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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC vs.
Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC

-+
+-05-07 16:36  gezelter
-+
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+        * libmdtools/: fSwitchingFunction.h, switch_module.F90: New module
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+        for fortran group-based switching function
-+
-+
+-05-07 16:35  gezelter
-+
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+        * libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp,
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+        Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp,
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+        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
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+        calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90,
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+        force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h,
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+        mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90,
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+        simulation_module.F90: Many changes to get group-based cutoffs to
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+        work
-+
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+-05-01 13:52  tim
-+
-+
+        * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp,
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+        libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90,
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+        libmdtools/do_Forces.F90, libmdtools/fSimulation.h,
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+        libmdtools/fortranWrapDefines.hpp,
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+        libmdtools/simulation_module.F90: C++ pass groupList to fortran
-+
-+
+-04-29 11:03  tim
-+
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+        * ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in
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+        calc_charge_charge when using molecular cutoff
-+
-+
+-04-28 21:11  tim
-+
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+        * libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an
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+        unmatched c/fortran interface
-+
-+
+-04-28 18:09  tim
-+
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+        * ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp:
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+        keep the previous position of cantilever in SMD
-+
-+
+-04-28 17:34  tim
-+
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+        * ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp,
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+        libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug
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+        in Molecule.cpp which initialize massRatio before creat the array.
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+        fix two bugs in ZconsVisitor
-+
-+
+-04-28 17:06  gezelter
-+
-+
+        * libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
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+        Adding molecular cutoffs
-+
-+
+-04-28 16:39  gezelter
-+
-+
+        * libmdtools/: calc_charge_charge.F90, do_Forces.F90,
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+        fSimulation.h, force_globals.F90, simulation_module.F90: work on
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+        molecular cutoffs
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-+
+-04-28 16:39  gezelter
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to
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+        Globals
-+
-+
+-04-27 11:26  tim
-+
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+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp,
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+        ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp,
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+        fSimulation.h, fortranWrapDefines.hpp: add center of mass of the
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+        molecule and massRation into atom class
-+
-+
+-04-26 16:16  mmeineke
-+
-+
+        * libBASS/Globals.cpp: modified the defaults for the system init
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+        time and system init state.
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-+
+-04-26 09:29  gezelter
-+
-+
+        * libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in
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+        calc_charge_charge.F90
-+
-+
+-04-23 23:31  tim
-+
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+        * ChangeLog, libmdtools/AtomVisitor.cpp,
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+        libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add
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+        reaction field correction to charge-charge interaction
-+
-+
+-04-22 16:33  tim
-+
-+
+        * libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp,
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+        Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the
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+        calculation of pressure tensor
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-+
+-04-22 09:55  tim
-+
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+        * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed
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+        another bug in InitFromFile. MPI verion of OOPSE is working again
-+
-+
+-04-21 22:29  tim
-+
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+        * libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp,
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+        InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp,
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+        SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two
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+        bugs in MPI version of InitfromFile and one unmatch MPI command in
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+        DumpWriter
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+-04-21 00:32  tim
-+
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+        * libmdtools/Functor.hpp, libmdtools/LinearCons.cpp,
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+        libmdtools/LinearCons.hpp, utils/CmdlineZsub.c,
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+        utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some
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+        useless files
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+-04-20 11:56  tim
-+
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+        * libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp,
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+        SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel  and
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+        velocitize at thermo
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+-04-20 00:39  tim
-+
-+
+        * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp,
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+        libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
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+        libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp,
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+        libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp,
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+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
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+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
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+        utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c,
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+        utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version
-+
-+
+-04-19 17:13  gezelter
-+
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+        * libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp,
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+        Thermo.cpp: Fixed a charge bug
-+
-+
+-04-19 15:54  tim
-+
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+        * libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp,
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+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
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+        libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed
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+        a bug in CompositeVisitor which cause the double counting problem
-+
-+
+-04-19 12:44  tim
-+
-+
+        * libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
