: Better tap |
476 |
> |
|
477 |
> |
2005-05-12 14:43 chrisfen |
478 |
> |
|
479 |
> |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
480 |
> |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
481 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
482 |
> |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
483 |
> |
Need to parametrize. |
484 |
> |
|
485 |
> |
2005-05-11 18:15 chuckv |
486 |
> |
|
487 |
> |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
488 |
> |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
489 |
> |
build issues under ifc7. |
490 |
> |
|
491 |
> |
2005-05-09 17:07 chuckv |
492 |
> |
|
493 |
> |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
494 |
> |
builder changes. |
495 |
> |
|
496 |
> |
2005-05-05 10:06 chrisfen |
497 |
> |
|
498 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
499 |
> |
to TAP |
500 |
> |
|
501 |
> |
2005-05-05 09:47 chrisfen |
502 |
> |
|
503 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
504 |
> |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
505 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
506 |
> |
src/UseTheForce/DarkSide/atype.F90, |
507 |
> |
src/UseTheForce/DarkSide/atype_interface.F90, |
508 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
509 |
> |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
510 |
> |
src/brains/fSimulation.h, src/io/Makefile, |
511 |
> |
src/io/StickyAtomTypesSectionParser.cpp, |
512 |
> |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
513 |
> |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
514 |
> |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
515 |
> |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
516 |
> |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
517 |
> |
not parametrized, but OOPSE will now let me run it... |
518 |
> |
|
519 |
> |
2005-05-03 17:55 chuckv |
520 |
> |
|
521 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
522 |
> |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
523 |
> |
Adding support for generic geometry to nanorodbuilder. |
524 |
> |
|
525 |
> |
2005-05-03 12:55 chuckv |
526 |
> |
|
527 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
528 |
> |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
529 |
> |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
530 |
> |
|
531 |
> |
2005-04-29 14:16 gezelter |
532 |
> |
|
533 |
> |
* make/Makefile.in: [no log message] |
534 |
> |
|
535 |
> |
2005-04-29 11:26 chrisfen |
536 |
> |
|
537 |
> |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
538 |
> |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
539 |
> |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
540 |
> |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
541 |
> |
samples/water/tip4p/water.md: Added TIP4P-Ew |
542 |
> |
|
543 |
> |
2005-04-27 19:24 chuckv |
544 |
> |
|
545 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
546 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
547 |
> |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
548 |
> |
nanoRodBuilder.... |
549 |
> |
|
550 |
> |
2005-04-27 15:13 chrisfen |
551 |
> |
|
552 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
553 |
> |
src/UseTheForce/DarkSide/atype.F90, |
554 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
555 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
556 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
557 |
> |
write statements and am closer to a working shapes |
558 |
> |
|
559 |
> |
2005-04-22 16:57 chuckv |
560 |
> |
|
561 |
> |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
562 |
> |
|
563 |
> |
2005-04-22 16:52 tim |
564 |
> |
|
565 |
> |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
566 |
> |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
567 |
> |
problem of c++ |
568 |
> |
|
569 |
> |
2005-04-21 09:12 chrisfen |
570 |
> |
|
571 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
572 |
> |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
573 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
574 |
> |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
575 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
576 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
577 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
578 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
579 |
> |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
580 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
581 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
582 |
> |
src/io/ShapeAtomTypesSectionParser.cpp, |
583 |
> |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
584 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
585 |
> |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
586 |
> |
bounds overwrite (I think...). At least the parser loads the |
587 |
> |
forcefield fine... |
588 |
> |
|
589 |
> |
2005-04-18 10:44 chrisfen |
590 |
> |
|
591 |
> |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
592 |
> |
Mac (capitalization confusion of filenames) |
593 |
> |
|
594 |
> |
2005-04-17 22:50 chrisfen |
595 |
> |
|
596 |
> |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
597 |
> |
UseTheForce/Shapes_FF.cpp, |
598 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
599 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
600 |
> |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
601 |
> |
|
602 |
> |
2005-04-15 17:43 gezelter |
603 |
> |
|
604 |
> |
* README: gmake in case people forget |
605 |
> |
|
606 |
> |
2005-04-15 17:40 gezelter |
607 |
> |
|
608 |
> |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
609 |
> |
banner. Vanity. |
610 |
> |
|
611 |
> |
2005-04-15 17:22 gezelter |
612 |
> |
|
613 |
> |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
614 |
> |
in banner (and version numbers in config.h) |
615 |
> |
|
616 |
> |
2005-04-15 17:22 gezelter |
617 |
> |
|
618 |
> |
* ChangeLog, LICENSE, README: Documentation changes |
619 |
> |
|
620 |
> |
2005-04-15 17:03 gezelter |
621 |
> |
|
622 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
623 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
624 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
625 |
> |
UseTheForce/ForceFieldCreator.hpp, |
626 |
> |
UseTheForce/ForceFieldFactory.cpp, |
627 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
628 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
629 |
> |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
630 |
> |
UseTheForce/notifyCutoffs.F90, |
631 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
632 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
633 |
> |
UseTheForce/DarkSide/atype.F90, |
634 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
635 |
> |
UseTheForce/DarkSide/eam.F90, |
636 |
> |
UseTheForce/DarkSide/eam_interface.F90, |
637 |
> |
UseTheForce/DarkSide/eam_interface.h, |
638 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
639 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
640 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
641 |
> |
UseTheForce/DarkSide/force_globals.F90, |
642 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
643 |
> |
UseTheForce/DarkSide/lj_interface.F90, |
644 |
> |
UseTheForce/DarkSide/lj_interface.h, |
645 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
646 |
> |
UseTheForce/DarkSide/reactionField.F90, |
647 |
> |
UseTheForce/DarkSide/shapes.F90, |
648 |
> |
UseTheForce/DarkSide/shapes_interface.F90, |
649 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
650 |
> |
UseTheForce/DarkSide/simParallel.F90, |
651 |
> |
UseTheForce/DarkSide/simParallel_interface.F90, |
652 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
653 |
> |
UseTheForce/DarkSide/simulation.F90, |
654 |
> |
UseTheForce/DarkSide/simulation_interface.F90, |
655 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
656 |
> |
UseTheForce/DarkSide/sticky.F90, |
657 |
> |
UseTheForce/DarkSide/sticky_interface.F90, |
658 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
659 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
660 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
661 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
662 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
663 |
> |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
664 |
> |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
665 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
666 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
667 |
> |
applications/dynamicProps/DynamicProps.cpp, |
668 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
669 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
670 |
> |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
671 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
672 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
673 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
674 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
675 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
676 |
> |
applications/dynamicProps/TimeCorrFunc.hpp, |
677 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
678 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
679 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
680 |
> |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
681 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
682 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
683 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
684 |
> |
applications/oopse/oopse.cpp, |
685 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
686 |
> |
applications/simpleBuilder/simpleBuilderCmd.c, |
687 |
> |
applications/simpleBuilder/simpleBuilderCmd.h, |
688 |
> |
applications/staticProps/GofAngle2.cpp, |
689 |
> |
applications/staticProps/GofAngle2.hpp, |
690 |
> |
applications/staticProps/GofR.cpp, |
691 |
> |
applications/staticProps/GofR.hpp, |
692 |
> |
applications/staticProps/GofRAngle.cpp, |
693 |
> |
applications/staticProps/GofRAngle.hpp, |
694 |
> |
applications/staticProps/GofXyz.cpp, |
695 |
> |
applications/staticProps/GofXyz.hpp, |
696 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
697 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
698 |
> |
applications/staticProps/StaticProps.cpp, |
699 |
> |
applications/staticProps/StaticPropsCmd.c, |
700 |
> |
applications/staticProps/StaticPropsCmd.h, |
701 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
702 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
703 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
704 |
> |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
705 |
> |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
706 |
> |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
707 |
> |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
708 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
709 |
> |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
710 |
> |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
711 |
> |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
712 |
> |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
713 |
> |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
714 |
> |
constraints/ZconstraintForceManager.cpp, |
715 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
716 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
717 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
718 |
> |
integrators/IntegratorFactory.cpp, |
719 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
720 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
721 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
722 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
723 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
724 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
725 |
> |
integrators/Velocitizer.hpp, |
726 |
> |
integrators/VelocityVerletIntegrator.cpp, |
727 |
> |
integrators/VelocityVerletIntegrator.hpp, |
728 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
729 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
730 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
731 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
732 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
733 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
734 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
735 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
736 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
737 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
738 |
> |
io/Globals.cpp, io/Globals.hpp, |
739 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
740 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
741 |
> |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
742 |
> |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
743 |
> |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
744 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
745 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
746 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
747 |
> |
io/StickyAtomTypesSectionParser.cpp, |
748 |
> |
io/StickyAtomTypesSectionParser.hpp, |
749 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
750 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
751 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
752 |
> |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
753 |
> |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
754 |
> |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
755 |
> |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
756 |
> |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
757 |
> |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
758 |
> |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
759 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
760 |
> |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
761 |
> |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
762 |
> |
math/Quaternion.hpp, math/RandNumGen.hpp, |
763 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
764 |
> |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
765 |
> |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
766 |
> |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
767 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
768 |
> |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
769 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
770 |
> |
minimizers/MinimizerFactory.hpp, |
771 |
> |
minimizers/MinimizerParameterSet.cpp, |
772 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
773 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
774 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
775 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
776 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
777 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
778 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
779 |
> |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
780 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
781 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
782 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
783 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
784 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
785 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
786 |
> |
profiling/timing.F90, restraints/Restraints.cpp, |
787 |
> |
restraints/Restraints.hpp, |
788 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
789 |
> |
restraints/ThermoIntegrationForceManager.hpp, |
790 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
791 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
792 |
> |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
793 |
> |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
794 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
795 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
796 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
797 |
> |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
798 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
799 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
800 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
801 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
802 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
803 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
804 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
805 |
> |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
806 |
> |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
807 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
808 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
809 |
> |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
810 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
811 |
> |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
812 |
> |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
813 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
814 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
815 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
816 |
> |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
817 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
818 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
819 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
820 |
> |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
821 |
> |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
822 |
> |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
823 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
824 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
825 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
826 |
> |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
827 |
> |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
828 |
> |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
829 |
> |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
830 |
> |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
831 |
> |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
832 |
> |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
833 |
> |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
834 |
> |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
835 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
836 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
837 |
> |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
838 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
839 |
> |
been drafted to perform our indentation services |
840 |
> |
|
841 |
> |
2005-04-15 17:03 gezelter |
842 |
> |
|
843 |
> |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
844 |
> |
messages have been added to make users ignore CGAL. |
845 |
> |
|
846 |
> |
2005-04-15 13:41 tim |
847 |
> |
|
848 |
> |
* make/Makefile.in: fix make install |
849 |
> |
|
850 |
> |
2005-04-15 13:41 tim |
851 |
> |
|
852 |
> |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
853 |
> |
add Makefile of samples |
854 |
> |
|
855 |
> |
2005-04-15 13:33 tim |
856 |
> |
|
857 |
> |
* samples/: lipid/Makefile, water/dimer/Makefile, |
858 |
> |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
859 |
> |
installed correctly |
860 |
> |
|
861 |
> |
2005-04-14 16:41 gezelter |
862 |
> |
|
863 |
> |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
864 |
> |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
865 |
> |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
866 |
> |
to use with filepp |
867 |
> |
|
868 |
> |
2005-04-14 16:20 gezelter |
869 |
> |
|
870 |
> |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
871 |
> |
MoLocator |
872 |
> |
|
873 |
> |
2005-04-14 14:12 gezelter |
874 |
> |
|
875 |
> |
* LICENSE: [no log message] |
876 |
> |
|
877 |
> |
2005-04-14 11:10 chuckv |
878 |
> |
|
879 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
880 |
> |
nanorodbuilder now exit's when libCGAL is not present. |
881 |
> |
|
882 |
> |
2005-04-14 10:20 tim |
883 |
> |
|
884 |
> |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
885 |
|
|
886 |
+ |
2005-04-13 18:36 chuckv |
887 |
+ |
|
888 |
+ |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
889 |
+ |
interface name for SGI Compiler |
890 |
+ |
|
891 |
+ |
2005-04-13 18:29 chrisfen |
892 |
+ |
|
893 |
+ |
* samples/water/ssde/ssde.md: oops... bad sample |
894 |
+ |
|
895 |
+ |
2005-04-13 18:00 chuckv |
896 |
+ |
|
897 |
+ |
* src/config.h.in: Change typo in CGAL. |
898 |
+ |
|
899 |
+ |
2005-04-13 17:43 tim |
900 |
+ |
|
901 |
+ |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
902 |
+ |
selection/SelectionCompiler.hpp: fix some warning messages |
903 |
+ |
|
904 |
+ |
2005-04-13 17:30 gezelter |
905 |
+ |
|
906 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
907 |
+ |
make/Makefile.in, src/config.h.in, |
908 |
+ |
src/applications/nanoRodBuilder/Makefile, |
909 |
+ |
src/applications/nanoRodBuilder/Makefile.in, |
910 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
911 |
+ |
checks |
912 |
+ |
|
913 |
+ |
2005-04-13 15:36 chuckv |
914 |
+ |
|
915 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
916 |
+ |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
917 |
+ |
DarkSide/electrostatic_interface.F90, |
918 |
+ |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
919 |
+ |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
920 |
+ |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
921 |
+ |
destroy methods for Fortran modules. |
922 |
+ |
|
923 |
+ |
2005-04-13 15:17 chuckv |
924 |
+ |
|
925 |
+ |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
926 |
+ |
shapes_interface.h: Added destroy method to clean up memory |
927 |
+ |
|
928 |
+ |
2005-04-13 13:41 tim |
929 |
+ |
|
930 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
931 |
+ |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
932 |
+ |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
933 |
+ |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
934 |
+ |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
935 |
+ |
fixed |
936 |
+ |
|
937 |
+ |
2005-04-12 17:44 chuckv |
938 |
+ |
|
939 |
+ |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
940 |
+ |
for nanoRodBuilder. |
941 |
+ |
|
942 |
+ |
2005-04-12 17:42 tim |
943 |
+ |
|
944 |
+ |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
945 |
+ |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
946 |
+ |
and simpleBuilder(forget to delete lattice) |
947 |
+ |
|
948 |
+ |
2005-04-12 17:33 tim |
949 |
+ |
|
950 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
951 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
952 |
+ |
refactory lattice |
953 |
+ |
|
954 |
+ |
2005-04-12 17:07 tim |
955 |
+ |
|
956 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
957 |
+ |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
958 |
+ |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
959 |
+ |
LatticeFactory and LatticeCreator |
960 |
+ |
|
961 |
+ |
2005-04-12 16:58 tim |
962 |
+ |
|
963 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
964 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
965 |
+ |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
966 |
+ |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
967 |
+ |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
968 |
+ |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
969 |
+ |
|
970 |
+ |
2005-04-12 16:28 gezelter |
971 |
+ |
|
972 |
+ |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
973 |
+ |
vector_class.F90: cleaned up vector_class memory leak fix by |
974 |
+ |
deallocating in reverse order of how we allocated. Also migrated |
975 |
+ |
MoLocator into utils directory |
976 |
+ |
|
977 |
+ |
2005-04-12 16:27 gezelter |
978 |
+ |
|
979 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
980 |
+ |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
981 |
+ |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
982 |
+ |
directory |
983 |
+ |
|
984 |
+ |
2005-04-12 16:27 gezelter |
985 |
+ |
|
986 |
+ |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
987 |
+ |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
988 |
+ |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
989 |
+ |
nanoRodBuilder/LatticeCreator.hpp, |
990 |
+ |
nanoRodBuilder/LatticeFactory.cpp, |
991 |
+ |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
992 |
+ |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
993 |
+ |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
994 |
+ |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
995 |
+ |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
996 |
+ |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
997 |
+ |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
998 |
+ |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
999 |
+ |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
1000 |
+ |
these files are now redundant |
1001 |
+ |
|
1002 |
+ |
2005-04-12 16:27 gezelter |
1003 |
+ |
|
1004 |
+ |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
1005 |
+ |
atype_interface.h: cleaned up memory leak fix |
1006 |
+ |
|
1007 |
+ |
2005-04-12 16:26 gezelter |
1008 |
+ |
|
1009 |
+ |
* make/Makefile.in: added lattice subdirectory |
1010 |
+ |
|
1011 |
+ |
2005-04-12 15:57 chrisfen |
1012 |
+ |
|
1013 |
+ |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
1014 |
+ |
a space by accident |
1015 |
+ |
|
1016 |
+ |
2005-04-12 15:56 chrisfen |
