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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs.
Revision 1057 by tim, Tue Feb 17 19:23:44 2004 UTC

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+-02-10 16:33  tim
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+        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
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+        libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp:
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+        single version of energy minimization is working.
-+
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+-02-09 15:38  mmeineke
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+        * staticProps/: AllCorr.cpp, staticProps.cpp:  started a bug fix on
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+        the massive memory overusage by OOPSE
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+-02-09 09:48  chrisfen
-+
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+        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the
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+        hardwired LJ_rcut
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+-02-06 19:14  tim
-+
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+        * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log
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+        message]
-+
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+-02-06 16:37  tim
-+
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+        * ChangeLog, libBASS/Globals.cpp,
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+        libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp,
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+        libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of
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+        energy minimization for argon is working, need to add constraint
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+-02-06 14:05  tim
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+        * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add
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+        one more file into Makefile.in
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+-02-06 13:58  tim
-+
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+        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
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+        libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp,
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+        libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp,
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+        libmdtools/Integrator.hpp, libmdtools/Makefile.in,
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+        libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp,
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+        libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp,
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+        libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp,
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+        libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp,
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+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
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+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add
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+        some lines into global.cpp to make it work with energy minimization
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+-02-04 17:26  tim
-+
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+        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
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+        Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp,
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+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp,
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+        NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs   :-)
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+        Single version of conjugate gradient with golden search linesearch
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+        pass a couple of functions test. Brent's  algorithm is still broken
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+-02-03 17:54  tim
-+
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+        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
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+        Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp,
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+        NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp,
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+        SteepestDescent.hpp: NLModel0, NLModel1 pass uit test
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+-02-03 15:47  tim
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+        * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp,
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+        ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp,
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+        NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp,
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+        SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp,
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+        SteepestDescent.hpp: [no log message]
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+-02-03 15:43  tim
-+
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+        * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp,
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+        Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp,
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+        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
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+        NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory
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+        constraint class
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+-02-03 12:10  tim
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+        * libmdtools/Functor.hpp: Functor.hpp pass unit test
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+-02-03 10:21  tim
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+        * ChangeLog, libmdtools/Minimizer1D.cpp,
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+        libmdtools/Minimizer1D.hpp: begin unit test of minimizer
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+-02-02 15:29  tim
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+        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
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+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
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+        Adding GoldenSection and Brent LineSearch Method
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+-01-30 16:47  tim
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+        * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp,
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+        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
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+        NLModel0.cpp, NLModel1.cpp: using class  Minimizer1D derived from
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+        MinimizerBase instead of a functor to do line seach
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+-01-30 10:00  chrisfen
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+        * forceFields/Makefile.in, libmdtools/Atom.cpp,
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+        libmdtools/Atom.hpp, libmdtools/ForceFields.hpp,
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+        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
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+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
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+        libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90,
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+        libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90,
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+        libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now
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+        has a working WATER.cpp forcefield and parser.  This involved
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+        changes to WATER.cpp and ForceFields amoung other files. One
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+        important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90.
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+        This will be removed on the next commit...
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+-01-29 18:00  gezelter
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+        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
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+        libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y,
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+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp,
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+        libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp,
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+        libBASS/RigidBodyStamp.hpp, libBASS/interface.c,
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+        libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c,
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+        libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h,
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+        libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl:
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+        member list fixes for rigid bodies
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+-01-29 16:44  tim
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+        * libmdtools/MinimizerParameterSet.hpp: Adding
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+        MinimizerParameterSet class.
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+-01-28 17:44  tim
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+        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
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+        NLModel0 and NLModel1
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+-01-28 15:40  tim
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+        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
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+        of NLModel
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+-01-27 15:34  gezelter
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+        * samples/water/: ssd.bass, water.mdl: Added point-charge models to
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+        water.mdl file, updated ssd.bass to use new SSD name
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+-01-27 15:34  gezelter
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+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
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+        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
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+        stuff
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+-01-27 14:39  gezelter
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+        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
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+-01-27 14:39  gezelter
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+        * samples/metals/Au.bass: Longer run time to test gold in MPI
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+-01-27 14:38  gezelter
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+        * samples/argon/argon.bass: Longer run time to test argon
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+-01-27 14:38  gezelter
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+        * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS
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+        changes to do new rigidBody scheme a copy of WATER.cpp from this
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+        morning
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+-01-27 14:37  gezelter
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+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
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+        BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
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+        MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp,
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+        MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp,
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+        interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h,
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+        node_list.h, parse_interface.h, parse_tree.c: More BASS changes to
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+        do new rigidBody scheme
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+-01-27 14:15  tim
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+        * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp,
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+        Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp,
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+        MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of
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+        constraint for Nonlinear Optimization Model
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+-01-26 17:01  gezelter
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+        * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use
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+        Euler angles for orientation instead of unit vectors required
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+        changes in MoLocator
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+-01-26 16:53  gezelter
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+        * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl,
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+        beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl,
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+        water/water.mdl: Changed orientation lines from unit vectors to
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+        euler angles
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+-01-26 16:52  gezelter
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+        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
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+-01-26 16:45  gezelter
-+
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+        * libmdtools/SimSetup.cpp: Changed default orientation in BASS to
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+        use Euler angles in the following order: phi, theta, psi Removed
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+        the ability to set orientation using a unit vector
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+-01-26 16:26  gezelter
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+        * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp,
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+        RigidBodyStamp.hpp: Changed default orientation in BASS to use
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+        Euler angles in the following order: phi, theta, psi Removed the
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+        ability to set orientation using a unit vector
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+-01-26 13:52  gezelter
-+
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+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
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+        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
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+-01-22 12:34  chrisfen
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+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp,
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+        TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h:
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+        Corrected spelling in several directories, and stated WATER.cpp
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+-01-21 17:16  tim
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+        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
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+        NLOPModel.hpp: constraint class in energy minimization
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+-01-20 15:34  tim
-+
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+        * libmdtools/MinimizerBase.hpp: Adding energy minimization
-+
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+-01-20 15:32  tim
-+
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+        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
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+        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
-+
-+
+-01-19 16:17  gezelter
-+
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+        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
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+        more user-friendly
-+
-+
+-01-19 13:51  chrisfen
-+
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+        * forceFields/DUFF.frc: Updated the default water to SSD/E
-+
-+
+-01-19 13:36  tim
-+
-+
+        * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample
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+        time, status time, thermal time and reset time are not divisible by
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+        dt
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+-01-19 11:10  gezelter
-+
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+        * third-party/Makefile.in: Added a bunch of dummy targets so make
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+        won't complain
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+-01-19 11:10  gezelter
-+
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+        * samples/lipid/5x5.bass: Fixed old bass file
-+
-+
+-01-19 11:09  gezelter
-+
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+        * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies
-+
+        required a change in how the MoleculeStamps are used by divideLabor
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+        in mpiSimulation.cpp
-+
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+-01-19 11:08  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
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+        BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp,