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+        libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp,
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+        libmdtools/DumpReader.cpp, libmdtools/Make.dep,
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+        libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp,
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+        libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in:
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+        Dump2XYZ is almost working except atoms in rigidbody are double
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+        counted
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+-04-18 22:52  tim
-+
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+        * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp,
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+        libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
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+        libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp,
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+        libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp,
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+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
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+        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
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+        libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp,
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+        libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp,
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+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
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+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
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+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
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+        libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp,
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+        libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp,
-+
+        libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp,
-+
+        libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp,
-+
+        utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new
-+
+        implement of quickLate using visitor and composite pattern
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-+
+-04-15 17:15  tim
-+
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+        * libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting
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+        exclude list
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+-04-15 11:18  tim
-+
-+
+        * ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp,
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+        libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp,
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+        libmdtools/Integrator.cpp, libmdtools/Molecule.cpp,
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+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
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+        libmdtools/Thermo.cpp, libmdtools/WATER.cpp,
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+        libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix
-+
+        whole bunch of bugs :-)
-+
-+
+-04-14 12:20  chrisfen
-+
-+
+        * forceFields/WATER.frc: Added the WATER.frc force field
-+
-+
+-04-14 11:32  gezelter
-+
-+
+        * libmdtools/Molecule.cpp: fixed for get_potential
-+
-+
+-04-14 10:37  tim
-+
-+
+        * AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/Make.dep,
-+
+        libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp,
-+
+        libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
-+
+        libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp,
-+
+        libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp,
-+
+        libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp:
-+
+        Change DumpWriter and InitFromFile
-+
-+
+-04-13 11:26  gezelter
-+
-+
+        * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now
-+
+        molecules can keep track of their own IntegrableObjects (and
-+
+        RigidBodies).  Also a bug-fix so that SimInfo can keep track of
-+
+        RigidBodies (which was done incorrectly before).
-+
-+
+-04-13 11:25  gezelter
-+
-+
+        * libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable
-+
+        (will back out momentarily)
-+
-+
+-04-13 10:10  gezelter
-+
-+
+        * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops.
-+
+        Those were old.
-+
-+
+-04-13 10:09  gezelter
-+
-+
+        * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot
-+
+        to add IntegrableObjects
-+
-+
+-04-12 16:02  gezelter
-+
-+
+        * libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code
-+
-+
+-04-12 15:32  gezelter
-+
-+
+        * samples/: alkane/butane.bass, water/ssd.bass: Slightly longer
-+
+        test run
-+
-+
+-04-12 15:32  gezelter
-+
-+
+        * libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp,
-+
+        DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp,
-+
+        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp,
-+
+        ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp,
-+
+        Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in,
-+
+        MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp,
-+
+        NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp,
-+
+        SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp,
-+
+        SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp,
-+
+        WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics
-+
+        (Somewhat extensive)
-+
-+
+-04-12 15:31  gezelter
-+
-+
+        * libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp,
-+
+        libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp,
-+
+        utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp:
-+
+        Changes for RigidBody dynamics
-+
-+
+-03-17 09:22  tim
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp,
-+
+        libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it
-+
+        does not sound a good choice, next commit will seperate SMD and
-+
+        ZConstraint
-+
-+
+-03-16 14:22  tim
-+
-+
+        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/GenericData.hpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp,
-+
+        libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint
-+
+        now can support sequential moving. Refactorying is needed to
-+
+        support SMD in ZConstraint
-+
-+
+-03-02 15:32  tim
-+
-+
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp,
-+
+        StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to
-+
+        support large file
-+
-+
+-03-01 16:17  tim
-+
-+
+        * utils/zsub.cpp: Fix a couple of bugs in zsub
-+
-+
+-03-01 15:01  tim
-+
-+
+        * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in,
-+
+        libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp,
-+
+        libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp,
-+
+        utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in,
-+
+        utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a
-+
+        program which can be used to replace atom type for zconstraint into
-+
+        OOPSE
-+
-+
+-02-24 11:36  tim
-+
-+
+        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log
-+
+        message]
-+
-+
+-02-24 10:49  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
-+
+        Constraint.cpp, Constraint.hpp, ConstraintList.cpp,
-+
+        ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp,
-+
+        Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp,
-+
+        NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp,
-+
+        OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp,
-+
+        SymMatrix.hpp: remove the old implement of minimizer from cvs tree
-+
-+
+-02-24 10:44  tim
-+
-+
+        * libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp,
-+
+        Integrator.hpp, Makefile.in, Minimizer1D.cpp,
-+
+        MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp,
-+
+        OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp,
-+
+        SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of
-+
+        compose to implement Minimizer both versions are working
-+
-+
+-02-17 14:23  tim
-+
-+
+        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
-+
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp,
-+
+        libmdtools/MinimizerParameterSet.hpp,
-+
+        libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order
-+
+        to remove the constraint force along bond direction
-+
-+
+-02-10 16:33  tim
-+
-+
+        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
-+
+        libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp:
-+
+        single version of energy minimization is working.
-+
-+
+-02-09 15:38  mmeineke
-+
-+
+        * staticProps/: AllCorr.cpp, staticProps.cpp:  started a bug fix on
-+
+        the massive memory overusage by OOPSE
-+
-+
+-02-09 09:48  chrisfen
-+
-+
+        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the
-+
+        hardwired LJ_rcut
-+
-+
+-02-06 19:14  tim
-+
-+
+        * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log
-+
+        message]
-+
-+
+-02-06 16:37  tim
-+
-+
+        * ChangeLog, libBASS/Globals.cpp,
-+
+        libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp,
-+
+        libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of
-+
+        energy minimization for argon is working, need to add constraint
-+
-+
+-02-06 14:05  tim
-+
-+
+        * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add
-+
+        one more file into Makefile.in
-+
-+
+-02-06 13:58  tim
-+
-+
+        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp,
-+
+        libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/Makefile.in,
-+
+        libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp,
-+
+        libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp,
-+
+        libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp,
-+
+        libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add
-+
+        some lines into global.cpp to make it work with energy minimization
-+
-+
+-02-04 17:26  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
-+
+        Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp,
-+
+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp,
-+
+        NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs   :-)
-+
+        Single version of conjugate gradient with golden search linesearch
-+
+        pass a couple of functions test. Brent's  algorithm is still broken
-+
-+
+-02-03 17:54  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp,
-+
+        Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp,
-+
+        NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp,
-+
+        SteepestDescent.hpp: NLModel0, NLModel1 pass uit test
-+
-+
+-02-03 15:47  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp,
-+
+        ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp,
-+
+        NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp,
-+
+        SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp,
-+
+        SteepestDescent.hpp: [no log message]
-+
-+
+-02-03 15:43  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp,
-+
+        Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp,
-+
+        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
-+
+        NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory
-+
+        constraint class
-+
-+
+-02-03 12:10  tim
-+
-+
+        * libmdtools/Functor.hpp: Functor.hpp pass unit test
-+
-+
+-02-03 10:21  tim
-+
-+
+        * ChangeLog, libmdtools/Minimizer1D.cpp,
-+
+        libmdtools/Minimizer1D.hpp: begin unit test of minimizer
-+
-+
+-02-02 15:29  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
-+
+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
-+
+        Adding GoldenSection and Brent LineSearch Method
-+
-+
+-01-30 16:47  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp,
-+
+        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
-+
+        NLModel0.cpp, NLModel1.cpp: using class  Minimizer1D derived from
-+
+        MinimizerBase instead of a functor to do line seach
-+
-+
+-01-30 10:00  chrisfen
-+
-+
+        * forceFields/Makefile.in, libmdtools/Atom.cpp,
-+
+        libmdtools/Atom.hpp, libmdtools/ForceFields.hpp,
-+
+        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90,
-+
+        libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90,
-+
+        libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now
-+
+        has a working WATER.cpp forcefield and parser.  This involved
-+
+        changes to WATER.cpp and ForceFields amoung other files. One
-+
+        important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90.
-+
+        This will be removed on the next commit...
-+
-+
+-01-29 18:00  gezelter
-+
-+
+        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
-+
+        libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y,
-+
+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp,
-+
+        libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp,
-+
+        libBASS/RigidBodyStamp.hpp, libBASS/interface.c,
-+
+        libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c,
-+
+        libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h,
-+
+        libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl:
-+
+        member list fixes for rigid bodies
-+
-+
+-01-29 16:44  tim
-+
-+
+        * libmdtools/MinimizerParameterSet.hpp: Adding
-+
+        MinimizerParameterSet class.
-+
-+
+-01-28 17:44  tim
-+
-+
+        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
-+
+        NLModel0 and NLModel1
-+
-+
+-01-28 15:40  tim
-+
-+
+        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
-+
+        of NLModel
-+
-+
+-01-27 15:34  gezelter
-+
-+
+        * samples/water/: ssd.bass, water.mdl: Added point-charge models to
-+
+        water.mdl file, updated ssd.bass to use new SSD name
-+
-+
+-01-27 15:34  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
-+
+        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
-+
+        stuff
-+
-+
+-01-27 14:39  gezelter
-+
-+
+        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
-+
-+
+-01-27 14:39  gezelter
-+
-+
+        * samples/metals/Au.bass: Longer run time to test gold in MPI
-+
-+
+-01-27 14:38  gezelter
-+
-+
+        * samples/argon/argon.bass: Longer run time to test argon
-+
-+
+-01-27 14:38  gezelter
-+
-+
+        * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS
-+
+        changes to do new rigidBody scheme a copy of WATER.cpp from this
-+
+        morning
-+
-+
+-01-27 14:37  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
-+
+        BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
-+
+        MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp,
-+
+        MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp,
-+
+        interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h,
-+
+        node_list.h, parse_interface.h, parse_tree.c: More BASS changes to
-+
+        do new rigidBody scheme
-+
-+
+-01-27 14:15  tim
-+
-+
+        * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp,
-+
+        Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp,
-+
+        MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of
-+
+        constraint for Nonlinear Optimization Model
-+
-+
+-01-26 17:01  gezelter
-+
-+
+        * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use
-+
+        Euler angles for orientation instead of unit vectors required
-+
+        changes in MoLocator
-+
-+
+-01-26 16:53  gezelter
-+
-+
+        * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl,
-+
+        beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl,
-+
+        water/water.mdl: Changed orientation lines from unit vectors to
-+
+        euler angles
-+
-+
+-01-26 16:52  gezelter
-+
-+
+        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
-+
-+
+-01-26 16:45  gezelter
-+
-+
+        * libmdtools/SimSetup.cpp: Changed default orientation in BASS to
-+
+        use Euler angles in the following order: phi, theta, psi Removed
-+
+        the ability to set orientation using a unit vector
-+
-+
+-01-26 16:26  gezelter
-+
-+
+        * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp,
-+
+        RigidBodyStamp.hpp: Changed default orientation in BASS to use
-+
+        Euler angles in the following order: phi, theta, psi Removed the
-+
+        ability to set orientation using a unit vector
-+
-+
+-01-26 13:52  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
-+
+        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
-+
-+
+-01-22 12:34  chrisfen
-+
-+
+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp,
-+
+        TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h:
-+
+        Corrected spelling in several directories, and stated WATER.cpp
-+
-+
+-01-21 17:16  tim
-+
-+
+        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
-+
+        NLOPModel.hpp: constraint class in energy minimization
-+
-+
+-01-20 15:34  tim
-+
-+
+        * libmdtools/MinimizerBase.hpp: Adding energy minimization
-+
-+
+-01-20 15:32  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
-+
+        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
-+
-+
+-01-19 16:17  gezelter
-+
-+
+        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
-+
+        more user-friendly
-+
-+
+-01-19 13:51  chrisfen
-+
-+
+        * forceFields/DUFF.frc: Updated the default water to SSD/E
-+
-+
+-01-19 13:36  tim
-+
-+
+        * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample
-+
+        time, status time, thermal time and reset time are not divisible by
-+
+        dt
-+
-+
+-01-19 11:10  gezelter
-+
-+
+        * third-party/Makefile.in: Added a bunch of dummy targets so make
-+
+        won't complain
-+
-+
+-01-19 11:10  gezelter
-+
-+
+        * samples/lipid/5x5.bass: Fixed old bass file
-+
-+
+-01-19 11:09  gezelter
-+
-+
+        * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies
-+
+        required a change in how the MoleculeStamps are used by divideLabor
-+
+        in mpiSimulation.cpp
-+
-+
+-01-19 11:08  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
-+
+        BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp,
-+
+        MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp,
-+
+        RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c,
-+
+        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
-+
+        parse_tree.c: BASS changes to add RigidBodies and LJrcut
-+
-+
+-01-16 16:55  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
-+
+        eor file
-+
-+
+-01-16 16:51  mmeineke
-+
-+
+        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
-+
+        write eor files
-+
-+
+-01-16 10:01  mmeineke
-+
-+
+        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
-+
+        initialization of the AtomStruct
-+
-+
+-01-15 16:57  chuckv
-+
-+
+        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
-+
-+
+-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
-+
-+
+-01-14 11:28  mmeineke
-+
-+
+        * 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
-+
+        switching function)
-+
-+
+-01-13 17:34  gezelter
-+
-+
+        * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90,
-+
+        oopseMPI_module.F90: Some changes for new MPI organization and
-+
+        direct charge-charge interactions
-+
-+
+-01-13 17:11  tim
-+
-+
+        * 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
-+
+        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,
+-10-10 12:10  mmeineke
-<
+        * props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp,
-<
+        props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp,
-<
+        props/PairCorrList.hpp, props/PairCorrType.cpp,
-<
+        props/PairCorrType.hpp, props/staticProps.cpp,
-<
+        staticProps/AllCorr.cpp, staticProps/AllCorr.hpp,
-<
+        staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp,
-<
+        staticProps/GofR.cpp, staticProps/Makefile.in,
-<
+        staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp,
-<
+        staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp,
-<
+        staticProps/staticProps.cpp: removed the props directory, and moved
-<
+        everything over to staticProps
->
+        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp,
->
+        CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp,
->
+        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
->
+        staticProps.cpp: removed the props directory, and moved everything
->
+        over to staticProps
+-10-09 17:09  mmeineke
-<
+        * libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp,
-<
+        props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp,
-<
+        props/PairCorrType.cpp, props/PairCorrType.hpp,
-<
+        props/staticProps.cpp: Contiuned work on staticProps. should be in
->
+        * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in
+        a position where it will compile and run first runs.
+-10-04 13:46  chuckv
+-10-03 17:02  mmeineke
-–
+        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
-–
+        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
-–
+        staticProps.cpp: changed the formating ogf the error statements in
-–
+        simError
-–
-–
+        added a function to get the maxCutoff
-–
-–
+        near completion of the staticProps code. still needs the pair loop,
-–
+        and the loop to allocate and read each frame.
-–
-–
+-10-03 17:02  mmeineke
-–
+        * libmdtools/SimInfo.hpp: changed the formating ogf the error
+        statements in simError
+        * libBASS/simError.c: changed the formating ogf the error
+        statements in simError
-–
+-10-02 17:06  mmeineke
-–
-–
+        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
-–
+        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
-–
+        staticProps.cpp: finishing up the constructs needed to get this
-–
+        program up and running
-–
+-09-30 11:00  mmeineke
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
+        utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
+        statWriter fix bug of vector wrapping at NPTi
-–
+-09-12 15:51  mmeineke
-–
-–
+        * props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp,
-–
+        PairCorrType.hpp: added AllCorr. It eill still need some work
-–
+-09-12 11:20  gezelter
+        * libmdtools/: Make.dep, Makefile.in: Added integrators to
+-09-12 11:20  gezelter
+        * ChangeLog: Entered changes for configure into ChangeLog
-–
-–
+-09-10 16:28  mmeineke
-–
-–
+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
-–
+        work on getting gofR working.
-–
-–
+-09-09 16:50  mmeineke
-–
-–
+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
-–
+        beginings of the GofR pair correlation.
-–
-–
+        added identification of identI in matchI.
+-09-09 15:35  mmeineke
+        * ChangeLog, libmdtools/GenericData.cpp,
+        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
+        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
-–
-–
+-08-28 11:59  mmeineke
-–
-–
+        * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp:
-–
+        added the first functional parts of the PairCorrType Abstract
-–
+        classes.
+-08-27 14:23  tim
+        samples/metals/Au.bass: EAM works...... Neighbor list also
+        works.....
-–
+-08-08 13:32  mmeineke
-–
-–
+        * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp:
-–
+        moved frameCount's functionality into DumpReader. also split props
-–
+        into staticProps and dynamicProps. (currently only have
-–
+        staticProps)
-–
+-08-08 12:48  mmeineke
+        * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
+-07-29 11:32  mmeineke
+        * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
-<
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
-<
+        props/frameCount.c, props/frameCount.h, props/props.cpp,
-<
+        src/Makefile: working on the props code
->
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
->
+        working on the props code
+-07-29 11:32  mmeineke
+-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
+-03-24 20:07  gezelter
-<
+        * samples/Makefile, tests/Makefile: moving tests to samples
->
+        * samples/Makefile: moving tests to samples
+-03-24 20:06  gezelter
-<
+        * samples/alkane/Makefile, samples/alkane/alkanes.mdl,
-<
+        samples/alkane/butane.bass, samples/alkane/init_butane.eor,
-<
+        samples/argon/Makefile, samples/argon/argon.bass,
-<
+        samples/argon/init_argon.eor, samples/argon/lj.mdl,
-<
+        samples/lipid/5x5.bass, samples/lipid/Makefile,
-<
+        samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl,
-<
+        samples/lipid/water.mdl, samples/water/Makefile,
-<
+        samples/water/init_ssd.eor, samples/water/ssd.bass,
-<
+        samples/water/water.mdl, tests/alkane/Makefile,
-<
+        tests/alkane/alkanes.mdl, tests/alkane/butane.bass,
-<
+        tests/alkane/init_butane.eor, tests/argon/Makefile,
-<
+        tests/argon/argon.bass, tests/argon/init_argon.eor,
-<
+        tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile,
-<
+        tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl,
-<
+        tests/lipid/water.mdl, tests/water/Makefile,
-<
+        tests/water/init_ssd.eor, tests/water/ssd.bass,
-<
+        tests/water/water.mdl: moved tests to samples
->
+        * samples/: alkane/Makefile, alkane/alkanes.mdl,
->
+        alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
->
+        argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
->
+        lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
->
+        lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
->
+        water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
->
+        samples
+-03-24 19:51  gezelter
+-03-24 19:46  gezelter
-<
+        * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile,
-<
+        tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile:
-<
+        Added makefiles in tests directories
->
+        * ac-tools/Make.conf.in: Added makefiles in tests directories
+-03-24 16:55  gezelter
+        * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
+        do_Forces.F90: little bug fixes here and there
-–
+-03-24 11:04  mmeineke
-–
-–
+        * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon
-–
+        test simulation
-–
-–
+-03-24 11:02  mmeineke
-–
-–
+        * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl,
-–
+        lipid/water.mdl, water/init_ssd.eor, water/ssd.bass,
-–
+        water/water.mdl: [no log message]
-–
-–
+-03-24 11:02  mmeineke
-–
-–
+        * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added
-–
+        some test bass files for experimenting with
-–
+-03-24 10:26  mmeineke
+        * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
+        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
+-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: New OOPSE
-<
+        Tree
->
+        libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial
->
+        revision

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+Removed lines
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+Added lines
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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC vs. Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC

Diff Legend

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC vs.
Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC