[ViewVC] Diff of: group/trunk/OOPSE-2.0/ChangeLog

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs.
Revision 2309 by chrisfen, Sun Sep 18 20:45:38 2005 UTC

-<
+-11-04 14:48  tim
->
+-09-16 18:04  chuckv
->
->
+        * 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
->
->
+        * 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
->
->
+        * 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
->
->
+        * 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
->
->
+        * 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
->
->
+        * 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
->
->
+        * src/UseTheForce/doForces.F90: bugfix on the grouptype finding
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+        algorithm
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->
+-09-07 15:46  gezelter
->
->
+        * 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
->
->
+        * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
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+        createGtypeCutoffMap
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->
+-08-30 13:23  chrisfen
->
->
+        * src/: UseTheForce/doForces.F90,
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+        UseTheForce/doForces_interface.F90,
->
+        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
->
->
+        * 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
->
->
+        * 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
->
->
+        * 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
->
->
+        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
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+        cutoffs... Segfaults nicely now...
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->
+-07-20 12:04  gezelter
->
->
+        * 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
->
->
+        * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
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+        <functional>
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->
+-07-13 10:54  tim
->
->
+        * 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,
->
+        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
->
->
+        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
->
+        UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
->
+        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
->
->
+        * src/UseTheForce/doForces.F90: [no log message]
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->
+-06-27 17:21  chuckv
->
->
+        * 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
->
->
+        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
->
+        UseTheForce/DarkSide/fInteractionMap.h,
->
+        UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
->
+        Breaky breaky!
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->
+-06-20 11:03  gezelter
->
->
+        * samples/water/ssd/ssd.md,
->
+        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
->
->
+        * src/: applications/staticProps/DensityPlot.cpp,
->
+        applications/staticProps/DensityPlot.hpp,
->
+        applications/staticProps/SCDOrderParameter.cpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        io/AtomTypesSectionParser.cpp: working version of DensityPlot
->
->
+-05-31 17:31  chuckv
->
->
+        * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
->
+        remove angular momentum.
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->
+-05-31 12:34  chuckv
->
->
+        * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
->
+        typo in nanorodBuilder.
->
->
+-05-30 09:01  chuckv
->
->
+        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
->
+        brains/Stats.hpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp: Added method to remove system angular
->
+        momentum to velocitizer and added method to calculate system
->
+        angular momentum to siminfo.
->
->
+-05-29 16:16  chrisfen
->
->
+        * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
->
+        balance from the Darkside (files)
->
->
+-05-29 16:15  chrisfen
->
->
+        * src/UseTheForce/doForces.F90: Removed balance from doForces
->
->
+-05-29 16:15  chrisfen
->
->
+        * samples/water/tap/: tap.in, tap.md: Updated tap sample
->
->
+-05-29 16:15  chrisfen
->
->
+        * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
->
+        dimer for testing purposes
->
->
+-05-29 16:14  chrisfen
->
->
+        * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
->
+        was apparently wiped earlier this month...
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->
+-05-29 16:13  chrisfen
->
->
+        * ChangeLog: ran make cvslog
->
->
+-05-28 19:16  tim
->
->
+        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
->
+        AtomNameVisitor
->
->
+-05-28 19:09  tim
->
->
+        * src/integrators/Integrator.cpp: dding resetIntegrator
->
->
+-05-28 19:06  tim
->
->
+        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
->
+        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
->
+        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
->
+        resetIntegrator
->
->
+-05-27 16:11  tim
->
->
+        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
->
+        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
->
+        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
->
+        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
->
+        StaticProps
->
->
+-05-26 23:41  tim
->
->
+        * src/: applications/staticProps/Makefile,
->
+        applications/staticProps/P2OrderParameter.cpp,
->
+        applications/staticProps/P2OrderParameter.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
->
+        utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
->
->
+-05-26 17:45  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h,
->
+        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
->
+        AtomNameVisitor to convert atom name to its base name;
->
+        wrappingvisitor now wrap back to the center of the mass; adding
->
+        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
->
->
+        * 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
->
->
+        * src/integrators/NPrT.cpp: NPrT in progress
->
->
+-05-20 11:01  tim
->
->
+        * 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,
->
+        io/Globals.hpp: NPAT is working
->
->
+-05-19 10:49  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
->
+        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
->
->
+-05-18 23:28  tim
->
->
+        * src/: brains/Register.cpp, integrators/NPAT.cpp,
->
+        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
->
+        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
->
+        MoLocator
->
->
+-04-14 14:12  gezelter
->
->
+        * LICENSE: [no log message]
->
->
+-04-14 11:10  chuckv
->
->
+        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
->
+        nanorodbuilder now exit's when libCGAL is not present.
->
->
+-04-14 10:20  tim
->
->
+        * src/io/make_nodes.h: fix one more warning message in make_nodes
->
->
+-04-13 18:36  chuckv
->
->
+        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
->
+        interface name for SGI Compiler
->
->
+-04-13 18:29  chrisfen
->
->
+        * samples/water/ssde/ssde.md: oops...  bad sample
->
->
+-04-13 18:00  chuckv
->
->
+        * src/config.h.in: Change typo in CGAL.
->
->
+-04-13 17:43  tim
->
->
+        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
->
+        selection/SelectionCompiler.hpp: fix some warning messages
->
->
+-04-13 17:30  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
->
+        make/Makefile.in, src/config.h.in,
->
+        src/applications/nanoRodBuilder/Makefile,
->
+        src/applications/nanoRodBuilder/Makefile.in,
->
+        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
->
+        checks
->
->
+-04-13 15:36  chuckv
->
->
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
->
+        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
->
+        DarkSide/electrostatic_interface.F90,
->
+        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
->
+        DarkSide/lj_interface.h, DarkSide/sticky.F90,
->
+        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
->
+        destroy methods for Fortran modules.
->
->
+-04-13 15:17  chuckv
->
->
+        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
->
+        shapes_interface.h: Added destroy method to clean up memory
->
->
+-04-13 13:41  tim
->
->
+        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
->
+        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
->
+        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
->
+        fixed
->
->
+-04-12 17:44  chuckv
->
->
+        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
->
+        for nanoRodBuilder.
->
->
+-04-12 17:42  tim
->
->
+        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
->
+        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
->
+        and simpleBuilder(forget to delete lattice)
->
->
+-04-12 17:33  tim
->
->
+        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
->
+        refactory lattice
->
->
+-04-12 17:07  tim
->
->
+        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
->
+        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
->
+        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
->
+        LatticeFactory and LatticeCreator
->
->
+-04-12 16:58  tim
->
->
+        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
->
+        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
->
+        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
->
+        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
->
+        lattice/Makefile: refactory LatticeFactory and LatticeCreator
->
->
+-04-12 16:28  gezelter
->
->
+        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
->
+        vector_class.F90: cleaned up vector_class memory leak fix by
->
+        deallocating in reverse order of how we allocated.  Also migrated
->
+        MoLocator into utils directory
->
->
+-04-12 16:27  gezelter
->
->
+        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
->
+        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
->
+        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
->
+        directory
->
->
+-04-12 16:27  gezelter
->
->
+        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
->
+        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
->
+        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
->
+        nanoRodBuilder/LatticeCreator.hpp,
->
+        nanoRodBuilder/LatticeFactory.cpp,
->
+        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
->
+        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
->
+        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
->
+        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
->
+        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
->
+        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
->
+        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
->
+        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
->
+        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
->
+        these files are now redundant
->
->
+-04-12 16:27  gezelter
->
->
+        * src/UseTheForce/DarkSide/: atype_interface.F90,
->
+        atype_interface.h: cleaned up memory leak fix
->
->
+-04-12 16:26  gezelter
->
->
+        * make/Makefile.in: added lattice subdirectory
->
->
+-04-12 15:57  chrisfen
->
->
+        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
->
+        a space by accident
->
->
+-04-12 15:56  chrisfen
->
->
+        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
->
+        quadrupole sample
->
->
+-04-12 15:56  chrisfen
->
->
+        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
->
+        samples
->
->
+-04-12 13:30  tim
->
->
+        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
->
+        type in fortran side
->
->
+-04-12 12:45  chuckv
->
->
+        * src/utils/vector_class.F90: Further changes to vector_class
->
+        destroy function.
->
->
+-04-12 12:39  chuckv
->
->
+        * src/utils/vector_class.F90: Fixed pointer memory leak in
->
+        vector_class.
->
->
+-04-12 12:12  chuckv
->
->
+        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
->
+        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
->
+        DarkSide/eam.F90, DarkSide/eam_interface.F90,
->
+        DarkSide/eam_interface.h: Updates to deallocate object in fortran.
->
->
+-04-12 09:24  chrisfen
->
->
+        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
->
+        output
->
->
+-04-11 19:29  chuckv
->
->
+        * src/: UseTheForce/DarkSide/atype.F90,
->
+        applications/nanoRodBuilder/Makefile: Changes to delete atypes...
->
->
+-04-11 19:28  chuckv
->
->
+        * src/utils/vector_class.F90: Added code to delete vector.
->
->
+-04-11 17:03  chuckv
->
->
+        * samples/metals/nanorod/: Au_nanoparticle.md,
->
+        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
->
+        aren't these here?
->
->
+-04-11 16:58  tim
->
->
+        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
->
+        basic_ifstrstream
->
->
+-04-11 16:37  chuckv
->
->
+        * make/Makefile.in,
->
+        src/applications/nanoRodBuilder/BaseLattice.cpp,
->
+        src/applications/nanoRodBuilder/BaseLattice.hpp,
->
+        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
->
+        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
->
+        src/applications/nanoRodBuilder/Lattice.cpp,
->
+        src/applications/nanoRodBuilder/Lattice.hpp,
->
+        src/applications/nanoRodBuilder/LatticeCreator.cpp,
->
+        src/applications/nanoRodBuilder/LatticeCreator.hpp,
->
+        src/applications/nanoRodBuilder/LatticeFactory.cpp,
->
+        src/applications/nanoRodBuilder/LatticeFactory.hpp,
->
+        src/applications/nanoRodBuilder/Makefile,
->
+        src/applications/nanoRodBuilder/MoLocator.cpp,
->
+        src/applications/nanoRodBuilder/MoLocator.hpp,
->
+        src/applications/nanoRodBuilder/nanoBuilder.ggo,
->
+        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
->
+        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
->
+        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
->
+        nanoRodBuilder application (may not work yet).  ((Doesn't work
->
+        yet.)) (((May never work....)))
->
->
+-04-11 15:54  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
->
+        prepareVisitor in Dump2XYZ
->
->
+-04-11 15:19  chrisfen
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
->
+        quadrupoles.  look!  it's divide by 3 like stone says!
->
->
+-04-11 15:18  chrisfen
->
->
+        * forceFields/DUFF2.frc: fixing of the quadrupoles
->
->
+-04-11 15:16  tim
->
->
+        * src/selection/Token.hpp: change the parameter name in
->
+        constructors
->
->
+-04-11 14:49  gezelter
->
->
+        * make/Makefile.in: One more bug fix for GNU make versions < 3.80
->
->
+-04-11 14:06  gezelter
->
->
+        * make/Makefile.in: Fixed the uc and lc functions for GNU make
->
+        versions < 3.80
->
->
+-04-11 11:13  gezelter
->
->
+        * make/Makefile.in, src/UseTheForce/Makefile,
->
+        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
->
+        some stuff to clean out module files during "make clean"
->
->
+-04-08 17:13  chrisfen
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
->
+        interactions should be working with a remaining question of
->
+        interaction magnitude
->
->
+-04-08 17:12  chrisfen
->
->
+        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
->
+        samples
->
->
+-04-08 13:48  chrisfen
->
->
+        * samples/water/ssd/ssd.md: oops...  messed up a sample
->
->
+-04-08 09:43  chrisfen
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
->
+        charge-dipole interactions
->
->
+-04-08 09:42  chrisfen
->
->
+        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
->
+        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
->
->
+-04-08 09:41  chrisfen
->
->
+        * forceFields/DUFF2.frc: added Cl- and Na+
->
->
+-04-06 18:59  tim
->
->
+        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
->
->
+-04-05 18:09  tim
->
->
+        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
->
+        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
->
+        in atom type name;clean the code a little bit
->
->
+-03-29 16:00  tim
->
->
+        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
->
+        in converting rotation matrix to quaternion
->
->
+-03-28 17:41  tim
->
->
+        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping
->
->
+-03-28 17:30  tim
->
->
+        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
->
+        the wrapping
->
->
+-03-28 10:54  tim
->
->
+        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
->
+        dimension of histogram
->
->
+-03-22 11:38  tim
->
->
+        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
->
+        src/applications/dynamicProps/Makefile,
->
+        src/applications/oopse/Makefile,
->
+        src/applications/simpleBuilder/Makefile,
->
+        src/applications/staticProps/Makefile: avoid building parallel
->
+        executable for dump2XYZ, simpleBuilder, staticProps and
->
+        dynamicProps
->
->
+-03-21 17:34  chrisfen
->
->
+        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
->
+        forcefield files
->
->
+-03-21 15:51  chrisfen
->
->
+        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
->
+        DarkSide/reactionField.F90: Make sure electrostatic_module provides
->
+        data for reaction_field
->
->
+-03-21 15:50  chrisfen
->
->
+        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
->
+        WILL CHANGE THIS BACK, RIGHT?
->
->
+-03-21 14:23  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
->
+        correct value
->
->
+-03-21 14:22  gezelter
->
->
+        * make/Makefile.in: fixed an install-related bug.
->
+        $(InstallCommand) had been set to $(InstallData)
->
->
+-03-15 09:21  gezelter
->
->
+        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
->
+        deletes and Nullifies restWriter, so Integrator shouldn't do it.
->
->
+-03-15 09:20  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos
->
->
+-03-13 02:39  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
->
+        charge-quadrupole interactions
->
->
+-03-12 14:12  chrisfen
->
->
+        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
->
+        thermoIntegration/solid/Makefile: forgot a couple of makefiles
->
->
+-03-12 14:05  chrisfen
->
->
+        * samples/thermoIntegration/liquid/ssde.in,
->
+        samples/thermoIntegration/liquid/ssde.md,
->
+        samples/thermoIntegration/liquid/water.md,
->
+        samples/thermoIntegration/solid/idealCrystal.in,
->
+        samples/thermoIntegration/solid/ssde.in,
->
+        samples/thermoIntegration/solid/ssde.md,
->
+        samples/thermoIntegration/solid/ssde.zang0,
->
+        samples/thermoIntegration/solid/water.md,
->
+        samples/water/tip3p_ice/tp3.md,
->
+        src/UseTheForce/DarkSide/sticky.F90,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: added some
->
+        samples
->
->
+-03-11 12:50  tim
->
->
+        * src/: brains/SimCreator.cpp,
->
+        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
->
+        MultipoleAtomTypesSectionParser
->
->
+-03-11 10:55  tim
->
->
+        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
->
+        excluded
->
->
+-03-11 10:53  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
->
+        quadrupoles
->
->
+-03-11 10:52  gezelter
->
->
+        * forceFields/DUFF2.frc: quadrupoles for SSD models
->
->
+-03-11 10:00  tim
->
->
+        * ChangeLog, doc/SelectionExpression.html,
->
+        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
->
+        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
->
+        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
->
+        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
->
+        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
->
+        SelectionExpression.html
->
->
+-03-10 19:43  chrisfen
->
->
+        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
->
+        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
->
+        MPI restraints
->
->
+-03-10 18:56  tim
->
->
+        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
->
+        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
->
+        and cutoff group
->
->
+-03-10 17:06  gezelter
->
->
+        * src/types/MorseBondType.hpp: fixed a doxygen problem
->
->
+-03-10 16:51  gezelter
->
->
+        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
->
+        the split dipole test cases
->
->
+-03-10 16:51  gezelter
->
->
+        * doc/SelectionExpression.html: updated some documentation
->
->
+-03-10 15:40  gezelter
->
->
+        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
->
+        Makefile: LinkedList removal project starts now
->
->
+-03-10 15:28  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
->
+        using map to replace link list
->
->
+-03-10 14:11  tim
->
->
+        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
->
+        case  of split dipole
->
->
+-03-10 14:10  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
->
+        src/io/RestWriter.cpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
->
+        builds...
->
->
+-03-10 13:44  tim
->
->
+        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
->
+        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
->
+        adding test case for split dipole
->
->
+-03-10 12:54  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
->
+        support for split dipoles
->
->
+-03-10 11:27  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
->
+        restraints
->
->
+-03-10 11:15  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
->
+        src/UseTheForce/ForceFields.hpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
->
->
+-03-10 11:14  tim
->
->
+        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
->
+        src/io/MultipoleAtomTypesSectionParser.cpp,
->
+        src/selection/SelectionEvaluator.cpp: minor change
->
->
+-03-10 10:10  chrisfen
->
->
+        * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
->
+        src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
->
+        src/integrators/Integrator.cpp, src/integrators/Integrator.hpp,
->
+        src/integrators/VelocityVerletIntegrator.cpp,
->
+        src/integrators/VelocityVerletIntegrator.hpp,
->
+        src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp,
->
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp,
->
+        src/io/RestReader.hpp, src/io/RestWriter.cpp,
->
+        src/io/RestWriter.hpp, src/io/RestraintReader.cpp,
->
+        src/io/RestraintWriter.cpp, src/restraints/Makefile,
->
+        src/restraints/Restraints.cpp, src/restraints/Restraints.hpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp,
->
+        src/restraints/ThermoIntegrationForceManager.hpp: First commit of
->
+        the new restraints code
->
->
+-03-09 13:48  tim
->
->
+        * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
->
+        IndexFinder
->
->
+-03-09 13:46  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.ggo,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h,
->
+        selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
->
+        fix compilation issue
->
->
+-03-09 12:58  tim
->
->
+        * forceFields/DUFF2.frc, scripts/filepp,
->
+        src/UseTheForce/EAM_FF.cpp,
->
+        src/io/MultipoleAtomTypesSectionParser.cpp,
->
+        src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
->
+        in SectionParser (lineNo is not updated)
->
->
+-03-09 12:30  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.ggo,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp,
->
+        io/ChargeAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile,
->
+        io/MultipoleAtomTypesSectionParser.cpp,
->
+        io/MultipoleAtomTypesSectionParser.hpp,
->
+        io/SectionParserManager.cpp, selection/Makefile,
->
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
->
+        types/AtomType.cpp, types/DirectionalAtomType.cpp,
->
+        visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp: adding IndexFinder which is used to
->
+        select the molecules; Seperate ElectrostaticAtomTypesSectionParser
->
+        into ChargeAtomTypesSectionParser and
->
+        MultipoleAtomTypesSectionParser;remove print dipole option from
->
+        Dump2XYZ;
->
->
+-03-09 12:28  tim
->
->
+        * forceFields/DUFF2.frc: change the format of DUFF2
->
->
+-03-09 10:44  gezelter
->
->
+        * src/UseTheForce/DarkSide/: electrostatic.F90,
->
+        electrostatic_interface.F90, electrostatic_interface.h: new
->
+        electrostatic module
->
->
+-03-09 09:26  gezelter
->
->
+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
->
+        DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
->
+        and fixed quadrupole stuff
->
->
+-03-09 09:25  gezelter
->
->
+        * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
->
+        for outdated charge and dipole interfaces
->
->
+-03-08 16:08  gezelter
->
->
+        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
->
+        mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
->
+        charge-dipole test cases
->
->
+-03-08 16:07  gezelter
->
->
+        * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
->
+        OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
->
+        strange icc8 bug (we think).
->
->
+-03-08 16:07  gezelter
->
->
+        * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!
->
->
+-03-08 16:07  gezelter
->
->
+        * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
->
+        Unification Project
->
->
+-03-08 16:07  gezelter
->
->
+        * src/io/Globals.cpp: Dunno
->
->
+-03-08 16:06  gezelter
->
->
+        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
->
+        OOPSE_itoa and checking a NULL left over from the LinkedList days
->
->
+-03-08 16:06  gezelter
->
->
+        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
->
+        atype_interface.F90, atype_interface.h, charge.F90,
->
+        charge_interface.F90, charge_interface.h, dipole.F90,
->
+        dipole_interface.F90, dipole_interface.h: electrostatic unification
->
+        project fixed an uninitialized variable in Lennard Jones mixing map
->
->
+-03-08 16:05  gezelter
->
->
+        * src/UseTheForce/doForces.F90: electrostatic unification project
->
->
+-03-08 16:05  gezelter
->
->
+        * samples/water/dimer/: two.md, water.md: making some cool test
->
+        cases
->
->
+-03-08 16:05  gezelter
->
->
+        * forceFields/DUFF2.frc: Added a charge for Chlorine
->
->
+-03-07 17:39  tim
->
->
+        * src/: brains/SimInfo.cpp, io/DumpReader.cpp,
->
+        math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
->
+        primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
->
+        Fixing a bug in BitSet.cpp
->
->
+-03-04 10:28  gezelter
->
->
+        * src/config.h.in: Cleaning up config.h.in by adding comments
->
->
+-03-04 10:28  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in,
->
+        src/brains/SimCreator.cpp: SPRNG eradication project
->
->
+-03-03 09:40  tim
->
->
+        * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
->
+        missing atom type problem)
->
->
+-03-02 11:29  tim
->
->
+        * src/math/RandNumGen.hpp: adding base class of Random Number
->
+        generator
->
->
+-03-02 11:28  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
->
+        Velocitizer is not initialized which causes a seg fault
->
->
+-03-02 10:36  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp, math/Makefile,
->
+        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
->
+        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp,
->
+        math/SeqRandNumGen.hpp: remove default parameter from
->
+        MersenneTwister.hpp which causes all kinds of trouble.  Refactory
->
+        random number generator
->
->
+-03-02 02:32  tim
->
->
+        * test/math/testRandNumGen.cpp: Adding unit test for random number
->
+        generator
->
->
+-03-01 18:17  tim
->
->
+        * src/brains/Thermo.hpp: fixed a file inclusion problem
->
->
+-03-01 18:17  tim
->
->
+        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
->
+        OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
->
+        ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
->
+        RandNumGenTestCase.hpp: fixed compilation problem
->
->
+-03-01 18:02  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp, math/Makefile,
->
+        math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp,
->
+        math/ParallelRandNumGen.hpp, math/mt19937ar.c,
->
+        math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand
->
->
+-03-01 18:00  tim
->
->
+        * test/math/: Makefile, ParallelandNumGenTestCase.cpp,
->
+        ParallelandNumGenTestCase.hpp: Change the name of test case
->
->
+-03-01 16:00  tim
->
->
+        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
->
+        OOPSERandNumGenTestCase.hpp: adding testcase for random number
->
+        generator
->
->
+-03-01 15:10  tim
->
->
+        * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
->
+        integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
->
+        math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp,
->
+        math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp,
->
+        math/Vector3.hpp, minimizers/MinimizerCreator.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
->
+        utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
->
+        visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4
->
->
+-03-01 14:11  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
->
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
->
+        math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
->
+        OOPSERandNumGen
->
->
+-03-01 10:44  gezelter
->
->
+        * make/Makefile.in: Fixed the damned build problem with the
->
+        libraries not being removed in make clean and make distclean (at
->
+        least we think it is fixed).
->
->
+-03-01 10:26  gezelter
->
->
+        * src/math/MersenneTwister.hpp: Making small modifications to allow
->
+        for use on MPI machines
->
->
+-03-01 09:45  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
->
+        integrators/Velocitizer.cpp, io/DumpReader.cpp,
->
+        math/MersenneTwister.hpp: adding MersenneTwister random number
->
+        generator
->
->
+-02-28 22:55  tim
->
->
+        * src/math/MersenneTwister.hpp: Adding a modified version of
->
+        MersenneTwister.hpp
->
->
+-02-28 12:24  tim
->
->
+        * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
->
+        definition.jpg: selection expression
->
->
+-02-25 16:22  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90,
->
+        UseTheForce/DarkSide/lj_interface.F90,
->
+        UseTheForce/DarkSide/lj_interface.h,
->
+        io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
->
+        types/AtomType.hpp: adding soft potential to LJ Module
->
->
+-02-25 11:38  tim
->
->
+        * doc/SelectionExpression.html: adding documentation for selection
->
+        expression
->
->
+-02-24 15:55  tim
->
->
+        * src/: applications/simpleBuilder/simpleBuilder.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
->
+        io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp:
->
+        adding basic_teebuf which can operate on multiple stream
->
+        simutaneously.
->
->
+-02-22 14:26  chrisfen
->
->
+        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
->
+        sample
->
->
+-02-22 13:56  tim
->
->
+        * src/: UseTheForce/DarkSide/reactionField.F90,
->
+        primitives/RigidBody.cpp: reactionfield get fixed
->
->
+-02-21 11:57  tim
->
->
+        * src/: applications/staticProps/GofRAngle.cpp,
->
+        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
->
+        a bug in GofRAngle
->
->
+-02-21 10:28  tim
->
->
+        * src/primitives/Molecule.cpp: Fix for compilation on the Sun
->
->
+-02-21 10:22  tim
->
->
+        * src/utils/next_combination.hpp: fix for compilation on the Sun
->
->
+-02-21 10:21  tim
->
->
+        * src/utils/GenericData.hpp: fix problem in sun
->
->
+-02-18 18:07  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.ggo,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/staticProps/GofXyz.cpp,
->
+        applications/staticProps/GofXyz.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
->
+        visitors/Makefile: adding LipidTransVisitor, GofXyz is working now
->
->
+-02-18 10:58  gezelter
->
->
+        * src/brains/Register.cpp: Corrected filename collision for EAM on
->
+        Mac OS X
->
->
+-02-18 10:58  gezelter
->
->
+        * src/applications/oopse/oopse.cpp: Updated copyright information
->
->
+-02-18 10:58  gezelter
->
->
+        * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
->
+        Makefile: corrected filename collision for EAM on operating systems
->
+        which are not case sensitive (aka Mac OS X)
->
->
+-02-17 15:15  tim
->
->
+        * src/applications/staticProps/GofXyz.cpp: more bug get fixed
->
->
+-02-17 14:50  tim
->
->
+        * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
->
+        in GofXyz
->
->
+-02-17 14:09  tim
->
->
+        * src/applications/staticProps/RadialDistrFunc.hpp: make
->
+        processHistogram non-abstrct function
->
->
+-02-17 13:41  tim
->
->
+        * src/applications/staticProps/GofXyz.cpp: [no log message]
->
->
+-02-17 13:30  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
->
+        GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
->
+        finish GofXyz
->
->
+-02-17 11:21  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
->
+        GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
->
+        distribution function
->
->
+-02-17 10:23  tim
->
->
+        * src/utils/BitSet.hpp: forget the const correctness for BitSet
->
->
+-02-17 10:18  tim
->
->
+        * src/: brains/BlockSnapshotManager.cpp,
->
+        selection/DistanceFinder.cpp: The change of interface of BitSet
->
+        cause a bug in SelectionEvaluation
->
->
+-02-16 16:13  tim
->
->
+        * src/utils/residentMem.c: return residentMem in byte
->
->
+-02-16 16:00  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
->
+        a bug in writing out the value of cosang
->
->
+-02-16 15:43  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
->
+        estimate avaliable memory
->
->
+-02-16 15:30  tim
->
->
+        * src/: 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/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h,
->
+        brains/BlockSnapshotManager.cpp: change the default bin number
->
->
+-02-16 14:36  tim
->
->
+        * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/dynamicProps/TimeCorrFunc.cpp,
->
+        applications/dynamicProps/VCorrFunc.cpp,
->
+        applications/staticProps/GofAngle2.cpp,
->
+        applications/staticProps/GofR.cpp,
->
+        applications/staticProps/GofR.hpp,
->
+        applications/staticProps/GofRAngle.cpp,
->
+        applications/staticProps/GofRAngle.hpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.hpp,
->
+        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
->
+        files;fix the problem of counting in staticProps
->
->
+-02-15 14:39  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: fix a bug in
->
+        BlockSnapshotManager
->
->
+-02-15 14:36  tim
->
->
+        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
->
+        reference counting now
->
->
+-02-15 12:49  tim
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        replace std::make_pair by VariablesType::value_type to make Sun
->
+        Compiler happy
->
->
+-02-15 12:35  tim
->
->
+        * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
->
+        TokenMap, using TokenMapType::value_type instead of std::make_pair
->
+        to make Sun compiler happy
->
->
+-02-15 12:24  tim
->
->
+        * src/applications/staticProps/: GofRAngle.cpp,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps
->
->
+-02-15 12:11  tim
->
->
+        * src/: applications/staticProps/GofR.cpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.hpp,
->
+        brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding
->
+        #ifdef __RWSTD to make sun compiler happy (2) fix pair density
->
+        calculation problem when two selections intersect with each other
->
->
+-02-15 10:24  gezelter
->
->
+        * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
->
+        xlc++
->
->
+-02-15 10:17  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/residentMem.c: [no log message]
->
->
+-02-15 01:17  gezelter
->
->
+        * src/utils/residentMem.c: bug fix for null termination
->
->
+-02-15 01:11  gezelter
->
->
+        * configure, ac-tools/configure.in, src/utils/residentMem.c:
->
+        bugfixing residentMem
->
->
+-02-15 00:59  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/residentMem.c: bugfixes for residentMem on LINUX
->
->
+-02-15 00:08  gezelter
->
->
+        * src/utils/Makefile.in: added residentMem
->
->
+-02-15 00:05  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in,
->
+        src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
->
+        src/utils/residentMem.h: modifications to estimate memory in use by
->
+        other processes autoconf fixes ps syntax checking config.h file
->
+        cleaning
->
->
+-02-14 18:26  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in: ps niceness
->
->
+-02-14 18:16  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
->
+        strangeness
->
->
+-02-14 14:42  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: fix a bug in
->
+        BlockSnapshotManager.hpp
->
->
+-02-14 13:51  tim
->
->
+        * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
->
+        StaticPropsCmd.c: default length for staticProps is 1/2 smallest
->
+        length of first frame
->
->
+-02-14 13:12  tim
->
->
+        * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
->
+        VelocityVerletIntegrator : last frame is written twice
->
->
+-02-14 12:57  tim
->
->
+        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
->
+        brains/SimInfo.cpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp: begin bug fix
->
->
+-02-14 12:35  tim
->
->
+        * src/applications/dynamicProps/: CorrelationFunction.cpp,
->
+        CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
->
+        CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp,
->
+        DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile,
->
+        ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp,
->
+        RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
->
+        VCorrFunc.hpp: refactory CorrelationFunction
->
->
+-02-14 10:18  gezelter
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
->
+        and start of switch for type of correlation function
->
->
+-02-13 16:18  tim
->
->
+        * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
->
+        calculating  bytes per stuntdouble
->
->
+-02-13 16:03  tim
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: more fix
->
->
+-02-13 15:57  tim
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
->
+        bug in CorrelationFunction
->
->
+-02-13 15:36  tim
->
->
+        * src/: applications/staticProps/GofR.cpp,
->
+        applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
->
+        bug in SimInfo::getCutoff()
->
->
+-02-13 15:08  tim
->
->
+        * make/Makefile.in: adding staticProps and dynamicProps into
->
+        Makefile.in
->
->
+-02-13 15:05  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
->
+        defaults to the cutoff radius
->
->
+-02-13 14:14  tim
->
->
+        * src/utils/Algorithm.hpp: adding Algorithm.hpp
->
->
+-02-13 14:10  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/dynamicProps/DynamicProps.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        integrators/Integrator.cpp, integrators/Integrator.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
->
+        visitors/OtherVisitor.cpp: dynamicProps get built
->
->
+-02-13 10:56  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
->
+        progress
->
->
+-02-13 03:04  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.hpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
->
+        brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
->
+        work in dynamicProps
->
->
+-02-13 02:25  tim
->
->
+        * src/applications/dynamicProps/DynamicProps.cpp: adding
->
+        dynamicProps
->
->
+-02-13 02:14  tim
->
->
+        * src/applications/dynamicProps/: DynamicPropsCmd.c,
->
+        DynamicPropsCmd.h: adding command line option to DynamicProps
->
->
+-02-13 02:13  tim
->
->
+        * src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
->
+        adding command line option for DynamicProps
->
->
+-02-13 01:57  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/dynamicProps/DipoleCorrFunc.cpp,
->
+        applications/dynamicProps/DipoleCorrFunc.hpp,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/dynamicProps/RCorrFunc.hpp,
->
+        applications/dynamicProps/VCorrFunc.cpp,
->
+        applications/dynamicProps/VCorrFunc.hpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
->
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
->
+        dynamicProps
->
->
+-02-12 15:09  tim
->
->
+        * src/selection/SelectionManager.cpp: adding SelectionManager.cpp
->
->
+-02-11 17:41  tim
->
->
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
->
+        more constructor to Snapshot to create customized DataStorage
->
->
+-02-11 17:39  tim
->
->
+        * src/selection/: DistanceFinder.hpp, Makefile,
->
+        SelectionManager.hpp: adding beginSelected, nextSelected method to
->
+        SelectionManager
->
->
+-02-11 17:36  tim
->
->
+        * src/config.h.in, configure: adding support for physmem
->
->
+-02-11 17:35  tim
->
->
+        * ac-tools/configure.in: adding supprot for physmem
->
->
+-02-11 17:35  tim
->
->
+        * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
->
+        physmem
->
->
+-02-10 17:37  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
->
+        GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
->
+        GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
->
+        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
->
+        StaticPropsCmd.h: more work in StaticProps
->
->
+-02-10 13:14  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
->
+        GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
->
+        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp,
->
+        Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
->
+        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
->
+        StaticPropsCmd.h: change the filenames
->
->
+-02-10 09:15  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
->
+        GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
->
+        RadialDistrFunc.hpp: adding GofRAngle
->
->
+-02-09 13:21  tim
->
->
+        * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
->
+        useless files
->
->
+-02-09 13:12  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, Makefile,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress
->
->
+-02-09 12:08  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
->
+        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR
->
->
+-02-07 17:39  tim
->
->
+        * src/primitives/Molecule.hpp: add getRigidBodyAt  function into
->
+        Molecule class
->
->
+-02-07 17:38  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info
->
->
+-02-07 17:36  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp: support select internal index selection, for
->
+        example, select DMPC.3
->
->
+-02-07 16:11  tim
->
->
+        * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
->
+        help info for Dump2XYZ
->
->
+-02-07 15:39  chrisfen
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        selection librarys added
->
->
+-02-07 15:31  tim
->
->
+        * src/selection/Makefile, make/Makefile.in: adding Makefile
->
->
+-02-07 15:20  chrisfen
->
->
+        * src/utils/wildcards.hpp: issue commented out in wildcards
->
->
+-02-07 15:06  tim
->
->
+        * src/selection/SelectionEvaluator.cpp: forget to reset the pc
->
+        which cause reevaluate return NULL
->
->
+-02-07 14:14  tim
->
->
+        * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
->
+        SimSnapshotManager.hpp: fix a bug in determing the global index for
->
+        rigidbodies
->
->
+-02-07 14:13  tim
->
->
+        * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
->
+        in Bitset
->
->
+-02-07 14:13  tim
->
->
+        * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
->
+        TokenMap.cpp: selection library is working
->
->
+-02-04 17:46  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor
->
->
+-02-04 17:45  tim
->
->
+        * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
->
+        and XYZVisitor now use selection library
->
->
+-02-04 17:44  tim
->
->
+        * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
->
+        adding SelectionManager into SimInfo
->
->
+-02-04 17:43  tim
->
->
+        * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
->
+        Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
->
+        selection library
->
->
+-02-04 17:42  tim
->
->
+        * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
->
+        in BitSet
->
->
+-02-04 17:41  tim
->
->
+        * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
->
+        implementation
->
->
+-02-04 17:39  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
->
+        SelectionManager.hpp, Token.hpp: half of the selection utility is
->
+        working need to debug within keyword and atomproperty keyword
->
->
+-02-04 00:42  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
->
+        get built
->
->
+-02-04 00:42  tim
->
->
+        * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet
->
->
+-02-04 00:26  tim
->
->
+        * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
->
+        remove some useless files
->
->
+-02-03 23:57  tim
->
->
+        * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
->
+        selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
->
+        adding wildcard class; NameFinder is finished
->
->
+-02-03 18:14  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
->
+        SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
->
+        selection library
->
->
+-02-03 09:04  tim
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        selection in progress
->
->
+-02-02 18:13  tim
->
->
+        * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
->
+        Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
->
+        progress, except SelectionEvaluator, other files are compiled
->
->
+-02-02 18:12  tim
->
->
+        * src/utils/: Makefile.in, any.hpp: adding boost::any
->
->
+-02-02 07:51  tim
->
->
+        * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp
->
->
+-02-01 17:49  tim
->
->
+        * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
->
+        selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
->
+        selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
->
+        selection/Token.hpp: Selection in progress
->
->
+-02-01 01:55  tim
->
->
+        * src/: selection/SelectionCompiler.hpp,
->
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
->
+        selection/SelectionManager.hpp, selection/Token.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp: adding selection library
->
->
+-01-26 10:26  tim
->
->
+        * src/integrators/: Integrator.cpp, Integrator.hpp,
->
+        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
->
+        to add eorWriter
->
->
+-01-26 10:15  tim
->
->
+        * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
->
+        (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
->
+        wrong column of electroframe
->
->
+-01-25 16:59  tim
->
->
+        * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
->
+        SimInfo, use number of cutoff stamp as counter to loop over
->
+        rigidbody stamp
->
->
+-01-25 12:45  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
->
+        integrators/DLM.cpp, io/AtomTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp,
->
+        io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp,
->
+        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.cpp,
->
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
->
+        math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp,
->
+        primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp,
->
+        primitives/GhostTorsion.hpp, primitives/Makefile,
->
+        primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete
->
+        section parser's error message (2) add GhostTorsion (3) accumulate
->
+        inertial tensor from the directional atoms before calculate
->
+        rigidbody's inertial tensor
->
->
+-01-17 17:17  tim
->
->
+        * forceFields/DUFF2.frc: forget to set dipole for lipid head group
->
->
+-01-17 11:58  tim
->
->
+        * src/integrators/NVT.cpp: fix a bug in loading initial extended
->
+        system parameters
->
->
+-01-17 11:05  tim
->
->
+        * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT
->
->
+-01-14 17:02  tim
->
->
+        * src/UseTheForce/WATER.cpp: remove WATER.cpp
->
->
+-01-14 16:37  tim
->
->
+        * forceFields/Makefile: sync Makefile
->
->
+-01-14 16:13  gezelter
->
->
+        * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
->
+        src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
->
+        src/applications/dump2Xyz/Makefile,
->
+        src/applications/oopse/Makefile,
->
+        src/applications/simpleBuilder/Makefile, src/brains/Makefile,
->
+        src/constraints/Makefile, src/integrators/Makefile,
->
+        src/io/Makefile, src/math/Makefile, src/minimizers/Makefile,
->
+        src/primitives/Makefile, src/profiling/Makefile,
->
+        src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in,
->
+        src/visitors/Makefile: moved Package variable into subdirectory
->
+        makefiles to speed up the building process
->
->
+-01-14 15:48  gezelter
->
->
+        * src/applications/oopse/oopse.cpp: Fixed publication details in
->
+        banner
->
->
+-01-14 15:48  gezelter
->
->
+        * src/UseTheForce/DarkSide/: simParallel_interface.F90,
->
+        simParallel_interface.h: added dummy subroutine to avoid empty
->
+        unit, synchronized this dummy routine between C and fortran
->
->
+-01-14 15:31  gezelter
->
->
+        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
->
+        notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
->
+        DarkSide/Makefile, DarkSide/atype.F90,
->
+        DarkSide/atype_interface.F90, DarkSide/charge.F90,
->
+        DarkSide/charge_interface.F90, DarkSide/dipole.F90,
->
+        DarkSide/dipole_interface.F90, DarkSide/eam.F90,
->
+        DarkSide/eam_interface.F90, DarkSide/gb.F90,
->
+        DarkSide/gb_interface.F90, DarkSide/lj_interface.F90,
->
+        DarkSide/shapes.F90, DarkSide/shapes_interface.F90,
->
+        DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90,
->
+        DarkSide/simulation.F90, DarkSide/simulation_interface.F90,
->
+        DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
->
+        modules and C/Fortran interface subroutines
->
->
+-01-14 15:15  gezelter
->
->
+        * configure, ac-tools/aclocal.m4: more fixes for gnugetopt
->
->
+-01-14 15:09  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt
->
->
+-01-14 11:49  tim
->
->
+        * src/: io/EAMAtomTypesSectionParser.cpp,
->
+        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
->
+        utils/StringUtils.hpp: using c library to do conversion instead of
->
+        using iostream due to a bug in libstdc++(GCC 3.2)
->
->
+-01-13 21:40  tim
->
->
+        * src/brains/SimSetup.cpp: no message
->
->
+-01-13 20:56  tim
->
->
+        * src/primitives/Molecule.hpp: fix a bug in global index
->
->
+-01-13 20:04  tim
->
->
+        * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
->
+        Integrator.hpp in Minimizer
->
->
+-01-13 17:14  gezelter
->
->
+        * src/utils/Makefile: compile getopt and getopt1 if we need to
->
->
+-01-13 16:56  gezelter
->
->
+        * make/Makefile.in: template flags
->
->
+-01-13 16:48  gezelter
->
->
+        * src/applications/oopse/Makefile: formatting
->
->
+-01-13 16:48  gezelter
->
->
+        * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
->
+        target
->
->
+-01-13 14:40  tim
->
->
+        * src/: UseTheForce/fSwitchingFunction.h,
->
+        UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
->
+        math/Makefile, math/RectMatrix.hpp, math/Vector.hpp,
->
+        primitives/RigidBody.cpp, types/AtomTypeProperties.h,
->
+        types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform
->
->
+-01-13 13:26  tim
->
->
+        * make/Makefile.in: change the order of linking (object file comes
->
+        first and then follow by user built library)
->
->
+-01-12 18:24  tim
->
->
+        * src/io/DumpWriter.cpp: remove useless debug info
->
->
+-01-12 18:21  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix
->
->
+-01-12 18:17  tim
->
->
+        * make/: Makefile.in, Makefile.in: missing tab
->
->
+-01-12 18:15  tim
->
->
+        * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
->
+        get fixed
->
->
+-01-12 17:40  gezelter
->
->
+        * make/Makefile.in, src/UseTheForce/DUFF.cpp,
->
+        src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
->
+        src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp,
->
+        src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp,
->
+        src/UseTheForce/ForceFieldCreator.hpp,
->
+        src/UseTheForce/ForceFieldFactory.cpp,
->
+        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp,
->
+        src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp,
->
+        src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h,
->
+        src/UseTheForce/fSwitchingFunction.h,
->
+        src/UseTheForce/mpiComponentPlan.h,
->
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
->
+        src/UseTheForce/notifyCutoffs.F90,
->
+        src/UseTheForce/notifyCutoffs_interface.h,
->
+        src/UseTheForce/DarkSide/LJ.F90,
->
+        src/UseTheForce/DarkSide/atype.F90,
->
+        src/UseTheForce/DarkSide/atype_interface.h,
->
+        src/UseTheForce/DarkSide/charge.F90,
->
+        src/UseTheForce/DarkSide/charge_interface.h,
->
+        src/UseTheForce/DarkSide/dipole.F90,
->
+        src/UseTheForce/DarkSide/dipole_interface.h,
->
+        src/UseTheForce/DarkSide/eam.F90,
->
+        src/UseTheForce/DarkSide/eam_interface.h,
->
+        src/UseTheForce/DarkSide/force_globals.F90,
->
+        src/UseTheForce/DarkSide/gb.F90,
->
+        src/UseTheForce/DarkSide/gb_interface.h,
->
+        src/UseTheForce/DarkSide/lj_interface.h,
->
+        src/UseTheForce/DarkSide/neighborLists.F90,
->
+        src/UseTheForce/DarkSide/reactionField.F90,
->
+        src/UseTheForce/DarkSide/shapes.F90,
->
+        src/UseTheForce/DarkSide/shapes_interface.h,
->
+        src/UseTheForce/DarkSide/simParallel.F90,
->
+        src/UseTheForce/DarkSide/simParallel_interface.h,
->
+        src/UseTheForce/DarkSide/simulation.F90,
->
+        src/UseTheForce/DarkSide/simulation_interface.h,
->
+        src/UseTheForce/DarkSide/sticky.F90,
->
+        src/UseTheForce/DarkSide/sticky_interface.h,
->
+        src/UseTheForce/DarkSide/switcheroo.F90,
->
+        src/applications/Makedepend, src/applications/quickLate.c,
->
+        src/applications/dump2Xyz/Dump2XYZ.cpp,
->
+        src/applications/oopse/oopse.cpp,
->
+        src/applications/simpleBuilder/BaseLattice.cpp,
->
+        src/applications/simpleBuilder/BaseLattice.hpp,
->
+        src/applications/simpleBuilder/Lattice.cpp,
->
+        src/applications/simpleBuilder/Lattice.hpp,
->
+        src/applications/simpleBuilder/LatticeCreator.cpp,
->
+        src/applications/simpleBuilder/LatticeCreator.hpp,
->
+        src/applications/simpleBuilder/LatticeFactory.cpp,
->
+        src/applications/simpleBuilder/LatticeFactory.hpp,
->
+        src/applications/simpleBuilder/MoLocator.cpp,
->
+        src/applications/simpleBuilder/MoLocator.hpp,
->
+        src/applications/simpleBuilder/simpleBuilder.cpp,
->
+        src/brains/DataStorage.cpp, src/brains/DataStorage.hpp,
->
+        src/brains/Exclude.cpp, src/brains/Exclude.hpp,
->
+        src/brains/ForceManager.cpp, src/brains/ForceManager.hpp,
->
+        src/brains/Makefile, src/brains/Migrator.hpp,
->
+        src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp,
->
+        src/brains/Register.cpp, src/brains/Register.hpp,
->
+        src/brains/SimCreator.cpp, src/brains/SimCreator.hpp,
->
+        src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
->
+        src/brains/SimModel.hpp, src/brains/SimSetup.hpp,
->
+        src/brains/SimSnapshotManager.cpp,
->
+        src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp,
->
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
->
+        src/brains/SkipList.hpp, src/brains/Snapshot.cpp,
->
+        src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp,
->
+        src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp,
->
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
->
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
->
+        src/constraints/AbstractClasses.hpp,
->
+        src/constraints/ConstraintElem.hpp,
->
+        src/constraints/ConstraintPair.hpp, src/constraints/Makefile,
->
+        src/constraints/Rattle.cpp, src/constraints/Rattle.hpp,
->
+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
->
+        src/constraints/ZconsStruct.hpp,
->
+        src/constraints/ZconstraintForceManager.cpp,
->
+        src/constraints/ZconstraintForceManager.hpp,
->
+        src/integrators/AbstractClasses.hpp,
->
+        src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp,
->
+        src/integrators/DLM.hpp, src/integrators/Integrator.cpp,
->
+        src/integrators/Integrator.hpp,
->
+        src/integrators/IntegratorCreator.hpp,
->
+        src/integrators/IntegratorFactory.cpp,
->
+        src/integrators/IntegratorFactory.hpp, src/integrators/Makefile,
->
+        src/integrators/NPT.cpp, src/integrators/NPT.hpp,
->
+        src/integrators/NPTf.cpp, src/integrators/NPTf.hpp,
->
+        src/integrators/NPTi.cpp, src/integrators/NPTi.hpp,
->
+        src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp,
->
+        src/integrators/NVE.cpp, src/integrators/NVE.hpp,
->
+        src/integrators/NVT.cpp, src/integrators/NVT.hpp,
->
+        src/integrators/RotationAlgorithm.hpp,
->
+        src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp,
->
+        src/integrators/VelocityVerletIntegrator.cpp,
->
+        src/integrators/VelocityVerletIntegrator.hpp,
->
+        src/io/AtomTypesSectionParser.cpp,
->
+        src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp,
->
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
->
+        src/io/BendTypesSectionParser.cpp,
->
+        src/io/BendTypesSectionParser.hpp,
->
+        src/io/BondTypesSectionParser.cpp,
->
+        src/io/BondTypesSectionParser.hpp,
->
+        src/io/DirectionalAtomTypesSectionParser.cpp,
->
+        src/io/DirectionalAtomTypesSectionParser.hpp,
->
+        src/io/DumpReader.cpp, src/io/DumpReader.hpp,
->
+        src/io/DumpWriter.cpp, src/io/DumpWriter.hpp,
->
+        src/io/EAMAtomTypesSectionParser.cpp,
->
+        src/io/EAMAtomTypesSectionParser.hpp,
->
+        src/io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp,
->
+        src/io/Globals.hpp, src/io/InitializeFromFile.cpp,
->
+        src/io/LennardJonesAtomTypesSectionParser.cpp,
->
+        src/io/LennardJonesAtomTypesSectionParser.hpp,
->
+        src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp,
->
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
->
+        src/io/Makefile, src/io/SectionParser.cpp,
->
+        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
->
+        src/io/SectionParserManager.hpp, src/io/StatWriter.cpp,
->
+        src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp,
->
+        src/io/StickyAtomTypesSectionParser.hpp,
->
+        src/io/TorsionTypesSectionParser.cpp,
->
+        src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp,
->
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
->
+        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp,
->
+        src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h,
->
+        src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h,
->
+        src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c,
->
+        src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp,
->
+        src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c,
->
+        src/math/MatVec3.h, src/math/Polynomial.hpp,
->
+        src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp,
->
+        src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp,
->
+        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
->
+        src/math/Vector.hpp, src/math/Vector3.hpp,
->
+        src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp,
->
+        src/minimizers/CGFamilyMinimizer.cpp,
->
+        src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile,
->
+        src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp,
->
+        src/minimizers/MinimizerCreator.hpp,
->
+        src/minimizers/MinimizerFactory.cpp,
->
+        src/minimizers/MinimizerFactory.hpp,
->
+        src/minimizers/MinimizerParameterSet.cpp,
->
+        src/minimizers/MinimizerParameterSet.hpp,
->
+        src/minimizers/OOPSEMinimizer.cpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
->
+        src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp,
->
+        src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp,
->
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
->
+        src/primitives/Bend.cpp, src/primitives/Bend.hpp,
->
+        src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp,
->
+        src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp,
->
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/primitives/GhostBend.hpp, src/primitives/Makefile,
->
+        src/primitives/Molecule.cpp, src/primitives/Molecule.hpp,
->
+        src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp,
->
+        src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp,
->
+        src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp,
->
+        src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp,
->
+        src/primitives/UreyBradleyBend.cpp,
->
+        src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp,
->
+        src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp,
->
+        src/types/AtomStamp.hpp, src/types/AtomType.cpp,
->
+        src/types/AtomType.hpp, src/types/AtomTypeProperties.h,
->
+        src/types/BendStamp.cpp, src/types/BendStamp.hpp,
->
+        src/types/BendType.hpp, src/types/BondStamp.cpp,
->
+        src/types/BondStamp.hpp, src/types/BondType.hpp,
->
+        src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp,
->
+        src/types/Component.cpp, src/types/Component.hpp,
->
+        src/types/CubicBendType.hpp, src/types/CubicBondType.hpp,
->
+        src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp,
->
+        src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp,
->
+        src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp,
->
+        src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp,
->
+        src/types/MakeStamps.cpp, src/types/MakeStamps.hpp,
->
+        src/types/Makefile, src/types/MoleculeStamp.cpp,
->
+        src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp,
->
+        src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp,
->
+        src/types/PolynomialBondType.hpp,
->
+        src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp,
->
+        src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp,
->
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
->
+        src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp,
->
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
->
+        src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp,
->
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
->
+        src/utils/GenericData.hpp, src/utils/GenericFactory.hpp,
->
+        src/utils/LocalIndexManager.hpp, src/utils/Makefile,
->
+        src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp,
->
+        src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp,
->
+        src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp,
->
+        src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp,
->
+        src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp,
->
+        src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp,
->
+        src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp,
->
+        src/utils/Utility.cpp, src/utils/Utility.hpp,
->
+        src/utils/definitions.F90, src/utils/fError.c,
->
+        src/utils/next_combination.hpp, src/utils/oopseMPI.F90,
->
+        src/utils/simError.c, src/utils/simError.h, src/utils/status.F90,
->
+        src/utils/vector_class.F90, src/visitors/AtomData.hpp,
->
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
->
+        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
->
+        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
->
+        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
->
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
->
+        src/visitors/ZconsVisitor.hpp: merging new_design branch into
->
+        OOPSE-2.0
->
->
+-01-12 13:13  tim
->
->
+        * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
->
+        utils/TypeContainer.hpp: forget to include <algorithm>
->
->
+-01-12 12:25  tim
->
->
+        * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
->
+        newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
->
+        fields
->
->
+-01-12 12:14  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/EAM.cpp, UseTheForce/EAM.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.h,
->
+        UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h,
->
+        UseTheForce/notifyCutoffs.F90,
->
+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
->
+        UseTheForce/DarkSide/atype.F90,
->
+        UseTheForce/DarkSide/atype_interface.h,
->
+        UseTheForce/DarkSide/charge.F90,
->
+        UseTheForce/DarkSide/charge_interface.h,
->
+        UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/dipole_interface.h,
->
+        UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h,
->
+        UseTheForce/DarkSide/force_globals.F90,
->
+        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
->
+        UseTheForce/DarkSide/lj_interface.h,
->
+        UseTheForce/DarkSide/neighborLists.F90,
->
+        UseTheForce/DarkSide/reactionField.F90,
->
+        UseTheForce/DarkSide/shapes.F90,
->
+        UseTheForce/DarkSide/shapes_interface.h,
->
+        UseTheForce/DarkSide/simParallel.F90,
->
+        UseTheForce/DarkSide/simParallel_interface.h,
->
+        UseTheForce/DarkSide/simulation.F90,
->
+        UseTheForce/DarkSide/simulation_interface.h,
->
+        UseTheForce/DarkSide/sticky.F90,
->
+        UseTheForce/DarkSide/sticky_interface.h,
->
+        UseTheForce/DarkSide/switcheroo.F90,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
->
+        brains/Exclude.hpp, brains/ForceManager.cpp,
->
+        brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp,
->
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp,
->
+        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/DirectionalAtomTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
->
+        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
->
+        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp,
->
+        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
->
+        io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.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/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, math/ChebyshevPolynomials.cpp,
->
+        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
->
+        math/Polynomial.hpp, math/Quaternion.hpp,
->
+        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
->
+        math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp,
->
+        math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp,
->
+        math/randomSPRNG.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/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,
->
+        restraints/Restraints.cpp, restraints/Restraints.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.cpp, 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/GenericData.hpp,
->
+        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
->
+        utils/MemoryUtils.hpp, utils/NumericConstant.hpp,
->
+        utils/OOPSEConstant.hpp, utils/PropertyMap.cpp,
->
+        utils/PropertyMap.hpp, utils/StringTokenizer.cpp,
->
+        utils/StringTokenizer.hpp, utils/StringUtils.cpp,
->
+        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
->
+        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
->
+        utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90,
->
+        utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90,
->
+        utils/simError.c, utils/simError.h, utils/status.F90,
->
+        utils/vector_class.F90, visitors/AtomData.hpp,
->
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp,
->
+        visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
->
+        visitors/ZconsVisitor.hpp: change license
->
->
+-01-12 12:14  tim
->
->
+        * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
->
+        branch new_design.
->
->
+-01-11 16:03  tim
->
->
+        * src/: constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        minimizers/MinimizerParameterSet.cpp,
->
+        minimizers/MinimizerParameterSet.hpp: change const static double
->
+        data member to const double
->
->
+-01-11 15:50  tim
->
->
+        * src/io/basic_ifstrstream.hpp: forget namespace qualifier std::
->
->
+-01-11 15:39  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
->
+        change data type from logical to integer in AtomTypeProperties.h
->
->
+-01-11 11:36  tim
->
->
+        * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
->
+        new format of EAM force field
->
->
+-01-11 11:24  tim
->
->
+        * src/UseTheForce/DUFF.cpp: change default name of DUFF force field
->
+        to DUFF2.frc
->
->
+-01-11 11:23  tim
->
->
+        * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
->
+        DUFF2.frc
->
->
+-01-11 11:09  tim
->
->
+        * make/Makefile.in: adding constraints and minimizers into
->
+        Makefile.in
->
->
+-01-11 11:03  tim
->
->
+        * src/io/: ChargeAtomTypesSectionParser.cpp,
->
+        ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
->
+        DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
->
+        files
->
->
+-01-11 10:59  tim
->
->
+        * src/io/ZConsWriter.cpp: [no log message]
->
->
+-01-11 10:53  tim
->
->
+        * src/UseTheForce/EAM.cpp: minor fix
->
->
+-01-11 10:52  tim
->
->
+        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
->
+        on branch new_design.
->
->
+-01-11 10:52  tim
->
->
+        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
->
+        on branch new_design.
->
->
+-01-11 10:52  tim
->
->
+        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
->
->
+-01-11 10:47  tim
->
->
+        * make/Makefile.in: forget a '$' sign
->
->
+-01-11 10:46  tim
->
->
+        * make/Makefile.in: missing tab in rules
->
->
+-01-10 17:04  tim
->
->
+        * src/: UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldCreator.hpp,
->
+        UseTheForce/ForceFieldFactory.cpp,
->
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile,
->
+        brains/Register.cpp, brains/Register.hpp,
->
+        integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorCreator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp,
->
+        minimizers/Makefile, minimizers/MinimizerCreator.cpp,
->
+        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
->
+        minimizers/MinimizerFactory.hpp: create a register module to
->
+        register force fields, integrators and minimizers
->
->
+-01-10 17:04  tim
->
->
+        * src/brains/Register.cpp: file Register.cpp was initially added on
->
+        branch new_design.
->
->
+-01-10 17:04  tim
->
->
+        * src/brains/Register.hpp: file Register.hpp was initially added on
->
+        branch new_design.
->
->
+-01-10 15:52  tim
->
->
+        * src/: UseTheForce/ForceFieldFactory.cpp,
->
+        applications/oopse/oopse.cpp, brains/ForceManager.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp,
->
+        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
->
+        method is working now
->
->
+-01-10 13:05  tim
->
->
+        * src/: constraints/ConstraintElem.hpp,
->
+        constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp,
->
+        io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp,
->
+        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
->
+        zconstraint
->
->
+-01-10 13:05  tim
->
->
+        * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
->
+        initially added on branch new_design.
->
->
+-01-07 16:50  tim
->
->
+        * src/constraints/ZconstraintForceManager.cpp: file
->
+        ZconstraintForceManager.cpp was initially added on branch
->
+        new_design.
->
->
+-01-07 16:50  tim
->
->
+        * src/constraints/ZconstraintForceManager.hpp: file
->
+        ZconstraintForceManager.hpp was initially added on branch
->
+        new_design.
->
->
+-01-07 16:50  tim
->
->
+        * src/: applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp,
->
+        constraints/ConstraintElem.hpp, constraints/Makefile,
->
+        constraints/ZConstraint.cpp, constraints/ZconsData.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
->
+        utils/NumericConstant.hpp: ZConstraintForceManager in progress
->
->
+-01-07 16:50  tim
->
->
+        * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
->
+        initially added on branch new_design.
->
->
+-01-06 17:31  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        constraints/ConstraintPair.hpp, integrators/Integrator.cpp,
->
+        integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp,
->
+        io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
->
+        constraint is almost working
->
->
+-01-05 19:36  tim
->
->
+        * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
->
+        working
->
->
+-01-05 19:16  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp,
->
+        minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
->
+        in progress
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
->
+        was initially added on branch new_design.
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
->
+        added on branch new_design.
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
->
+        Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
->
+        MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
->
+        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
->
+        SDMinimizer.hpp: minimizer in progress
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
->
+        was initially added on branch new_design.
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-01-05 12:35  tim
->
->
+        * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
->
+        added on branch new_design.
->
->
+-01-04 17:18  tim
->
->
+        * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
->
+        brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
->
+        brains/Thermo.cpp, constraints/ConstraintPair.hpp,
->
+        constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp,
->
+        integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp,
->
+        primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
->
+        progress
->
->
+-01-04 17:18  tim
->
->
+        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
->
+        initially added on branch new_design.
->
->
+-01-04 17:18  tim
->
->
+        * src/minimizers/MinimizerParameterSet.cpp: file
->
+        MinimizerParameterSet.cpp was initially added on branch new_design.
->
->
+-01-04 17:18  tim
->
->
+        * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
->
+        initially added on branch new_design.
->
->
+-01-04 17:18  tim
->
->
+        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
->
+        was initially added on branch new_design.
->
->
+-01-04 17:18  tim
->
->
+        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
->
+        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
->
+        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
->
+        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
->
->
+-01-04 17:18  tim
->
->
+        * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
->
+        branch new_design.
->
->
+-12-20 15:50  chuckv
->
->
+        * make/Makefile.in: Fixed Makefile test bug under OSX and possibly
->
+        other BSD's, replaced test -f *.mod with ls function since BSD test
->
+        apparently doesn't support wildcards.
->
->
+-12-20 15:36  tim
->
->
+        * make/Makefile.in: fix a test command incompatiable problem
->
->
+-12-20 14:49  tim
->
->
+        * src/integrators/NPTi.cpp: NPT is working now
->
->
+-12-16 14:20  tim
->
->
+        * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
->
+        invalid stamp id
->
->
+-12-16 14:00  tim
->
->
+        * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
->
+        newEAM.u6.frc: adding new EAM force field files
->
->
+-12-16 13:55  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
->
+        in  EAM parameter file is incorrect
->
->
+-12-16 12:27  tim
->
->
+        * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
->
+        brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
->
+        utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM
->
->
+-12-15 17:34  tim
->
->
+        * src/: applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream
->
->
+-12-15 16:07  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
->
+        add EAM Force Field
->
->
+-12-15 14:40  tim
->
->
+        * src/applications/oopse/oopse.cpp: add more force fields
->
->
+-12-15 11:44  tim
->
->
+        * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
->
+        to call All_reduce in MPI version)
->
->
+-12-15 11:13  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
->
+        io/DumpReader.cpp: MPI in NVE is working
->
->
+-12-14 16:57  tim
->
->
+        * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
->
+        Master nodes does not brocast the total number of frames
->
->
+-12-14 14:08  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
->
+        integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
->
+        minimizers/CGFamilyMinimizer.cpp,
->
+        minimizers/MinimizerParameterSet.hpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
->
+        minimizers/SDMinimizer.cpp: more fix in MPI version
->
->
+-12-13 17:30  tim
->
->
+        * src/: UseTheForce/DarkSide/simParallel.F90,
->
+        applications/oopse/oopse.cpp, brains/SimCreator.cpp,
->
+        brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp,
->
+        integrators/DLM.cpp, integrators/Integrator.cpp,
->
+        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp,
->
+        io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp,
->
+        io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp,
->
+        math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp,
->
+        primitives/RigidBody.cpp, primitives/StuntDouble.cpp,
->
+        primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp,
->
+        utils/LocalIndexManager.hpp, utils/PropertyMap.cpp,
->
+        utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
->
+        is built
->
->
+-12-10 13:41  tim
->
->
+        * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp
->
->
+-12-10 11:14  tim
->
->
+        * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
->
+        primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
->
+        and Dipole is working now
->
->
+-12-09 18:15  tim
->
->
+        * src/: UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
->
+        fix an index problem in eFrame matrix
->
->
+-12-09 18:09  tim
->
->
+        * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
->
+        initializing the new Charge AtomType
->
->
+-12-09 16:15  tim
->
->
+        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
->
+        types/DirectionalAtomType.cpp: sticky module get compiled
->
->
+-12-09 15:43  gezelter
->
->
+        * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
->
+        reactionField.F90: u_l -> eFrame  for electrostatics u_l -> A for
->
+        GB
->
->
+-12-09 15:42  gezelter
->
->
+        * src/UseTheForce/doForces.F90: u_l -> eFrame
->
->
+-12-09 15:27  gezelter
->
->
+        * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
->
+        module now has the option for multiple sticky types
->
->
+-12-09 15:27  gezelter
->
->
+        * src/UseTheForce/doForces.F90: sticky
->
->
+-12-09 11:22  tim
->
->
+        * src/integrators/: NPT.cpp, NVT.cpp: fix an interface
->
+        inconsistency in lab2Bidy
->
->
+-12-09 10:45  tim
->
->
+        * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
->
+        in calculating torque in rigid body
->
->
+-12-08 15:37  tim
->
->
+        * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
->
+        brains/SnapShot.cpp, brains/Snapshot.hpp,
->
+        integrators/Integrator.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
->
+        fix a parsing bug in ElectroStaticAtomTypesSectionParser
->
->
+-12-08 12:03  tim
->
->
+        * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
->
+        in  NVT is working
->
->
+-12-07 18:08  tim
->
->
+        * src/: UseTheForce/Makefile, brains/SimInfo.hpp,
->
+        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
->
+        io/DumpWriter.cpp: NPT in progress
->
->
+-12-07 09:43  tim
->
->
+        * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
->
+        message]
->
->
+-12-07 00:12  tim
->
->
+        * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
->
+        UseInitXSstate
->
->
+-12-07 00:00  tim
->
->
+        * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message
->
->
+-12-06 23:47  tim
->
->
+        * src/types/DirectionalAtomType.cpp: [no log message]
->
->
+-12-06 21:18  tim
->
->
+        * forceFields/newDUFF.frc: merge WATER force field into DUFF
->
->
+-12-06 20:33  tim
->
->
+        * forceFields/newDUFF.frc: change the force constant of bonds
->
->
+-12-06 18:29  tim
->
->
+        * src/: UseTheForce/DarkSide/charge.F90,
->
+        UseTheForce/DarkSide/charge_interface.h,
->
+        UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
->
+        fix atom type ident in Charge and Dipole Module
->
->
+-12-06 17:56  tim
->
->
+        * src/primitives/Torsion.cpp: butane is working now
->
->
+-12-06 15:15  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
->
+        primitives/Bond.hpp, primitives/Torsion.cpp: short range
->
+        interaction for butane is correct.Still something wrong with long
->
+        range one
->
->
+-12-05 23:49  tim
->
->
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
->
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        io/BendTypesSectionParser.cpp, math/Polynomial.hpp,
->
+        primitives/Atom.hpp, utils/NumericConstant.hpp,
->
+        utils/TypeContainer.hpp: fix a bug in Exclude List
->
->
+-12-05 17:21  tim
->
->
+        * forceFields/newDUFF.frc: minor fix in DUFF
->
->
+-12-05 17:02  tim
->
->
+        * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
->
+        utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
->
+        fix a bug in filling MolMembership
->
->
+-12-05 12:12  tim
->
->
+        * forceFields/newDUFF.frc: minor fix in force field file
->
->
+-12-05 12:09  tim
->
->
+        * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp
->
->
+-12-04 15:09  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
->
+        math/Vector3.hpp: NVE is working now, get the same result as
->
+        OOPSE-1.0
->
->
+-12-04 14:29  tim
->
->
+        * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy
->
->
+-12-04 14:24  gezelter
->
->
+        * src/primitives/: Bend.cpp, Torsion.cpp: What?
->
->
+-12-04 14:24  gezelter
->
->
+        * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion
->
->
+-12-04 00:24  tim
->
->
+        * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
->
+        integrators/Integrator.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp,
->
+        utils/TypeContainer.hpp: NVE conserved energy, however, potential
->
+        is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf
->
+        and NPTxyz to test integrator Step 2 SSD in NVE to test DLM,
->
+        dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
->
+EAM Step 5 Shape Step 6 Constraint & Restraint
->
->
+-12-03 19:01  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
->
+        io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
->
+        energy of NVE is not conserved
->
->
+-12-03 17:36  tim
->
->
+        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
->
+        primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running
->
->
+-12-03 16:30  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
->
+        integrators/NVE.cpp, primitives/Molecule.cpp,
->
+        primitives/Molecule.hpp, primitives/StuntDouble.hpp,
->
+        primitives/Torsion.hpp: more missing function get implemented
->
->
+-12-03 15:30  tim
->
->
+        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
->
+        SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo
->
->
+-12-03 12:59  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp,
->
+        io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
->
+        io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
->
+        utils/TypeContainer.hpp: begin to fix bugs
->
->
+-12-02 19:26  tim
->
->
+        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
->
+        new_design.
->
->
+-12-02 19:26  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
->
+        integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp,
->
+        io/SectionParserManager.hpp, utils/Makefile,
->
+        utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
->
+        bug in countTokens in StringTokenizer
->
->
+-12-02 19:06  tim
->
->
+        * forceFields/newDUFF.frc: minor fix
->
->
+-12-02 18:15  tim
->
->
+        * forceFields/newDUFF.frc: new ForceField format
->
->
+-12-02 17:15  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldCreator.hpp,
->
+        UseTheForce/ForceFieldFactory.cpp,
->
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
->
+        applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorCreator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        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,
->
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
->
+        types/Makefile: refine factory pattern to make it initialized
->
+        correctly
->
->
+-12-02 17:15  tim
->
->
+        * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-12-02 17:15  tim
->
->
+        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-12-02 17:15  tim
->
->
+        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-12-02 17:15  tim
->
->
+        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-12-02 11:53  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
->
+        types/DirectionalAtomType.cpp, types/Makefile: oopse get built
->
->
+-12-02 11:04  tim
->
->
+        * src/: applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapshotManager.hpp, brains/Stats.cpp,
->
+        constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp,
->
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp,
->
+        io/basic_ifstrstream.hpp, primitives/Bend.hpp,
->
+        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
->
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
->
+        types/OplsTorsionType.hpp, types/ShapeAtomType.hpp,
->
+        utils/PropertyMap.hpp, utils/TypeContainer.hpp,
->
+        visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
->
+        have two linking problem
->
->
+-12-02 00:17  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp,
->
+        restraints/Restraints.cpp, visitors/AtomVisitor.cpp,
->
+        visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/ZconsVisitor.cpp: change endl to std::endl
->
->
+-12-02 00:14  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
->
+        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
->
+        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
->
+        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp: minor fix
->
->
+-12-02 00:09  tim
->
->
+        * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
->
+        remove StreamTokenizer
->
->
+-12-02 00:06  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp,
->
+        io/ZConsWriter.cpp, math/randomSPRNG.cpp,
->
+        restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
->
+        namespace std in .cpp file
->
->
+-12-02 00:04  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp,
->
+        brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, io/ZConsWriter.hpp,
->
+        minimizers/MinimizerParameterSet.hpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
->
+        minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp,
->
+        restraints/Restraints.cpp, restraints/Restraints.hpp,
->
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
->
+        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
->
+        utils/GenericData.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
->
+        qulified name prefix std
->
->
+-12-01 23:55  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
->
+        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
->
+        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
->
+        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp: replace string by std::string
->
->
+-12-01 22:12  tim
->
->
+        * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
->
+        src/applications/simpleBuilder/BaseLattice.hpp,
->
+        src/applications/simpleBuilder/Lattice.hpp,
->
+        src/applications/simpleBuilder/LatticeCreator.hpp,
->
+        src/applications/simpleBuilder/LatticeFactory.hpp,
->
+        src/applications/simpleBuilder/MoLocator.hpp,
->
+        src/brains/SimInfo.cpp, src/brains/SkipList.hpp,
->
+        src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp,
->
+        src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp,
->
+        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp,
->
+        src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp,
->
+        src/utils/Makefile, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp,
->
+        src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp,
->
+        src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp,
->
+        test/brains/RigidBody.cpp: replace misuse of using namespace std in
->
+        header files
->
->
+-12-01 21:23  tim
->
->
+        * src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
->
+        primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
->
+        utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
->
+        begin to fix linking problem
->
->
+-12-01 21:08  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
->
+        brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
->
+        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
->
+        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
->
+        integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp,
->
+        math/SquareMatrix3.hpp, primitives/Atom.hpp,
->
+        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
->
+        utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
->
+        still has some linking problem
->
->
+-12-01 19:26  tim
->
->
+        * src/: integrators/NVT.cpp, integrators/NVT.hpp,
->
+        utils/OOPSEConstant.hpp: NVT get built
->
->
+-12-01 19:09  tim
->
->
+        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
->
+        branch new_design.
->
->
+-12-01 19:09  tim
->
->
+        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
->
+        branch new_design.
->
->
+-12-01 19:09  tim
->
->
+        * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
->
+        brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
->
+        brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
->
+        integrators/Integrator.hpp, integrators/Makefile,
->
+        integrators/NVE.cpp, integrators/NVE.hpp,
->
+        integrators/RotationAlgorithm.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
->
+        get built
->
->
+-12-01 19:09  tim
->
->
+        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
->
+        was initially added on branch new_design.
->
->
+-12-01 17:45  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp,
->
+        io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
->
+        io/StatWriter.hpp: rename DumpWrite to DumpWriter
->
->
+-12-01 17:45  tim
->
->
+        * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
->
+        branch new_design.
->
->
+-12-01 15:05  tim
->
->
+        * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
->
+        io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
->
+        utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp,
->
+        visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
->
+        visitors/ZconsVisitor.hpp: visitors get built
->
->
+-12-01 14:32  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: fixed a sample
->
->
+-12-01 14:10  tim
->
->
+        * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/types/AtomType.hpp, src/utils/Utility.hpp,
->
+        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
->
+        src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
->
+        spell check
->
->
+-12-01 13:42  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
->
+        and constraint, other directories get built
->
->
+-12-01 12:38  tim
->
->
+        * src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
->
+        brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
->
+        primitives/GhostBend.cpp, primitives/RigidBody.cpp,
->
+        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
->
+        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
->
+        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
->
+        refactory AtomType
->
->
+-11-30 22:11  tim
->
->
+        * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change
->
->
+-11-30 21:30  tim
->
->
+        * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
->
+        NumericConstant
->
->
+-11-30 21:24  tim
->
->
+        * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
->
+        primitives/RigidBody.cpp: minor fix
->
->
+-11-30 18:14  tim
->
->
+        * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
->
+        io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
->
+        io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
->
+        get built, next is integrator
->
->
+-11-30 17:43  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        io/BASS_interface.cpp, primitives/StuntDouble.hpp,
->
+        utils/StringUtils.hpp: brains get built
->
->
+-11-30 15:50  tim
->
->
+        * src/: brains/ForceManager.cpp, brains/Makefile,
->
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
->
+        utils/StringUtils.hpp: brains get built, io is next
->
->
+-11-30 14:58  tim
->
->
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
->
+        brains/ForceManager.cpp, brains/ForceManager.hpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp,
->
+        brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
->
+        math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
->
->
+-11-30 14:58  tim
->
->
+        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
->
+        added on branch new_design.
->
->
+-11-30 12:54  tim
->
->
+        * src/: primitives/Bend.hpp, primitives/Bond.hpp,
->
+        primitives/StuntDouble.hpp, primitives/Torsion.hpp,
->
+        utils/LocalIndexManager.hpp: more get fixed
->
->
+-11-30 00:03  tim
->
->
+        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
->
+        initially added on branch new_design.
->
->
+-11-30 00:03  tim
->
->
+        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
->
+        LocalndexManager.hpp to LocalIndexManager.hpp
->
->
+-11-29 23:43  tim
->
->
+        * src/: io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp,
->
+        io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
->
+        types/PolynomialTorsionType.hpp: Section Parsers get compiled
->
->
+-11-29 23:14  tim
->
->
+        * src/: io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
->
+        fixed
->
->
+-11-29 22:49  tim
->
->
+        * src/: io/TorsionTypesSectionParser.cpp,
->
+        io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
->
+        types/CubicTorsionType.hpp, types/PolynomialBendType.hpp,
->
+        types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
->
+        types/QuarticTorsionType.hpp: minor fixed
->
->
+-11-29 22:32  tim
->
->
+        * src/: io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
->
+        types/PolynomialTorsionType.hpp: #inlcude statement can not be
->
+        embedded
->
->
+-11-29 16:42  tim
->
->
+        * test/math/: Makefile, PolynomialTestCase.cpp,
->
+        PolynomialTestCase.hpp: add PolynomialTestCase
->
->
+-11-29 16:42  tim
->
->
+        * src/math/Polynomial.hpp: Polynomial passes unit test
->
->
+-11-29 15:03  tim
->
->
+        * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
->
+        QuarticTorsion.hpp to QuarticTorsionType.hpp
->
->
+-11-29 15:03  tim
->
->
+        * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 14:56  tim
->
->
+        * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 14:56  tim
->
->
+        * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
->
+        CubicTorsionType and QuarticTorsionType
->
->
+-11-29 14:56  tim
->
->
+        * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 13:00  tim
->
->
+        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
->
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
->
+        types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
->
+        fixed
->
->
+-11-29 12:59  tim
->
->
+        * src/utils/Trim.hpp: file Trim.hpp was initially added on branch
->
+        new_design.
->
->
+-11-29 12:59  tim
->
->
+        * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
->
+        Algorithm for std::string
->
->
+-11-29 10:52  tim
->
->
+        * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
->
+        some useless files
->
->
+-11-29 10:50  tim
->
->
+        * src/io/: BondTypesSectionParser.cpp,
->
+        ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
->
+        ElectrostaticAtomTypesSectionParser.cpp,
->
+        HarmonicBondTypesSectionParser.cpp,
->
+        HarmonicBondTypesSectionParser.hpp,
->
+        LennardJonesAtomTypesSectionParser.cpp, Makefile,
->
+        SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
->
+        StickyAtomTypesSectionParser.hpp: more files get fixed
->
->
+-11-29 10:27  tim
->
->
+        * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
->
+        DirectionalAtomTypesSectionParser.cpp,
->
+        EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp,
->
+        Makefile, SectionParser.cpp, SectionParser.hpp,
->
+        SectionParserManager.cpp, SectionParserManager.hpp: part of io get
->
+        built
->
->
+-11-29 09:49  tim
->
->
+        * src/types/UreyBradleyBendType.hpp: types get built
->
->
+-11-29 09:40  tim
->
->
+        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
->
+        types  get built
->
->
+-11-25 21:13  tim
->
->
+        * src/: UseTheForce/ForceField.hpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
->
+        types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
->
+        files
->
->
+-11-25 15:18  tim
->
->
+        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-25 15:18  tim
->
->
+        * src/: io/AtomTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp,
->
+        types/QuadraticBendType.hpp, types/QuadraticBondType.hpp,
->
+        types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
->
+        files
-<
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
-<
+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
-<
+        class
->
+-11-25 15:18  tim
->
->
+        * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-24 17:12  tim
->
->
+        * src/: io/AtomTypesSectionParser.cpp,
->
+        io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
->
+        io/ChargeAtomTypesSectionParser.hpp,
->
+        io/DipoleAtomTypesSectionParser.cpp,
->
+        io/DipoleAtomTypesSectionParser.hpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
->
+        io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp,
->
+        io/EAMAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp,
->
+        io/HarmonicBondTypesSectionParser.hpp,
->
+        io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile,
->
+        io/SectionParser.hpp, io/SectionParserManager.hpp,
->
+        io/StickyAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.hpp,
->
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
->
+        utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built
->
->
+-11-24 16:33  tim
->
->
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
->
+        ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
->
+        LJFF.cpp, Makefile: UseTheForce get built
->
->
+-11-24 15:55  tim
->
->
+        * src/: math/RectMatrix.hpp, primitives/Bend.cpp,
->
+        primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
->
+        primitives/Makefile, primitives/Molecule.cpp,
->
+        primitives/Molecule.hpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp, primitives/Torsion.cpp,
->
+        primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
->
+        primitives/UreyBradleyBend.hpp: types and primitives get built
->
->
+-11-24 14:49  tim
->
->
+        * test/utils/: Makefile, NextCombinationTestCase.cpp,
->
+        StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
->
+        StringTokenizerTestCase
->
->
+-11-24 14:49  tim
->
->
+        * src/utils/: GenericData.hpp, StringTokenizer.cpp,
->
+        StringTokenizer.hpp: StringTokenizer passes unit test
->
->
+-11-24 13:20  tim
->
->
+        * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
->
+        src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
->
+        change Makefile
->
->
+-11-24 13:06  chrisfen
->
->
+        * src/io/RestraintReader.cpp: improved restraints - mpi should work
->
+        fine
->
->
+-11-24 13:06  chrisfen
->
->
+        * src/integrators/Integrator.cpp: improved restraints
->
->
+-11-24 13:05  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: oops...
->
->
+-11-24 12:42  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
->
+        brains/DataStorage.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, integrators/Integrator.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        primitives/DirectionalAtom.cpp: add SetForceManager method to
->
+        integrator
->
->
+-11-23 18:12  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, integrators/Integrator.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/Velocitizer.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp,
->
+        types/UreyBradleyBendType.hpp: refactory NPT integrator
->
->
+-11-23 17:50  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
->
+        Restraints should work in parallel now
->
->
+-11-23 17:48  chrisfen
->
->
+        * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
->
+        brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
->
+        integrators/Integrator.cpp, integrators/Integrator.hpp,
->
+        io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp,
->
+        io/RestraintReader.cpp, io/RestraintWriter.cpp,
->
+        restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
->
+        to restraints
->
->
+-11-23 17:47  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
->
+        return to the original on next commit
->
->
+-11-23 12:53  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        io/ChargeAtomTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp,
->
+        io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp,
->
+        io/SectionParser.hpp, types/DirectionalAtomType.cpp,
->
+        utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
->
->
+-11-23 12:53  tim
->
->
+        * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
->
+        ElectrostaticAtomTypesSectionParser.hpp was initially added on
->
+        branch new_design.
->
->
+-11-23 12:53  tim
->
->
+        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
->
+        ElectrostaticAtomTypesSectionParser.cpp was initially added on
->
+        branch new_design.
->
->
+-11-23 01:03  tim
->
->
+        * src/: io/EAMAtomTypesSectionParser.cpp,
->
+        io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
->
+        types/AtomType.hpp, types/DirectionalAtomType.cpp,
->
+        types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
->
->
+-11-23 01:03  tim
->
->
+        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
->
+        was initially added on branch new_design.
->
->
+-11-23 01:03  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.hpp: file
->
+        EAMAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-23 01:03  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.cpp: file
->
+        EAMAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/TorsionTypesSectionParser.hpp: file
->
+        TorsionTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/BendTypesSectionParser.hpp: file
->
+        BendTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/BondTypesSectionParser.hpp: file
->
+        BondTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/BondTypesSectionParser.cpp: file
->
+        BondTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/TorsionTypesSectionParser.cpp: file
->
+        TorsionTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:35  tim
->
->
+        * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
->
+        BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
->
+        TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add
->
+        BondTypesSectionParser, BendTypesSectionParser and
->
+        TorsionTypeSectionParser
->
->
+-11-22 23:35  tim
->
->
+        * src/io/BendTypesSectionParser.cpp: file
->
+        BendTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 18:04  tim
->
->
+        * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
->
+        DUFF and EAM
->
->
+-11-22 18:02  tim
->
->
+        * src/io/: DirectionalAtomTypesParser.hpp,
->
+        DirectionalAtomTypesSectionParser.hpp: adding section parsers
->
->
+-11-22 18:02  tim
->
->
+        * src/io/DirectionalAtomTypesSectionParser.hpp: file
->
+        DirectionalAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 15:55  tim
->
->
+        * src/io/DipoleAtomTypesSectionParser.hpp: file
->
+        DipoleAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 15:55  tim
->
->
+        * src/io/AtomTypesSectionParser.hpp: file
->
+        AtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 15:55  tim
->
->
+        * src/io/HarmonicBondTypesSectionParser.hpp: file
->
+        HarmonicBondTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 15:55  tim
->
->
+        * src/io/StickyAtomTypesSectionParser.cpp: file
->
+        StickyAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 15:55  tim
-+
+        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
-+
+        LennardJonesAtomTypesSectionParser.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/HarmonicBondTypesSectionParser.cpp: file
-+
+        HarmonicBondTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DirectionalAtomTypesSectionParser.cpp: file
-+
+        DirectionalAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/AtomTypesSectionParser.cpp: file
-+
+        AtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/ChargeAtomTypesSectionParser.cpp: file
-+
+        ChargeAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DipoleAtomTypesSectionParser.cpp: file
-+
+        DipoleAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
-+
+        LennardJonesAtomTypesSectionParser.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/ChargeAtomTypesSectionParser.hpp: file
-+
+        ChargeAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/StickyAtomTypesSectionParser.hpp: file
-+
+        StickyAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
-+
+        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
-+
+        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
-+
+        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
-+
+        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
-+
+        io/ChargeAtomTypesSectionParser.hpp,
-+
+        io/DipoleAtomTypesSectionParser.cpp,
-+
+        io/DipoleAtomTypesSectionParser.hpp,
-+
+        io/DirectionalAtomTypesParser.hpp,
-+
+        io/DirectionalAtomTypesSectionParser.cpp,
-+
+        io/HarmonicBondTypesSectionParser.cpp,
-+
+        io/HarmonicBondTypesSectionParser.hpp,
-+
+        io/LennardJonesAtomTypesSectionParser.cpp,
-+
+        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
-+
+        io/SectionParser.hpp, io/SectionParserManager.cpp,
-+
+        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
-+
+        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
-+
+        types/AtomType.hpp, types/DirectionalAtomType.hpp,
-+
+        utils/GenericData.hpp: adding section parsers
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DirectionalAtomTypesParser.hpp: file
-+
+        DirectionalAtomTypesParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-19 17:12  tim
-+
-+
+        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-19 17:12  tim
-+
-+
+        * src/: brains/SimState.cpp, brains/SimState.hpp,
-+
+        io/InitializeFromFile.cpp, types/FixBondType.hpp,
-+
+        types/FixedBondType.hpp: remove more useless files
-+
-+
+-11-19 16:47  tim
-+
-+
+        * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
-+
+        integrators/Integrator.cpp, applications/Makedepend: remove more
-+
+        useless files
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
-+
+        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
-+
+        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
-+
+        integrators/NVT.hpp: refactory integrator
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 15:37  tim
-+
-+
+        * forceFields/newDUFF.frc: new DUFF forcefield
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
-+
+        UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
-+
+        utils/TypeContainer.hpp: add EAM
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 13:02  tim
-+
-+
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
-+
+        error checking
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/types/FixBondType.hpp: file FixBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
-+
+        UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
-+
+        UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp,
-+
+        integrators/IntegratorFactory.cpp,
-+
+        integrators/IntegratorFactory.hpp, integrators/NVE.hpp,
-+
+        integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp,
-+
+        utils/StringTokenizer.cpp: DUFF is almost done except error
-+
+        checking
-+
-+
+-11-18 19:11  tim
-+
-+
+        * src/UseTheForce/DUFF.cpp: adding DUFF parser
-+
-+
+-11-18 18:26  tim
-+
-+
+        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 18:26  tim
-+
-+
+        * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
-+
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
-+
+        integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp,
-+
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
-+
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
-+
+        types/HarmonicBondType.hpp, types/QuadraticBendType.hpp,
-+
+        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
-+
+        DUFF parser
-+
-+
+-11-18 16:42  tim
-+
-+
+        * forceFields/newDUFF.frc: adding new format DUFF force field
-+
-+
+-11-18 10:57  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
-+
+        slowed down the force loop
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
-+
+        primitives/Bend.cpp, utils/NumericConstant.cpp,
-+
+        utils/NumericConstant.hpp: Adding NumericConstant class
-+
-+
+-11-17 23:16  tim
-+
-+
+        * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
-+
+        UseTheForce/ForceFields.hpp: remove more junk files
-+
-+
+-11-17 23:12  tim
-+
-+
+        * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
-+
+        brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
-+
+        integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp,
-+
+        primitives/AbstractClasses.hpp, primitives/Bond.cpp,
-+
+        primitives/BondExtensions.cpp, primitives/SRI.hpp,
-+
+        primitives/TorsionExtensions.cpp: remove some junk files
-+
-+
+-11-17 23:07  tim
-+
-+
+        * src/primitives/BendExtensions.cpp: remove some junk files
-+
-+
+-11-17 23:04  tim
-+
-+
+        * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
-+
+        QuadraticBondType.hpp: refine QudraticBond
-+
-+
+-11-17 22:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
-+
-+
+-11-17 22:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/: math/ChebyshevPolynomials.cpp,
-+
+        math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
-+
+        primitives/Bend.hpp, primitives/GhostBend.cpp,
-+
+        primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp,
-+
+        primitives/UreyBradleyBend.hpp, types/BondType.hpp,
-+
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
-+
+        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
-+
+        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
-+
+        UreyBradleyBend and GhostBend
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/: math/ChebyshevPolynomials.cpp,
-+
+        math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
-+
+        primitives/Bond.hpp, types/CharmmTorsionType.hpp,
-+
+        types/OplsTorsionType.hpp, types/PolynomialBondType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
-+
+        stuff and Chebyshev Polynomial
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/PolynomialTorsionType.hpp: file
-+
+        PolynomialTorsionType.hpp was initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/: math/Polynomial.hpp, primitives/Bend.cpp,
-+
+        primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
-+
+        types/BondType.hpp, types/CharmmTorsionType.cpp,
-+
+        types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp,
-+
+        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
-+
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/TorsionType.hpp,
-+
+        utils/StringTokenizer.hpp: add  PolynomialBondType,
-+
+        PolynomialBendType, PolynomialTorsionType, HarmonicBendType and
-+
+        CharmmTorsionType. Need to refine the design and add document for
-+
+        them
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 20:11  tim
-+
-+
+        * src/types/: BendType.hpp, PolynomialBondType.hpp,
-+
+        TorsionType.hpp: add PolynomialBondType
-+
-+
+-11-16 20:11  tim
-+
-+
+        * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 18:20  tim
-+
-+
+        * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-16 18:20  tim
-+
-+
+        * src/math/Polynomial.hpp: Adding Polynomial class
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
-+
+        MorseBondType.hpp, TorsionType.hpp: added some new stuff
-+
-+
+-11-16 15:36  tim
-+
-+
+        * src/: primitives/Bend.cpp, primitives/Bend.hpp,
-+
+        primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
-+
+        types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
-+
+        TorsionType
-+
-+
+-11-15 21:07  tim
-+
-+
+        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 21:07  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
-+
+        utils/StringTokenizer.cpp: adding DUFF class; adding checking
-+
+        statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
-+
+        UseTheForce/ForceFieldFactory.cpp,
-+
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
-+
+        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
-+
+        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
-+
+        integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
-+
+        io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
-+
+        DumpWriter.Next Step is LJFF and integrators
-+
-+
+-11-13 00:08  tim
-+
-+
+        * src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, primitives/Molecule.cpp,
-+
+        primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
-+
+        refactory, refactory
-+
-+
+-11-12 17:43  tim
-+
-+
+        * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
-+
+        StringTokenizer.cpp: bug fix in hasMoreTokens
-+
-+
+-11-12 17:28  tim
-+
-+
+        * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-12 17:28  tim
-+
-+
+        * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
-+
+        StringUtils, a c-style strtok like class, need unit test
-+
-+
+-11-12 12:40  tim
-+
-+
+        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp: SimCreator and SimInfo are  ready for unit test
-+
-+
+-11-12 02:05  tim
-+
-+
+        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
-+
+        primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
-+
+        MoleculeCreator forget to create CutoffGroups for free atoms
-+
-+
+-11-12 01:19  tim
-+
-+
+        * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
-+
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
-+
+        io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
-+
+        OOPSE = Object-Obfuscated Parallel Simulation Engine
-+
-+
+-11-11 16:48  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: working sample
-+
-+
+-11-11 16:47  chrisfen
-+
-+
+        * src/restraints/Restraints.cpp: working towards parallel
-+
+        restraints
-+
-+
+-11-11 16:47  chrisfen
-+
-+
+        * src/integrators/Integrator.cpp: Commented out some write
-+
+        statements
-+
-+
+-11-11 16:46  chrisfen
-+
-+
+        * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
-+
+        write statements
-+
-+
+-11-11 16:46  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: Fun with ice
-+
-+
+-11-11 11:41  tim
-+
-+
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h,
-+
+        brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp,
-+
+        io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
-+
+        useless mpiSimulation
-+
-+
+-11-11 11:41  tim
-+
-+
+        * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-10 17:50  tim
-+
-+
+        * src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
-+
+        integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo
-+
-+
+-11-10 17:01  tim
-+
-+
+        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
-+
+        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
-+
+        brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
-+
+        brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
-+
+        io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp,
-+
+        visitors/AtomVisitor.cpp: another painful day (1) SimCreator,
-+
+        SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom
-+
+        File will be removed) (3) ForceField (at least LJ) and BondType,
-+
+        BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
-+
+        Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
-+
-+
+-11-10 09:52  tim
-+
-+
+        * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
-+
+        configurable StatWriter
-+
-+
+-11-10 09:52  tim
-+
-+
+        * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-09 21:58  tim
-+
-+
+        * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
-+
+        in progress
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.cpp: file
-+
+        VelocityVerletIntegrator.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
-+
+        brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
-+
+        brains/mpiSimulation.hpp, integrators/Integrator.hpp,
-+
+        integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp: adding ForceManager
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/integrators/NVE.cpp: file NVE.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-08 20:08  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.hpp: file
-+
+        VelocityVerletIntegrator.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-08 20:08  tim
-+
-+
+        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-08 20:08  tim
-+
-+
+        * src/: brains/Exclude.hpp, brains/Stats.hpp,
-+
+        integrators/Integrator.hpp, integrators/NVE.hpp,
-+
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
-+
+        utils/TypeContainer.hpp: More to break
-+
-+
+-11-06 00:21  tim
-+
-+
+        * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-06 00:21  tim
-+
-+
+        * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
-+
+        UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
-+
+        utils/TypeContainer.hpp, utils/next_combination.hpp: adding
-+
+        ForceField and TypeContainer classes
-+
-+
+-11-05 18:38  tim
-+
-+
+        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-05 18:38  tim
-+
-+
+        * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-05 18:38  tim
-+
-+
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
-+
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, primitives/Molecule.hpp,
-+
+        utils/LocalndexManager.hpp: Fix Exclude class etc.
-+
-+
+-11-05 16:45  chrisfen
-+
-+
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
-+
+        linear visitor
-+
-+
+-11-05 16:04  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/shapes.F90: current status of the
-+
+        debugging process
-+
-+
+-11-05 16:04  chrisfen
-+
-+
+        * make/Makefile.in: included visitors and minimizer
-+
-+
+-11-05 16:03  chrisfen
-+
-+
+        * ChangeLog: new changes
-+
-+
+-11-04 21:56  tim
-+
-+
+        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
-+
+        primitives/Molecule.hpp: Pain......
-+
-+
+-11-04 15:55  tim
-+
-+
+        * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
-+
+        src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
-+
+        src/brains/Stats.hpp: time to break SimSetup
-+
-+
+-11-04 15:51  gezelter
-+
-+
+        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
-+
+        classes in progress
-+
+-11-04 14:48  tim
+        * src/brains/Stats.cpp: file Stats.cpp was initially added on
+        * src/brains/Stats.hpp: file Stats.hpp was initially added on
+        branch new_design.
-+
+-11-04 14:48  tim
-+
-+
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
-+
+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
-+
+        class
-+
+-11-04 11:22  gezelter
+        * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
+-11-03 14:56  tim
-–
+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
-–
+        added on branch new_design.
-–
-–
+-11-03 14:56  tim
-–
+        * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
+        class(similar as SimSetup)
+        * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
+        added on branch new_design.
-+
+-11-03 14:56  tim
-+
-+
+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
-+
+        added on branch new_design.
-+
+-11-03 13:00  tim
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+-11-02 17:41  tim
-+
+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
-+
+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
-+
+        Need unit test
-+
-+
+-11-02 17:41  tim
-+
+        * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
+        initially added on branch new_design.
+        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
+        branch new_design.
-<
+-11-02 17:41  tim
->
+-11-02 11:59  tim
-<
+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
-<
+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
-<
+        Need unit test
->
+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
->
+        branch new_design.
+-11-02 11:59  tim
+        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
+        SimSnapshotManager.hpp: SimModel in progress
-–
+-11-02 11:59  tim
-–
-–
+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
-–
+        branch new_design.
-–
+-11-02 10:28  chrisfen
+        * src/: UseTheForce/DarkSide/shapes.F90,
+-11-02 10:27  tim
-<
+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
-<
+        added on branch new_design.
->
+        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
->
+        functions for dealing with memory issue
+-11-02 10:27  tim
-<
+        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
-<
+        functions for dealing with memory issue
->
+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
->
+        added on branch new_design.
+-11-02 10:23  tim
+-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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Comparing trunk/OOPSE-2.0/ChangeLog (file contents): Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs. Revision 2309 by chrisfen, Sun Sep 18 20:45:38 2005 UTC

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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs.
Revision 2309 by chrisfen, Sun Sep 18 20:45:38 2005 UTC