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+        MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp,
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+        RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c,
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+        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
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+        parse_tree.c: BASS changes to add RigidBodies and LJrcut
-+
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+-01-16 16:55  tim
-+
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+        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
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+        eor file
-+
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+-01-16 16:51  mmeineke
-+
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+        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
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+        write eor files
-+
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+-01-16 10:01  mmeineke
-+
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+        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
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+        initialization of the AtomStruct
-+
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+-01-15 16:57  chuckv
-+
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+        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
-+
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+-01-15 10:51  gezelter
-+
-+
+        * ac-tools/aclocal.m4: Changes for altivec
-+
-+
+-01-15 09:22  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: Documented the Spud Toss
-+
-+
+-01-14 23:33  gezelter
-+
-+
+        * libmdtools/do_Forces.F90: changes for charge charge interactions
-+
-+
+-01-14 20:14  gezelter
-+
-+
+        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
-+
+        notifyCutoffs.F90: More work for adding charges
-+
-+
+-01-14 17:41  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        src/Makefile.in: autoconf fixes
-+
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+-01-14 11:28  mmeineke
-+
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+        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug
-+
-+
+-01-14 10:48  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        src/Makefile.in, third-party/Makefile.in: autoconf compatibility
-+
+        changes for icc8
-+
-+
+-01-13 18:01  gezelter
-+
-+
+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp,
-+
+        SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90,
-+
+        fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90:
-+
+        Changes for adding direct charge-charge interactions (with
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+        switching function)
-+
-+
+-01-13 17:34  gezelter
-+
-+
+        * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90,
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+        oopseMPI_module.F90: Some changes for new MPI organization and
-+
+        direct charge-charge interactions
-+
-+
+-01-13 17:11  tim
-+
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+        * Functor.hpp, libmdtools/Functor.hpp: [no log message]
-+
-+
+-01-13 16:22  tim
-+
-+
+        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method
-+
-+
+-01-13 15:35  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
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+        eor file whenever it is used instead of rewinding it
-+
-+
+-01-13 15:04  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
-+
+        of writeFrame
-+
-+
+-01-13 10:46  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp:
-+
+        Merge the code of writeFinal and writeDump;
-+
+         Adding sortingIndex into DumpWriter;
-+
+         Fix a bug of writing last frame twice in integrator
-+
-+
+-01-12 17:54  tim
-+
-+
+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
-+
+        a bug in copying string
-+
-+
+-01-12 15:37  tim
-+
-+
+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
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+        samples/water/ssd.bass: Dumpwriter only write out the atoms on
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+        master nodes
-+
-+
+-01-10 04:46  tim
-+
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+        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
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+        roll it back fix a bug of copying string to a pointer Still have
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+        Seg fault, it looks like a random MPI seg fault in totalview
-+
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+-01-09 21:15  tim
-+
-+
+        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
-+
-+
+-01-09 15:29  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
-+
-+
+-01-08 17:25  chuckv
-+
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+        * libmdtools/DumpWriter.cpp: A work in progress...
-+
-+
+-01-08 13:59  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: null terminate some strings just in
-+
+        case
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-+
+-01-08 13:13  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
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+        state bug.
-+
-+
+-01-08 13:05  gezelter
-+
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+        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
-+
-+
+-01-08 12:57  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
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+        exstended state bug
-+
-+
+-01-08 12:40  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
-+
-+
+-01-08 10:44  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: added support for the ignore
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+        XS state info  flag
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+-01-07 14:26  tim
-+
-+
+        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
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+        samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
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+        sending message from master node to itself in DumpWriter.cpp and
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+        InitializeFromFile.cpp
-+
-+
+-01-06 14:49  chuckv
-+
-+
+        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
-+
+        performance fixes in the dipole dipole and reaction field code
-+
-+
+-01-06 13:54  chuckv
-+
-+
+        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
-+
+        little more sane
-+
-+
+-01-05 17:49  chuckv
-+
-+
+        * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90,
-+
+        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
-+
+        calc_sticky_pair.F90, do_Forces.F90: Attempting to increase
-+
+        performance by reducing spurious function calls
-+
-+
+-01-05 17:18  chuckv
-+
-+
+        * libmdtools/do_Forces.F90: mangling forces even further
-+
-+
+-01-05 17:18  chuckv
-+
-+
+        * configure, ac-tools/configure.in: mpich mucking
-+
-+
+-01-05 17:12  chuckv
-+
-+
+        * libmdtools/do_Forces.F90: mangled do_forces...
-+
-+
+-01-05 16:00  chuckv
-+
-+
+        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
-+
+        libmdtools/do_Forces.F90: Added bitmask to do_forces property
-+
+        lookup
-+
+-12-29 14:56  chuckv
+        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
+-03-25 09:29  mmeineke
-<
+        * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
->
+        * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy,
+        src/MPIobj/dummy, src/obj/dummy: [no log message]
+-03-25 09:29  mmeineke
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
+        libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
+        libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-<
+        libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
-<
+        Tree
->
+        libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
->
+        revision
+-03-21 12:42  mmeineke
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
+        libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
+        libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-<
+        libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
-<
+        revision
->
+        libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE
->
+        Tree

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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs. Revision 1057 by tim, Tue Feb 17 19:23:44 2004 UTC

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Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs.
Revision 1057 by tim, Tue Feb 17 19:23:44 2004 UTC