1017 |
+ |
|
1018 |
+ |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
1019 |
+ |
quadrupole sample |
1020 |
+ |
|
1021 |
+ |
2005-04-12 15:56 chrisfen |
1022 |
+ |
|
1023 |
+ |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
1024 |
+ |
samples |
1025 |
+ |
|
1026 |
+ |
2005-04-12 13:30 tim |
1027 |
+ |
|
1028 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
1029 |
+ |
type in fortran side |
1030 |
+ |
|
1031 |
+ |
2005-04-12 12:45 chuckv |
1032 |
+ |
|
1033 |
+ |
* src/utils/vector_class.F90: Further changes to vector_class |
1034 |
+ |
destroy function. |
1035 |
+ |
|
1036 |
+ |
2005-04-12 12:39 chuckv |
1037 |
+ |
|
1038 |
+ |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
1039 |
+ |
vector_class. |
1040 |
+ |
|
1041 |
+ |
2005-04-12 12:12 chuckv |
1042 |
+ |
|
1043 |
+ |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
1044 |
+ |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
1045 |
+ |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
1046 |
+ |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
1047 |
+ |
|
1048 |
+ |
2005-04-12 09:24 chrisfen |
1049 |
+ |
|
1050 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
1051 |
+ |
output |
1052 |
+ |
|
1053 |
+ |
2005-04-11 19:29 chuckv |
1054 |
+ |
|
1055 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
1056 |
+ |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
1057 |
+ |
|
1058 |
+ |
2005-04-11 19:28 chuckv |
1059 |
+ |
|
1060 |
+ |
* src/utils/vector_class.F90: Added code to delete vector. |
1061 |
+ |
|
1062 |
+ |
2005-04-11 17:03 chuckv |
1063 |
+ |
|
1064 |
+ |
* samples/metals/nanorod/: Au_nanoparticle.md, |
1065 |
+ |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
1066 |
+ |
aren't these here? |
1067 |
+ |
|
1068 |
+ |
2005-04-11 16:58 tim |
1069 |
+ |
|
1070 |
+ |
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
1071 |
+ |
basic_ifstrstream |
1072 |
+ |
|
1073 |
+ |
2005-04-11 16:37 chuckv |
1074 |
+ |
|
1075 |
+ |
* make/Makefile.in, |
1076 |
+ |
src/applications/nanoRodBuilder/BaseLattice.cpp, |
1077 |
+ |
src/applications/nanoRodBuilder/BaseLattice.hpp, |
1078 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
1079 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
1080 |
+ |
src/applications/nanoRodBuilder/Lattice.cpp, |
1081 |
+ |
src/applications/nanoRodBuilder/Lattice.hpp, |
1082 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
1083 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
1084 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
1085 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
1086 |
+ |
src/applications/nanoRodBuilder/Makefile, |
1087 |
+ |
src/applications/nanoRodBuilder/MoLocator.cpp, |
1088 |
+ |
src/applications/nanoRodBuilder/MoLocator.hpp, |
1089 |
+ |
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
1090 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
1091 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
1092 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
1093 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
1094 |
+ |
nanoRodBuilder application (may not work yet). ((Doesn't work |
1095 |
+ |
yet.)) (((May never work....))) |
1096 |
+ |
|
1097 |
+ |
2005-04-11 15:54 tim |
1098 |
+ |
|
1099 |
+ |
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
1100 |
+ |
prepareVisitor in Dump2XYZ |
1101 |
+ |
|
1102 |
+ |
2005-04-11 15:19 chrisfen |
1103 |
+ |
|
1104 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
1105 |
+ |
quadrupoles. look! it's divide by 3 like stone says! |
1106 |
+ |
|
1107 |
+ |
2005-04-11 15:18 chrisfen |
1108 |
+ |
|
1109 |
+ |
* forceFields/DUFF2.frc: fixing of the quadrupoles |
1110 |
+ |
|
1111 |
+ |
2005-04-11 15:16 tim |
1112 |
+ |
|
1113 |
+ |
* src/selection/Token.hpp: change the parameter name in |
1114 |
+ |
constructors |
1115 |
+ |
|
1116 |
+ |
2005-04-11 14:49 gezelter |
1117 |
+ |
|
1118 |
+ |
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
1119 |
+ |
|
1120 |
+ |
2005-04-11 14:06 gezelter |
1121 |
+ |
|
1122 |
+ |
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
1123 |
+ |
versions < 3.80 |
1124 |
+ |
|
1125 |
+ |
2005-04-11 11:13 gezelter |
1126 |
+ |
|
1127 |
+ |
* make/Makefile.in, src/UseTheForce/Makefile, |
1128 |
+ |
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
1129 |
+ |
some stuff to clean out module files during "make clean" |
1130 |
+ |
|
1131 |
+ |
2005-04-08 17:13 chrisfen |
1132 |
+ |
|
1133 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
1134 |
+ |
interactions should be working with a remaining question of |
1135 |
+ |
interaction magnitude |
1136 |
+ |
|
1137 |
+ |
2005-04-08 17:12 chrisfen |
1138 |
+ |
|
1139 |
+ |
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
1140 |
+ |
samples |
1141 |
+ |
|
1142 |
+ |
2005-04-08 13:48 chrisfen |
1143 |
+ |
|
1144 |
+ |
* samples/water/ssd/ssd.md: oops... messed up a sample |
1145 |
+ |
|
1146 |
+ |
2005-04-08 09:43 chrisfen |
1147 |
+ |
|
1148 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
1149 |
+ |
charge-dipole interactions |
1150 |
+ |
|
1151 |
+ |
2005-04-08 09:42 chrisfen |
1152 |
+ |
|
1153 |
+ |
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
1154 |
+ |
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
1155 |
+ |
|
1156 |
+ |
2005-04-08 09:41 chrisfen |
1157 |
+ |
|
1158 |
+ |
* forceFields/DUFF2.frc: added Cl- and Na+ |
1159 |
+ |
|
1160 |
+ |
2005-04-06 18:59 tim |
1161 |
+ |
|
1162 |
+ |
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
1163 |
+ |
|
1164 |
+ |
2005-04-05 18:09 tim |
1165 |
+ |
|
1166 |
+ |
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
1167 |
+ |
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
1168 |
+ |
in atom type name;clean the code a little bit |
1169 |
+ |
|
1170 |
+ |
2005-03-29 16:00 tim |
1171 |
+ |
|
1172 |
+ |
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
1173 |
+ |
in converting rotation matrix to quaternion |
1174 |
+ |
|
1175 |
+ |
2005-03-28 17:41 tim |
1176 |
+ |
|
1177 |
+ |
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
1178 |
+ |
|
1179 |
+ |
2005-03-28 17:30 tim |
1180 |
+ |
|
1181 |
+ |
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
1182 |
+ |
the wrapping |
1183 |
+ |
|
1184 |
+ |
2005-03-28 10:54 tim |
1185 |
+ |
|
1186 |
+ |
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
1187 |
+ |
dimension of histogram |
1188 |
+ |
|
1189 |
+ |
2005-03-22 11:38 tim |
1190 |
+ |
|
1191 |
+ |
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
1192 |
+ |
src/applications/dynamicProps/Makefile, |
1193 |
+ |
src/applications/oopse/Makefile, |
1194 |
+ |
src/applications/simpleBuilder/Makefile, |
1195 |
+ |
src/applications/staticProps/Makefile: avoid building parallel |
1196 |
+ |
executable for dump2XYZ, simpleBuilder, staticProps and |
1197 |
+ |
dynamicProps |
1198 |
+ |
|
1199 |
+ |
2005-03-21 17:34 chrisfen |
1200 |
+ |
|
1201 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
1202 |
+ |
forcefield files |
1203 |
+ |
|
1204 |
+ |
2005-03-21 15:51 chrisfen |
1205 |
+ |
|
1206 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
1207 |
+ |
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
1208 |
+ |
data for reaction_field |
1209 |
+ |
|
1210 |
+ |
2005-03-21 15:50 chrisfen |
1211 |
+ |
|
1212 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
1213 |
+ |
WILL CHANGE THIS BACK, RIGHT? |
1214 |
+ |
|
1215 |
+ |
2005-03-21 14:23 gezelter |
1216 |
+ |
|
1217 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
1218 |
+ |
correct value |
1219 |
+ |
|
1220 |
+ |
2005-03-21 14:22 gezelter |
1221 |
+ |
|
1222 |
+ |
* make/Makefile.in: fixed an install-related bug. |
1223 |
+ |
$(InstallCommand) had been set to $(InstallData) |
1224 |
+ |
|
1225 |
+ |
2005-03-15 09:21 gezelter |
1226 |
+ |
|
1227 |
+ |
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
1228 |
+ |
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
1229 |
+ |
|
1230 |
+ |
2005-03-15 09:20 gezelter |
1231 |
+ |
|
1232 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
1233 |
+ |
|
1234 |
+ |
2005-03-13 02:39 gezelter |
1235 |
+ |
|
1236 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
1237 |
+ |
charge-quadrupole interactions |
1238 |
+ |
|
1239 |
+ |
2005-03-12 14:12 chrisfen |
1240 |
+ |
|
1241 |
+ |
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
1242 |
+ |
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
1243 |
+ |
|
1244 |
+ |
2005-03-12 14:05 chrisfen |
1245 |
+ |
|
1246 |
+ |
* samples/thermoIntegration/liquid/ssde.in, |
1247 |
+ |
samples/thermoIntegration/liquid/ssde.md, |
1248 |
+ |
samples/thermoIntegration/liquid/water.md, |
1249 |
+ |
samples/thermoIntegration/solid/idealCrystal.in, |
1250 |
+ |
samples/thermoIntegration/solid/ssde.in, |
1251 |
+ |
samples/thermoIntegration/solid/ssde.md, |
1252 |
+ |
samples/thermoIntegration/solid/ssde.zang0, |
1253 |
+ |
samples/thermoIntegration/solid/water.md, |
1254 |
+ |
samples/water/tip3p_ice/tp3.md, |
1255 |
+ |
src/UseTheForce/DarkSide/sticky.F90, |
1256 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: added some |
1257 |
+ |
samples |
1258 |
+ |
|
1259 |
+ |
2005-03-11 12:50 tim |
1260 |
+ |
|
1261 |
+ |
* src/: brains/SimCreator.cpp, |
1262 |
+ |
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
1263 |
+ |
MultipoleAtomTypesSectionParser |
1264 |
+ |
|
1265 |
+ |
2005-03-11 10:55 tim |
1266 |
+ |
|
1267 |
+ |
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
1268 |
+ |
excluded |
1269 |
+ |
|
1270 |
+ |
2005-03-11 10:53 gezelter |
1271 |
+ |
|
1272 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
1273 |
+ |
quadrupoles |
1274 |
+ |
|
1275 |
+ |
2005-03-11 10:52 gezelter |
1276 |
+ |
|
1277 |
+ |
* forceFields/DUFF2.frc: quadrupoles for SSD models |
1278 |
+ |
|
1279 |
+ |
2005-03-11 10:00 tim |
1280 |
+ |
|
1281 |
+ |
* ChangeLog, doc/SelectionExpression.html, |
1282 |
+ |
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
1283 |
+ |
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
1284 |
+ |
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
1285 |
+ |
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
1286 |
+ |
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
1287 |
+ |
SelectionExpression.html |
1288 |
+ |
|
1289 |
+ |
2005-03-10 19:43 chrisfen |
1290 |
+ |
|
1291 |
|
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
1292 |
|
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
1293 |
|
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
1294 |
|
MPI restraints |
1295 |
|
|
1296 |
< |
2005-03-10 23:56 tim |
1296 |
> |
2005-03-10 18:56 tim |
1297 |
|
|
1298 |
|
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
1299 |
|
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
1300 |
|
and cutoff group |
1301 |
|
|
1302 |
< |
2005-03-10 22:06 gezelter |
1302 |
> |
2005-03-10 17:06 gezelter |
1303 |
|
|
1304 |
|
* src/types/MorseBondType.hpp: fixed a doxygen problem |
1305 |
|
|
1306 |
< |
2005-03-10 21:51 gezelter |
1306 |
> |
2005-03-10 16:51 gezelter |
1307 |
|
|
1308 |
|
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
1309 |
|
the split dipole test cases |
1310 |
|
|
1311 |
< |
2005-03-10 21:51 gezelter |
1311 |
> |
2005-03-10 16:51 gezelter |
1312 |
|
|
1313 |
|
* doc/SelectionExpression.html: updated some documentation |
1314 |
|
|
1315 |
< |
2005-03-10 20:40 gezelter |
1315 |
> |
2005-03-10 15:40 gezelter |
1316 |
|
|
1317 |
|
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
1318 |
|
Makefile: LinkedList removal project starts now |
1319 |
|
|
1320 |
< |
2005-03-10 20:28 tim |
1320 |
> |
2005-03-10 15:28 tim |
1321 |
|
|
1322 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
1323 |
|
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
1324 |
|
using map to replace link list |
1325 |
|
|
1326 |
< |
2005-03-10 19:11 tim |
1326 |
> |
2005-03-10 14:11 tim |
1327 |
|
|
1328 |
|
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
1329 |
|
case of split dipole |
1330 |
|
|
1331 |
< |
2005-03-10 19:10 chrisfen |
1331 |
> |
2005-03-10 14:10 chrisfen |
1332 |
|
|
1333 |
|
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
1334 |
|
src/io/RestWriter.cpp, |
1335 |
|
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
1336 |
|
builds... |
1337 |
|
|
1338 |
< |
2005-03-10 18:44 tim |
1338 |
> |
2005-03-10 13:44 tim |
1339 |
|
|
1340 |
|
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
1341 |
|
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
1342 |
|
adding test case for split dipole |
1343 |
|
|
1344 |
< |
2005-03-10 17:54 gezelter |
1344 |
> |
2005-03-10 12:54 gezelter |
1345 |
|
|
1346 |
|
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
1347 |
|
support for split dipoles |
1348 |
|
|
1349 |
< |
2005-03-10 16:27 chrisfen |
1349 |
> |
2005-03-10 11:27 chrisfen |
1350 |
|
|
1351 |
|
* samples/water/tip3p_ice/tp3.md, |
1352 |
|
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
1353 |
|
restraints |
1354 |
|
|
1355 |
< |
2005-03-10 16:15 chrisfen |
1355 |
> |
2005-03-10 11:15 chrisfen |
1356 |
|
|
1357 |
|
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
1358 |
|
src/UseTheForce/ForceFields.hpp, |
1359 |
|
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
1360 |
|
|
1361 |
< |
2005-03-10 16:14 tim |
1361 |
> |
2005-03-10 11:14 tim |
1362 |
|
|
1363 |
|
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
1364 |
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
1365 |
|
src/selection/SelectionEvaluator.cpp: minor change |
1366 |
|
|
1367 |
< |
2005-03-10 15:10 chrisfen |
1367 |
> |
2005-03-10 10:10 chrisfen |
1368 |
|
|
1369 |
|
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
1370 |
|
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
1381 |
|
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
1382 |
|
the new restraints code |
1383 |
|
|
1384 |
< |
2005-03-09 18:48 tim |
1384 |
> |
2005-03-09 13:48 tim |
1385 |
|
|
1386 |
|
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
1387 |
|
IndexFinder |
1388 |
|
|
1389 |
< |
2005-03-09 18:46 tim |
1389 |
> |
2005-03-09 13:46 tim |
1390 |
|
|
1391 |
|
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
1392 |
|
applications/dump2Xyz/Dump2XYZCmd.c, |
1394 |
|
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
1395 |
|
fix compilation issue |
1396 |
|
|
1397 |
< |
2005-03-09 17:58 tim |
1397 |
> |
2005-03-09 12:58 tim |
1398 |
|
|
1399 |
|
* forceFields/DUFF2.frc, scripts/filepp, |
1400 |
|
src/UseTheForce/EAM_FF.cpp, |
1402 |
|
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
1403 |
|
in SectionParser (lineNo is not updated) |
1404 |
|
|
1405 |
< |
2005-03-09 17:30 tim |
1405 |
> |
2005-03-09 12:30 tim |
1406 |
|
|
1407 |
|
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
1408 |
|
applications/dump2Xyz/Dump2XYZ.ggo, |
1424 |
|
MultipoleAtomTypesSectionParser;remove print dipole option from |
1425 |
|
Dump2XYZ; |
1426 |
|
|
1427 |
< |
2005-03-09 17:28 tim |
1427 |
> |
2005-03-09 12:28 tim |
1428 |
|
|
1429 |
|
* forceFields/DUFF2.frc: change the format of DUFF2 |
1430 |
|
|
1431 |
< |
2005-03-09 15:44 gezelter |
1431 |
> |
2005-03-09 10:44 gezelter |
1432 |
|
|
1433 |
|
* src/UseTheForce/DarkSide/: electrostatic.F90, |
1434 |
|
electrostatic_interface.F90, electrostatic_interface.h: new |
1435 |
|
electrostatic module |
1436 |
|
|
1437 |
< |
2005-03-09 14:26 gezelter |
1437 |
> |
2005-03-09 09:26 gezelter |
1438 |
|
|
1439 |
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
1440 |
|
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
1441 |
|
and fixed quadrupole stuff |
1442 |
|
|
1443 |
< |
2005-03-09 14:25 gezelter |
1443 |
> |
2005-03-09 09:25 gezelter |
1444 |
|
|
1445 |
|
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
1446 |
|
for outdated charge and dipole interfaces |
1447 |
|
|
1448 |
< |
2005-03-08 21:08 gezelter |
1448 |
> |
2005-03-08 16:08 gezelter |
1449 |
|
|
1450 |
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
1451 |
|
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
1452 |
|
charge-dipole test cases |
1453 |
|
|
1454 |
< |
2005-03-08 21:07 gezelter |
1454 |
> |
2005-03-08 16:07 gezelter |
1455 |
|
|
1456 |
|
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
1457 |
|
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
1458 |
|
strange icc8 bug (we think). |
1459 |
|
|
1460 |
< |
2005-03-08 21:07 gezelter |
1460 |
> |
2005-03-08 16:07 gezelter |
1461 |
|
|
1462 |
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
1463 |
|
|
1464 |
< |
2005-03-08 21:07 gezelter |
1464 |
> |
2005-03-08 16:07 gezelter |
1465 |
|
|
1466 |
|
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
1467 |
|
Unification Project |
1468 |
|
|
1469 |
< |
2005-03-08 21:07 gezelter |
1469 |
> |
2005-03-08 16:07 gezelter |
1470 |
|
|
1471 |
|
* src/io/Globals.cpp: Dunno |
1472 |
|
|
1473 |
< |
2005-03-08 21:06 gezelter |
1473 |
> |
2005-03-08 16:06 gezelter |
1474 |
|
|
1475 |
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
1476 |
|
OOPSE_itoa and checking a NULL left over from the LinkedList days |
1477 |
|
|
1478 |
< |
2005-03-08 21:06 gezelter |
1478 |
> |
2005-03-08 16:06 gezelter |
1479 |
|
|
1480 |
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
1481 |
|
atype_interface.F90, atype_interface.h, charge.F90, |
1483 |
|
dipole_interface.F90, dipole_interface.h: electrostatic unification |
1484 |
|
project fixed an uninitialized variable in Lennard Jones mixing map |
1485 |
|
|
1486 |
< |
2005-03-08 21:05 gezelter |
1486 |
> |
2005-03-08 16:05 gezelter |
1487 |
|
|
1488 |
|
* src/UseTheForce/doForces.F90: electrostatic unification project |
1489 |
|
|
1490 |
< |
2005-03-08 21:05 gezelter |
1490 |
> |
2005-03-08 16:05 gezelter |
1491 |
|
|
1492 |
|
* samples/water/dimer/: two.md, water.md: making some cool test |
1493 |
|
cases |
1494 |
|
|
1495 |
< |
2005-03-08 21:05 gezelter |
1495 |
> |
2005-03-08 16:05 gezelter |
1496 |
|
|
1497 |
|
* forceFields/DUFF2.frc: Added a charge for Chlorine |
1498 |
|
|
1499 |
< |
2005-03-07 22:39 tim |
1499 |
> |
2005-03-07 17:39 tim |
1500 |
|
|
1501 |
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
1502 |
|
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
1503 |
|
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
1504 |
|
Fixing a bug in BitSet.cpp |
1505 |
|
|
1506 |
< |
2005-03-04 15:28 gezelter |
1506 |
> |
2005-03-04 10:28 gezelter |
1507 |
|
|
1508 |
|
* src/config.h.in: Cleaning up config.h.in by adding comments |
1509 |
|
|
1510 |
< |
2005-03-04 15:28 gezelter |
1510 |
> |
2005-03-04 10:28 gezelter |
1511 |
|
|
1512 |
|
* configure, ac-tools/configure.in, make/Makefile.in, |
1513 |
|
src/brains/SimCreator.cpp: SPRNG eradication project |
1514 |
|
|
1515 |
< |
2005-03-03 14:40 tim |
1515 |
> |
2005-03-03 09:40 tim |
1516 |
|
|
1517 |
|
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
1518 |
|
missing atom type problem) |
1519 |
|
|
1520 |
< |
2005-03-02 16:29 tim |
1520 |
> |
2005-03-02 11:29 tim |
1521 |
|
|
1522 |
|
* src/math/RandNumGen.hpp: adding base class of Random Number |
1523 |
|
generator |
1524 |
|
|
1525 |
< |
2005-03-02 16:28 tim |
1525 |
> |
2005-03-02 11:28 tim |
1526 |
|
|
1527 |
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
1528 |
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
1529 |
|
Velocitizer is not initialized which causes a seg fault |
1530 |
|
|
1531 |
< |
2005-03-02 15:36 tim |
1531 |
> |
2005-03-02 10:36 tim |
1532 |
|
|
1533 |
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
1534 |
|
integrators/Velocitizer.hpp, math/Makefile, |
1538 |
|
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
1539 |
|
random number generator |
1540 |
|
|
1541 |
< |
2005-03-02 07:32 tim |
1541 |
> |
2005-03-02 02:32 tim |
1542 |
|
|
1543 |
|
* test/math/testRandNumGen.cpp: Adding unit test for random number |
1544 |
|
generator |
1545 |
|
|
1546 |
< |
2005-03-01 23:17 tim |
1546 |
> |
2005-03-01 18:17 tim |
1547 |
|
|
1548 |
|
* src/brains/Thermo.hpp: fixed a file inclusion problem |
1549 |
|
|
1550 |
< |
2005-03-01 23:17 tim |
1550 |
> |
2005-03-01 18:17 tim |
1551 |
|
|
1552 |
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
1553 |
|
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
1554 |
|
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
1555 |
|
RandNumGenTestCase.hpp: fixed compilation problem |
1556 |
|
|
1557 |
< |
2005-03-01 23:02 tim |
1557 |
> |
2005-03-01 18:02 tim |
1558 |
|
|
1559 |
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
1560 |
|
integrators/Velocitizer.hpp, math/Makefile, |
1562 |
|
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
1563 |
|
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
1564 |
|
|
1565 |
< |
2005-03-01 23:00 tim |
1565 |
> |
2005-03-01 18:00 tim |
1566 |
|
|
1567 |
|
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
1568 |
|
ParallelandNumGenTestCase.hpp: Change the name of test case |
1569 |
|
|
1570 |
< |
2005-03-01 21:00 tim |
1570 |
> |
2005-03-01 16:00 tim |
1571 |
|
|
1572 |
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
1573 |
|
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
1574 |
|
generator |
1575 |
|
|
1576 |
< |
2005-03-01 20:10 tim |
1576 |
> |
2005-03-01 15:10 tim |
1577 |
|
|
1578 |
|
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
1579 |
|
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
1584 |
|
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
1585 |
|
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
1586 |
|
|
1587 |
< |
2005-03-01 19:11 tim |
1587 |
> |
2005-03-01 14:11 tim |
1588 |
|
|
1589 |
|
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
1590 |
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
1591 |
|
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
1592 |
|
OOPSERandNumGen |
1593 |
|
|
1594 |
< |
2005-03-01 15:44 gezelter |
1594 |
> |
2005-03-01 10:44 gezelter |
1595 |
|
|
1596 |
|
* make/Makefile.in: Fixed the damned build problem with the |
1597 |
|
libraries not being removed in make clean and make distclean (at |
1598 |
|
least we think it is fixed). |
1599 |
|
|
1600 |
< |
2005-03-01 15:26 gezelter |
1600 |
> |
2005-03-01 10:26 gezelter |
1601 |
|
|
1602 |
|
* src/math/MersenneTwister.hpp: Making small modifications to allow |
1603 |
|
for use on MPI machines |
1604 |
|
|
1605 |
< |
2005-03-01 14:45 tim |
1605 |
> |
2005-03-01 09:45 tim |
1606 |
|
|
1607 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
1608 |
|
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
1609 |
|
math/MersenneTwister.hpp: adding MersenneTwister random number |
1610 |
|
generator |
1611 |
|
|
1612 |
< |
2005-03-01 03:55 tim |
1612 |
> |
2005-02-28 22:55 tim |
1613 |
|
|
1614 |
|
* src/math/MersenneTwister.hpp: Adding a modified version of |
1615 |
|
MersenneTwister.hpp |
1616 |
|
|
1617 |
< |
2005-02-28 17:24 tim |
1617 |
> |
2005-02-28 12:24 tim |
1618 |
|
|
1619 |
|
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
1620 |
|
definition.jpg: selection expression |
1621 |
|
|
1622 |
< |
2005-02-25 21:22 tim |
1622 |
> |
2005-02-25 16:22 tim |
1623 |
|
|
1624 |
|
* src/: UseTheForce/DarkSide/LJ.F90, |
1625 |
|
UseTheForce/DarkSide/lj_interface.F90, |
1627 |
|
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
1628 |
|
types/AtomType.hpp: adding soft potential to LJ Module |
1629 |
|
|
1630 |
< |
2005-02-25 16:38 tim |
1630 |
> |
2005-02-25 11:38 tim |
1631 |
|
|
1632 |
|
* doc/SelectionExpression.html: adding documentation for selection |
1633 |
|
expression |
1634 |
|
|
1635 |
< |
2005-02-24 20:55 tim |
1635 |
> |
2005-02-24 15:55 tim |
1636 |
|
|
1637 |
|
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
1638 |
|
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
1640 |
|
adding basic_teebuf which can operate on multiple stream |
1641 |
|
simutaneously. |
1642 |
|
|
1643 |
< |
2005-02-22 18:56 tim |
1643 |
> |
2005-02-22 14:26 chrisfen |
1644 |
|
|
1645 |
+ |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
1646 |
+ |
sample |
1647 |
+ |
|
1648 |
+ |
2005-02-22 13:56 tim |
1649 |
+ |
|
1650 |
|
* src/: UseTheForce/DarkSide/reactionField.F90, |
1651 |
|
primitives/RigidBody.cpp: reactionfield get fixed |
1652 |
|
|
1653 |
< |
2005-02-21 16:57 tim |
1653 |
> |
2005-02-21 11:57 tim |
1654 |
|
|
1655 |
|
* src/: applications/staticProps/GofRAngle.cpp, |
1656 |
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
1657 |
|
a bug in GofRAngle |
1658 |
|
|
1659 |
< |
2005-02-21 15:28 tim |
1659 |
> |
2005-02-21 10:28 tim |
1660 |
|
|
1661 |
|
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
1662 |
|
|
1663 |
< |
2005-02-21 15:22 tim |
1663 |
> |
2005-02-21 10:22 tim |
1664 |
|
|
1665 |
|
* src/utils/next_combination.hpp: fix for compilation on the Sun |
1666 |
|
|
1667 |
< |
2005-02-21 15:21 tim |
1667 |
> |
2005-02-21 10:21 tim |
1668 |
|
|
1669 |
|
* src/utils/GenericData.hpp: fix problem in sun |
1670 |
|
|
1671 |
< |
2005-02-18 23:07 tim |
1671 |
> |
2005-02-18 18:07 tim |
1672 |
|
|
1673 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1674 |
|
applications/dump2Xyz/Dump2XYZ.ggo, |
1685 |
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
1686 |
|
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
1687 |
|
|
1688 |
< |
2005-02-18 15:58 gezelter |
1688 |
> |
2005-02-18 10:58 gezelter |
1689 |
|
|
1690 |
|
* src/brains/Register.cpp: Corrected filename collision for EAM on |
1691 |
|
Mac OS X |
1692 |
|
|
1693 |
< |
2005-02-18 15:58 gezelter |
1693 |
> |
2005-02-18 10:58 gezelter |
1694 |
|
|
1695 |
|
* src/applications/oopse/oopse.cpp: Updated copyright information |
1696 |
|
|
1697 |
< |
2005-02-18 15:58 gezelter |
1697 |
> |
2005-02-18 10:58 gezelter |
1698 |
|
|
1699 |
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
1700 |
|
Makefile: corrected filename collision for EAM on operating systems |
1701 |
|
which are not case sensitive (aka Mac OS X) |
1702 |
|
|
1703 |
< |
2005-02-17 20:15 tim |
1703 |
> |
2005-02-17 15:15 tim |
1704 |
|
|
1705 |
|
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
1706 |
|
|
1707 |
< |
2005-02-17 19:50 tim |
1707 |
> |
2005-02-17 14:50 tim |
1708 |
|
|
1709 |
|
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
1710 |
|
in GofXyz |
1711 |
|
|
1712 |
< |
2005-02-17 19:09 tim |
1712 |
> |
2005-02-17 14:09 tim |
1713 |
|
|
1714 |
|
* src/applications/staticProps/RadialDistrFunc.hpp: make |
1715 |
|
processHistogram non-abstrct function |
1716 |
|
|
1717 |
< |
2005-02-17 18:41 tim |
1717 |
> |
2005-02-17 13:41 tim |
1718 |
|
|
1719 |
|
* src/applications/staticProps/GofXyz.cpp: [no log message] |
1720 |
|
|
1721 |
< |
2005-02-17 18:30 tim |
1721 |
> |
2005-02-17 13:30 tim |
1722 |
|
|
1723 |
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
1724 |
|
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
1725 |
|
finish GofXyz |
1726 |
|
|
1727 |
< |
2005-02-17 16:21 tim |
1727 |
> |
2005-02-17 11:21 tim |
1728 |
|
|
1729 |
|
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
1730 |
|
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
1731 |
|
distribution function |
1732 |
|
|
1733 |
< |
2005-02-17 15:23 tim |
1733 |
> |
2005-02-17 10:23 tim |
1734 |
|
|
1735 |
|
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
1736 |
|
|
1737 |
< |
2005-02-17 15:18 tim |
1737 |
> |
2005-02-17 10:18 tim |
1738 |
|
|
1739 |
|
* src/: brains/BlockSnapshotManager.cpp, |
1740 |
|
selection/DistanceFinder.cpp: The change of interface of BitSet |
1741 |
|
cause a bug in SelectionEvaluation |
1742 |
|
|
1743 |
< |
2005-02-16 21:13 tim |
1743 |
> |
2005-02-16 16:13 tim |
1744 |
|
|
1745 |
|
* src/utils/residentMem.c: return residentMem in byte |
1746 |
|
|
1747 |
< |
2005-02-16 21:00 tim |
1747 |
> |
2005-02-16 16:00 tim |
1748 |
|
|
1749 |
|
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
1750 |
|
a bug in writing out the value of cosang |
1751 |
|
|
1752 |
< |
2005-02-16 20:43 tim |
1752 |
> |
2005-02-16 15:43 tim |
1753 |
|
|
1754 |
|
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
1755 |
|
estimate avaliable memory |
1756 |
|
|
1757 |
< |
2005-02-16 20:30 tim |
1757 |
> |
2005-02-16 15:30 tim |
1758 |
|
|
1759 |
|
* src/: applications/staticProps/GofAngle2.cpp, |
1760 |
|
applications/staticProps/GofAngle2.hpp, |
1770 |
|
applications/staticProps/StaticPropsCmd.h, |
1771 |
|
brains/BlockSnapshotManager.cpp: change the default bin number |
1772 |
|
|
1773 |
< |
2005-02-16 19:36 tim |
1773 |
> |
2005-02-16 14:36 tim |
1774 |
|
|
1775 |
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
1776 |
|
applications/dynamicProps/RCorrFunc.cpp, |
1787 |
|
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
1788 |
|
files;fix the problem of counting in staticProps |
1789 |
|
|
1790 |
< |
2005-02-15 19:39 tim |
1790 |
> |
2005-02-15 14:39 tim |
1791 |
|
|
1792 |
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
1793 |
|
BlockSnapshotManager |
1794 |
|
|
1795 |
< |
2005-02-15 19:36 tim |
1795 |
> |
2005-02-15 14:36 tim |
1796 |
|
|
1797 |
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
1798 |
|
applications/staticProps/RadialDistrFunc.cpp, |
1800 |
|
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
1801 |
|
reference counting now |
1802 |
|
|
1803 |
< |
2005-02-15 17:49 tim |
1803 |
> |
2005-02-15 12:49 tim |
1804 |
|
|
1805 |
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
1806 |
|
replace std::make_pair by VariablesType::value_type to make Sun |
1807 |
|
Compiler happy |
1808 |
|
|
1809 |
< |
2005-02-15 17:35 tim |
1809 |
> |
2005-02-15 12:35 tim |
1810 |
|
|
1811 |
|
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
1812 |
|
TokenMap, using TokenMapType::value_type instead of std::make_pair |
1813 |
|
to make Sun compiler happy |
1814 |
|
|
1815 |
< |
2005-02-15 17:24 tim |
1815 |
> |
2005-02-15 12:24 tim |
1816 |
|
|
1817 |
|
* src/applications/staticProps/: GofRAngle.cpp, |
1818 |
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
1819 |
|
|
1820 |
< |
2005-02-15 17:11 tim |
1820 |
> |
2005-02-15 12:11 tim |
1821 |
|
|
1822 |
|
* src/: applications/staticProps/GofR.cpp, |
1823 |
|
applications/staticProps/RadialDistrFunc.cpp, |
1826 |
|
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
1827 |
|
calculation problem when two selections intersect with each other |
1828 |
|
|
1829 |
< |
2005-02-15 15:24 gezelter |
1829 |
> |
2005-02-15 10:24 gezelter |
1830 |
|
|
1831 |
|
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
1832 |
|
xlc++ |
1833 |
|
|
1834 |
< |
2005-02-15 15:17 gezelter |
1834 |
> |
2005-02-15 10:17 gezelter |
1835 |
|
|
1836 |
|
* configure, ac-tools/configure.in, src/config.h.in, |
1837 |
|
src/utils/residentMem.c: [no log message] |
1838 |
|
|
1839 |
< |
2005-02-15 06:17 gezelter |
1839 |
> |
2005-02-15 01:17 gezelter |
1840 |
|
|
1841 |
|
* src/utils/residentMem.c: bug fix for null termination |
1842 |
|
|
1843 |
< |
2005-02-15 06:11 gezelter |
1843 |
> |
2005-02-15 01:11 gezelter |
1844 |
|
|
1845 |
|
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
1846 |
|
bugfixing residentMem |
1847 |
|
|
1848 |
< |
2005-02-15 05:59 gezelter |
1848 |
> |
2005-02-15 00:59 gezelter |
1849 |
|
|
1850 |
|
* configure, ac-tools/configure.in, src/config.h.in, |
1851 |
|
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
1852 |
|
|
1853 |
< |
2005-02-15 05:08 gezelter |
1853 |
> |
2005-02-15 00:08 gezelter |
1854 |
|
|
1855 |
|
* src/utils/Makefile.in: added residentMem |
1856 |
|
|
1857 |
< |
2005-02-15 05:05 gezelter |
1857 |
> |
2005-02-15 00:05 gezelter |
1858 |
|
|
1859 |
|
* configure, ac-tools/configure.in, make/Makefile.in, |
1860 |
|
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
1862 |
|
other processes autoconf fixes ps syntax checking config.h file |
1863 |
|
cleaning |
1864 |
|
|
1865 |
< |
2005-02-14 23:26 gezelter |
1865 |
> |
2005-02-14 18:26 gezelter |
1866 |
|
|
1867 |
|
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
1868 |
|
|
1869 |
< |
2005-02-14 23:16 gezelter |
1869 |
> |
2005-02-14 18:16 gezelter |
1870 |
|
|
1871 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
1872 |
|
strangeness |
1873 |
|
|
1874 |
< |
2005-02-14 19:42 tim |
1874 |
> |
2005-02-14 14:42 tim |
1875 |
|
|
1876 |
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
1877 |
|
BlockSnapshotManager.hpp |
1878 |
|
|
1879 |
< |
2005-02-14 18:51 tim |
1879 |
> |
2005-02-14 13:51 tim |
1880 |
|
|
1881 |
|
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
1882 |
|
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
1883 |
|
length of first frame |
1884 |
|
|
1885 |
< |
2005-02-14 18:12 tim |
1885 |
> |
2005-02-14 13:12 tim |
1886 |
|
|
1887 |
|
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
1888 |
|
VelocityVerletIntegrator : last frame is written twice |
1889 |
|
|
1890 |
< |
2005-02-14 17:57 tim |
1890 |
> |
2005-02-14 12:57 tim |
1891 |
|
|
1892 |
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
1893 |
|
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
1894 |
|
primitives/StuntDouble.hpp: begin bug fix |
1895 |
|
|
1896 |
< |
2005-02-14 17:35 tim |
1896 |
> |
2005-02-14 12:35 tim |
1897 |
|
|
1898 |
|
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
1899 |
|
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
1903 |
|
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
1904 |
|
VCorrFunc.hpp: refactory CorrelationFunction |
1905 |
|
|
1906 |
< |
2005-02-14 15:18 gezelter |
1906 |
> |
2005-02-14 10:18 gezelter |
1907 |
|
|
1908 |
|
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
1909 |
|
and start of switch for type of correlation function |
1910 |
|
|
1911 |
< |
2005-02-13 21:18 tim |
1911 |
> |
2005-02-13 16:18 tim |
1912 |
|
|
1913 |
|
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
1914 |
|
calculating bytes per stuntdouble |
1915 |
|
|
1916 |
< |
2005-02-13 21:03 tim |
1916 |
> |
2005-02-13 16:03 tim |
1917 |
|
|
1918 |
|
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
1919 |
|
|
1920 |
< |
2005-02-13 20:57 tim |
1920 |
> |
2005-02-13 15:57 tim |
1921 |
|
|
1922 |
|
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
1923 |
|
bug in CorrelationFunction |
1924 |
|
|
1925 |
< |
2005-02-13 20:36 tim |
1925 |
> |
2005-02-13 15:36 tim |
1926 |
|
|
1927 |
|
* src/: applications/staticProps/GofR.cpp, |
1928 |
|
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
1929 |
|
bug in SimInfo::getCutoff() |
1930 |
|
|
1931 |
< |
2005-02-13 20:08 tim |
1931 |
> |
2005-02-13 15:08 tim |
1932 |
|
|
1933 |
|
* make/Makefile.in: adding staticProps and dynamicProps into |
1934 |
|
Makefile.in |
1935 |
|
|
1936 |
< |
2005-02-13 20:05 tim |
1936 |
> |
2005-02-13 15:05 tim |
1937 |
|
|
1938 |
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1939 |
|
applications/dynamicProps/CorrelationFunction.hpp, |
1944 |
|
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
1945 |
|
defaults to the cutoff radius |
1946 |
|
|
1947 |
< |
2005-02-13 19:14 tim |
1947 |
> |
2005-02-13 14:14 tim |
1948 |
|
|
1949 |
|
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
1950 |
|
|
1951 |
< |
2005-02-13 19:10 tim |
1951 |
> |
2005-02-13 14:10 tim |
1952 |
|
|
1953 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1954 |
|
applications/dynamicProps/CorrelationFunction.cpp, |
1962 |
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
1963 |
|
visitors/OtherVisitor.cpp: dynamicProps get built |
1964 |
|
|
1965 |
< |
2005-02-13 15:56 tim |
1965 |
> |
2005-02-13 10:56 tim |
1966 |
|
|
1967 |
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1968 |
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1969 |
|
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
1970 |
|
progress |
1971 |
|
|
1972 |
< |
2005-02-13 08:04 tim |
1972 |
> |
2005-02-13 03:04 tim |
1973 |
|
|
1974 |
|
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
1975 |
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1977 |
|
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
1978 |
|
work in dynamicProps |
1979 |
|
|
1980 |
< |
2005-02-13 07:25 tim |
1980 |
> |
2005-02-13 02:25 tim |
1981 |
|
|
1982 |
|
* src/applications/dynamicProps/DynamicProps.cpp: adding |
1983 |
|
dynamicProps |
1984 |
|
|
1985 |
< |
2005-02-13 07:14 tim |
1985 |
> |
2005-02-13 02:14 tim |
1986 |
|
|
1987 |
|
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
1988 |
|
DynamicPropsCmd.h: adding command line option to DynamicProps |
1989 |
|
|
1990 |
< |
2005-02-13 07:13 tim |
1990 |
> |
2005-02-13 02:13 tim |
1991 |
|
|
1992 |
|
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
1993 |
|
adding command line option for DynamicProps |
1994 |
|
|
1995 |
< |
2005-02-13 06:57 tim |
1995 |
> |
2005-02-13 01:57 tim |
1996 |
|
|
1997 |
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1998 |
|
applications/dynamicProps/CorrelationFunction.hpp, |
2009 |
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
2010 |
|
dynamicProps |
2011 |
|
|
2012 |
< |
2005-02-12 20:09 tim |
2012 |
> |
2005-02-12 15:09 tim |
2013 |
|
|
2014 |
|
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
2015 |
|
|
2016 |
< |
2005-02-11 22:41 tim |
2016 |
> |
2005-02-11 17:41 tim |
2017 |
|
|
2018 |
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
2019 |
|
more constructor to Snapshot to create customized DataStorage |
2020 |
|
|
2021 |
< |
2005-02-11 22:39 tim |
2021 |
> |
2005-02-11 17:39 tim |
2022 |
|
|
2023 |
|
* src/selection/: DistanceFinder.hpp, Makefile, |
2024 |
|
SelectionManager.hpp: adding beginSelected, nextSelected method to |
2025 |
|
SelectionManager |
2026 |
|
|
2027 |
< |
2005-02-11 22:36 tim |
2027 |
> |
2005-02-11 17:36 tim |
2028 |
|
|
2029 |
|
* src/config.h.in, configure: adding support for physmem |
2030 |
|
|
2031 |
< |
2005-02-11 22:35 tim |
2031 |
> |
2005-02-11 17:35 tim |
2032 |
|
|
2033 |
|
* ac-tools/configure.in: adding supprot for physmem |
2034 |
|
|
2035 |
< |
2005-02-11 22:35 tim |
2035 |
> |
2005-02-11 17:35 tim |
2036 |
|
|
2037 |
|
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
2038 |
|
physmem |
2039 |
|
|
2040 |
< |
2005-02-10 22:37 tim |
2040 |
> |
2005-02-10 17:37 tim |
2041 |
|
|
2042 |
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
2043 |
|
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
2045 |
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
2046 |
|
StaticPropsCmd.h: more work in StaticProps |
2047 |
|
|
2048 |
< |
2005-02-10 18:14 tim |
2048 |
> |
2005-02-10 13:14 tim |
2049 |
|
|
2050 |
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
2051 |
|
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
2054 |
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
2055 |
|
StaticPropsCmd.h: change the filenames |
2056 |
|
|
2057 |
< |
2005-02-10 14:15 tim |
2057 |
> |
2005-02-10 09:15 tim |
2058 |
|
|
2059 |
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
2060 |
|
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
2061 |
|
RadialDistrFunc.hpp: adding GofRAngle |
2062 |
|
|
2063 |
< |
2005-02-09 18:21 tim |
2063 |
> |
2005-02-09 13:21 tim |
2064 |
|
|
2065 |
|
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
2066 |
|
useless files |
2067 |
|
|
2068 |
< |
2005-02-09 18:12 tim |
2068 |
> |
2005-02-09 13:12 tim |
2069 |
|
|
2070 |
|
* src/applications/staticProps/: GofR.cpp, Makefile, |
2071 |
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
2072 |
|
|
2073 |
< |
2005-02-09 17:08 tim |
2073 |
> |
2005-02-09 12:08 tim |
2074 |
|
|
2075 |
|
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
2076 |
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
2077 |
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
2078 |
|
|
2079 |
< |
2005-02-07 22:39 tim |
2079 |
> |
2005-02-07 17:39 tim |
2080 |
|
|
2081 |
|
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
2082 |
|
Molecule class |
2083 |
|
|
2084 |
< |
2005-02-07 22:38 tim |
2084 |
> |
2005-02-07 17:38 tim |
2085 |
|
|
2086 |
|
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
2087 |
|
|
2088 |
< |
2005-02-07 22:36 tim |
2088 |
> |
2005-02-07 17:36 tim |
2089 |
|
|
2090 |
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
2091 |
|
SelectionCompiler.cpp: support select internal index selection, for |
2092 |
|
example, select DMPC.3 |
2093 |
|
|
2094 |
< |
2005-02-07 21:11 tim |
2094 |
> |
2005-02-07 16:11 tim |
2095 |
|
|
2096 |
|
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
2097 |
|
help info for Dump2XYZ |
2098 |
|
|
2099 |
< |
2005-02-07 20:39 chrisfen |
2099 |
> |
2005-02-07 15:39 chrisfen |
2100 |
|
|
2101 |
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
2102 |
|
selection librarys added |
2103 |
|
|
2104 |
< |
2005-02-07 20:31 tim |
2104 |
> |
2005-02-07 15:31 tim |
2105 |
|
|
2106 |
|
* src/selection/Makefile, make/Makefile.in: adding Makefile |
2107 |
|
|
2108 |
< |
2005-02-07 20:20 chrisfen |
2108 |
> |
2005-02-07 15:20 chrisfen |
2109 |
|
|
2110 |
|
* src/utils/wildcards.hpp: issue commented out in wildcards |
2111 |
|
|
2112 |
< |
2005-02-07 20:06 tim |
2112 |
> |
2005-02-07 15:06 tim |
2113 |
|
|
2114 |
|
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
2115 |
|
which cause reevaluate return NULL |
2116 |
|
|
2117 |
< |
2005-02-07 19:14 tim |
2117 |
> |
2005-02-07 14:14 tim |
2118 |
|
|
2119 |
|
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
2120 |
|
SimSnapshotManager.hpp: fix a bug in determing the global index for |
2121 |
|
rigidbodies |
2122 |
|
|
2123 |
< |
2005-02-07 19:13 tim |
2123 |
> |
2005-02-07 14:13 tim |
2124 |
|
|
2125 |
|
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
2126 |
|
in Bitset |
2127 |
|
|
2128 |
< |
2005-02-07 19:13 tim |
2128 |
> |
2005-02-07 14:13 tim |
2129 |
|
|
2130 |
|
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
2131 |
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
2132 |
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
2133 |
|
TokenMap.cpp: selection library is working |
2134 |
|
|
2135 |
< |
2005-02-04 22:46 tim |
2135 |
> |
2005-02-04 17:46 tim |
2136 |
|
|
2137 |
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
2138 |
|
|
2139 |
< |
2005-02-04 22:45 tim |
2139 |
> |
2005-02-04 17:45 tim |
2140 |
|
|
2141 |
|
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
2142 |
|
and XYZVisitor now use selection library |
2143 |
|
|
2144 |
< |
2005-02-04 22:44 tim |
2144 |
> |
2005-02-04 17:44 tim |
2145 |
|
|
2146 |
|
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
2147 |
|
adding SelectionManager into SimInfo |
2148 |
|
|
2149 |
< |
2005-02-04 22:43 tim |
2149 |
> |
2005-02-04 17:43 tim |
2150 |
|
|
2151 |
|
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
2152 |
|
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
2153 |
|
selection library |
2154 |
|
|
2155 |
< |
2005-02-04 22:42 tim |
2155 |
> |
2005-02-04 17:42 tim |
2156 |
|
|
2157 |
|
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
2158 |
|
in BitSet |
2159 |
|
|
2160 |
< |
2005-02-04 22:41 tim |
2160 |
> |
2005-02-04 17:41 tim |
2161 |
|
|
2162 |
|
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
2163 |
|
implementation |
2164 |
|
|
2165 |
< |
2005-02-04 22:39 tim |
2165 |
> |
2005-02-04 17:39 tim |
2166 |
|
|
2167 |
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
2168 |
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
2170 |
|
SelectionManager.hpp, Token.hpp: half of the selection utility is |
2171 |
|
working need to debug within keyword and atomproperty keyword |
2172 |
|
|
2173 |
< |
2005-02-04 05:42 tim |
2173 |
> |
2005-02-04 00:42 tim |
2174 |
|
|
2175 |
|
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
2176 |
|
get built |
2177 |
|
|
2178 |
< |
2005-02-04 05:42 tim |
2178 |
> |
2005-02-04 00:42 tim |
2179 |
|
|
2180 |
|
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
2181 |
|
|
2182 |
< |
2005-02-04 05:26 tim |
2182 |
> |
2005-02-04 00:26 tim |
2183 |
|
|
2184 |
|
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
2185 |
|
remove some useless files |
2186 |
|
|
2187 |
< |
2005-02-04 04:57 tim |
2187 |
> |
2005-02-03 23:57 tim |
2188 |
|
|
2189 |
|
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
2190 |
|
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
2191 |
|
adding wildcard class; NameFinder is finished |
2192 |
|
|
2193 |
< |
2005-02-03 23:14 tim |
2193 |
> |
2005-02-03 18:14 tim |
2194 |
|
|
2195 |
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
2196 |
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
2198 |
|
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
2199 |
|
selection library |
2200 |
|
|
2201 |
< |
2005-02-03 14:04 tim |
2201 |
> |
2005-02-03 09:04 tim |
2202 |
|
|
2203 |
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
2204 |
|
selection in progress |
2205 |
|
|
2206 |
< |
2005-02-02 23:13 tim |
2206 |
> |
2005-02-02 18:13 tim |
2207 |
|
|
2208 |
|
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
2209 |
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
2210 |
|
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
2211 |
|
progress, except SelectionEvaluator, other files are compiled |
2212 |
|
|
2213 |
< |
2005-02-02 23:12 tim |
2213 |
> |
2005-02-02 18:12 tim |
2214 |
|
|
2215 |
|
* src/utils/: Makefile.in, any.hpp: adding boost::any |
2216 |
|
|
2217 |
< |
2005-02-02 12:51 tim |
2217 |
> |
2005-02-02 07:51 tim |
2218 |
|
|
2219 |
|
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
2220 |
|
|
2221 |
< |
2005-02-01 22:49 tim |
2221 |
> |
2005-02-01 17:49 tim |
2222 |
|
|
2223 |
|
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
2224 |
|
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
2225 |
|
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
2226 |
|
selection/Token.hpp: Selection in progress |
2227 |
|
|
2228 |
< |
2005-02-01 06:55 tim |
2228 |
> |
2005-02-01 01:55 tim |
2229 |
|
|
2230 |
|
* src/: selection/SelectionCompiler.hpp, |
2231 |
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
2232 |
|
selection/SelectionManager.hpp, selection/Token.hpp, |
2233 |
|
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
2234 |
|
|
2235 |
< |
2005-01-26 15:26 tim |
2235 |
> |
2005-01-26 10:26 tim |
2236 |
|
|
2237 |
|
* src/integrators/: Integrator.cpp, Integrator.hpp, |
2238 |
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
2239 |
|
to add eorWriter |
2240 |
|
|
2241 |
< |
2005-01-26 15:15 tim |
2241 |
> |
2005-01-26 10:15 tim |
2242 |
|
|
2243 |
|
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
2244 |
|
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
2245 |
|
wrong column of electroframe |
2246 |
|
|
2247 |
< |
2005-01-25 21:59 tim |
2247 |
> |
2005-01-25 16:59 tim |
2248 |
|
|
2249 |
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
2250 |
|
SimInfo, use number of cutoff stamp as counter to loop over |
2251 |
|
rigidbody stamp |
2252 |
|
|
2253 |
< |
2005-01-25 17:45 tim |
2253 |
> |
2005-01-25 12:45 tim |
2254 |
|
|
2255 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2256 |
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
2270 |
|
inertial tensor from the directional atoms before calculate |
2271 |
|
rigidbody's inertial tensor |
2272 |
|
|
2273 |
< |
2005-01-17 22:17 tim |
2273 |
> |
2005-01-17 17:17 tim |
2274 |
|
|
2275 |
|
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
2276 |
|
|
2277 |
< |
2005-01-17 16:58 tim |
2277 |
> |
2005-01-17 11:58 tim |
2278 |
|
|
2279 |
|
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
2280 |
|
system parameters |
2281 |
|
|
2282 |
< |
2005-01-17 16:05 tim |
2282 |
> |
2005-01-17 11:05 tim |
2283 |
|
|
2284 |
|
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
2285 |
|
|
2286 |
< |
2005-01-14 22:02 tim |
2286 |
> |
2005-01-14 17:02 tim |
2287 |
|
|
2288 |
|
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
2289 |
|
|
2290 |
< |
2005-01-14 21:37 tim |
2290 |
> |
2005-01-14 16:37 tim |
2291 |
|
|
2292 |
|
* forceFields/Makefile: sync Makefile |
2293 |
|
|
2294 |
< |
2005-01-14 21:13 gezelter |
2294 |
> |
2005-01-14 16:13 gezelter |
2295 |
|
|
2296 |
|
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
2297 |
|
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
2305 |
|
src/visitors/Makefile: moved Package variable into subdirectory |
2306 |
|
makefiles to speed up the building process |
2307 |
|
|
2308 |
< |
2005-01-14 20:48 gezelter |
2308 |
> |
2005-01-14 15:48 gezelter |
2309 |
|
|
2310 |
|
* src/applications/oopse/oopse.cpp: Fixed publication details in |
2311 |
|
banner |
2312 |
|
|
2313 |
< |
2005-01-14 20:48 gezelter |
2313 |
> |
2005-01-14 15:48 gezelter |
2314 |
|
|
2315 |
|
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
2316 |
|
simParallel_interface.h: added dummy subroutine to avoid empty |
2317 |
|
unit, synchronized this dummy routine between C and fortran |
2318 |
|
|
2319 |
< |
2005-01-14 20:31 gezelter |
2319 |
> |
2005-01-14 15:31 gezelter |
2320 |
|
|
2321 |
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
2322 |
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
2332 |
|
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
2333 |
|
modules and C/Fortran interface subroutines |
2334 |
|
|
2335 |
< |
2005-01-14 20:15 gezelter |
2335 |
> |
2005-01-14 15:15 gezelter |
2336 |
|
|
2337 |
|
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
2338 |
|
|
2339 |
< |
2005-01-14 20:09 gezelter |
2339 |
> |
2005-01-14 15:09 gezelter |
2340 |
|
|
2341 |
|
* configure, ac-tools/configure.in, src/config.h.in, |
2342 |
|
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
2343 |
|
|
2344 |
< |
2005-01-14 16:49 tim |
2344 |
> |
2005-01-14 11:49 tim |
2345 |
|
|
2346 |
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
2347 |
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
2348 |
|
utils/StringUtils.hpp: using c library to do conversion instead of |
2349 |
|
using iostream due to a bug in libstdc++(GCC 3.2) |
2350 |
|
|
2351 |
< |
2005-01-14 02:40 tim |
2351 |
> |
2005-01-13 21:40 tim |
2352 |
|
|
2353 |
|
* src/brains/SimSetup.cpp: no message |
2354 |
|
|
2355 |
< |
2005-01-14 01:56 tim |
2355 |
> |
2005-01-13 20:56 tim |
2356 |
|
|
2357 |
|
* src/primitives/Molecule.hpp: fix a bug in global index |
2358 |
|
|
2359 |
< |
2005-01-14 01:04 tim |
2359 |
> |
2005-01-13 20:04 tim |
2360 |
|
|
2361 |
|
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
2362 |
|
Integrator.hpp in Minimizer |
2363 |
|
|
2364 |
< |
2005-01-13 22:14 gezelter |
2364 |
> |
2005-01-13 17:14 gezelter |
2365 |
|
|
2366 |
|
* src/utils/Makefile: compile getopt and getopt1 if we need to |
2367 |
|
|
2368 |
< |
2005-01-13 21:56 gezelter |
2368 |
> |
2005-01-13 16:56 gezelter |
2369 |
|
|
2370 |
|
* make/Makefile.in: template flags |
2371 |
|
|
2372 |
< |
2005-01-13 21:48 gezelter |
2372 |
> |
2005-01-13 16:48 gezelter |
2373 |
|
|
2374 |
|
* src/applications/oopse/Makefile: formatting |
2375 |
|
|
2376 |
< |
2005-01-13 21:48 gezelter |
2376 |
> |
2005-01-13 16:48 gezelter |
2377 |
|
|
2378 |
|
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
2379 |
|
target |
2380 |
|
|
2381 |
< |
2005-01-13 19:40 tim |
2381 |
> |
2005-01-13 14:40 tim |
2382 |
|
|
2383 |
|
* src/: UseTheForce/fSwitchingFunction.h, |
2384 |
|
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
2386 |
|
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
2387 |
|
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
2388 |
|
|
2389 |
< |
2005-01-13 18:26 tim |
2389 |
> |
2005-01-13 13:26 tim |
2390 |
|
|
2391 |
|
* make/Makefile.in: change the order of linking (object file comes |
2392 |
|
first and then follow by user built library) |
2393 |
|
|
2394 |
< |
2005-01-12 23:24 tim |
2394 |
> |
2005-01-12 18:24 tim |
2395 |
|
|
2396 |
|
* src/io/DumpWriter.cpp: remove useless debug info |
2397 |
|
|
2398 |
< |
2005-01-12 23:21 tim |
2398 |
> |
2005-01-12 18:21 tim |
2399 |
|
|
2400 |
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
2401 |
|
|
2402 |
< |
2005-01-12 23:17 tim |
2402 |
> |
2005-01-12 18:17 tim |
2403 |
|
|
2404 |
|
* make/: Makefile.in, Makefile.in: missing tab |
2405 |
|
|
2406 |
< |
2005-01-12 23:15 tim |
2406 |
> |
2005-01-12 18:15 tim |
2407 |
|
|
2408 |
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
2409 |
|
get fixed |
2410 |
|
|
2411 |
< |
2005-01-12 22:40 gezelter |
2411 |
> |
2005-01-12 17:40 gezelter |
2412 |
|
|
2413 |
|
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
2414 |
|
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
2618 |
|
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
2619 |
|
OOPSE-2.0 |
2620 |
|
|
2621 |
< |
2005-01-12 18:13 tim |
2621 |
> |
2005-01-12 13:13 tim |
2622 |
|
|
2623 |
|
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
2624 |
|
utils/TypeContainer.hpp: forget to include <algorithm> |
2625 |
|
|
2626 |
< |
2005-01-12 17:25 tim |
2626 |
> |
2005-01-12 12:25 tim |
2627 |
|
|
2628 |
|
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
2629 |
|
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
2630 |
|
fields |
2631 |
|
|
2632 |
< |
2005-01-12 17:14 tim |
2632 |
> |
2005-01-12 12:14 tim |
2633 |
|
|
2634 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2635 |
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
2791 |
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
2792 |
|
visitors/ZconsVisitor.hpp: change license |
2793 |
|
|
2794 |
< |
2005-01-12 17:14 tim |
2794 |
> |
2005-01-12 12:14 tim |
2795 |
|
|
2796 |
|
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
2797 |
|
branch new_design. |
2798 |
|
|
2799 |
< |
2005-01-11 21:03 tim |
2799 |
> |
2005-01-11 16:03 tim |
2800 |
|
|
2801 |
|
* src/: constraints/ZconstraintForceManager.cpp, |
2802 |
|
constraints/ZconstraintForceManager.hpp, |
2804 |
|
minimizers/MinimizerParameterSet.hpp: change const static double |
2805 |
|
data member to const double |
2806 |
|
|
2807 |
< |
2005-01-11 20:50 tim |
2807 |
> |
2005-01-11 15:50 tim |
2808 |
|
|
2809 |
|
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
2810 |
|
|
2811 |
< |
2005-01-11 20:39 tim |
2811 |
> |
2005-01-11 15:39 tim |
2812 |
|
|
2813 |
|
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
2814 |
|
change data type from logical to integer in AtomTypeProperties.h |
2815 |
|
|
2816 |
< |
2005-01-11 16:36 tim |
2816 |
> |
2005-01-11 11:36 tim |
2817 |
|
|
2818 |
|
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
2819 |
|
new format of EAM force field |
2820 |
|
|
2821 |
< |
2005-01-11 16:24 tim |
2821 |
> |
2005-01-11 11:24 tim |
2822 |
|
|
2823 |
|
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
2824 |
|
to DUFF2.frc |
2825 |
|
|
2826 |
< |
2005-01-11 16:23 tim |
2826 |
> |
2005-01-11 11:23 tim |
2827 |
|
|
2828 |
|
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
2829 |
|
DUFF2.frc |
2830 |
|
|
2831 |
< |
2005-01-11 16:09 tim |
2831 |
> |
2005-01-11 11:09 tim |
2832 |
|
|
2833 |
|
* make/Makefile.in: adding constraints and minimizers into |
2834 |
|
Makefile.in |
2835 |
|
|
2836 |
< |
2005-01-11 16:03 tim |
2836 |
> |
2005-01-11 11:03 tim |
2837 |
|
|
2838 |
|
* src/io/: ChargeAtomTypesSectionParser.cpp, |
2839 |
|
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
2840 |
|
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
2841 |
|
files |
2842 |
|
|
2843 |
< |
2005-01-11 15:59 tim |
2843 |
> |
2005-01-11 10:59 tim |
2844 |
|
|
2845 |
|
* src/io/ZConsWriter.cpp: [no log message] |
2846 |
|
|
2847 |
< |
2005-01-11 15:53 tim |
2847 |
> |
2005-01-11 10:53 tim |
2848 |
|
|
2849 |
|
* src/UseTheForce/EAM.cpp: minor fix |
2850 |
|
|
2851 |
< |
2005-01-11 15:52 tim |
2851 |
> |
2005-01-11 10:52 tim |
2852 |
|
|
2853 |
|
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
2854 |
|
on branch new_design. |
2855 |
|
|
2856 |
< |
2005-01-11 15:52 tim |
2856 |
> |
2005-01-11 10:52 tim |
2857 |
|
|
2858 |
|
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
2859 |
|
on branch new_design. |
2860 |
|
|
2861 |
< |
2005-01-11 15:52 tim |
2861 |
> |
2005-01-11 10:52 tim |
2862 |
|
|
2863 |
|
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
2864 |
|
|
2865 |
< |
2005-01-11 15:47 tim |
2865 |
> |
2005-01-11 10:47 tim |
2866 |
|
|
2867 |
|
* make/Makefile.in: forget a '$' sign |
2868 |
|
|
2869 |
< |
2005-01-11 15:46 tim |
2869 |
> |
2005-01-11 10:46 tim |
2870 |
|
|
2871 |
|
* make/Makefile.in: missing tab in rules |
2872 |
|
|
2873 |
< |
2005-01-10 22:04 tim |
2873 |
> |
2005-01-10 17:04 tim |
2874 |
|
|
2875 |
|
* src/: UseTheForce/ForceFieldCreator.cpp, |
2876 |
|
UseTheForce/ForceFieldCreator.hpp, |
2889 |
|
minimizers/MinimizerFactory.hpp: create a register module to |
2890 |
|
register force fields, integrators and minimizers |
2891 |
|
|
2892 |
< |
2005-01-10 22:04 tim |
2892 |
> |
2005-01-10 17:04 tim |
2893 |
|
|
2894 |
|
* src/brains/Register.cpp: file Register.cpp was initially added on |
2895 |
|
branch new_design. |
2896 |
|
|
2897 |
< |
2005-01-10 22:04 tim |
2897 |
> |
2005-01-10 17:04 tim |
2898 |
|
|
2899 |
|
* src/brains/Register.hpp: file Register.hpp was initially added on |
2900 |
|
branch new_design. |
2901 |
|
|
2902 |
< |
2005-01-10 20:52 tim |
2902 |
> |
2005-01-10 15:52 tim |
2903 |
|
|
2904 |
|
* src/: UseTheForce/ForceFieldFactory.cpp, |
2905 |
|
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
2911 |
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
2912 |
|
method is working now |
2913 |
|
|
2914 |
< |
2005-01-10 18:05 tim |
2914 |
> |
2005-01-10 13:05 tim |
2915 |
|
|
2916 |
|
* src/: constraints/ConstraintElem.hpp, |
2917 |
|
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
2921 |
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
2922 |
|
zconstraint |
2923 |
|
|
2924 |
< |
2005-01-10 18:05 tim |
2924 |
> |
2005-01-10 13:05 tim |
2925 |
|
|
2926 |
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
2927 |
|
initially added on branch new_design. |
2928 |
|
|
2929 |
< |
2005-01-07 21:50 tim |
2929 |
> |
2005-01-07 16:50 tim |
2930 |
|
|
2931 |
|
* src/constraints/ZconstraintForceManager.cpp: file |
2932 |
|
ZconstraintForceManager.cpp was initially added on branch |
2933 |
|
new_design. |
2934 |
|
|
2935 |
< |
2005-01-07 21:50 tim |
2935 |
> |
2005-01-07 16:50 tim |
2936 |
|
|
2937 |
|
* src/constraints/ZconstraintForceManager.hpp: file |
2938 |
|
ZconstraintForceManager.hpp was initially added on branch |
2939 |
|
new_design. |
2940 |
|
|
2941 |
< |
2005-01-07 21:50 tim |
2941 |
> |
2005-01-07 16:50 tim |
2942 |
|
|
2943 |
|
* src/: applications/simpleBuilder/BaseLattice.hpp, |
2944 |
|
applications/simpleBuilder/Lattice.hpp, |
2952 |
|
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
2953 |
|
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
2954 |
|
|
2955 |
< |
2005-01-07 21:50 tim |
2955 |
> |
2005-01-07 16:50 tim |
2956 |
|
|
2957 |
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
2958 |
|
initially added on branch new_design. |
2959 |
|
|
2960 |
< |
2005-01-06 22:31 tim |
2960 |
> |
2005-01-06 17:31 tim |
2961 |
|
|
2962 |
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
2963 |
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2966 |
|
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
2967 |
|
constraint is almost working |
2968 |
|
|
2969 |
< |
2005-01-06 00:36 tim |
2969 |
> |
2005-01-05 19:36 tim |
2970 |
|
|
2971 |
|
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
2972 |
|
working |
2973 |
|
|
2974 |
< |
2005-01-06 00:16 tim |
2974 |
> |
2005-01-05 19:16 tim |
2975 |
|
|
2976 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2977 |
|
applications/oopse/oopse.cpp, |
2986 |
|
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
2987 |
|
in progress |
2988 |
|
|
2989 |
< |
2005-01-05 17:35 tim |
2989 |
> |
2005-01-05 12:35 tim |
2990 |
|
|
2991 |
|
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
2992 |
|
was initially added on branch new_design. |
2993 |
|
|
2994 |
< |
2005-01-05 17:35 tim |
2994 |
> |
2005-01-05 12:35 tim |
2995 |
|
|
2996 |
|
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
2997 |
|
added on branch new_design. |
2998 |
|
|
2999 |
< |
2005-01-05 17:35 tim |
2999 |
> |
2005-01-05 12:35 tim |
3000 |
|
|
3001 |
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
3002 |
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
3004 |
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
3005 |
|
SDMinimizer.hpp: minimizer in progress |
3006 |
|
|
3007 |
< |
2005-01-05 17:35 tim |
3007 |
> |
2005-01-05 12:35 tim |
3008 |
|
|
3009 |
|
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
3010 |
|
was initially added on branch new_design. |
3011 |
|
|
3012 |
< |
2005-01-05 17:35 tim |
3012 |
> |
2005-01-05 12:35 tim |
3013 |
|
|
3014 |
|
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
3015 |
|
was initially added on branch new_design. |
3016 |
|
|
3017 |
< |
2005-01-05 17:35 tim |
3017 |
> |
2005-01-05 12:35 tim |
3018 |
|
|
3019 |
|
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
3020 |
|
was initially added on branch new_design. |
3021 |
|
|
3022 |
< |
2005-01-05 17:35 tim |
3022 |
> |
2005-01-05 12:35 tim |
3023 |
|
|
3024 |
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
3025 |
|
added on branch new_design. |
3026 |
|
|
3027 |
< |
2005-01-04 22:18 tim |
3027 |
> |
2005-01-04 17:18 tim |
3028 |
|
|
3029 |
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
3030 |
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
3035 |
|
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
3036 |
|
progress |
3037 |
|
|
3038 |
< |
2005-01-04 22:18 tim |
3038 |
> |
2005-01-04 17:18 tim |
3039 |
|
|
3040 |
|
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
3041 |
|
initially added on branch new_design. |
3042 |
|
|
3043 |
< |
2005-01-04 22:18 tim |
3043 |
> |
2005-01-04 17:18 tim |
3044 |
|
|
3045 |
|
* src/minimizers/MinimizerParameterSet.cpp: file |
3046 |
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
3047 |
|
|
3048 |
< |
2005-01-04 22:18 tim |
3048 |
> |
2005-01-04 17:18 tim |
3049 |
|
|
3050 |
|
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
3051 |
|
initially added on branch new_design. |
3052 |
|
|
3053 |
< |
2005-01-04 22:18 tim |
3053 |
> |
2005-01-04 17:18 tim |
3054 |
|
|
3055 |
|
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
3056 |
|
was initially added on branch new_design. |
3057 |
|
|
3058 |
< |
2005-01-04 22:18 tim |
3058 |
> |
2005-01-04 17:18 tim |
3059 |
|
|
3060 |
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
3061 |
|
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
3062 |
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
3063 |
|
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
3064 |
|
|
3065 |
< |
2005-01-04 22:18 tim |
3065 |
> |
2005-01-04 17:18 tim |
3066 |
|
|
3067 |
|
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
3068 |
|
branch new_design. |
3069 |
|
|
3070 |
< |
2004-12-20 20:50 chuckv |
3070 |
> |
2004-12-20 15:50 chuckv |
3071 |
|
|
3072 |
|
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
3073 |
|
other BSD's, replaced test -f *.mod with ls function since BSD test |
3074 |
|
apparently doesn't support wildcards. |
3075 |
|
|
3076 |
< |
2004-12-20 20:36 tim |
3076 |
> |
2004-12-20 15:36 tim |
3077 |
|
|
3078 |
|
* make/Makefile.in: fix a test command incompatiable problem |
3079 |
|
|
3080 |
< |
2004-12-20 19:49 tim |
3080 |
> |
2004-12-20 14:49 tim |
3081 |
|
|
3082 |
|
* src/integrators/NPTi.cpp: NPT is working now |
3083 |
|
|
3084 |
< |
2004-12-16 19:20 tim |
3084 |
> |
2004-12-16 14:20 tim |
3085 |
|
|
3086 |
|
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
3087 |
|
invalid stamp id |
3088 |
|
|
3089 |
< |
2004-12-16 19:00 tim |
3089 |
> |
2004-12-16 14:00 tim |
3090 |
|
|
3091 |
|
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
3092 |
|
newEAM.u6.frc: adding new EAM force field files |
3093 |
|
|
3094 |
< |
2004-12-16 18:55 tim |
3094 |
> |
2004-12-16 13:55 tim |
3095 |
|
|
3096 |
|
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
3097 |
|
in EAM parameter file is incorrect |
3098 |
|
|
3099 |
< |
2004-12-16 17:27 tim |
3099 |
> |
2004-12-16 12:27 tim |
3100 |
|
|
3101 |
|
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
3102 |
|
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
3103 |
|
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
3104 |
|
|
3105 |
< |
2004-12-15 22:34 tim |
3105 |
> |
2004-12-15 17:34 tim |
3106 |
|
|
3107 |
|
* src/: applications/simpleBuilder/BaseLattice.cpp, |
3108 |
|
applications/simpleBuilder/BaseLattice.hpp, |
3115 |
|
applications/simpleBuilder/simpleBuilder.cpp, |
3116 |
|
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
3117 |
|
|
3118 |
< |
2004-12-15 21:07 tim |
3118 |
> |
2004-12-15 16:07 tim |
3119 |
|
|
3120 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3121 |
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
3122 |
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
3123 |
|
add EAM Force Field |
3124 |
|
|
3125 |
< |
2004-12-15 19:40 tim |
3125 |
> |
2004-12-15 14:40 tim |
3126 |
|
|
3127 |
|
* src/applications/oopse/oopse.cpp: add more force fields |
3128 |
|
|
3129 |
< |
2004-12-15 16:44 tim |
3129 |
> |
2004-12-15 11:44 tim |
3130 |
|
|
3131 |
|
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
3132 |
|
to call All_reduce in MPI version) |
3133 |
|
|
3134 |
< |
2004-12-15 16:13 tim |
3134 |
> |
2004-12-15 11:13 tim |
3135 |
|
|
3136 |
|
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
3137 |
|
io/DumpReader.cpp: MPI in NVE is working |
3138 |
|
|
3139 |
< |
2004-12-14 21:57 tim |
3139 |
> |
2004-12-14 16:57 tim |
3140 |
|
|
3141 |
|
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
3142 |
|
Master nodes does not brocast the total number of frames |
3143 |
|
|
3144 |
< |
2004-12-14 19:08 tim |
3144 |
> |
2004-12-14 14:08 tim |
3145 |
|
|
3146 |
|
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
3147 |
|
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
3150 |
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
3151 |
|
minimizers/SDMinimizer.cpp: more fix in MPI version |
3152 |
|
|
3153 |
< |
2004-12-13 22:30 tim |
3153 |
> |
2004-12-13 17:30 tim |
3154 |
|
|
3155 |
|
* src/: UseTheForce/DarkSide/simParallel.F90, |
3156 |
|
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
3168 |
|
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
3169 |
|
is built |
3170 |
|
|
3171 |
< |
2004-12-10 18:41 tim |
3171 |
> |
2004-12-10 13:41 tim |
3172 |
|
|
3173 |
|
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
3174 |
|
|
3175 |
< |
2004-12-10 16:14 tim |
3175 |
> |
2004-12-10 11:14 tim |
3176 |
|
|
3177 |
|
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
3178 |
|
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
3179 |
|
and Dipole is working now |
3180 |
|
|
3181 |
< |
2004-12-09 23:15 tim |
3181 |
> |
2004-12-09 18:15 tim |
3182 |
|
|
3183 |
|
* src/: UseTheForce/DarkSide/dipole.F90, |
3184 |
|
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
3185 |
|
fix an index problem in eFrame matrix |
3186 |
|
|
3187 |
< |
2004-12-09 23:09 tim |
3187 |
> |
2004-12-09 18:09 tim |
3188 |
|
|
3189 |
|
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
3190 |
|
initializing the new Charge AtomType |
3191 |
|
|
3192 |
< |
2004-12-09 21:15 tim |
3192 |
> |
2004-12-09 16:15 tim |
3193 |
|
|
3194 |
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
3195 |
|
types/DirectionalAtomType.cpp: sticky module get compiled |
3196 |
|
|
3197 |
< |
2004-12-09 20:43 gezelter |
3197 |
> |
2004-12-09 15:43 gezelter |
3198 |
|
|
3199 |
|
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
3200 |
|
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
3201 |
|
GB |
3202 |
|
|
3203 |
< |
2004-12-09 20:42 gezelter |
3203 |
> |
2004-12-09 15:42 gezelter |
3204 |
|
|
3205 |
|
* src/UseTheForce/doForces.F90: u_l -> eFrame |
3206 |
|
|
3207 |
< |
2004-12-09 20:27 gezelter |
3207 |
> |
2004-12-09 15:27 gezelter |
3208 |
|
|
3209 |
|
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
3210 |
|
module now has the option for multiple sticky types |
3211 |
|
|
3212 |
< |
2004-12-09 20:27 gezelter |
3212 |
> |
2004-12-09 15:27 gezelter |
3213 |
|
|
3214 |
|
* src/UseTheForce/doForces.F90: sticky |
3215 |
|
|
3216 |
< |
2004-12-09 16:22 tim |
3216 |
> |
2004-12-09 11:22 tim |
3217 |
|
|
3218 |
|
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
3219 |
|
inconsistency in lab2Bidy |
3220 |
|
|
3221 |
< |
2004-12-09 15:45 tim |
3221 |
> |
2004-12-09 10:45 tim |
3222 |
|
|
3223 |
|
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
3224 |
|
in calculating torque in rigid body |
3225 |
|
|
3226 |
< |
2004-12-08 20:37 tim |
3226 |
> |
2004-12-08 15:37 tim |
3227 |
|
|
3228 |
|
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
3229 |
|
brains/SnapShot.cpp, brains/Snapshot.hpp, |
3231 |
|
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
3232 |
|
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
3233 |
|
|
3234 |
< |
2004-12-08 17:03 tim |
3234 |
> |
2004-12-08 12:03 tim |
3235 |
|
|
3236 |
|
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
3237 |
|
in NVT is working |
3238 |
|
|
3239 |
< |
2004-12-07 23:08 tim |
3239 |
> |
2004-12-07 18:08 tim |
3240 |
|
|
3241 |
|
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
3242 |
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
3243 |
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
3244 |
|
io/DumpWriter.cpp: NPT in progress |
3245 |
|
|
3246 |
< |
2004-12-07 14:43 tim |
3246 |
> |
2004-12-07 09:43 tim |
3247 |
|
|
3248 |
|
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
3249 |
|
message] |
3250 |
|
|
3251 |
< |
2004-12-07 05:12 tim |
3251 |
> |
2004-12-07 00:12 tim |
3252 |
|
|
3253 |
|
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
3254 |
|
UseInitXSstate |
3255 |
|
|
3256 |
< |
2004-12-07 05:00 tim |
3256 |
> |
2004-12-07 00:00 tim |
3257 |
|
|
3258 |
|
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
3259 |
|
|
3260 |
< |
2004-12-07 04:47 tim |
3260 |
> |
2004-12-06 23:47 tim |
3261 |
|
|
3262 |
|
* src/types/DirectionalAtomType.cpp: [no log message] |
3263 |
|
|
3264 |
< |
2004-12-07 02:18 tim |
3264 |
> |
2004-12-06 21:18 tim |
3265 |
|
|
3266 |
|
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
3267 |
|
|
3268 |
< |
2004-12-07 01:33 tim |
3268 |
> |
2004-12-06 20:33 tim |
3269 |
|
|
3270 |
|
* forceFields/newDUFF.frc: change the force constant of bonds |
3271 |
|
|
3272 |
< |
2004-12-06 23:29 tim |
3272 |
> |
2004-12-06 18:29 tim |
3273 |
|
|
3274 |
|
* src/: UseTheForce/DarkSide/charge.F90, |
3275 |
|
UseTheForce/DarkSide/charge_interface.h, |
3277 |
|
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
3278 |
|
fix atom type ident in Charge and Dipole Module |
3279 |
|
|
3280 |
< |
2004-12-06 22:56 tim |
3280 |
> |
2004-12-06 17:56 tim |
3281 |
|
|
3282 |
|
* src/primitives/Torsion.cpp: butane is working now |
3283 |
|
|
3284 |
< |
2004-12-06 20:15 tim |
3284 |
> |
2004-12-06 15:15 tim |
3285 |
|
|
3286 |
|
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
3287 |
|
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
3288 |
|
interaction for butane is correct.Still something wrong with long |
3289 |
|
range one |
3290 |
|
|
3291 |
< |
2004-12-06 04:49 tim |
3291 |
> |
2004-12-05 23:49 tim |
3292 |
|
|
3293 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3294 |
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3296 |
|
primitives/Atom.hpp, utils/NumericConstant.hpp, |
3297 |
|
utils/TypeContainer.hpp: fix a bug in Exclude List |
3298 |
|
|
3299 |
< |
2004-12-05 22:21 tim |
3299 |
> |
2004-12-05 17:21 tim |
3300 |
|
|
3301 |
|
* forceFields/newDUFF.frc: minor fix in DUFF |
3302 |
|
|
3303 |
< |
2004-12-05 22:02 tim |
3303 |
> |
2004-12-05 17:02 tim |
3304 |
|
|
3305 |
|
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
3306 |
|
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
3307 |
|
fix a bug in filling MolMembership |
3308 |
|
|
3309 |
< |
2004-12-05 17:12 tim |
3309 |
> |
2004-12-05 12:12 tim |
3310 |
|
|
3311 |
|
* forceFields/newDUFF.frc: minor fix in force field file |
3312 |
|
|
3313 |
< |
2004-12-05 17:09 tim |
3313 |
> |
2004-12-05 12:09 tim |
3314 |
|
|
3315 |
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
3316 |
|
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
3317 |
|
|
3318 |
< |
2004-12-04 20:09 tim |
3318 |
> |
2004-12-04 15:09 tim |
3319 |
|
|
3320 |
|
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
3321 |
|
math/Vector3.hpp: NVE is working now, get the same result as |
3322 |
|
OOPSE-1.0 |
3323 |
|
|
3324 |
< |
2004-12-04 19:29 tim |
3324 |
> |
2004-12-04 14:29 tim |
3325 |
|
|
3326 |
|
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
3327 |
|
|
3328 |
< |
2004-12-04 19:24 gezelter |
3328 |
> |
2004-12-04 14:24 gezelter |
3329 |
|
|
3330 |
|
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
3331 |
|
|
3332 |
< |
2004-12-04 19:24 gezelter |
3332 |
> |
2004-12-04 14:24 gezelter |
3333 |
|
|
3334 |
|
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
3335 |
|
|
3336 |
< |
2004-12-04 05:24 tim |
3336 |
> |
2004-12-04 00:24 tim |
3337 |
|
|
3338 |
|
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
3339 |
|
integrators/Integrator.hpp, |
3344 |
|
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
3345 |
|
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
3346 |
|
|
3347 |
< |
2004-12-04 00:01 tim |
3347 |
> |
2004-12-03 19:01 tim |
3348 |
|
|
3349 |
|
* src/: UseTheForce/DarkSide/LJ.F90, |
3350 |
|
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
3353 |
|
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
3354 |
|
energy of NVE is not conserved |
3355 |
|
|
3356 |
< |
2004-12-03 22:36 tim |
3356 |
> |
2004-12-03 17:36 tim |
3357 |
|
|
3358 |
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
3359 |
|
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
3360 |
|
|
3361 |
< |
2004-12-03 21:30 tim |
3361 |
> |
2004-12-03 16:30 tim |
3362 |
|
|
3363 |
|
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
3364 |
|
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
3366 |
|
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
3367 |
|
primitives/Torsion.hpp: more missing function get implemented |
3368 |
|
|
3369 |
< |
2004-12-03 20:30 tim |
3369 |
> |
2004-12-03 15:30 tim |
3370 |
|
|
3371 |
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
3372 |
|
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
3373 |
|
|
3374 |
< |
2004-12-03 17:59 tim |
3374 |
> |
2004-12-03 12:59 tim |
3375 |
|
|
3376 |
|
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
3377 |
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3380 |
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
3381 |
|
utils/TypeContainer.hpp: begin to fix bugs |
3382 |
|
|
3383 |
< |
2004-12-03 00:26 tim |
3383 |
> |
2004-12-02 19:26 tim |
3384 |
|
|
3385 |
|
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
3386 |
|
new_design. |
3387 |
|
|
3388 |
< |
2004-12-03 00:26 tim |
3388 |
> |
2004-12-02 19:26 tim |
3389 |
|
|
3390 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3391 |
|
UseTheForce/ForceFieldCreator.cpp, |
3396 |
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
3397 |
|
bug in countTokens in StringTokenizer |
3398 |
|
|
3399 |
< |
2004-12-03 00:06 tim |
3399 |
> |
2004-12-02 19:06 tim |
3400 |
|
|
3401 |
|
* forceFields/newDUFF.frc: minor fix |
3402 |
|
|
3403 |
< |
2004-12-02 23:15 tim |
3403 |
> |
2004-12-02 18:15 tim |
3404 |
|
|
3405 |
|
* forceFields/newDUFF.frc: new ForceField format |
3406 |
|
|
3407 |
< |
2004-12-02 22:15 tim |
3407 |
> |
2004-12-02 17:15 tim |
3408 |
|
|
3409 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3410 |
|
UseTheForce/ForceFieldCreator.cpp, |
3423 |
|
types/Makefile: refine factory pattern to make it initialized |
3424 |
|
correctly |
3425 |
|
|
3426 |
< |
2004-12-02 22:15 tim |
3426 |
> |
2004-12-02 17:15 tim |
3427 |
|
|
3428 |
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
3429 |
|
was initially added on branch new_design. |
3430 |
|
|
3431 |
< |
2004-12-02 22:15 tim |
3431 |
> |
2004-12-02 17:15 tim |
3432 |
|
|
3433 |
|
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
3434 |
|
was initially added on branch new_design. |
3435 |
|
|
3436 |
< |
2004-12-02 22:15 tim |
3436 |
> |
2004-12-02 17:15 tim |
3437 |
|
|
3438 |
|
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
3439 |
|
was initially added on branch new_design. |
3440 |
|
|
3441 |
< |
2004-12-02 22:15 tim |
3441 |
> |
2004-12-02 17:15 tim |
3442 |
|
|
3443 |
|
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
3444 |
|
was initially added on branch new_design. |
3445 |
|
|
3446 |
< |
2004-12-02 16:53 tim |
3446 |
> |
2004-12-02 11:53 tim |
3447 |
|
|
3448 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
3449 |
|
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
3450 |
|
|
3451 |
< |
2004-12-02 16:04 tim |
3451 |
> |
2004-12-02 11:04 tim |
3452 |
|
|
3453 |
|
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
3454 |
|
applications/simpleBuilder/LatticeCreator.hpp, |
3472 |
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
3473 |
|
have two linking problem |
3474 |
|
|
3475 |
< |
2004-12-02 05:17 tim |
3475 |
> |
2004-12-02 00:17 tim |
3476 |
|
|
3477 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3478 |
|
applications/simpleBuilder/Lattice.cpp, |
3484 |
|
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
3485 |
|
visitors/ZconsVisitor.cpp: change endl to std::endl |
3486 |
|
|
3487 |
< |
2004-12-02 05:14 tim |
3487 |
> |
2004-12-02 00:14 tim |
3488 |
|
|
3489 |
|
* src/: UseTheForce/Shapes_FF.cpp, |
3490 |
|
applications/dump2Xyz/Dump2XYZ.cpp, |
3500 |
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
3501 |
|
visitors/RigidBodyVisitor.hpp: minor fix |
3502 |
|
|
3503 |
< |
2004-12-02 05:09 tim |
3503 |
> |
2004-12-02 00:09 tim |
3504 |
|
|
3505 |
|
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
3506 |
|
remove StreamTokenizer |
3507 |
|
|
3508 |
< |
2004-12-02 05:06 tim |
3508 |
> |
2004-12-02 00:06 tim |
3509 |
|
|
3510 |
|
* src/: UseTheForce/Shapes_FF.cpp, |
3511 |
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
3514 |
|
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
3515 |
|
namespace std in .cpp file |
3516 |
|
|
3517 |
< |
2004-12-02 05:04 tim |
3517 |
> |
2004-12-02 00:04 tim |
3518 |
|
|
3519 |
|
* src/: UseTheForce/Shapes_FF.cpp, |
3520 |
|
applications/dump2Xyz/Dump2XYZ.cpp, |
3538 |
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
3539 |
|
qulified name prefix std |
3540 |
|
|
3541 |
< |
2004-12-02 04:55 tim |
3541 |
> |
2004-12-01 23:55 tim |
3542 |
|
|
3543 |
|
* src/: UseTheForce/Shapes_FF.cpp, |
3544 |
|
applications/dump2Xyz/Dump2XYZ.cpp, |
3554 |
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
3555 |
|
visitors/RigidBodyVisitor.hpp: replace string by std::string |
3556 |
|
|
3557 |
< |
2004-12-02 03:12 tim |
3557 |
> |
2004-12-01 22:12 tim |
3558 |
|
|
3559 |
|
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
3560 |
|
src/applications/simpleBuilder/BaseLattice.hpp, |
3575 |
|
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
3576 |
|
header files |
3577 |
|
|
3578 |
< |
2004-12-02 02:23 tim |
3578 |
> |
2004-12-01 21:23 tim |
3579 |
|
|
3580 |
|
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
3581 |
|
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
3582 |
|
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
3583 |
|
begin to fix linking problem |
3584 |
|
|
3585 |
< |
2004-12-02 02:08 tim |
3585 |
> |
2004-12-01 21:08 tim |
3586 |
|
|
3587 |
|
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
3588 |
|
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
3594 |
|
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
3595 |
|
still has some linking problem |
3596 |
|
|
3597 |
< |
2004-12-02 00:26 tim |
3597 |
> |
2004-12-01 19:26 tim |
3598 |
|
|
3599 |
|
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
3600 |
|
utils/OOPSEConstant.hpp: NVT get built |
3601 |
|
|
3602 |
< |
2004-12-02 00:09 tim |
3602 |
> |
2004-12-01 19:09 tim |
3603 |
|
|
3604 |
|
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
3605 |
|
branch new_design. |
3606 |
|
|
3607 |
< |
2004-12-02 00:09 tim |
3607 |
> |
2004-12-01 19:09 tim |
3608 |
|
|
3609 |
|
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
3610 |
|
branch new_design. |
3611 |
|
|
3612 |
< |
2004-12-02 00:09 tim |
3612 |
> |
2004-12-01 19:09 tim |
3613 |
|
|
3614 |
|
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
3615 |
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
3621 |
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
3622 |
|
get built |
3623 |
|
|
3624 |
< |
2004-12-02 00:09 tim |
3624 |
> |
2004-12-01 19:09 tim |
3625 |
|
|
3626 |
|
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
3627 |
|
was initially added on branch new_design. |
3628 |
|
|
3629 |
< |
2004-12-01 22:45 tim |
3629 |
> |
2004-12-01 17:45 tim |
3630 |
|
|
3631 |
|
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
3632 |
|
integrators/IntegratorFactory.cpp, |
3637 |
|
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
3638 |
|
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
3639 |
|
|
3640 |
< |
2004-12-01 22:45 tim |
3640 |
> |
2004-12-01 17:45 tim |
3641 |
|
|
3642 |
|
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
3643 |
|
branch new_design. |
3644 |
|
|
3645 |
< |
2004-12-01 20:05 tim |
3645 |
> |
2004-12-01 15:05 tim |
3646 |
|
|
3647 |
|
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
3648 |
|
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
3651 |
|
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
3652 |
|
visitors/ZconsVisitor.hpp: visitors get built |
3653 |
|
|
3654 |
< |
2004-12-01 19:32 chrisfen |
3654 |
> |
2004-12-01 14:32 chrisfen |
3655 |
|
|
3656 |
|
* samples/water/tip3p_ice/tp3.md: fixed a sample |
3657 |
|
|
3658 |
< |
2004-12-01 19:10 tim |
3658 |
> |
2004-12-01 14:10 tim |
3659 |
|
|
3660 |
|
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
3661 |
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
3664 |
|
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
3665 |
|
spell check |
3666 |
|
|
3667 |
< |
2004-12-01 18:42 tim |
3667 |
> |
2004-12-01 13:42 tim |
3668 |
|
|
3669 |
|
* src/: UseTheForce/DarkSide/atype.F90, |
3670 |
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3673 |
|
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
3674 |
|
and constraint, other directories get built |
3675 |
|
|
3676 |
< |
2004-12-01 17:38 tim |
3676 |
> |
2004-12-01 12:38 tim |
3677 |
|
|
3678 |
|
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
3679 |
|
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
3686 |
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
3687 |
|
refactory AtomType |
3688 |
|
|
3689 |
< |
2004-12-01 03:11 tim |
3689 |
> |
2004-11-30 22:11 tim |
3690 |
|
|
3691 |
|
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
3692 |
|
|
3693 |
< |
2004-12-01 02:30 tim |
3693 |
> |
2004-11-30 21:30 tim |
3694 |
|
|
3695 |
|
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
3696 |
|
NumericConstant |
3697 |
|
|
3698 |
< |
2004-12-01 02:24 tim |
3698 |
> |
2004-11-30 21:24 tim |
3699 |
|
|
3700 |
|
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
3701 |
|
primitives/RigidBody.cpp: minor fix |
3702 |
|
|
3703 |
< |
2004-11-30 23:14 tim |
3703 |
> |
2004-11-30 18:14 tim |
3704 |
|
|
3705 |
|
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
3706 |
|
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
3707 |
|
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
3708 |
|
get built, next is integrator |
3709 |
|
|
3710 |
< |
2004-11-30 22:43 tim |
3710 |
> |
2004-11-30 17:43 tim |
3711 |
|
|
3712 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3713 |
|
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
3715 |
|
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
3716 |
|
utils/StringUtils.hpp: brains get built |
3717 |
|
|
3718 |
< |
2004-11-30 20:50 tim |
3718 |
> |
2004-11-30 15:50 tim |
3719 |
|
|
3720 |
|
* src/: brains/ForceManager.cpp, brains/Makefile, |
3721 |
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
3722 |
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
3723 |
|
utils/StringUtils.hpp: brains get built, io is next |
3724 |
|
|
3725 |
< |
2004-11-30 19:58 tim |
3725 |
> |
2004-11-30 14:58 tim |
3726 |
|
|
3727 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3728 |
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
3733 |
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
3734 |
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
3735 |
|
|
3736 |
< |
2004-11-30 19:58 tim |
3736 |
> |
2004-11-30 14:58 tim |
3737 |
|
|
3738 |
|
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
3739 |
|
added on branch new_design. |
3740 |
|
|
3741 |
< |
2004-11-30 17:54 tim |
3741 |
> |
2004-11-30 12:54 tim |
3742 |
|
|
3743 |
|
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
3744 |
|
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
3745 |
|
utils/LocalIndexManager.hpp: more get fixed |
3746 |
|
|
3747 |
< |
2004-11-30 05:03 tim |
3747 |
> |
2004-11-30 00:03 tim |
3748 |
|
|
3749 |
|
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
3750 |
|
initially added on branch new_design. |
3751 |
|
|
3752 |
< |
2004-11-30 05:03 tim |
3752 |
> |
2004-11-30 00:03 tim |
3753 |
|
|
3754 |
|
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
3755 |
|
LocalndexManager.hpp to LocalIndexManager.hpp |
3756 |
|
|
3757 |
< |
2004-11-30 04:43 tim |
3757 |
> |
2004-11-29 23:43 tim |
3758 |
|
|
3759 |
|
* src/: io/BendTypesSectionParser.cpp, |
3760 |
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
3763 |
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
3764 |
|
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
3765 |
|
|
3766 |
< |
2004-11-30 04:14 tim |
3766 |
> |
2004-11-29 23:14 tim |
3767 |
|
|
3768 |
|
* src/: io/BendTypesSectionParser.cpp, |
3769 |
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
3771 |
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
3772 |
|
fixed |
3773 |
|
|
3774 |
< |
2004-11-30 03:49 tim |
3774 |
> |
2004-11-29 22:49 tim |
3775 |
|
|
3776 |
|
* src/: io/TorsionTypesSectionParser.cpp, |
3777 |
|
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
3779 |
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
3780 |
|
types/QuarticTorsionType.hpp: minor fixed |
3781 |
|
|
3782 |
< |
2004-11-30 03:32 tim |
3782 |
> |
2004-11-29 22:32 tim |
3783 |
|
|
3784 |
|
* src/: io/TorsionTypesSectionParser.cpp, |
3785 |
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
3786 |
|
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
3787 |
|
embedded |
3788 |
|
|
3789 |
< |
2004-11-29 21:42 tim |
3789 |
> |
2004-11-29 16:42 tim |
3790 |
|
|
3791 |
|
* test/math/: Makefile, PolynomialTestCase.cpp, |
3792 |
|
PolynomialTestCase.hpp: add PolynomialTestCase |
3793 |
|
|
3794 |
< |
2004-11-29 21:42 tim |
3794 |
> |
2004-11-29 16:42 tim |
3795 |
|
|
3796 |
|
* src/math/Polynomial.hpp: Polynomial passes unit test |
3797 |
|
|
3798 |
< |
2004-11-29 20:03 tim |
3798 |
> |
2004-11-29 15:03 tim |
3799 |
|
|
3800 |
|
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
3801 |
|
QuarticTorsion.hpp to QuarticTorsionType.hpp |
3802 |
|
|
3803 |
< |
2004-11-29 20:03 tim |
3803 |
> |
2004-11-29 15:03 tim |
3804 |
|
|
3805 |
|
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
3806 |
|
initially added on branch new_design. |
3807 |
|
|
3808 |
< |
2004-11-29 19:56 tim |
3808 |
> |
2004-11-29 14:56 tim |
3809 |
|
|
3810 |
|
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
3811 |
|
initially added on branch new_design. |
3812 |
|
|
3813 |
< |
2004-11-29 19:56 tim |
3813 |
> |
2004-11-29 14:56 tim |
3814 |
|
|
3815 |
|
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
3816 |
|
CubicTorsionType and QuarticTorsionType |
3817 |
|
|
3818 |
< |
2004-11-29 19:56 tim |
3818 |
> |
2004-11-29 14:56 tim |
3819 |
|
|
3820 |
|
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
3821 |
|
initially added on branch new_design. |
3822 |
|
|
3823 |
< |
2004-11-29 18:00 tim |
3823 |
> |
2004-11-29 13:00 tim |
3824 |
|
|
3825 |
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
3826 |
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
3827 |
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
3828 |
|
fixed |
3829 |
|
|
3830 |
< |
2004-11-29 17:59 tim |
3830 |
> |
2004-11-29 12:59 tim |
3831 |
|
|
3832 |
|
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
3833 |
|
new_design. |
3834 |
|
|
3835 |
< |
2004-11-29 17:59 tim |
3835 |
> |
2004-11-29 12:59 tim |
3836 |
|
|
3837 |
|
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
3838 |
|
Algorithm for std::string |
3839 |
|
|
3840 |
< |
2004-11-29 15:52 tim |
3840 |
> |
2004-11-29 10:52 tim |
3841 |
|
|
3842 |
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
3843 |
|
some useless files |
3844 |
|
|
3845 |
< |
2004-11-29 15:50 tim |
3845 |
> |
2004-11-29 10:50 tim |
3846 |
|
|
3847 |
|
* src/io/: BondTypesSectionParser.cpp, |
3848 |
|
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
3853 |
|
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
3854 |
|
StickyAtomTypesSectionParser.hpp: more files get fixed |
3855 |
|
|
3856 |
< |
2004-11-29 15:27 tim |
3856 |
> |
2004-11-29 10:27 tim |
3857 |
|
|
3858 |
|
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
3859 |
|
DirectionalAtomTypesSectionParser.cpp, |
3862 |
|
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
3863 |
|
built |
3864 |
|
|
3865 |
< |
2004-11-29 14:49 tim |
3865 |
> |
2004-11-29 09:49 tim |
3866 |
|
|
3867 |
|
* src/types/UreyBradleyBendType.hpp: types get built |
3868 |
|
|
3869 |
< |
2004-11-29 14:40 tim |
3869 |
> |
2004-11-29 09:40 tim |
3870 |
|
|
3871 |
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
3872 |
|
types get built |
3873 |
|
|
3874 |
< |
2004-11-26 02:13 tim |
3874 |
> |
2004-11-25 21:13 tim |
3875 |
|
|
3876 |
|
* src/: UseTheForce/ForceField.hpp, |
3877 |
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
3878 |
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
3879 |
|
files |
3880 |
|
|
3881 |
< |
2004-11-25 20:18 tim |
3881 |
> |
2004-11-25 15:18 tim |
3882 |
|
|
3883 |
|
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
3884 |
|
initially added on branch new_design. |
3885 |
|
|
3886 |
< |
2004-11-25 20:18 tim |
3886 |
> |
2004-11-25 15:18 tim |
3887 |
|
|
3888 |
|
* src/: io/AtomTypesSectionParser.cpp, |
3889 |
|
io/BondTypesSectionParser.cpp, |
3892 |
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
3893 |
|
files |
3894 |
|
|
3895 |
< |
2004-11-25 20:18 tim |
3895 |
> |
2004-11-25 15:18 tim |
3896 |
|
|
3897 |
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
3898 |
|
initially added on branch new_design. |
3899 |
|
|
3900 |
< |
2004-11-24 22:12 tim |
3900 |
> |
2004-11-24 17:12 tim |
3901 |
|
|
3902 |
|
* src/: io/AtomTypesSectionParser.cpp, |
3903 |
|
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
3920 |
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
3921 |
|
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
3922 |
|
|
3923 |
< |
2004-11-24 21:33 tim |
3923 |
> |
2004-11-24 16:33 tim |
3924 |
|
|
3925 |
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
3926 |
|
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
3927 |
|
LJFF.cpp, Makefile: UseTheForce get built |
3928 |
|
|
3929 |
< |
2004-11-24 20:55 tim |
3929 |
> |
2004-11-24 15:55 tim |
3930 |
|
|
3931 |
|
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
3932 |
|
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
3936 |
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
3937 |
|
primitives/UreyBradleyBend.hpp: types and primitives get built |
3938 |
|
|
3939 |
< |
2004-11-24 19:49 tim |
3939 |
> |
2004-11-24 14:49 tim |
3940 |
|
|
3941 |
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
3942 |
|
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
3943 |
|
StringTokenizerTestCase |
3944 |
|
|
3945 |
< |
2004-11-24 19:49 tim |
3945 |
> |
2004-11-24 14:49 tim |
3946 |
|
|
3947 |
|
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
3948 |
|
StringTokenizer.hpp: StringTokenizer passes unit test |
3949 |
|
|
3950 |
< |
2004-11-24 18:20 tim |
3950 |
> |
2004-11-24 13:20 tim |
3951 |
|
|
3952 |
|
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
3953 |
|
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
3954 |
|
change Makefile |
3955 |
|
|
3956 |
< |
2004-11-24 18:06 chrisfen |
3956 |
> |
2004-11-24 13:06 chrisfen |
3957 |
|
|
3958 |
|
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
3959 |
|
fine |
3960 |
|
|
3961 |
< |
2004-11-24 18:06 chrisfen |
3961 |
> |
2004-11-24 13:06 chrisfen |
3962 |
|
|
3963 |
|
* src/integrators/Integrator.cpp: improved restraints |
3964 |
|
|
3965 |
< |
2004-11-24 18:05 chrisfen |
3965 |
> |
2004-11-24 13:05 chrisfen |
3966 |
|
|
3967 |
|
* samples/water/tip3p_ice/tp3.md: oops... |
3968 |
|
|
3969 |
< |
2004-11-24 17:42 tim |
3969 |
> |
2004-11-24 12:42 tim |
3970 |
|
|
3971 |
|
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
3972 |
|
brains/DataStorage.hpp, brains/SimCreator.cpp, |
3975 |
|
primitives/DirectionalAtom.cpp: add SetForceManager method to |
3976 |
|
integrator |
3977 |
|
|
3978 |
< |
2004-11-23 23:12 tim |
3978 |
> |
2004-11-23 18:12 tim |
3979 |
|
|
3980 |
|
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
3981 |
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
3987 |
|
integrators/VelocityVerletIntegrator.hpp, |
3988 |
|
types/UreyBradleyBendType.hpp: refactory NPT integrator |
3989 |
|
|
3990 |
< |
2004-11-23 22:50 chrisfen |
3990 |
> |
2004-11-23 17:50 chrisfen |
3991 |
|
|
3992 |
|
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
3993 |
|
Restraints should work in parallel now |
3994 |
|
|
3995 |
< |
2004-11-23 22:48 chrisfen |
3995 |
> |
2004-11-23 17:48 chrisfen |
3996 |
|
|
3997 |
|
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
3998 |
|
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
4002 |
|
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
4003 |
|
to restraints |
4004 |
|
|
4005 |
< |
2004-11-23 22:47 chrisfen |
4005 |
> |
2004-11-23 17:47 chrisfen |
4006 |
|
|
4007 |
|
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
4008 |
|
return to the original on next commit |
4009 |
|
|
4010 |
< |
2004-11-23 17:53 tim |
4010 |
> |
2004-11-23 12:53 tim |
4011 |
|
|
4012 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4013 |
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
4020 |
|
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
4021 |
|
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
4022 |
|
|
4023 |
< |
2004-11-23 17:53 tim |
4023 |
> |
2004-11-23 12:53 tim |
4024 |
|
|
4025 |
|
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
4026 |
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
4027 |
|
branch new_design. |
4028 |
|
|
4029 |
< |
2004-11-23 17:53 tim |
4029 |
> |
2004-11-23 12:53 tim |
4030 |
|
|
4031 |
|
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
4032 |
|
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
4033 |
|
branch new_design. |
4034 |
|
|
4035 |
< |
2004-11-23 06:03 tim |
4035 |
> |
2004-11-23 01:03 tim |
4036 |
|
|
4037 |
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
4038 |
|
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
4039 |
|
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
4040 |
|
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
4041 |
|
|
4042 |
< |
2004-11-23 06:03 tim |
4042 |
> |
2004-11-23 01:03 tim |
4043 |
|
|
4044 |
|
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
4045 |
|
was initially added on branch new_design. |
4046 |
|
|
4047 |
< |
2004-11-23 06:03 tim |
4047 |
> |
2004-11-23 01:03 tim |
4048 |
|
|
4049 |
|
* src/io/EAMAtomTypesSectionParser.hpp: file |
4050 |
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
4051 |
|
new_design. |
4052 |
|
|
4053 |
< |
2004-11-23 06:03 tim |
4053 |
> |
2004-11-23 01:03 tim |
4054 |
|
|
4055 |
|
* src/io/EAMAtomTypesSectionParser.cpp: file |
4056 |
|
EAMAtomTypesSectionParser.cpp was initially added on branch |
4057 |
|
new_design. |
4058 |
|
|
4059 |
< |
2004-11-23 04:35 tim |
4059 |
> |
2004-11-22 23:35 tim |
4060 |
|
|
4061 |
|
* src/io/TorsionTypesSectionParser.hpp: file |
4062 |
|
TorsionTypesSectionParser.hpp was initially added on branch |
4063 |
|
new_design. |
4064 |
|
|
4065 |
< |
2004-11-23 04:35 tim |
4065 |
> |
2004-11-22 23:35 tim |
4066 |
|
|
4067 |
|
* src/io/BendTypesSectionParser.hpp: file |
4068 |
|
BendTypesSectionParser.hpp was initially added on branch |
4069 |
|
new_design. |
4070 |
|
|
4071 |
< |
2004-11-23 04:35 tim |
4071 |
> |
2004-11-22 23:35 tim |
4072 |
|
|
4073 |
|
* src/io/BondTypesSectionParser.hpp: file |
4074 |
|
BondTypesSectionParser.hpp was initially added on branch |
4075 |
|
new_design. |
4076 |
|
|
4077 |
< |
2004-11-23 04:35 tim |
4077 |
> |
2004-11-22 23:35 tim |
4078 |
|
|
4079 |
|
* src/io/BondTypesSectionParser.cpp: file |
4080 |
|
BondTypesSectionParser.cpp was initially added on branch |
4081 |
|
new_design. |
4082 |
|
|
4083 |
< |
2004-11-23 04:35 tim |
4083 |
> |
2004-11-22 23:35 tim |
4084 |
|
|
4085 |
|
* src/io/TorsionTypesSectionParser.cpp: file |
4086 |
|
TorsionTypesSectionParser.cpp was initially added on branch |
4087 |
|
new_design. |
4088 |
|
|
4089 |
< |
2004-11-23 04:35 tim |
4089 |
> |
2004-11-22 23:35 tim |
4090 |
|
|
4091 |
|
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
4092 |
|
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
4094 |
|
BondTypesSectionParser, BendTypesSectionParser and |
4095 |
|
TorsionTypeSectionParser |
4096 |
|
|
4097 |
< |
2004-11-23 04:35 tim |
4097 |
> |
2004-11-22 23:35 tim |
4098 |
|
|
4099 |
|
* src/io/BendTypesSectionParser.cpp: file |
4100 |
|
BendTypesSectionParser.cpp was initially added on branch |
4101 |
|
new_design. |
4102 |
|
|
4103 |
< |
2004-11-22 23:04 tim |
4103 |
> |
2004-11-22 18:04 tim |
4104 |
|
|
4105 |
|
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
4106 |
|
DUFF and EAM |
4107 |
|
|
4108 |
< |
2004-11-22 23:02 tim |
4108 |
> |
2004-11-22 18:02 tim |
4109 |
|
|
4110 |
|
* src/io/: DirectionalAtomTypesParser.hpp, |
4111 |
|
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
4112 |
|
|
4113 |
< |
2004-11-22 23:02 tim |
4113 |
> |
2004-11-22 18:02 tim |
4114 |
|
|
4115 |
|
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
4116 |
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
4117 |
|
new_design. |
4118 |
|
|
4119 |
< |
2004-11-22 20:55 tim |
4119 |
> |
2004-11-22 15:55 tim |
4120 |
|
|
4121 |
|
* src/io/DipoleAtomTypesSectionParser.hpp: file |
4122 |
|
DipoleAtomTypesSectionParser.hpp was initially added on branch |
4123 |
|
new_design. |
4124 |
|
|
4125 |
< |
2004-11-22 20:55 tim |
4125 |
> |
2004-11-22 15:55 tim |
4126 |
|
|
4127 |
|
* src/io/AtomTypesSectionParser.hpp: file |
4128 |
|
AtomTypesSectionParser.hpp was initially added on branch |
4129 |
|
new_design. |
4130 |
|
|
4131 |
< |
2004-11-22 20:55 tim |
4131 |
> |
2004-11-22 15:55 tim |
4132 |
|
|
4133 |
|
* src/io/HarmonicBondTypesSectionParser.hpp: file |
4134 |
|
HarmonicBondTypesSectionParser.hpp was initially added on branch |
4135 |
|
new_design. |
4136 |
|
|
4137 |
< |
2004-11-22 20:55 tim |
4137 |
> |
2004-11-22 15:55 tim |
4138 |
|
|
4139 |
|
* src/io/StickyAtomTypesSectionParser.cpp: file |
4140 |
|
StickyAtomTypesSectionParser.cpp was initially added on branch |
4141 |
|
new_design. |
4142 |
|
|
4143 |
< |
2004-11-22 20:55 tim |
4143 |
> |
2004-11-22 15:55 tim |
4144 |
|
|
4145 |
|
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
4146 |
|
LennardJonesAtomTypesSectionParser.hpp was initially added on |
4147 |
|
branch new_design. |
4148 |
|
|
4149 |
< |
2004-11-22 20:55 tim |
4149 |
> |
2004-11-22 15:55 tim |
4150 |
|
|
4151 |
|
* src/io/HarmonicBondTypesSectionParser.cpp: file |
4152 |
|
HarmonicBondTypesSectionParser.cpp was initially added on branch |
4153 |
|
new_design. |
4154 |
|
|
4155 |
< |
2004-11-22 20:55 tim |
4155 |
> |
2004-11-22 15:55 tim |
4156 |
|
|
4157 |
|
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
4158 |
|
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
4159 |
|
new_design. |
4160 |
|
|
4161 |
< |
2004-11-22 20:55 tim |
4161 |
> |
2004-11-22 15:55 tim |
4162 |
|
|
4163 |
|
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
4164 |
|
was initially added on branch new_design. |
4165 |
|
|
4166 |
< |
2004-11-22 20:55 tim |
4166 |
> |
2004-11-22 15:55 tim |
4167 |
|
|
4168 |
|
* src/io/AtomTypesSectionParser.cpp: file |
4169 |
|
AtomTypesSectionParser.cpp was initially added on branch |
4170 |
|
new_design. |
4171 |
|
|
4172 |
< |
2004-11-22 20:55 tim |
4172 |
> |
2004-11-22 15:55 tim |
4173 |
|
|
4174 |
|
* src/io/ChargeAtomTypesSectionParser.cpp: file |
4175 |
|
ChargeAtomTypesSectionParser.cpp was initially added on branch |
4176 |
|
new_design. |
4177 |
|
|
4178 |
< |
2004-11-22 20:55 tim |
4178 |
> |
2004-11-22 15:55 tim |
4179 |
|
|
4180 |
|
* src/io/DipoleAtomTypesSectionParser.cpp: file |
4181 |
|
DipoleAtomTypesSectionParser.cpp was initially added on branch |
4182 |
|
new_design. |
4183 |
|
|
4184 |
< |
2004-11-22 20:55 tim |
4184 |
> |
2004-11-22 15:55 tim |
4185 |
|
|
4186 |
|
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
4187 |
|
LennardJonesAtomTypesSectionParser.cpp was initially added on |
4188 |
|
branch new_design. |
4189 |
|
|
4190 |
< |
2004-11-22 20:55 tim |
4190 |
> |
2004-11-22 15:55 tim |
4191 |
|
|
4192 |
|
* src/io/ChargeAtomTypesSectionParser.hpp: file |
4193 |
|
ChargeAtomTypesSectionParser.hpp was initially added on branch |
4194 |
|
new_design. |
4195 |
|
|
4196 |
< |
2004-11-22 20:55 tim |
4196 |
> |
2004-11-22 15:55 tim |
4197 |
|
|
4198 |
|
* src/io/StickyAtomTypesSectionParser.hpp: file |
4199 |
|
StickyAtomTypesSectionParser.hpp was initially added on branch |
4200 |
|
new_design. |
4201 |
|
|
4202 |
< |
2004-11-22 20:55 tim |
4202 |
> |
2004-11-22 15:55 tim |
4203 |
|
|
4204 |
|
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
4205 |
|
added on branch new_design. |
4206 |
|
|
4207 |
< |
2004-11-22 20:55 tim |
4207 |
> |
2004-11-22 15:55 tim |
4208 |
|
|
4209 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
4210 |
|
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
4226 |
|
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
4227 |
|
utils/GenericData.hpp: adding section parsers |
4228 |
|
|
4229 |
< |
2004-11-22 20:55 tim |
4229 |
> |
2004-11-22 15:55 tim |
4230 |
|
|
4231 |
|
* src/io/DirectionalAtomTypesParser.hpp: file |
4232 |
|
DirectionalAtomTypesParser.hpp was initially added on branch |
4233 |
|
new_design. |
4234 |
|
|
4235 |
< |
2004-11-22 20:55 tim |
4235 |
> |
2004-11-22 15:55 tim |
4236 |
|
|
4237 |
|
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
4238 |
|
was initially added on branch new_design. |
4239 |
|
|
4240 |
< |
2004-11-22 20:55 tim |
4240 |
> |
2004-11-22 15:55 tim |
4241 |
|
|
4242 |
|
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
4243 |
|
added on branch new_design. |
4244 |
|
|
4245 |
< |
2004-11-19 22:12 tim |
4245 |
> |
2004-11-19 17:12 tim |
4246 |
|
|
4247 |
|
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
4248 |
|
added on branch new_design. |
4249 |
|
|
4250 |
< |
2004-11-19 22:12 tim |
4250 |
> |
2004-11-19 17:12 tim |
4251 |
|
|
4252 |
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
4253 |
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
4254 |
|
types/FixedBondType.hpp: remove more useless files |
4255 |
|
|
4256 |
< |
2004-11-19 21:47 tim |
4256 |
> |
2004-11-19 16:47 tim |
4257 |
|
|
4258 |
|
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
4259 |
|
integrators/Integrator.cpp, applications/Makedepend: remove more |
4260 |
|
useless files |
4261 |
|
|
4262 |
< |
2004-11-19 21:38 tim |
4262 |
> |
2004-11-19 16:38 tim |
4263 |
|
|
4264 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4265 |
|
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
4266 |
|
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
4267 |
|
integrators/NVT.hpp: refactory integrator |
4268 |
|
|
4269 |
< |
2004-11-19 21:38 tim |
4269 |
> |
2004-11-19 16:38 tim |
4270 |
|
|
4271 |
|
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
4272 |
|
branch new_design. |
4273 |
|
|
4274 |
< |
2004-11-19 21:38 tim |
4274 |
> |
2004-11-19 16:38 tim |
4275 |
|
|
4276 |
|
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
4277 |
|
branch new_design. |
4278 |
|
|
4279 |
< |
2004-11-19 21:38 tim |
4279 |
> |
2004-11-19 16:38 tim |
4280 |
|
|
4281 |
|
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
4282 |
|
branch new_design. |
4283 |
|
|
4284 |
< |
2004-11-19 21:38 tim |
4284 |
> |
2004-11-19 16:38 tim |
4285 |
|
|
4286 |
|
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
4287 |
|
on branch new_design. |
4288 |
|
|
4289 |
< |
2004-11-19 21:38 tim |
4289 |
> |
2004-11-19 16:38 tim |
4290 |
|
|
4291 |
|
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
4292 |
|
branch new_design. |
4293 |
|
|
4294 |
< |
2004-11-19 20:37 tim |
4294 |
> |
2004-11-19 15:37 tim |
4295 |
|
|
4296 |
|
* forceFields/newDUFF.frc: new DUFF forcefield |
4297 |
|
|
4298 |
< |
2004-11-19 20:23 tim |
4298 |
> |
2004-11-19 15:23 tim |
4299 |
|
|
4300 |
|
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
4301 |
|
branch new_design. |
4302 |
|
|
4303 |
< |
2004-11-19 20:23 tim |
4303 |
> |
2004-11-19 15:23 tim |
4304 |
|
|
4305 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
4306 |
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
4307 |
|
utils/TypeContainer.hpp: add EAM |
4308 |
|
|
4309 |
< |
2004-11-19 20:23 tim |
4309 |
> |
2004-11-19 15:23 tim |
4310 |
|
|
4311 |
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
4312 |
|
branch new_design. |
4313 |
|
|
4314 |
< |
2004-11-19 18:02 tim |
4314 |
> |
2004-11-19 13:02 tim |
4315 |
|
|
4316 |
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
4317 |
|
error checking |
4318 |
|
|
4319 |
< |
2004-11-19 17:56 tim |
4319 |
> |
2004-11-19 12:56 tim |
4320 |
|
|
4321 |
|
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
4322 |
|
was initially added on branch new_design. |
4323 |
|
|
4324 |
< |
2004-11-19 17:56 tim |
4324 |
> |
2004-11-19 12:56 tim |
4325 |
|
|
4326 |
|
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
4327 |
|
was initially added on branch new_design. |
4328 |
|
|
4329 |
< |
2004-11-19 17:56 tim |
4329 |
> |
2004-11-19 12:56 tim |
4330 |
|
|
4331 |
|
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
4332 |
|
added on branch new_design. |
4333 |
|
|
4334 |
< |
2004-11-19 17:56 tim |
4334 |
> |
2004-11-19 12:56 tim |
4335 |
|
|
4336 |
|
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
4337 |
|
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
4342 |
|
utils/StringTokenizer.cpp: DUFF is almost done except error |
4343 |
|
checking |
4344 |
|
|
4345 |
< |
2004-11-19 00:11 tim |
4345 |
> |
2004-11-18 19:11 tim |
4346 |
|
|
4347 |
|
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
4348 |
|
|
4349 |
< |
2004-11-18 23:26 tim |
4349 |
> |
2004-11-18 18:26 tim |
4350 |
|
|
4351 |
|
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
4352 |
|
initially added on branch new_design. |
4353 |
|
|
4354 |
< |
2004-11-18 23:26 tim |
4354 |
> |
2004-11-18 18:26 tim |
4355 |
|
|
4356 |
|
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
4357 |
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
4363 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
4364 |
|
DUFF parser |
4365 |
|
|
4366 |
< |
2004-11-18 21:42 tim |
4366 |
> |
2004-11-18 16:42 tim |
4367 |
|
|
4368 |
|
* forceFields/newDUFF.frc: adding new format DUFF force field |
4369 |
|
|
4370 |
< |
2004-11-18 15:57 chrisfen |
4370 |
> |
2004-11-18 10:57 chrisfen |
4371 |
|
|
4372 |
|
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
4373 |
|
slowed down the force loop |
4374 |
|
|
4375 |
< |
2004-11-18 05:42 tim |
4375 |
> |
2004-11-18 00:42 tim |
4376 |
|
|
4377 |
|
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
4378 |
|
initially added on branch new_design. |
4379 |
|
|
4380 |
< |
2004-11-18 05:42 tim |
4380 |
> |
2004-11-18 00:42 tim |
4381 |
|
|
4382 |
|
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
4383 |
|
initially added on branch new_design. |
4384 |
|
|
4385 |
< |
2004-11-18 05:42 tim |
4385 |
> |
2004-11-18 00:42 tim |
4386 |
|
|
4387 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
4388 |
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
4389 |
|
utils/NumericConstant.hpp: Adding NumericConstant class |
4390 |
|
|
4391 |
< |
2004-11-18 04:16 tim |
4391 |
> |
2004-11-17 23:16 tim |
4392 |
|
|
4393 |
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
4394 |
|
UseTheForce/ForceFields.hpp: remove more junk files |
4395 |
|
|
4396 |
< |
2004-11-18 04:12 tim |
4396 |
> |
2004-11-17 23:12 tim |
4397 |
|
|
4398 |
|
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
4399 |
|
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
4402 |
|
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
4403 |
|
primitives/TorsionExtensions.cpp: remove some junk files |
4404 |
|
|
4405 |
< |
2004-11-18 04:07 tim |
4405 |
> |
2004-11-17 23:07 tim |
4406 |
|
|
4407 |
|
* src/primitives/BendExtensions.cpp: remove some junk files |
4408 |
|
|
4409 |
< |
2004-11-18 04:04 tim |
4409 |
> |
2004-11-17 23:04 tim |
4410 |
|
|
4411 |
|
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
4412 |
|
QuadraticBondType.hpp: refine QudraticBond |
4413 |
|
|
4414 |
< |
2004-11-18 03:57 tim |
4414 |
> |
2004-11-17 22:57 tim |
4415 |
|
|
4416 |
|
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
4417 |
|
|
4418 |
< |
2004-11-18 03:57 tim |
4418 |
> |
2004-11-17 22:57 tim |
4419 |
|
|
4420 |
|
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
4421 |
|
initially added on branch new_design. |
4422 |
|
|
4423 |
< |
2004-11-17 21:47 tim |
4423 |
> |
2004-11-17 16:47 tim |
4424 |
|
|
4425 |
|
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
4426 |
|
was initially added on branch new_design. |
4427 |
|
|
4428 |
< |
2004-11-17 21:47 tim |
4428 |
> |
2004-11-17 16:47 tim |
4429 |
|
|
4430 |
|
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
4431 |
|
added on branch new_design. |
4432 |
|
|
4433 |
< |
2004-11-17 21:47 tim |
4433 |
> |
2004-11-17 16:47 tim |
4434 |
|
|
4435 |
|
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
4436 |
|
added on branch new_design. |
4437 |
|
|
4438 |
< |
2004-11-17 21:47 tim |
4438 |
> |
2004-11-17 16:47 tim |
4439 |
|
|
4440 |
|
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
4441 |
|
initially added on branch new_design. |
4442 |
|
|
4443 |
< |
2004-11-17 21:47 tim |
4443 |
> |
2004-11-17 16:47 tim |
4444 |
|
|
4445 |
|
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
4446 |
|
initially added on branch new_design. |
4447 |
|
|
4448 |
< |
2004-11-17 21:47 tim |
4448 |
> |
2004-11-17 16:47 tim |
4449 |
|
|
4450 |
|
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
4451 |
|
initially added on branch new_design. |
4452 |
|
|
4453 |
< |
2004-11-17 21:47 tim |
4453 |
> |
2004-11-17 16:47 tim |
4454 |
|
|
4455 |
|
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
4456 |
|
added on branch new_design. |
4457 |
|
|
4458 |
< |
2004-11-17 21:47 tim |
4458 |
> |
2004-11-17 16:47 tim |
4459 |
|
|
4460 |
|
* src/: math/ChebyshevPolynomials.cpp, |
4461 |
|
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
4467 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
4468 |
|
UreyBradleyBend and GhostBend |
4469 |
|
|
4470 |
< |
2004-11-17 18:58 tim |
4470 |
> |
2004-11-17 13:58 tim |
4471 |
|
|
4472 |
|
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
4473 |
|
was initially added on branch new_design. |
4474 |
|
|
4475 |
< |
2004-11-17 18:58 tim |
4475 |
> |
2004-11-17 13:58 tim |
4476 |
|
|
4477 |
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
4478 |
|
was initially added on branch new_design. |
4479 |
|
|
4480 |
< |
2004-11-17 18:58 tim |
4480 |
> |
2004-11-17 13:58 tim |
4481 |
|
|
4482 |
|
* src/: math/ChebyshevPolynomials.cpp, |
4483 |
|
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
4486 |
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
4487 |
|
stuff and Chebyshev Polynomial |
4488 |
|
|
4489 |
< |
2004-11-17 18:58 tim |
4489 |
> |
2004-11-17 13:58 tim |
4490 |
|
|
4491 |
|
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
4492 |
|
initially added on branch new_design. |
4493 |
|
|
4494 |
< |
2004-11-17 06:37 tim |
4494 |
> |
2004-11-17 01:37 tim |
4495 |
|
|
4496 |
|
* src/types/PolynomialTorsionType.hpp: file |
4497 |
|
PolynomialTorsionType.hpp was initially added on branch new_design. |
4498 |
|
|
4499 |
< |
2004-11-17 06:37 tim |
4499 |
> |
2004-11-17 01:37 tim |
4500 |
|
|
4501 |
|
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
4502 |
|
initially added on branch new_design. |
4503 |
|
|
4504 |
< |
2004-11-17 06:37 tim |
4504 |
> |
2004-11-17 01:37 tim |
4505 |
|
|
4506 |
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
4507 |
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
4515 |
|
CharmmTorsionType. Need to refine the design and add document for |
4516 |
|
them |
4517 |
|
|
4518 |
< |
2004-11-17 06:37 tim |
4518 |
> |
2004-11-17 01:37 tim |
4519 |
|
|
4520 |
|
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
4521 |
|
initially added on branch new_design. |
4522 |
|
|
4523 |
< |
2004-11-17 06:37 tim |
4523 |
> |
2004-11-17 01:37 tim |
4524 |
|
|
4525 |
|
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
4526 |
|
initially added on branch new_design. |
4527 |
|
|
4528 |
< |
2004-11-17 06:37 tim |
4528 |
> |
2004-11-17 01:37 tim |
4529 |
|
|
4530 |
|
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
4531 |
|
initially added on branch new_design. |
4532 |
|
|
4533 |
< |
2004-11-17 01:11 tim |
4533 |
> |
2004-11-16 20:11 tim |
4534 |
|
|
4535 |
|
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
4536 |
|
TorsionType.hpp: add PolynomialBondType |
4537 |
|
|
4538 |
< |
2004-11-17 01:11 tim |
4538 |
> |
2004-11-16 20:11 tim |
4539 |
|
|
4540 |
|
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
4541 |
|
initially added on branch new_design. |
4542 |
|
|
4543 |
< |
2004-11-16 23:20 tim |
4543 |
> |
2004-11-16 18:20 tim |
4544 |
|
|
4545 |
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
4546 |
|
on branch new_design. |
4547 |
|
|
4548 |
< |
2004-11-16 23:20 tim |
4548 |
> |
2004-11-16 18:20 tim |
4549 |
|
|
4550 |
|
* src/math/Polynomial.hpp: Adding Polynomial class |
4551 |
|
|
4552 |
< |
2004-11-16 22:04 gezelter |
4552 |
> |
2004-11-16 17:04 gezelter |
4553 |
|
|
4554 |
|
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
4555 |
|
added on branch new_design. |
4556 |
|
|
4557 |
< |
2004-11-16 22:04 gezelter |
4557 |
> |
2004-11-16 17:04 gezelter |
4558 |
|
|
4559 |
|
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
4560 |
|
initially added on branch new_design. |
4561 |
|
|
4562 |
< |
2004-11-16 22:04 gezelter |
4562 |
> |
2004-11-16 17:04 gezelter |
4563 |
|
|
4564 |
|
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
4565 |
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
4566 |
|
|
4567 |
< |
2004-11-16 20:36 tim |
4567 |
> |
2004-11-16 15:36 tim |
4568 |
|
|
4569 |
|
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
4570 |
|
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
4571 |
|
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
4572 |
|
TorsionType |
4573 |
|
|
4574 |
< |
2004-11-16 02:07 tim |
4574 |
> |
2004-11-15 21:07 tim |
4575 |
|
|
4576 |
|
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
4577 |
|
branch new_design. |
4578 |
|
|
4579 |
< |
2004-11-16 02:07 tim |
4579 |
> |
2004-11-15 21:07 tim |
4580 |
|
|
4581 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4582 |
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
4583 |
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
4584 |
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
4585 |
|
|
4586 |
< |
2004-11-15 23:00 tim |
4586 |
> |
2004-11-15 18:00 tim |
4587 |
|
|
4588 |
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
4589 |
|
UseTheForce/ForceFieldFactory.cpp, |
4591 |
|
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
4592 |
|
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
4593 |
|
|
4594 |
< |
2004-11-15 23:00 tim |
4594 |
> |
2004-11-15 18:00 tim |
4595 |
|
|
4596 |
|
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
4597 |
|
was initially added on branch new_design. |
4598 |
|
|
4599 |
< |
2004-11-15 23:00 tim |
4599 |
> |
2004-11-15 18:00 tim |
4600 |
|
|
4601 |
|
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
4602 |
|
was initially added on branch new_design. |
4603 |
|
|
4604 |
< |
2004-11-15 23:00 tim |
4604 |
> |
2004-11-15 18:00 tim |
4605 |
|
|
4606 |
|
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
4607 |
|
branch new_design. |
4608 |
|
|
4609 |
< |
2004-11-15 18:02 tim |
4609 |
> |
2004-11-15 13:02 tim |
4610 |
|
|
4611 |
|
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
4612 |
|
initially added on branch new_design. |
4613 |
|
|
4614 |
< |
2004-11-15 18:02 tim |
4614 |
> |
2004-11-15 13:02 tim |
4615 |
|
|
4616 |
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
4617 |
|
branch new_design. |
4618 |
|
|
4619 |
< |
2004-11-15 18:02 tim |
4619 |
> |
2004-11-15 13:02 tim |
4620 |
|
|
4621 |
|
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
4622 |
|
branch new_design. |
4623 |
|
|
4624 |
< |
2004-11-15 18:02 tim |
4624 |
> |
2004-11-15 13:02 tim |
4625 |
|
|
4626 |
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
4627 |
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
4629 |
|
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
4630 |
|
DumpWriter.Next Step is LJFF and integrators |
4631 |
|
|
4632 |
< |
2004-11-13 05:08 tim |
4632 |
> |
2004-11-13 00:08 tim |
4633 |
|
|
4634 |
|
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
4635 |
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
4637 |
|
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
4638 |
|
refactory, refactory |
4639 |
|
|
4640 |
< |
2004-11-12 22:43 tim |
4640 |
> |
2004-11-12 17:43 tim |
4641 |
|
|
4642 |
|
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
4643 |
|
StringTokenizer.cpp: bug fix in hasMoreTokens |
4644 |
|
|
4645 |
< |
2004-11-12 22:28 tim |
4645 |
> |
2004-11-12 17:28 tim |
4646 |
|
|
4647 |
|
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
4648 |
|
initially added on branch new_design. |
4649 |
|
|
4650 |
< |
2004-11-12 22:28 tim |
4650 |
> |
2004-11-12 17:28 tim |
4651 |
|
|
4652 |
|
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
4653 |
|
StringUtils, a c-style strtok like class, need unit test |
4654 |
|
|
4655 |
< |
2004-11-12 17:40 tim |
4655 |
> |
2004-11-12 12:40 tim |
4656 |
|
|
4657 |
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
4658 |
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
4659 |
|
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
4660 |
|
|
4661 |
< |
2004-11-12 07:05 tim |
4661 |
> |
2004-11-12 02:05 tim |
4662 |
|
|
4663 |
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
4664 |
|
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
4665 |
|
MoleculeCreator forget to create CutoffGroups for free atoms |
4666 |
|
|
4667 |
< |
2004-11-12 06:19 tim |
4667 |
> |
2004-11-12 01:19 tim |
4668 |
|
|
4669 |
|
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
4670 |
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4672 |
|
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
4673 |
|
OOPSE = Object-Obfuscated Parallel Simulation Engine |
4674 |
|
|
4675 |
< |
2004-11-11 21:48 chrisfen |
4675 |
> |
2004-11-11 16:48 chrisfen |
4676 |
|
|
4677 |
|
* samples/water/tip3p_ice/tp3.md: working sample |
4678 |
|
|
4679 |
< |
2004-11-11 21:47 chrisfen |
4679 |
> |
2004-11-11 16:47 chrisfen |
4680 |
|
|
4681 |
|
* src/restraints/Restraints.cpp: working towards parallel |
4682 |
|
restraints |
4683 |
|
|
4684 |
< |
2004-11-11 21:47 chrisfen |
4684 |
> |
2004-11-11 16:47 chrisfen |
4685 |
|
|
4686 |
|
* src/integrators/Integrator.cpp: Commented out some write |
4687 |
|
statements |
4688 |
|
|
4689 |
< |
2004-11-11 21:46 chrisfen |
4689 |
> |
2004-11-11 16:46 chrisfen |
4690 |
|
|
4691 |
|
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
4692 |
|
write statements |
4693 |
|
|
4694 |
< |
2004-11-11 21:46 chrisfen |
4694 |
> |
2004-11-11 16:46 chrisfen |
4695 |
|
|
4696 |
|
* samples/water/tip3p_ice/tp3.md: Fun with ice |
4697 |
|
|
4698 |
< |
2004-11-11 16:41 tim |
4698 |
> |
2004-11-11 11:41 tim |
4699 |
|
|
4700 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
4701 |
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
4704 |
|
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
4705 |
|
useless mpiSimulation |
4706 |
|
|
4707 |
< |
2004-11-11 16:41 tim |
4707 |
> |
2004-11-11 11:41 tim |
4708 |
|
|
4709 |
|
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
4710 |
|
branch new_design. |
4711 |
|
|
4712 |
< |
2004-11-10 22:50 tim |
4712 |
> |
2004-11-10 17:50 tim |
4713 |
|
|
4714 |
|
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
4715 |
|
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
4716 |
|
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
4717 |
|
|
4718 |
< |
2004-11-10 22:01 tim |
4718 |
> |
2004-11-10 17:01 tim |
4719 |
|
|
4720 |
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
4721 |
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
4729 |
|
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
4730 |
|
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
4731 |
|
|
4732 |
< |
2004-11-10 14:52 tim |
4732 |
> |
2004-11-10 09:52 tim |
4733 |
|
|
4734 |
|
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
4735 |
|
configurable StatWriter |
4736 |
|
|
4737 |
< |
2004-11-10 14:52 tim |
4737 |
> |
2004-11-10 09:52 tim |
4738 |
|
|
4739 |
|
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
4740 |
|
branch new_design. |
4741 |
|
|
4742 |
< |
2004-11-10 02:58 tim |
4742 |
> |
2004-11-09 21:58 tim |
4743 |
|
|
4744 |
|
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
4745 |
|
in progress |
4746 |
|
|
4747 |
< |
2004-11-09 23:11 tim |
4747 |
> |
2004-11-09 18:11 tim |
4748 |
|
|
4749 |
|
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
4750 |
|
added on branch new_design. |
4751 |
|
|
4752 |
< |
2004-11-09 23:11 tim |
4752 |
> |
2004-11-09 18:11 tim |
4753 |
|
|
4754 |
|
* src/integrators/VelocityVerletIntegrator.cpp: file |
4755 |
|
VelocityVerletIntegrator.cpp was initially added on branch |
4756 |
|
new_design. |
4757 |
|
|
4758 |
< |
2004-11-09 23:11 tim |
4758 |
> |
2004-11-09 18:11 tim |
4759 |
|
|
4760 |
|
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
4761 |
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4764 |
|
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
4765 |
|
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
4766 |
|
|
4767 |
< |
2004-11-09 23:11 tim |
4767 |
> |
2004-11-09 18:11 tim |
4768 |
|
|
4769 |
|
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
4770 |
|
added on branch new_design. |
4771 |
|
|
4772 |
< |
2004-11-09 23:11 tim |
4772 |
> |
2004-11-09 18:11 tim |
4773 |
|
|
4774 |
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
4775 |
|
branch new_design. |
4776 |
|
|
4777 |
< |
2004-11-09 01:08 tim |
4777 |
> |
2004-11-08 20:08 tim |
4778 |
|
|
4779 |
|
* src/integrators/VelocityVerletIntegrator.hpp: file |
4780 |
|
VelocityVerletIntegrator.hpp was initially added on branch |
4781 |
|
new_design. |
4782 |
|
|
4783 |
< |
2004-11-09 01:08 tim |
4783 |
> |
2004-11-08 20:08 tim |
4784 |
|
|
4785 |
|
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
4786 |
|
branch new_design. |
4787 |
|
|
4788 |
< |
2004-11-09 01:08 tim |
4788 |
> |
2004-11-08 20:08 tim |
4789 |
|
|
4790 |
|
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
4791 |
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
4792 |
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
4793 |
|
utils/TypeContainer.hpp: More to break |
4794 |
|
|
4795 |
< |
2004-11-06 05:21 tim |
4795 |
> |
2004-11-06 00:21 tim |
4796 |
|
|
4797 |
|
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
4798 |
|
added on branch new_design. |
4799 |
|
|
4800 |
< |
2004-11-06 05:21 tim |
4800 |
> |
2004-11-06 00:21 tim |
4801 |
|
|
4802 |
|
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
4803 |
|
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
4804 |
|
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
4805 |
|
ForceField and TypeContainer classes |
4806 |
|
|
4807 |
< |
2004-11-05 23:38 tim |
4807 |
> |
2004-11-05 18:38 tim |
4808 |
|
|
4809 |
|
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
4810 |
|
initially added on branch new_design. |
4811 |
|
|
4812 |
< |
2004-11-05 23:38 tim |
4812 |
> |
2004-11-05 18:38 tim |
4813 |
|
|
4814 |
|
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
4815 |
|
initially added on branch new_design. |
4816 |
|
|
4817 |
< |
2004-11-05 23:38 tim |
4817 |
> |
2004-11-05 18:38 tim |
4818 |
|
|
4819 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
4820 |
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
4822 |
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
4823 |
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
4824 |
|
|
4825 |
< |
2004-11-05 21:45 chrisfen |
4825 |
> |
2004-11-05 16:45 chrisfen |
4826 |
|
|
4827 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
4828 |
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
4829 |
|
linear visitor |
4830 |
|
|
4831 |
< |
2004-11-05 21:04 chrisfen |
4831 |
> |
2004-11-05 16:04 chrisfen |
4832 |
|
|
4833 |
|
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
4834 |
|
debugging process |
4835 |
|
|
4836 |
< |
2004-11-05 21:04 chrisfen |
4836 |
> |
2004-11-05 16:04 chrisfen |
4837 |
|
|
4838 |
|
* make/Makefile.in: included visitors and minimizer |
4839 |
|
|
4840 |
< |
2004-11-05 21:03 chrisfen |
4840 |
> |
2004-11-05 16:03 chrisfen |
4841 |
|
|
4842 |
|
* ChangeLog: new changes |
4843 |
|
|
4844 |
< |
2004-11-05 02:56 tim |
4844 |
> |
2004-11-04 21:56 tim |
4845 |
|
|
4846 |
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
4847 |
|
primitives/Molecule.hpp: Pain...... |
4848 |
|
|
4849 |
< |
2004-11-04 20:55 tim |
4849 |
> |
2004-11-04 15:55 tim |
4850 |
|
|
4851 |
|
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
4852 |
|
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
4853 |
|
src/brains/Stats.hpp: time to break SimSetup |
4854 |
|
|
4855 |
< |
2004-11-04 20:51 gezelter |
4855 |
> |
2004-11-04 15:51 gezelter |
4856 |
|
|
4857 |
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
4858 |
|
classes in progress |
4859 |
|
|
4860 |
< |
2004-11-04 19:48 tim |
4860 |
> |
2004-11-04 14:48 tim |
4861 |
|
|
4862 |
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
4863 |
|
branch new_design. |
4864 |
|
|
4865 |
< |
2004-11-04 19:48 tim |
4865 |
> |
2004-11-04 14:48 tim |
4866 |
|
|
4867 |
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
4868 |
|
branch new_design. |
4869 |
|
|
4870 |
< |
2004-11-04 19:48 tim |
4870 |
> |
2004-11-04 14:48 tim |
4871 |
|
|
4872 |
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
4873 |
|
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
4874 |
|
class |
4875 |
|
|
4876 |
< |
2004-11-04 16:22 gezelter |
4876 |
> |
2004-11-04 11:22 gezelter |
4877 |
|
|
4878 |
|
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
4879 |
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
4882 |
|
false and "-1" but there should be logic to figure them out in the |
4883 |
|
other two classes |
4884 |
|
|
4885 |
< |
2004-11-04 16:20 gezelter |
4885 |
> |
2004-11-04 11:20 gezelter |
4886 |
|
|
4887 |
|
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
4888 |
|
remember what I did |
4889 |
|
|
4890 |
< |
2004-11-04 16:20 gezelter |
4890 |
> |
2004-11-04 11:20 gezelter |
4891 |
|
|
4892 |
|
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
4893 |
|
|
4894 |
< |
2004-11-04 16:20 gezelter |
4894 |
> |
2004-11-04 11:20 gezelter |
4895 |
|
|
4896 |
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
4897 |
|
in the entry_plug so that it only is set if the atoms really are in |
4898 |
|
the simulation |
4899 |
|
|
4900 |
< |
2004-11-04 16:20 gezelter |
4900 |
> |
2004-11-04 11:20 gezelter |
4901 |
|
|
4902 |
|
* samples/water/ssd/ssd.md: testing force fields |
4903 |
|
|
4904 |
< |
2004-11-04 16:19 gezelter |
4904 |
> |
2004-11-04 11:19 gezelter |
4905 |
|
|
4906 |
|
* samples/shape/linear.in: testing shapes |
4907 |
|
|
4908 |
< |
2004-11-03 19:56 tim |
4908 |
> |
2004-11-03 14:56 tim |
4909 |
|
|
4910 |
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
4911 |
|
class(similar as SimSetup) |
4912 |
|
|
4913 |
< |
2004-11-03 19:56 tim |
4913 |
> |
2004-11-03 14:56 tim |
4914 |
|
|
4915 |
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
4916 |
|
added on branch new_design. |
4917 |
|
|
4918 |
< |
2004-11-03 19:56 tim |
4918 |
> |
2004-11-03 14:56 tim |
4919 |
|
|
4920 |
|
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
4921 |
|
added on branch new_design. |
4922 |
|
|
4923 |
< |
2004-11-03 18:00 tim |
4923 |
> |
2004-11-03 13:00 tim |
4924 |
|
|
4925 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4926 |
|
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
4930 |
|
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
4931 |
|
compiled. Still a long way to go ...... |
4932 |
|
|
4933 |
< |
2004-11-03 16:08 tim |
4933 |
> |
2004-11-03 11:08 tim |
4934 |
|
|
4935 |
|
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
4936 |
|
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
4945 |
|
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
4946 |
|
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
4947 |
|
|
4948 |
< |
2004-11-02 22:41 tim |
4948 |
> |
2004-11-02 17:41 tim |
4949 |
|
|
4950 |
|
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
4951 |
|
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
4952 |
|
Need unit test |
4953 |
|
|
4954 |
< |
2004-11-02 22:41 tim |
4954 |
> |
2004-11-02 17:41 tim |
4955 |
|
|
4956 |
|
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
4957 |
|
initially added on branch new_design. |
4958 |
|
|
4959 |
< |
2004-11-02 22:41 tim |
4959 |
> |
2004-11-02 17:41 tim |
4960 |
|
|
4961 |
|
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
4962 |
|
branch new_design. |
4963 |
|
|
4964 |
< |
2004-11-02 16:59 tim |
4964 |
> |
2004-11-02 11:59 tim |
4965 |
|
|
4966 |
|
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
4967 |
|
branch new_design. |
4968 |
|
|
4969 |
< |
2004-11-02 16:59 tim |
4969 |
> |
2004-11-02 11:59 tim |
4970 |
|
|
4971 |
|
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
4972 |
|
SimSnapshotManager.hpp: SimModel in progress |
4973 |
|
|
4974 |
< |
2004-11-02 15:28 chrisfen |
4974 |
> |
2004-11-02 10:28 chrisfen |
4975 |
|
|
4976 |
|
* src/: UseTheForce/DarkSide/shapes.F90, |
4977 |
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
4978 |
|
looks like it's working |
4979 |
|
|
4980 |
< |
2004-11-02 15:27 tim |
4980 |
> |
2004-11-02 10:27 tim |
4981 |
|
|
4982 |
|
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
4983 |
|
functions for dealing with memory issue |
4984 |
|
|
4985 |
< |
2004-11-02 15:27 tim |
4985 |
> |
2004-11-02 10:27 tim |
4986 |
|
|
4987 |
|
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
4988 |
|
added on branch new_design. |
4989 |
|
|
4990 |
< |
2004-11-02 15:23 tim |
4990 |
> |
2004-11-02 10:23 tim |
4991 |
|
|
4992 |
|
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
4993 |
|
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
4994 |
|
SimModel(something similar as SimInfo) |
4995 |
|
|
4996 |
< |
2004-11-01 22:52 tim |
4996 |
> |
2004-11-01 17:52 tim |
4997 |
|
|
4998 |
|
* src/: applications/simpleBuilder/MoLocator.hpp, |
4999 |
|
applications/simpleBuilder/simpleBuilder.cpp, |
5012 |
|
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
5013 |
|
RigidBody and StuntDouble classes get compiled |
5014 |
|
|
5015 |
< |
2004-11-01 21:40 tim |
5015 |
> |
2004-11-01 16:40 tim |
5016 |
|
|
5017 |
|
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
5018 |
|
on branch new_design. |
5019 |
|
|
5020 |
< |
2004-11-01 21:40 tim |
5020 |
> |
2004-11-01 16:40 tim |
5021 |
|
|
5022 |
|
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
5023 |
|
branch new_design. |
5024 |
|
|
5025 |
< |
2004-11-01 21:40 tim |
5025 |
> |
2004-11-01 16:40 tim |
5026 |
|
|
5027 |
|
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
5028 |
|
branch new_design. |
5029 |
|
|
5030 |
< |
2004-11-01 21:40 tim |
5030 |
> |
2004-11-01 16:40 tim |
5031 |
|
|
5032 |
|
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
5033 |
|
version of Bond, Bend and Torsion. |
5034 |
|
|
5035 |
< |
2004-11-01 21:37 tim |
5035 |
> |
2004-11-01 16:37 tim |
5036 |
|
|
5037 |
|
* src/types/BendType.hpp: file BendType.hpp was initially added on |
5038 |
|
branch new_design. |
5039 |
|
|
5040 |
< |
2004-11-01 21:37 tim |
5040 |
> |
2004-11-01 16:37 tim |
5041 |
|
|
5042 |
|
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
5043 |
|
BondType, BendType, TorsionType |
5044 |
|
|
5045 |
< |
2004-11-01 21:37 tim |
5045 |
> |
2004-11-01 16:37 tim |
5046 |
|
|
5047 |
|
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
5048 |
|
added on branch new_design. |
5049 |
|
|
5050 |
< |
2004-11-01 21:37 tim |
5050 |
> |
2004-11-01 16:37 tim |
5051 |
|
|
5052 |
|
* src/types/BondType.hpp: file BondType.hpp was initially added on |
5053 |
|
branch new_design. |
5054 |
|
|
5055 |
< |
2004-11-01 20:15 tim |
5055 |
> |
2004-11-01 15:15 tim |
5056 |
|
|
5057 |
|
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
5058 |
|
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
5060 |
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
5061 |
|
break, break and break..... |
5062 |
|
|
5063 |
< |
2004-11-01 19:57 tim |
5063 |
> |
2004-11-01 14:57 tim |
5064 |
|
|
5065 |
|
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
5066 |
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
5067 |
|
StuntDouble.hpp: these core classes get compiled |
5068 |
|
|
5069 |
< |
2004-10-29 22:37 tim |
5069 |
> |
2004-10-29 17:37 tim |
5070 |
|
|
5071 |
|
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
5072 |
|
class |
5073 |
|
|
5074 |
< |
2004-10-29 22:28 chrisfen |
5074 |
> |
2004-10-29 17:28 chrisfen |
5075 |
|
|
5076 |
|
* src/: UseTheForce/DarkSide/atype.F90, |
5077 |
|
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
5078 |
|
types/ShapeAtomType.cpp: still debugging |
5079 |
|
|
5080 |
< |
2004-10-29 22:28 chrisfen |
5080 |
> |
2004-10-29 17:28 chrisfen |
5081 |
|
|
5082 |
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
5083 |
|
shapes rcut calculator added |
5084 |
|
|
5085 |
< |
2004-10-29 22:27 chrisfen |
5085 |
> |
2004-10-29 17:27 chrisfen |
5086 |
|
|
5087 |
|
* samples/shape/linear.md: shorter run |
5088 |
|
|
5089 |
< |
2004-10-29 20:54 tim |
5089 |
> |
2004-10-29 15:54 tim |
5090 |
|
|
5091 |
|
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
5092 |
|
|
5093 |
< |
2004-10-29 16:22 tim |
5093 |
> |
2004-10-29 11:22 tim |
5094 |
|
|
5095 |
|
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
5096 |
|
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
5097 |
|
some deprecated files |
5098 |
|
|
5099 |
< |
2004-10-29 16:20 tim |
5099 |
> |
2004-10-29 11:20 tim |
5100 |
|
|
5101 |
|
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
5102 |
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
5103 |
|
More painful reconstruction is coming !!! |
5104 |
|
|
5105 |
< |
2004-10-28 22:34 tim |
5105 |
> |
2004-10-28 17:34 tim |
5106 |
|
|
5107 |
|
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
5108 |
|
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
5110 |
|
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
5111 |
|
DirectionalAtom and RigidBody |
5112 |
|
|
5113 |
< |
2004-10-28 22:26 tim |
5113 |
> |
2004-10-28 17:26 tim |
5114 |
|
|
5115 |
|
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
5116 |
|
src/applications/simpleBuilder/MoLocator.cpp, |
5118 |
|
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
5119 |
|
remove old Vector3d.hpp from application/simpleBuilder |
5120 |
|
|
5121 |
< |
2004-10-28 21:42 tim |
5121 |
> |
2004-10-28 16:42 tim |
5122 |
|
|
5123 |
|
* src/utils/next_combination.hpp: Minor change in next_combination |
5124 |
|
|
5125 |
< |
2004-10-28 21:28 tim |
5125 |
> |
2004-10-28 16:28 tim |
5126 |
|
|
5127 |
|
* src/utils/next_combination.hpp, |
5128 |
|
test/utils/NextCombinationTestCase.cpp, |
5129 |
|
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
5130 |
|
|
5131 |
< |
2004-10-28 21:11 tim |
5131 |
> |
2004-10-28 16:11 tim |
5132 |
|
|
5133 |
|
* src/utils/next_combination.hpp: change documentation of |
5134 |
|
next_combination.hpp |
5135 |
|
|
5136 |
< |
2004-10-28 20:41 tim |
5136 |
> |
2004-10-28 15:41 tim |
5137 |
|
|
5138 |
|
* ChangeLog, src/utils/next_combination.hpp, |
5139 |
|
test/utils/NextCombinationTestCase.cpp, |
5140 |
|
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
5141 |
|
|
5142 |
< |
2004-10-28 20:01 tim |
5142 |
> |
2004-10-28 15:01 tim |
5143 |
|
|
5144 |
|
* src/utils/next_combination.hpp: adding replace wildcard function |
5145 |
|
|
5146 |
< |
2004-10-28 19:33 tim |
5146 |
> |
2004-10-28 14:33 tim |
5147 |
|
|
5148 |
|
* src/utils/next_combination.hpp: Minor change |
5149 |
|
|
5150 |
< |
2004-10-28 19:06 tim |
5150 |
> |
2004-10-28 14:06 tim |
5151 |
|
|
5152 |
|
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
5153 |
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
5157 |
|
test/utils/next_combination.hpp: STL next_permutation like |
5158 |
|
next_combination is working |
5159 |
|
|
5160 |
< |
2004-10-28 17:22 chrisfen |
5160 |
> |
2004-10-28 12:22 chrisfen |
5161 |
|
|
5162 |
|
* src/UseTheForce/WATER.cpp: fix of setDipoles |
5163 |
|
|
5164 |
< |
2004-10-28 17:20 gezelter |
5164 |
> |
2004-10-28 12:20 gezelter |
5165 |
|
|
5166 |
|
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
5167 |
|
shapeFile |
5168 |
|
|
5169 |
< |
2004-10-28 17:20 gezelter |
5169 |
> |
2004-10-28 12:20 gezelter |
5170 |
|
|
5171 |
|
* samples/shape/linear.md: forgot the orientation line |
5172 |
|
|
5173 |
< |
2004-10-28 16:56 gezelter |
5173 |
> |
2004-10-28 11:56 gezelter |
5174 |
|
|
5175 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5176 |
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
5177 |
|
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
5178 |
|
declaration foo |
5179 |
|
|
5180 |
< |
2004-10-28 16:55 gezelter |
5180 |
> |
2004-10-28 11:55 gezelter |
5181 |
|
|
5182 |
|
* samples/lipid/5x5.md: uncommented .in line |
5183 |
|
|
5184 |
< |
2004-10-28 15:42 tim |
5184 |
> |
2004-10-28 10:42 tim |
5185 |
|
|
5186 |
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
5187 |
|
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
5188 |
|
in progress |
5189 |
|
|
5190 |
< |
2004-10-28 15:15 tim |
5190 |
> |
2004-10-28 10:15 tim |
5191 |
|
|
5192 |
|
* test/utils/: NextCombinationTestCase.cpp, |
5193 |
|
NextCombinationTestCase.hpp: adding next_combination test case |
5194 |
|
|
5195 |
< |
2004-10-28 15:02 tim |
5195 |
> |
2004-10-28 10:02 tim |
5196 |
|
|
5197 |
|
* test/utils/next_combination.hpp: STL Compatible combination |
5198 |
|
sequence generator |
5199 |
|
|
5200 |
< |
2004-10-28 06:23 tim |
5200 |
> |
2004-10-28 01:23 tim |
5201 |
|
|
5202 |
|
* test/utils/: GenerateCombination.hpp, |
5203 |
|
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
5204 |
|
|
5205 |
< |
2004-10-28 06:16 tim |
5205 |
> |
2004-10-28 01:16 tim |
5206 |
|
|
5207 |
|
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
5208 |
|
next_combination function. |
5209 |
|
|
5210 |
< |
2004-10-28 03:27 tim |
5210 |
> |
2004-10-27 22:27 tim |
5211 |
|
|
5212 |
|
* test/utils/ReplaceWildCard.hpp: no message |
5213 |
|
|
5214 |
< |
2004-10-28 03:14 tim |
5214 |
> |
2004-10-27 22:14 tim |
5215 |
|
|
5216 |
|
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
5217 |
|
ReplaceWildCard(recursive version) is working, need refactoring. An |
5218 |
|
iterative version is on the way |
5219 |
|
|
5220 |
< |
2004-10-28 02:28 tim |
5220 |
> |
2004-10-27 21:28 tim |
5221 |
|
|
5222 |
|
* test/utils/: Makefile, ReplaceWildCard.hpp, |
5223 |
|
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
5224 |
|
|
5225 |
< |
2004-10-28 02:08 tim |
5225 |
> |
2004-10-27 21:08 tim |
5226 |
|
|
5227 |
|
* test/utils/: ReplaceWildCardTestCase.cpp, |
5228 |
|
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
5229 |
|
|
5230 |
< |
2004-10-27 23:17 tim |
5230 |
> |
2004-10-27 18:17 tim |
5231 |
|
|
5232 |
|
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
5233 |
|
test |
5234 |
|
|
5235 |
< |
2004-10-27 06:25 tim |
5235 |
> |
2004-10-27 01:25 tim |
5236 |
|
|
5237 |
|
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
5238 |
|
char matching is on the way |
5239 |
|
|
5240 |
< |
2004-10-27 06:07 tim |
5240 |
> |
2004-10-27 01:07 tim |
5241 |
|
|
5242 |
|
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
5243 |
|
|
5244 |
< |
2004-10-27 03:00 gezelter |
5244 |
> |
2004-10-26 22:00 gezelter |
5245 |
|
|
5246 |
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
5247 |
|
|
5248 |
< |
2004-10-27 02:20 gezelter |
5248 |
> |
2004-10-26 21:20 gezelter |
5249 |
|
|
5250 |
|
* src/UseTheForce/ForceFields.hpp: subclass foo |
5251 |
|
|
5252 |
< |
2004-10-27 02:16 gezelter |
5252 |
> |
2004-10-26 21:16 gezelter |
5253 |
|
|
5254 |
|
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
5255 |
|
string conversion |
5256 |
|
|
5257 |
< |
2004-10-27 00:01 gezelter |
5257 |
> |
2004-10-26 19:01 gezelter |
5258 |
|
|
5259 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5260 |
|
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
5261 |
|
brains/SimSetup.hpp: char* -> string |
5262 |
|
|
5263 |
< |
2004-10-26 22:25 gezelter |
5263 |
> |
2004-10-26 17:25 gezelter |
5264 |
|
|
5265 |
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
5266 |
|
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
5267 |
|
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
5268 |
|
isXXX |
5269 |
|
|
5270 |
< |
2004-10-26 22:25 gezelter |
5270 |
> |
2004-10-26 17:25 gezelter |
5271 |
|
|
5272 |
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
5273 |
|
define name collision |
5274 |
|
|
5275 |
< |
2004-10-26 22:24 gezelter |
5275 |
> |
2004-10-26 17:24 gezelter |
5276 |
|
|
5277 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5278 |
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
5281 |
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
5282 |
|
forcefield refactoring for shapes |
5283 |
|
|
5284 |
< |
2004-10-26 22:24 gezelter |
5284 |
> |
2004-10-26 17:24 gezelter |
5285 |
|
|
5286 |
|
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
5287 |
|
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
5288 |
|
linear.md, linear.shape, toluene.shape: adding sample shape |
5289 |
|
directory |
5290 |
|
|
5291 |
< |
2004-10-26 22:19 tim |
5291 |
> |
2004-10-26 17:19 tim |
5292 |
|
|
5293 |
|
* ChangeLog, src/brains/DataStorage.cpp, |
5294 |
|
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
5296 |
|
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
5297 |
|
DataStorage passes unit test |
5298 |
|
|
5299 |
< |
2004-10-26 18:03 chrisfen |
5299 |
> |
2004-10-26 13:03 chrisfen |
5300 |
|
|
5301 |
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
5302 |
|
Changes to help advance shapes |
5303 |
|
|
5304 |
< |
2004-10-26 18:02 chrisfen |
5304 |
> |
2004-10-26 13:02 chrisfen |
5305 |
|
|
5306 |
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
5307 |
|
Shapes force field reader |
5308 |
|
|
5309 |
< |
2004-10-26 17:28 tim |
5309 |
> |
2004-10-26 12:28 tim |
5310 |
|
|
5311 |
|
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
5312 |
|
SnapshotTestCase in progress |
5313 |
|
|
5314 |
< |
2004-10-25 22:46 tim |
5314 |
> |
2004-10-25 17:46 tim |
5315 |
|
|
5316 |
|
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
5317 |
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
5320 |
|
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
5321 |
|
and Vector classes |
5322 |
|
|
5323 |
< |
2004-10-25 17:03 tim |
5323 |
> |
2004-10-25 12:03 tim |
5324 |
|
|
5325 |
|
* ChangeLog, src/utils/GenericFactory.hpp, |
5326 |
|
test/utils/GenericFactoryTestCase.cpp, |
5328 |
|
GenericFactory Test Case. GenericFactory now can bed used to creat |
5329 |
|
ForcefieldFactory and IntegratorFactory etc. |
5330 |
|
|
5331 |
< |
2004-10-25 04:08 tim |
5331 |
> |
2004-10-24 23:08 tim |
5332 |
|
|
5333 |
|
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
5334 |
|
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
5335 |
|
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
5336 |
|
get reconstructed |
5337 |
|
|
5338 |
< |
2004-10-24 07:55 tim |
5338 |
> |
2004-10-24 02:55 tim |
5339 |
|
|
5340 |
|
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
5341 |
|
|
5342 |
< |
2004-10-23 23:09 tim |
5342 |
> |
2004-10-23 18:09 tim |
5343 |
|
|
5344 |
|
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
5345 |
|
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
5346 |
|
RigidBody.cpp: Refactoring in progress |
5347 |
|
|
5348 |
< |
2004-10-22 23:09 tim |
5348 |
> |
2004-10-22 18:09 tim |
5349 |
|
|
5350 |
|
* ChangeLog, src/brains/Snapshot.hpp, |
5351 |
|
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
5352 |
|
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
5353 |
|
test/brains/StuntDouble.hpp: more work in Snapshot |
5354 |
|
|
5355 |
< |
2004-10-22 22:59 chrisfen |
5355 |
> |
2004-10-22 17:59 chrisfen |
5356 |
|
|
5357 |
|
* src/: UseTheForce/LJFF.cpp, |
5358 |
|
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
5359 |
|
god! It runs and conserves energy! |
5360 |
|
|
5361 |
< |
2004-10-22 22:54 chrisfen |
5361 |
> |
2004-10-22 17:54 chrisfen |
5362 |
|
|
5363 |
|
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
5364 |
|
|
5365 |
< |
2004-10-22 22:53 chrisfen |
5365 |
> |
2004-10-22 17:53 chrisfen |
5366 |
|
|
5367 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5368 |
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
5370 |
|
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
5371 |
|
breakey |
5372 |
|
|
5373 |
< |
2004-10-22 22:53 chrisfen |
5373 |
> |
2004-10-22 17:53 chrisfen |
5374 |
|
|
5375 |
|
* make/Makefile.in: compiler flags |
5376 |
|
|
5377 |
< |
2004-10-22 21:20 gezelter |
5377 |
> |
2004-10-22 16:20 gezelter |
5378 |
|
|
5379 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5380 |
|
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
5381 |
|
brains/fSimulation.h, types/AtomType.hpp, |
5382 |
|
types/DirectionalAtomType.hpp: fixey fixey |
5383 |
|
|
5384 |
< |
2004-10-22 20:22 gezelter |
5384 |
> |
2004-10-22 15:22 gezelter |
5385 |
|
|
5386 |
|
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
5387 |
|
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
5388 |
|
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
5389 |
|
fortran files and c/Fortran interfaces |
5390 |
|
|
5391 |
< |
2004-10-22 20:21 gezelter |
5391 |
> |
2004-10-22 15:21 gezelter |
5392 |
|
|
5393 |
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
5394 |
|
DirectionalAtomType.hpp, Makefile: More on AtomType and |
5395 |
|
DirectionalAtomType |
5396 |
|
|
5397 |
< |
2004-10-22 14:47 gezelter |
5397 |
> |
2004-10-22 09:47 gezelter |
5398 |
|
|
5399 |
|
* src/types/AtomType.hpp: Adding AtomType |
5400 |
|
|
5401 |
< |
2004-10-21 21:31 tim |
5401 |
> |
2004-10-21 16:31 tim |
5402 |
|
|
5403 |
|
* ChangeLog, src/brains/Snapshot.hpp, |
5404 |
|
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
5407 |
|
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
5408 |
|
Snapshot and SnapshotManager in progress |
5409 |
|
|
5410 |
< |
2004-10-21 21:30 tim |
5410 |
> |
2004-10-21 16:30 tim |
5411 |
|
|
5412 |
|
* test/brains/: BrainsTest.cpp, Makefile, |
5413 |
|
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
5414 |
|
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
5415 |
|
Snapshot and snapshotManager. |
5416 |
|
|
5417 |
< |
2004-10-21 20:15 gezelter |
5417 |
> |
2004-10-21 15:15 gezelter |
5418 |
|
|
5419 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5420 |
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
5425 |
|
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
5426 |
|
Fixey Fixey. |
5427 |
|
|
5428 |
< |
2004-10-21 16:32 tim |
5428 |
> |
2004-10-21 11:32 tim |
5429 |
|
|
5430 |
|
* src/utils/GenericData.cpp, src/utils/Makefile, |
5431 |
|
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
5432 |
|
|
5433 |
< |
2004-10-21 16:24 tim |
5433 |
> |
2004-10-21 11:24 tim |
5434 |
|
|
5435 |
|
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
5436 |
|
|
5437 |
< |
2004-10-21 16:22 tim |
5437 |
> |
2004-10-21 11:22 tim |
5438 |
|
|
5439 |
|
* ChangeLog, src/brains/SimSetup.cpp, |
5440 |
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
5452 |
|
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
5453 |
|
GenericData |
5454 |
|
|
5455 |
< |
2004-10-21 15:25 chuckv |
5455 |
> |
2004-10-21 10:25 chuckv |
5456 |
|
|
5457 |
|
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
5458 |
|
module. |
5459 |
|
|
5460 |
< |
2004-10-21 15:24 chuckv |
5460 |
> |
2004-10-21 10:24 chuckv |
5461 |
|
|
5462 |
|
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
5463 |
|
fortran lj module. |
5464 |
|
|
5465 |
< |
2004-10-20 22:54 tim |
5465 |
> |
2004-10-20 17:54 tim |
5466 |
|
|
5467 |
|
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
5468 |
|
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
5470 |
|
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
5471 |
|
GenericData and PropertyMap pass unit test. |
5472 |
|
|
5473 |
< |
2004-10-20 21:52 gezelter |
5473 |
> |
2004-10-20 16:52 gezelter |
5474 |
|
|
5475 |
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
5476 |
|
DarkSide/sticky_interface.h: fixed a fortran name problem |
5477 |
|
|
5478 |
< |
2004-10-20 21:38 tim |
5478 |
> |
2004-10-20 16:38 tim |
5479 |
|
|
5480 |
|
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
5481 |
|
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
5482 |
|
UtilTest, UtilTest.cpp: adding generic data test case |
5483 |
|
|
5484 |
< |
2004-10-20 21:16 chuckv |
5484 |
> |
2004-10-20 16:16 chuckv |
5485 |
|
|
5486 |
|
* configure, ac-tools/aclocal.m4, |
5487 |
|
src/UseTheForce/DarkSide/Makefile, |
5493 |
|
Fortran/C++ interface de-obfuscation project appears to be |
5494 |
|
complete! Woo hoo! |
5495 |
|
|
5496 |
< |
2004-10-20 20:47 chuckv |
5496 |
> |
2004-10-20 15:47 chuckv |
5497 |
|
|
5498 |
|
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
5499 |
|
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
5500 |
|
continues |
5501 |
|
|
5502 |
< |
2004-10-20 20:46 chuckv |
5502 |
> |
2004-10-20 15:46 chuckv |
5503 |
|
|
5504 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5505 |
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
5516 |
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
5517 |
|
de-obfuscation project (It is a very long story) |
5518 |
|
|
5519 |
< |
2004-10-20 18:07 tim |
5519 |
> |
2004-10-20 13:07 tim |
5520 |
|
|
5521 |
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
5522 |
|
test/math/SquareMatrix3TestCase.cpp, |
5523 |
|
test/math/SquareMatrixTestCase.cpp, |
5524 |
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
5525 |
|
|
5526 |
< |
2004-10-20 05:52 tim |
5526 |
> |
2004-10-20 00:52 tim |
5527 |
|
|
5528 |
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
5529 |
|
SnapshotManager in design phase |
5530 |
|
|
5531 |
< |
2004-10-20 04:54 gezelter |
5531 |
> |
2004-10-19 23:54 gezelter |
5532 |
|
|
5533 |
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
5534 |
|
problem prevented linking |
5535 |
|
|
5536 |
< |
2004-10-20 04:54 gezelter |
5536 |
> |
2004-10-19 23:54 gezelter |
5537 |
|
|
5538 |
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
5539 |
|
|
5540 |
< |
2004-10-20 04:26 gezelter |
5540 |
> |
2004-10-19 23:26 gezelter |
5541 |
|
|
5542 |
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
5543 |
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
5544 |
|
more fortran name mangling |
5545 |
|
|
5546 |
< |
2004-10-20 04:23 gezelter |
5546 |
> |
2004-10-19 23:23 gezelter |
5547 |
|
|
5548 |
|
* src/profiling/timing.F90: yet more fortran renaming |
5549 |
|
|
5550 |
< |
2004-10-20 04:19 gezelter |
5550 |
> |
2004-10-19 23:19 gezelter |
5551 |
|
|
5552 |
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
5553 |
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
5554 |
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
5555 |
|
wrappers.F90: Fortran name cleanup continues |
5556 |
|
|
5557 |
< |
2004-10-20 04:12 gezelter |
5557 |
> |
2004-10-19 23:12 gezelter |
5558 |
|
|
5559 |
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
5560 |
|
broken fortran stuff |
5561 |
|
|
5562 |
< |
2004-10-20 04:02 gezelter |
5562 |
> |
2004-10-19 23:02 gezelter |
5563 |
|
|
5564 |
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
5565 |
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
5576 |
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
5577 |
|
name sanity on the fortran side |
5578 |
|
|
5579 |
< |
2004-10-20 00:18 tim |
5579 |
> |
2004-10-19 19:18 tim |
5580 |
|
|
5581 |
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
5582 |
|
|
5583 |
< |
2004-10-19 23:01 tim |
5583 |
> |
2004-10-19 18:01 tim |
5584 |
|
|
5585 |
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
5586 |
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
5587 |
|
except diagonalize(), all of functions in math library pass the |
5588 |
|
test |
5589 |
|
|
5590 |
< |
2004-10-19 22:43 chuckv |
5590 |
> |
2004-10-19 17:43 chuckv |
5591 |
|
|
5592 |
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
5593 |
|
C-fortran interface functions. |
5594 |
|
|
5595 |
< |
2004-10-19 22:37 chuckv |
5595 |
> |
2004-10-19 17:37 chuckv |
5596 |
|
|
5597 |
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
5598 |
|
eam_module_inteface.h, gb_module_interface.h, |
5600 |
|
sticky_pair_module_interface.h: Added correct prototypes for |
5601 |
|
C-fortran interface functions. |
5602 |
|
|
5603 |
< |
2004-10-19 21:28 tim |
5603 |
> |
2004-10-19 16:28 tim |
5604 |
|
|
5605 |
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
5606 |
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
5610 |
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
5611 |
|
bugs get fixed at math library |
5612 |
|
|
5613 |
< |
2004-10-19 20:43 chuckv |
5613 |
> |
2004-10-19 15:43 chuckv |
5614 |
|
|
5615 |
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
5616 |
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
5624 |
|
notifycutoffs_module_interface.h: Added new files for fortran |
5625 |
|
interface. |
5626 |
|
|
5627 |
< |
2004-10-19 20:43 gezelter |
5627 |
> |
2004-10-19 15:43 gezelter |
5628 |
|
|
5629 |
|
* src/UseTheForce/Makefile: regressing |
5630 |
|
|
5631 |
< |
2004-10-19 20:40 gezelter |
5631 |
> |
2004-10-19 15:40 gezelter |
5632 |
|
|
5633 |
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
5634 |
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
5635 |
|
working on shapes for portability |
5636 |
|
|
5637 |
< |
2004-10-19 20:40 gezelter |
5637 |
> |
2004-10-19 15:40 gezelter |
5638 |
|
|
5639 |
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
5640 |
|
|
5641 |
< |
2004-10-19 18:21 chrisfen |
5641 |
> |
2004-10-19 13:21 chrisfen |
5642 |
|
|
5643 |
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
5644 |
|
findBegin |
5645 |
|
|
5646 |
< |
2004-10-19 04:34 tim |
5646 |
> |
2004-10-18 23:34 tim |
5647 |
|
|
5648 |
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
5649 |
|
are fixed in Vector class |
5650 |
|
|
5651 |
< |
2004-10-19 04:28 tim |
5651 |
> |
2004-10-18 23:28 tim |
5652 |
|
|
5653 |
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
5654 |
|
some bugs in RectMatrixTestCase |
5655 |
|
|
5656 |
< |
2004-10-19 04:21 tim |
5656 |
> |
2004-10-18 23:21 tim |
5657 |
|
|
5658 |
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
5659 |
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
5660 |
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
5661 |
|
test/math/VectorTestCase.hpp: implement more test cases |
5662 |
|
|
5663 |
< |
2004-10-18 23:13 tim |
5663 |
> |
2004-10-18 18:13 tim |
5664 |
|
|
5665 |
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
5666 |
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
5669 |
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
5670 |
|
tests on math library |
5671 |
|
|
5672 |
< |
2004-10-18 21:03 tim |
5672 |
> |
2004-10-18 16:03 tim |
5673 |
|
|
5674 |
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
5675 |
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
5677 |
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
5678 |
|
more testing units |
5679 |
|
|
5680 |
< |
2004-10-18 17:07 tim |
5680 |
> |
2004-10-18 12:07 tim |
5681 |
|
|
5682 |
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
5683 |
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
5684 |
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
5685 |
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
5686 |
|
|
5687 |
< |
2004-10-18 16:30 gezelter |
5687 |
> |
2004-10-18 11:30 gezelter |
5688 |
|
|
5689 |
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
5690 |
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
5691 |
|
\phi) |
5692 |
|
|
5693 |
< |
2004-10-18 16:29 gezelter |
5693 |
> |
2004-10-18 11:29 gezelter |
5694 |
|
|
5695 |
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
5696 |
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
5697 |
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
5698 |
|
Shapes into OOPSE |
5699 |
|
|
5700 |
< |
2004-10-18 15:21 gezelter |
5700 |
> |
2004-10-18 10:21 gezelter |
5701 |
|
|
5702 |
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
5703 |
|
|
5704 |
< |
2004-10-18 05:23 tim |
5704 |
> |
2004-10-18 00:23 tim |
5705 |
|
|
5706 |
|
* test/math/VectorTestCase.hpp: adding vector test case |
5707 |
|
|
5708 |
< |
2004-10-18 05:23 tim |
5708 |
> |
2004-10-18 00:23 tim |
5709 |
|
|
5710 |
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
5711 |
|
test case |
5712 |
|
|
5713 |
< |
2004-10-17 01:19 tim |
5713 |
> |
2004-10-16 20:19 tim |
5714 |
|
|
5715 |
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
5716 |
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
5717 |
|
progress |
5718 |
|
|
5719 |
< |
2004-10-16 01:31 tim |
5719 |
> |
2004-10-15 20:31 tim |
5720 |
|
|
5721 |
|
* src/math/Quaternion.hpp: add quaternion class |
5722 |
|
|
5723 |
< |
2004-10-15 21:11 tim |
5723 |
> |
2004-10-15 16:11 tim |
5724 |
|
|
5725 |
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
5726 |
|
IfstrstreamTestCase.hpp: adding test file |
5727 |
|
|
5728 |
< |
2004-10-15 21:10 tim |
5728 |
> |
2004-10-15 16:10 tim |
5729 |
|
|
5730 |
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
5731 |
|
|
5732 |
< |
2004-10-15 20:42 tim |
5732 |
> |
2004-10-15 15:42 tim |
5733 |
|
|
5734 |
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
5735 |
|
|
5736 |
< |
2004-10-15 20:35 tim |
5736 |
> |
2004-10-15 15:35 tim |
5737 |
|
|
5738 |
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
5739 |
|
|
5740 |
< |
2004-10-15 20:34 tim |
5740 |
> |
2004-10-15 15:34 tim |
5741 |
|
|
5742 |
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
5743 |
|
namespace oopse |
5744 |
|
|
5745 |
< |
2004-10-15 19:38 chuckv |
5745 |
> |
2004-10-15 14:38 chuckv |
5746 |
|
|
5747 |
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
5748 |
|
XLF and XLC. |
5749 |
|
|
5750 |
< |
2004-10-15 18:28 tim |
5750 |
> |
2004-10-15 13:28 tim |
5751 |
|
|
5752 |
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
5753 |
|
adding ifstrstream test case |
5754 |
|
|
5755 |
< |
2004-10-15 18:20 tim |
5755 |
> |
2004-10-15 13:20 tim |
5756 |
|
|
5757 |
|
* src/io/basic_ifstrstream.hpp: fix include |
5758 |
|
|
5759 |
< |
2004-10-15 18:18 tim |
5759 |
> |
2004-10-15 13:18 tim |
5760 |
|
|
5761 |
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
5762 |
|
|
5763 |
< |
2004-10-15 18:17 tim |
5763 |
> |
2004-10-15 13:17 tim |
5764 |
|
|
5765 |
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
5766 |
|
|
5767 |
< |
2004-10-15 18:16 tim |
5767 |
> |
2004-10-15 13:16 tim |
5768 |
|
|
5769 |
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
5770 |
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
5771 |
|
|
5772 |
< |
2004-10-15 15:37 tim |
5772 |
> |
2004-10-15 10:37 tim |
5773 |
|
|
5774 |
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
5775 |
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
5776 |
|
|
5777 |
< |
2004-10-15 15:20 tim |
5777 |
> |
2004-10-15 10:20 tim |
5778 |
|
|
5779 |
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
5780 |
|
|
5781 |
< |
2004-10-15 15:19 tim |
5781 |
> |
2004-10-15 10:19 tim |
5782 |
|
|
5783 |
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
5784 |
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
5785 |
|
SquareMatrixTestCase class |
5786 |
|
|
5787 |
< |
2004-10-15 07:52 tim |
5787 |
> |
2004-10-15 02:52 tim |
5788 |
|
|
5789 |
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
5790 |
|
|
5791 |
< |
2004-10-14 23:28 tim |
5791 |
> |
2004-10-14 18:28 tim |
5792 |
|
|
5793 |
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
5794 |
|
Vector.hpp: math library in progress |
5795 |
|
|
5796 |
< |
2004-10-14 23:27 tim |
5796 |
> |
2004-10-14 18:27 tim |
5797 |
|
|
5798 |
|
* src/io/FileReader.hpp: FileReader in progress |
5799 |
|
|
5800 |
< |
2004-10-13 23:53 tim |
5800 |
> |
2004-10-13 18:53 tim |
5801 |
|
|
5802 |
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
5803 |
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
5804 |
|
|
5805 |
< |
2004-10-13 22:28 tim |
5805 |
> |
2004-10-13 17:28 tim |
5806 |
|
|
5807 |
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
5808 |
|
class |
5809 |
|
|
5810 |
< |
2004-10-13 22:27 tim |
5810 |
> |
2004-10-13 17:27 tim |
5811 |
|
|
5812 |
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
5813 |
|
RectMatrixTestCase.hpp: adding testing unit |
5814 |
|
|
5815 |
< |
2004-10-13 22:24 tim |
5815 |
> |
2004-10-13 17:24 tim |
5816 |
|
|
5817 |
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
5818 |
|
|
5819 |
< |
2004-10-13 06:51 tim |
5819 |
> |
2004-10-13 01:51 tim |
5820 |
|
|
5821 |
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
5822 |
|
Vector3.hpp: refactory vector and matrix classes |
5823 |
|
|
5824 |
< |
2004-10-13 06:50 tim |
5824 |
> |
2004-10-13 01:50 tim |
5825 |
|
|
5826 |
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
5827 |
|
|
5828 |
< |
2004-10-12 23:57 tim |
5828 |
> |
2004-10-12 18:57 tim |
5829 |
|
|
5830 |
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
5831 |
|
Matrix3x3d.hpp |
5832 |
|
|
5833 |
< |
2004-10-12 19:08 tim |
5833 |
> |
2004-10-12 14:08 tim |
5834 |
|
|
5835 |
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
5836 |
|
|
5837 |
< |
2004-10-11 22:15 tim |
5837 |
> |
2004-10-11 17:15 tim |
5838 |
|
|
5839 |
|
* src/: constraints/AbstractClasses.hpp, |
5840 |
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
5841 |
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
5842 |
|
|
5843 |
< |
2004-10-11 21:54 tim |
5843 |
> |
2004-10-11 16:54 tim |
5844 |
|
|
5845 |
|
* scripts/filepp: fix a bug in filepp |
5846 |
|
|
5847 |
< |
2004-10-11 21:13 tim |
5847 |
> |
2004-10-11 16:13 tim |
5848 |
|
|
5849 |
|
* make/Makefile.in: using filepp to generate dependencies instead |
5850 |
|
of compilers |
5851 |
|
|
5852 |
< |
2004-10-11 21:10 tim |
5852 |
> |
2004-10-11 16:10 tim |
5853 |
|
|
5854 |
|
* scripts/filepp: filepp can be used to generate dependencies for |
5855 |
|
c/c++ now |
5856 |
|
|
5857 |
< |
2004-10-11 18:40 tim |
5857 |
> |
2004-10-11 13:40 tim |
5858 |
|
|
5859 |
|
* make/Makefile.in: remove -module from F90Options |
5860 |
|
|
5861 |
< |
2004-10-11 18:01 tim |
5861 |
> |
2004-10-11 13:01 tim |
5862 |
|
|
5863 |
|
* make/Makefile.in: adding rules to move fortran 90 module to |
5864 |
|
target directory |
5865 |
|
|
5866 |
< |
2004-10-11 15:43 gezelter |
5866 |
> |
2004-10-11 10:43 gezelter |
5867 |
|
|
5868 |
|
* make/Makefile.in: fixed makefile.in |
5869 |
|
|
5870 |
< |
2004-10-11 14:51 tim |
5870 |
> |
2004-10-11 09:51 tim |
5871 |
|
|
5872 |
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
5873 |
|
machine |
5874 |
|
|
5875 |
< |
2004-10-11 14:26 tim |
5875 |
> |
2004-10-11 09:26 tim |
5876 |
|
|
5877 |
|
* forceFields/Makefile: add Makefile |
5878 |
|
|
5879 |
< |
2004-10-11 14:23 tim |
5879 |
> |
2004-10-11 09:23 tim |
5880 |
|
|
5881 |
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
5882 |
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
5883 |
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
5884 |
|
directory |
5885 |
|
|
5886 |
< |
2004-10-09 06:01 tim |
5886 |
> |
2004-10-11 09:23 tim |
5887 |
|
|
5888 |
< |
* samples/: alkane/Makefile.in, lipid/Makefile.in, |
5889 |
< |
metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in |
5888 |
> |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
5889 |
> |
Makefile |
5890 |
|
|
5891 |
< |
2004-10-08 23:15 tim |
5891 |
> |
2004-10-09 01:01 tim |
5892 |
> |
|
5893 |
> |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
5894 |
> |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
5895 |
> |
Remove some Makefile.in |
5896 |
|
|
5897 |
+ |
2004-10-08 18:15 tim |
5898 |
+ |
|
5899 |
|
* make/Makefile.in: [no log message] |
5900 |
|
|
5901 |
< |
2004-10-08 22:51 tim |
5901 |
> |
2004-10-08 17:51 tim |
5902 |
|
|
5903 |
|
* make/Makefile.in: fix make install |
5904 |
|
|
5905 |
< |
2004-10-08 22:10 tim |
5905 |
> |
2004-10-08 17:10 tim |
5906 |
|
|
5907 |
|
* make/Makefile.in: adding make install |
5908 |
|
|
5909 |
< |
2004-10-08 22:04 tim |
5909 |
> |
2004-10-08 17:04 tim |
5910 |
|
|
5911 |
< |
* samples/: alkane/Makefile, lipid/Makefile, metals/Makefile, |
5912 |
< |
minimizer/Makefile, water/Makefile.in, water/dimer/Makefile, |
5913 |
< |
water/dimer/Makefile.in, water/spce/Makefile, |
5911 |
> |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
5912 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
5913 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
5914 |
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
5915 |
|
water/ssde/Makefile, water/ssde/Makefile.in, |
5916 |
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
5917 |
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
5918 |
|
zcons/Makefile.in: add Makefile to sample directory |
5919 |
|
|
5920 |
< |
2004-10-06 23:03 gezelter |
5920 |
> |
2004-10-06 18:03 gezelter |
5921 |
|
|
5922 |
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
5923 |
|
stuff |
5924 |
|
|
5925 |
< |
2004-10-06 23:03 gezelter |
5925 |
> |
2004-10-06 18:03 gezelter |
5926 |
|
|
5927 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
5928 |
|
make/Doxyfile, src/applications/getopt.c, |
5929 |
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
5930 |
|
build fixes |
5931 |
|
|
5932 |
< |
2004-10-06 22:20 tim |
5932 |
> |
2004-10-06 17:20 tim |
5933 |
|
|
5934 |
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
5935 |
|
|
5936 |
< |
2004-10-06 22:19 tim |
5936 |
> |
2004-10-06 17:19 tim |
5937 |
|
|
5938 |
|
* scripts/filepp: filepp can handle different fortran module case |
5939 |
|
and suffix |
5940 |
|
|
5941 |
< |
2004-10-06 21:27 gezelter |
5941 |
> |
2004-10-06 16:27 gezelter |
5942 |
|
|
5943 |
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
5944 |
|
OOPSE-2.0 directory structure yet |
5945 |
|
|
5946 |
< |
2004-10-06 21:27 gezelter |
5946 |
> |
2004-10-06 16:27 gezelter |
5947 |
|
|
5948 |
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
5949 |
|
|
5950 |
< |
2004-10-06 21:22 gezelter |
5950 |
> |
2004-10-06 16:22 gezelter |
5951 |
|
|
5952 |
|
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
5953 |
|
make/Makefile.in: cleaning up build process |
5954 |
|
|
5955 |
< |
2004-10-06 20:01 chrisfen |
5955 |
> |
2004-10-06 15:01 chrisfen |
5956 |
|
|
5957 |
|
* src/restraints/Restraints.cpp: made the file reading in |
5958 |
|
restraints more intelligent - no longer gives uninformative seg |
5959 |
|
faults |
5960 |
|
|
5961 |
< |
2004-10-06 19:55 gezelter |
5961 |
> |
2004-10-06 14:55 gezelter |
5962 |
|
|
5963 |
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
5964 |
|
|
5965 |
< |
2004-10-06 19:51 gezelter |
5965 |
> |
2004-10-06 14:51 gezelter |
5966 |
|
|
5967 |
|
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
5968 |
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
5969 |
|
|
5970 |
< |
2004-10-06 18:53 tim |
5970 |
> |
2004-10-06 13:53 tim |
5971 |
|
|
5972 |
|
* make/: Makefile, Makefile.in: fix make statistics |
5973 |
|
|
5974 |
< |
2004-10-06 18:18 tim |
5974 |
> |
2004-10-06 13:18 tim |
5975 |
|
|
5976 |
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
5977 |
|
combine all of the static libraries to a big library |
5978 |
|
|
5979 |
< |
2004-10-05 22:57 tim |
5979 |
> |
2004-10-05 17:57 tim |
5980 |
|
|
5981 |
|
* make/: Makefile, Makefile.in: adding shared library flag |
5982 |
|
|
5983 |
< |
2004-10-05 19:37 tim |
5983 |
> |
2004-10-05 14:37 tim |
5984 |
|
|
5985 |
|
* src/: Makefile, UseTheForce/Makefile, |
5986 |
|
UseTheForce/mpiSimulation_module.F90, |
5988 |
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
5989 |
|
mpiSimulation_module to DarkSide |
5990 |
|
|
5991 |
< |
2004-10-05 19:35 tim |
5991 |
> |
2004-10-05 14:35 tim |
5992 |
|
|
5993 |
|
* make/: Makefile, Makefile.in: building MPI version;using static |
5994 |
|
library instead of shared library |
5995 |
|
|
5996 |
< |
2004-10-05 14:14 tim |
5996 |
> |
2004-10-05 09:14 tim |
5997 |
|
|
5998 |
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
5999 |
|
to filepp |
6000 |
|
|
6001 |
< |
2004-10-04 20:56 tim |
6001 |
> |
2004-10-04 15:56 tim |
6002 |
|
|
6003 |
|
* make/: Makefile, Makefile.in: add make cvslog |
6004 |
|
|
6005 |
< |
2004-10-04 16:24 gezelter |
6005 |
> |
2004-10-04 11:24 gezelter |
6006 |
|
|
6007 |
|
* make/: Makefile, Makefile.in: more work on the parallel build |
6008 |
|
|
6009 |
< |
2004-10-04 16:06 gezelter |
6009 |
> |
2004-10-04 11:06 gezelter |
6010 |
|
|
6011 |
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
6012 |
|
|
6013 |
< |
2004-10-04 15:27 gezelter |
6013 |
> |
2004-10-04 10:27 gezelter |
6014 |
|
|
6015 |
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
6016 |
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
6017 |
|
shapes |
6018 |
|
|
6019 |
< |
2004-10-02 04:40 tim |
6019 |
> |
2004-10-01 23:40 tim |
6020 |
|
|
6021 |
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
6022 |
|
|
6023 |
< |
2004-10-02 04:22 tim |
6023 |
> |
2004-10-01 23:22 tim |
6024 |
|
|
6025 |
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
6026 |
|
|
6027 |
< |
2004-10-01 21:59 tim |
6027 |
> |
2004-10-01 16:59 tim |
6028 |
|
|
6029 |
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
6030 |
|
|
6031 |
< |
2004-10-01 21:22 gezelter |
6031 |
> |
2004-10-01 16:22 gezelter |
6032 |
|
|
6033 |
|
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
6034 |
|
few minor build changes |
6035 |
|
|
6036 |
< |
2004-10-01 21:11 tim |
6036 |
> |
2004-10-01 16:11 tim |
6037 |
|
|
6038 |
|
* scripts/filepp: adding fortran90 make dependency tool |
6039 |
|
|
6040 |
< |
2004-09-30 15:41 tim |
6040 |
> |
2004-09-30 10:41 tim |
6041 |
|
|
6042 |
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
6043 |
|
remove object files belong to current package. turn off silent |
6044 |
|
mode |
6045 |
|
|
6046 |
< |
2004-09-29 21:55 tim |
6046 |
> |
2004-09-29 16:55 tim |
6047 |
|
|
6048 |
|
* src/: Makefile, UseTheForce/Makefile, |
6049 |
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
6054 |
|
restraints/Makefile, types/Makefile, utils/Makefile, |
6055 |
|
visitors/Makefile: define DEV_ROOT as relative path |
6056 |
|
|
6057 |
< |
2004-09-29 21:54 tim |
6057 |
> |
2004-09-29 16:54 tim |
6058 |
|
|
6059 |
|
* make/: Makefile, Makefile.in: get the relative path by shell |
6060 |
|
script |
6061 |
|
|
6062 |
< |
2004-09-29 21:32 tim |
6062 |
> |
2004-09-29 16:32 tim |
6063 |
|
|
6064 |
|
* make/Makefile: eliminate DEV_ROOT by relative path |
6065 |
|
|
6066 |
< |
2004-09-29 18:37 tim |
6066 |
> |
2004-09-29 13:37 tim |
6067 |
|
|
6068 |
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
6069 |
|
|
6070 |
< |
2004-09-29 17:57 gezelter |
6070 |
> |
2004-09-29 12:57 gezelter |
6071 |
|
|
6072 |
|
* configure, ac-tools/configure.in: updates |
6073 |
|
|
6074 |
< |
2004-09-29 17:56 gezelter |
6074 |
> |
2004-09-29 12:56 gezelter |
6075 |
|
|
6076 |
|
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
6077 |
|
make stuff |
6078 |
|
|
6079 |
< |
2004-09-29 17:46 tim |
6079 |
> |
2004-09-29 12:46 tim |
6080 |
|
|
6081 |
|
* Makefile: If makefile does not exist, print error message |
6082 |
|
|
6083 |
< |
2004-09-29 17:12 tim |
6083 |
> |
2004-09-29 12:12 tim |
6084 |
|
|
6085 |
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
6086 |
|
|
6087 |
< |
2004-09-29 15:58 gezelter |
6087 |
> |
2004-09-29 10:58 gezelter |
6088 |
|
|
6089 |
|
* Makefile, make/Makefile: still working on build process |
6090 |
|
|
6091 |
< |
2004-09-29 15:00 tim |
6091 |
> |
2004-09-29 10:00 tim |
6092 |
|
|
6093 |
|
* make/Makefile: add print statment to rules |
6094 |
|
|
6095 |
< |
2004-09-29 14:59 tim |
6095 |
> |
2004-09-29 09:59 tim |
6096 |
|
|
6097 |
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
6098 |
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
6102 |
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
6103 |
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
6104 |
|
|
6105 |
< |
2004-09-29 02:55 tim |
6105 |
> |
2004-09-28 21:55 tim |
6106 |
|
|
6107 |
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
6108 |
|
which cause headache in bulding libutils |
6109 |
|
|
6110 |
< |
2004-09-28 23:24 tim |
6110 |
> |
2004-09-28 18:24 tim |
6111 |
|
|
6112 |
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
6113 |
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
6130 |
|
change directory structure of application. Every executable file is |
6131 |
|
replaced in seperate directory |
6132 |
|
|
6133 |
< |
2004-09-28 22:15 gezelter |
6133 |
> |
2004-09-28 17:15 gezelter |
6134 |
|
|
6135 |
|
* lib/dummy: Keep that lib around, please. |
6136 |
|
|
6137 |
< |
2004-09-28 22:14 gezelter |
6137 |
> |
2004-09-28 17:14 gezelter |
6138 |
|
|
6139 |
|
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
6140 |
|
starting a configure version |
6141 |
|
|
6142 |
< |
2004-09-28 21:08 tim |
6142 |
> |
2004-09-28 16:08 tim |
6143 |
|
|
6144 |
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
6145 |
|
UseTheForce/DarkSide/Makefile, |
6148 |
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
6149 |
|
around to solve dependency problem |
6150 |
|
|
6151 |
< |
2004-09-28 20:43 tim |
6151 |
> |
2004-09-28 15:43 tim |
6152 |
|
|
6153 |
|
* Makefile, src/UseTheForce/ForceFields.hpp, |
6154 |
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
6158 |
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
6159 |
|
src/utils/Makefile: [no log message] |
6160 |
|
|
6161 |
< |
2004-09-28 20:41 tim |
6161 |
> |
2004-09-28 15:41 tim |
6162 |
|
|
6163 |
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
6164 |
|
problem |
6165 |
|
|
6166 |
< |
2004-09-28 16:13 tim |
6166 |
> |
2004-09-28 11:13 tim |
6167 |
|
|
6168 |
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
6169 |
|
src/io/Makefile: add yacc and lex rules |
6170 |
|
|
6171 |
< |
2004-09-27 20:24 tim |
6171 |
> |
2004-09-27 15:24 tim |
6172 |
|
|
6173 |
|
* make/Makefile: adding include path to F90Options |
6174 |
|
|
6175 |
< |
2004-09-27 20:13 tim |
6175 |
> |
2004-09-27 15:13 tim |
6176 |
|
|
6177 |
|
* make/Makefile: change suffix from .cc to .cpp |
6178 |
|
|
6179 |
< |
2004-09-24 16:27 tim |
6179 |
> |
2004-09-24 11:27 tim |
6180 |
|
|
6181 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6182 |
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
6243 |
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
6244 |
|
visitors/ZconsVisitor.hpp: change the #include in source files |
6245 |
|
|
6246 |
< |
2004-09-24 04:16 gezelter |
6246 |
> |
2004-09-23 23:16 gezelter |
6247 |
|
|
6248 |
|
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
6249 |
|
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
6389 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
6390 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
6391 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
6392 |
+ |
samples/argon/500.in, samples/argon/500.md, |
6393 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
6394 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
6395 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
6396 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
6397 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
6398 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
6419 |
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
6420 |
|
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
6421 |
|
|
6422 |
< |
2004-09-24 04:16 gezelter |
6422 |
> |
2004-09-23 23:16 gezelter |
6423 |
|
|
6424 |
|
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
6425 |
|
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
6565 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
6566 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
6567 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
6568 |
+ |
samples/argon/500.in, samples/argon/500.md, |
6569 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
6570 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
6571 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
6572 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
6573 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
6574 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |