[ViewVC] Diff of: group/trunk/OOPSE-4/ChangeLog

Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2199 by gezelter, Thu Apr 14 21:41:56 2005 UTC vs.
Revision 2310 by chrisfen, Mon Sep 19 23:21:46 2005 UTC

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+-09-18 15:45  chrisfen
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+        * ChangeLog, samples/water/ssdrf/ssdrf.md,
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+        src/UseTheForce/doForces.F90,
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+        src/UseTheForce/doForces_interface.F90,
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+        src/UseTheForce/doForces_interface.h,
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+        src/UseTheForce/DarkSide/electrostatic.F90,
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+        src/UseTheForce/DarkSide/electrostatic_interface.h,
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+        src/brains/SimInfo.cpp: reaction field seems to work now, still
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+        need to do some testing...
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+-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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+-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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+-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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+-09-16 14:35  chrisfen
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+        * src/brains/SimInfo.cpp: fixed a capitalization error
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+-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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+-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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+-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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+-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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+-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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+-09-15 08:47  chrisfen
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+        * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
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+-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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+-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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+-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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+-09-14 19:13  chrisfen
-+
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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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+-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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+-09-14 19:11  chrisfen
-+
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+        * samples/argon/: 500.in, 500.md: Equilibrated the sample
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+-09-14 19:10  chrisfen
-+
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+        * forceFields/DUFF2.frc: re-added Cl- and Na+
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+-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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+-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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+-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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+-09-07 17:44  chuckv
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+        * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
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+-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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+-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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+-09-07 15:46  gezelter
-+
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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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+-09-07 14:18  gezelter
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+        * src/UseTheForce/doForces.F90: Some bug hunting
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+-09-07 14:18  gezelter
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+        * samples/argon/argonNVT.md: Just a longer test
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+-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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+-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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+-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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+-08-30 13:23  chrisfen
-+
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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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+-08-26 17:39  chrisfen
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+        * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
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+-08-26 16:30  chrisfen
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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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+-08-26 15:34  chuckv
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+        * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
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+-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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+-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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+-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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+-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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+-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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+-08-09 17:33  gezelter
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+        * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
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+-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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+-07-29 14:38  gezelter
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+        * src/UseTheForce/doForces.F90: fixes in progress
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+-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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+-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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+-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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+-07-13 11:48  tim
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+        * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
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+        <functional>
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+-07-13 10:54  tim
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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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+-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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+-06-28 08:58  gezelter
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+        * src/UseTheForce/doForces.F90: [no log message]
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+-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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+-06-27 16:01  gezelter
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+        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
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+        UseTheForce/DarkSide/fInteractionMap.h,
-+
+        UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
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+        Breaky breaky!
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+-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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+-06-13 13:25  tim
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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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+-05-31 17:31  chuckv
-+
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+        * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
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+        remove angular momentum.
-+
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+-05-31 12:34  chuckv
-+
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+        * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
-+
+        typo in nanorodBuilder.
-+
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+-05-30 09:01  chuckv
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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,
-+
+        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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+-05-29 16:16  chrisfen
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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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+-05-29 16:15  chrisfen
-+
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+        * src/UseTheForce/doForces.F90: Removed balance from doForces
-+
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+-05-29 16:15  chrisfen
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+        * samples/water/tap/: tap.in, tap.md: Updated tap sample
-+
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+-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
-+
-+
+-05-29 16:14  chrisfen
-+
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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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+-05-29 16:13  chrisfen
-+
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+        * ChangeLog: ran make cvslog
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+-05-28 19:16  tim
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+        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
-+
+        AtomNameVisitor
-+
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+-05-28 19:09  tim
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+        * src/integrators/Integrator.cpp: dding resetIntegrator
-+
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+-05-28 19:06  tim
-+
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+        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
-+
+        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
-+
+        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
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+        resetIntegrator
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+-05-27 16:11  tim
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+        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
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+        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
-+
+        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
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+        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
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+        StaticProps
-+
-+
+-05-26 23:41  tim
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+        * src/: applications/staticProps/Makefile,
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+        applications/staticProps/P2OrderParameter.cpp,
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+        applications/staticProps/P2OrderParameter.hpp,
-+
+        applications/staticProps/StaticProps.cpp,
-+
+        applications/staticProps/StaticProps.ggo,
-+
+        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
-+
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+-05-26 17:45  tim
-+
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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,
-+
+        applications/staticProps/P2OrderParameter.cpp,
-+
+        applications/staticProps/P2OrderParameter.hpp,
-+
+        applications/staticProps/RadialDistrFunc.cpp,
-+
+        applications/staticProps/RadialDistrFunc.hpp,
-+
+        applications/staticProps/StaticAnalyser.hpp,
-+
+        applications/staticProps/StaticProps.cpp,
-+
+        applications/staticProps/StaticProps.ggo,
-+
+        applications/staticProps/StaticPropsCmd.c,
-+
+        applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
-+
+        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
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+        AtomNameVisitor to convert atom name to its base name;
-+
+        wrappingvisitor now wrap back to the center of the mass; adding
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+        P2OrderParameter into StaticProps
-+
-+
+-05-22 16:36  chuckv
-+
-+
+        * samples/metals/nanorod/Au_nanoparticle_FCC.md,
-+
+        src/applications/nanoRodBuilder/Geometry.cpp,
-+
+        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
-+
+        src/applications/nanoRodBuilder/GeometryFactory.cpp,
-+
+        src/applications/nanoRodBuilder/GeometryFactory.hpp,
-+
+        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
-+
+        src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
-+
+        tensor.
-+
-+
+-05-22 16:05  tim
-+
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+        * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
-+
+        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
-+
+        io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
-+
+        printPressureTensor
-+
-+
+-05-20 14:27  tim
-+
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+        * src/integrators/NPrT.cpp: NPrT in progress
-+
-+
+-05-20 11:01  tim
-+
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+        * src/: integrators/NPrT.cpp, io/Globals.cpp,
-+
+        utils/OOPSEConstant.hpp: NPrT in progress
-+
-+
+-05-19 16:31  tim
-+
-+
+        * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
-+
+        integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
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+        io/Globals.hpp: NPAT is working
-+
-+
+-05-19 10:49  tim
-+
-+
+        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
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+        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
-+
-+
+-05-18 23:28  tim
-+
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+        * src/: brains/Register.cpp, integrators/NPAT.cpp,
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+        integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
-+
+        io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
-+
-+
+-05-18 14:06  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
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+        some tap changes
-+
-+
+-05-18 13:31  chrisfen
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
-+
+        DarkSide/sticky.F90: Modifications to temper the dipolar strength
-+
+        in the first solvation shell for tap
-+
-+
+-05-18 07:35  chrisfen
-+
-+
+        * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
-+
+        for testing purposes
-+
-+
+-05-17 17:35  chrisfen
-+
-+
+        * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
-+
+        samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
-+
+        src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
-+
+        correcting changes to the previous merge that were not caught
-+
-+
+-05-16 23:20  chuckv
-+
-+
+        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
-+
+        Fixed merge issues between Kyle and Chris so OOPSE will actually
-+
+        build.
-+
-+
+-05-16 22:46  kdaily
-+
-+
+        * src/io/: GayBerneAtomTypesSectionParser.cpp,
-+
+        GayBerneAtomTypesSectionParser.hpp, Makefile: help
-+
-+
+-05-16 21:08  kdaily
-+
-+
+        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
-+
+        src/types/DirectionalAtomType.cpp,
-+
+        src/types/DirectionalAtomType.hpp: added gb
-+
-+
+-05-13 15:36  chrisfen
-+
-+
+        * forceFields/DUFF2.frc: Better tap
-+
-+
+-05-12 14:43  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
-+
+        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
-+
+        src/applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
-+
+        Need to parametrize.
-+
-+
+-05-11 18:15  chuckv
-+
-+
+        * src/: io/ShapeAtomTypesSectionParser.cpp,
-+
+        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
-+
+        build issues under ifc7.
-+
-+
+-05-09 17:07  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
-+
+        builder changes.
-+
-+
+-05-05 10:06  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
-+
+        to TAP
-+
-+
+-05-05 09:47  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
-+
+        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
-+
+        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
-+
+        src/UseTheForce/DarkSide/atype.F90,
-+
+        src/UseTheForce/DarkSide/atype_interface.F90,
-+
+        src/UseTheForce/DarkSide/simulation.F90,
-+
+        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
-+
+        src/brains/fSimulation.h, src/io/Makefile,
-+
+        src/io/StickyAtomTypesSectionParser.cpp,
-+
+        src/io/StickyPowerAtomTypesSectionParser.cpp,
-+
+        src/io/StickyPowerAtomTypesSectionParser.hpp,
-+
+        src/types/AtomType.cpp, src/types/AtomType.hpp,
-+
+        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
-+
+        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
-+
+        not parametrized, but OOPSE will now let me run it...
-+
-+
+-05-03 17:55  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
-+
+        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
-+
+        Adding support for generic geometry to nanorodbuilder.
-+
-+
+-05-03 12:55  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
-+
+        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
-+
+        nanorodBuilderCmd.h: More changes to nanoRodBuilder....
-+
-+
+-04-29 14:16  gezelter
-+
-+
+        * make/Makefile.in: [no log message]
-+
-+
+-04-29 11:26  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, samples/water/spce/water.md,
-+
+        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
-+
+        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
-+
+        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
-+
+        samples/water/tip4p/water.md: Added TIP4P-Ew
-+
-+
+-04-27 19:24  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
-+
+        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
-+
+        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
-+
+        nanoRodBuilder....
-+
-+
+-04-27 15:13  chrisfen
-+
-+
+        * samples/shape/Shapes.frc, samples/shape/linear.shape,
-+
+        src/UseTheForce/DarkSide/atype.F90,
-+
+        src/UseTheForce/DarkSide/shapes.F90,
-+
+        src/UseTheForce/DarkSide/shapes_interface.F90,
-+
+        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
-+
+        write statements and am closer to a working shapes
-+
-+
+-04-22 16:57  chuckv
-+
-+
+        * src/utils/Predicate.hpp: Fixed gcc4 bug...
-+
-+
+-04-22 16:52  tim
-+
-+
+        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
-+
+        Trim.hpp: adding CharClassificationFunctor to fix the locale
-+
+        problem  of c++
-+
-+
+-04-21 09:12  chrisfen
-+
-+
+        * samples/shape/Shapes.frc, samples/shape/linear.in,
-+
+        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
-+
+        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
-+
+        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
-+
+        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
-+
+        src/UseTheForce/DarkSide/shapes.F90,
-+
+        src/UseTheForce/DarkSide/shapes_interface.F90,
-+
+        src/UseTheForce/DarkSide/shapes_interface.h,
-+
+        src/brains/Register.cpp, src/brains/SimCreator.cpp,
-+
+        src/io/Makefile, src/io/SectionParser.cpp,
-+
+        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
-+
+        src/io/ShapeAtomTypesSectionParser.cpp,
-+
+        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
-+
+        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
-+
+        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
-+
+        bounds overwrite (I think...). At least the parser loads the
-+
+        forcefield fine...
-+
-+
+-04-18 10:44  chrisfen
-+
-+
+        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
-+
+        Mac (capitalization confusion of filenames)
-+
-+
+-04-17 22:50  chrisfen
-+
-+
+        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
-+
+        UseTheForce/Shapes_FF.cpp,
-+
+        io/DirectionalAtomTypesSectionParser.cpp,
-+
+        io/ShapeAtomTypesSectionParser.cpp,
-+
+        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
-+
-+
+-04-15 17:43  gezelter
-+
-+
+        * README: gmake in case people forget
-+
-+
+-04-15 17:40  gezelter
-+
-+
+        * src/applications/oopse/oopse.cpp: fixed the spacing on the
-+
+        banner.  Vanity.
-+
-+
+-04-15 17:22  gezelter
-+
-+
+        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
-+
+        in banner (and version numbers in config.h)
-+
-+
+-04-15 17:22  gezelter
-+
-+
+        * ChangeLog, LICENSE, README: Documentation changes
-+
-+
+-04-15 17:03  gezelter
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
-+
+        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
-+
+        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
-+
+        UseTheForce/ForceFieldCreator.hpp,
-+
+        UseTheForce/ForceFieldFactory.cpp,
-+
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
-+
+        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
-+
+        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
-+
+        UseTheForce/notifyCutoffs.F90,
-+
+        UseTheForce/notifyCutoffs_interface.F90,
-+
+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
-+
+        UseTheForce/DarkSide/atype.F90,
-+
+        UseTheForce/DarkSide/atype_interface.F90,
-+
+        UseTheForce/DarkSide/eam.F90,
-+
+        UseTheForce/DarkSide/eam_interface.F90,
-+
+        UseTheForce/DarkSide/eam_interface.h,
-+
+        UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        UseTheForce/DarkSide/force_globals.F90,
-+
+        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
-+
+        UseTheForce/DarkSide/lj_interface.F90,
-+
+        UseTheForce/DarkSide/lj_interface.h,
-+
+        UseTheForce/DarkSide/neighborLists.F90,
-+
+        UseTheForce/DarkSide/reactionField.F90,
-+
+        UseTheForce/DarkSide/shapes.F90,
-+
+        UseTheForce/DarkSide/shapes_interface.F90,
-+
+        UseTheForce/DarkSide/shapes_interface.h,
-+
+        UseTheForce/DarkSide/simParallel.F90,
-+
+        UseTheForce/DarkSide/simParallel_interface.F90,
-+
+        UseTheForce/DarkSide/simParallel_interface.h,
-+
+        UseTheForce/DarkSide/simulation.F90,
-+
+        UseTheForce/DarkSide/simulation_interface.F90,
-+
+        UseTheForce/DarkSide/simulation_interface.h,
-+
+        UseTheForce/DarkSide/sticky.F90,
-+
+        UseTheForce/DarkSide/sticky_interface.F90,
-+
+        UseTheForce/DarkSide/sticky_interface.h,
-+
+        UseTheForce/DarkSide/switcheroo.F90,
-+
+        applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        applications/dump2Xyz/Dump2XYZCmd.c,
-+
+        applications/dump2Xyz/Dump2XYZCmd.h,
-+
+        applications/dynamicProps/CrossTimeCorrFunc.cpp,
-+
+        applications/dynamicProps/CrossTimeCorrFunc.hpp,
-+
+        applications/dynamicProps/DipoleCorrFunc.cpp,
-+
+        applications/dynamicProps/DipoleCorrFunc.hpp,
-+
+        applications/dynamicProps/DynamicProps.cpp,
-+
+        applications/dynamicProps/DynamicPropsCmd.c,
-+
+        applications/dynamicProps/DynamicPropsCmd.h,
-+
+        applications/dynamicProps/FrameTimeCorrFunc.hpp,
-+
+        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
-+
+        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
-+
+        applications/dynamicProps/RCorrFunc.cpp,
-+
+        applications/dynamicProps/RCorrFunc.hpp,
-+
+        applications/dynamicProps/TimeCorrFunc.cpp,
-+
+        applications/dynamicProps/TimeCorrFunc.hpp,
-+
+        applications/dynamicProps/VCorrFunc.cpp,
-+
+        applications/dynamicProps/VCorrFunc.hpp,
-+
+        applications/nanoRodBuilder/GeometryBuilder.cpp,
-+
+        applications/nanoRodBuilder/GeometryBuilder.hpp,
-+
+        applications/nanoRodBuilder/nanorodBuilder.cpp,
-+
+        applications/nanoRodBuilder/nanorodBuilderCmd.c,
-+
+        applications/nanoRodBuilder/nanorodBuilderCmd.h,
-+
+        applications/oopse/oopse.cpp,
-+
+        applications/simpleBuilder/simpleBuilder.cpp,
-+
+        applications/simpleBuilder/simpleBuilderCmd.c,
-+
+        applications/simpleBuilder/simpleBuilderCmd.h,
-+
+        applications/staticProps/GofAngle2.cpp,
-+
+        applications/staticProps/GofAngle2.hpp,
-+
+        applications/staticProps/GofR.cpp,
-+
+        applications/staticProps/GofR.hpp,
-+
+        applications/staticProps/GofRAngle.cpp,
-+
+        applications/staticProps/GofRAngle.hpp,
-+
+        applications/staticProps/GofXyz.cpp,
-+
+        applications/staticProps/GofXyz.hpp,
-+
+        applications/staticProps/RadialDistrFunc.cpp,
-+
+        applications/staticProps/RadialDistrFunc.hpp,
-+
+        applications/staticProps/StaticProps.cpp,
-+
+        applications/staticProps/StaticPropsCmd.c,
-+
+        applications/staticProps/StaticPropsCmd.h,
-+
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
-+
+        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
-+
+        brains/Exclude.hpp, brains/ForceManager.cpp,
-+
+        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
-+
+        brains/MoleculeCreator.hpp, brains/Register.cpp,
-+
+        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
-+
+        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
-+
+        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
-+
+        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
-+
+        brains/fSimulation.h, constraints/ConstraintElem.hpp,
-+
+        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
-+
+        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
-+
+        constraints/ZconstraintForceManager.cpp,
-+
+        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
-+
+        integrators/DLM.hpp, integrators/Integrator.cpp,
-+
+        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
-+
+        integrators/IntegratorFactory.cpp,
-+
+        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
-+
+        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
-+
+        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
-+
+        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
-+
+        integrators/NVT.cpp, integrators/NVT.hpp,
-+
+        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
-+
+        integrators/Velocitizer.hpp,
-+
+        integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp,
-+
+        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
-+
+        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
-+
+        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
-+
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
-+
+        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
-+
+        io/ChargeAtomTypesSectionParser.hpp,
-+
+        io/DirectionalAtomTypesSectionParser.cpp,
-+
+        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
-+
+        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
-+
+        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
-+
+        io/Globals.cpp, io/Globals.hpp,
-+
+        io/LennardJonesAtomTypesSectionParser.cpp,
-+
+        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
-+
+        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
-+
+        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
-+
+        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
-+
+        io/SectionParser.cpp, io/SectionParser.hpp,
-+
+        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
-+
+        io/StatWriter.cpp, io/StatWriter.hpp,
-+
+        io/StickyAtomTypesSectionParser.cpp,
-+
+        io/StickyAtomTypesSectionParser.hpp,
-+
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
-+
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
-+
+        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
-+
+        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
-+
+        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
-+
+        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
-+
+        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
-+
+        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
-+
+        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
-+
+        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
-+
+        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
-+
+        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
-+
+        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
-+
+        math/Quaternion.hpp, math/RandNumGen.hpp,
-+
+        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
-+
+        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
-+
+        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
-+
+        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
-+
+        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
-+
+        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
-+
+        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
-+
+        minimizers/MinimizerFactory.hpp,
-+
+        minimizers/MinimizerParameterSet.cpp,
-+
+        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
-+
+        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
-+
+        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
-+
+        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
-+
+        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
-+
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
-+
+        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
-+
+        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
-+
+        primitives/Molecule.cpp, primitives/Molecule.hpp,
-+
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
-+
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
-+
+        primitives/Torsion.cpp, primitives/Torsion.hpp,
-+
+        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
-+
+        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
-+
+        profiling/timing.F90, restraints/Restraints.cpp,
-+
+        restraints/Restraints.hpp,
-+
+        restraints/ThermoIntegrationForceManager.cpp,
-+
+        restraints/ThermoIntegrationForceManager.hpp,
-+
+        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
-+
+        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
-+
+        selection/NameFinder.cpp, selection/NameFinder.hpp,
-+
+        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
-+
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
-+
+        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
-+
+        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
-+
+        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
-+
+        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
-+
+        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
-+
+        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
-+
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
-+
+        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
-+
+        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
-+
+        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
-+
+        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
-+
+        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
-+
+        types/MakeStamps.cpp, types/MakeStamps.hpp,
-+
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
-+
+        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
-+
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
-+
+        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
-+
+        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
-+
+        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
-+
+        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
-+
+        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
-+
+        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
-+
+        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
-+
+        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
-+
+        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
-+
+        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
-+
+        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
-+
+        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
-+
+        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
-+
+        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
-+
+        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
-+
+        utils/any.hpp, utils/definitions.F90, utils/fError.c,
-+
+        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
-+
+        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
-+
+        utils/residentMem.h, utils/simError.c, utils/simError.h,
-+
+        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
-+
+        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
-+
+        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
-+
+        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
-+
+        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
-+
+        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
-+
+        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
-+
+        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
-+
+        been drafted to perform our indentation services
-+
-+
+-04-15 17:03  gezelter
-+
-+
+        * configure, ac-tools/configure.in: Jedi mind-trick warning
-+
+        messages have been added to make users ignore CGAL.
-+
-+
+-04-15 13:41  tim
-+
-+
+        * make/Makefile.in: fix make install
-+
-+
+-04-15 13:41  tim
-+
-+
+        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
-+
+        add  Makefile of samples
-+
-+
+-04-15 13:33  tim
-+
-+
+        * samples/: lipid/Makefile, water/dimer/Makefile,
-+
+        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
-+
+        installed correctly
-+
-+
+-04-14 16:41  gezelter
-+
-+
+        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
-+
+        scripts/filepp, scripts/filepp.in: configure now searches for perl
-+
+        to use with filepp
-+
+-04-14 16:20  gezelter
+        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
+-09-29 12:56  gezelter
-<
+        * make/: Make.conf.in, Makefile.in: Working on make stuff
->
+        * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
->
+        make stuff
+-09-29 12:46  tim
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
+        src/visitors/RigidBodyVisitor.cpp,
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-<
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
->
+        src/visitors/ZconsVisitor.hpp, make/Makefile,
->
+        make/_files/style.css, samples/Makefile.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
+        src/visitors/RigidBodyVisitor.cpp,
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-<
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
->
+        src/visitors/ZconsVisitor.hpp, make/Makefile,
->
+        make/_files/style.css, samples/Makefile.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,

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+Removed lines
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Comparing trunk/OOPSE-4/ChangeLog (file contents): Revision 2199 by gezelter, Thu Apr 14 21:41:56 2005 UTC vs. Revision 2310 by chrisfen, Mon Sep 19 23:21:46 2005 UTC

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Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2199 by gezelter, Thu Apr 14 21:41:56 2005 UTC vs.
Revision 2310 by chrisfen, Mon Sep 19 23:21:46 2005 UTC