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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

-<
+-09-10 16:28  mmeineke
->
+-06-03 21:38  gezelter
-<
+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
-<
+        work on getting gofR working.
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
->
+        libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c,
->
+        libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in,
->
+        libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for
->
+        fortran access to SimError
-<
+-09-09 16:50  mmeineke
->
+-06-03 16:51  tim
-<
+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
-<
+        beginings of the GofR pair correlation.
->
+        * libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp,
->
+        ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp,
->
+        ConstraintElement.cpp, ConstraintElement.hpp,
->
+        ConstraintIterator.hpp, ConstraintManager.cpp,
->
+        ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp,
->
+        Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new
->
+        implementation of constraint
->
->
+-06-03 16:06  tim
->
->
+        * libmdtools/DumpWriter.cpp: fixed a bug which only writes out the
->
+        first atom of a molecule
->
->
+-06-03 15:02  gezelter
->
->
+        * libmdtools/SimSetup.cpp: Fixed groupOffset bug
->
->
+-06-03 15:02  gezelter
->
->
+        * ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for
->
+        autoconf
->
->
+-06-02 13:28  gezelter
->
->
+        * samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't
->
+        have been in CVS
->
->
+-06-02 13:28  gezelter
->
->
+        * samples/: argon/Makefile, minimizer/argon/Makefile: Why is this
->
+        in CVS?
->
->
+-06-02 13:27  gezelter
->
->
+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep,
->
+        Makefile.in, WATER.cpp: formatting error messages, dependency fixes
->
->
+-06-02 13:27  gezelter
->
->
+        * libBASS/simError.h: starting fortran-usable version of simError
->
->
+-06-02 09:56  chrisfen
->
->
+        * samples/: argon/Makefile, minimizer/argon/Makefile: Probably
->
+        shouldn't be in CVS
->
->
+-06-02 09:56  chrisfen
->
->
+        * libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp,
->
+        Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes,
->
+        removed writeRaw
->
->
+-06-02 09:56  chrisfen
->
->
+        * libBASS/simError.c: Formatting Changes
->
->
+-06-02 09:21  gezelter
->
->
+        * libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp:
->
+        severity levels in simError
->
->
+-06-01 16:45  gezelter
->
->
+        * libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90,
->
+        do_Forces.F90, mpiSimulation.cpp, neighborLists.F90,
->
+        simulation_module.F90: Bug fix (fixes of skipList and neighbor list
->
+        under MPI)
->
->
+-06-01 16:44  gezelter
->
->
+        * libBASS/MoleculeStamp.cpp: Bug fix (memory leak)
->
->
+-06-01 13:43  gezelter
->
->
+        * samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing
->
->
+-06-01 13:42  gezelter
->
->
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
->
+        SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp,
->
+        mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90:
->
+        Cutoff Groups for MPI
->
->
+-06-01 13:07  chrisfen
->
->
+        * libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in
->
+        useLiquidThermInt routine in ForceFields.cpp
->
->
+-06-01 12:15  chrisfen
->
->
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
->
+        SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate
->
+        solid and liquid thermodynamic integration routines
->
->
+-06-01 10:57  tim
->
->
+        * libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in
->
+        progress
->
->
+-06-01 09:27  chrisfen
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt
->
+        keyword and changed useThermInt to useSolidThermInt
->
->
+-06-01 09:21  chrisfen
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate
->
+        solid and liquid thermodynamic integration routines
->
->
+-05-28 10:21  gezelter
->
->
+        * libmdtools/do_Forces.F90: bugfix starting
->
->
+-05-27 15:06  chrisfen
->
->
+        * libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in
->
+        Integrator.cpp where it called writeRaw() when useThermInt =
->
+        false...
->
->
+-05-27 14:51  tim
->
->
+        * ChangeLog, libmdtools/do_Forces.F90,
->
+        libmdtools/simulation_module.F90: Bug fix for SkipList
->
->
+-05-27 14:26  gezelter
->
->
+        * libmdtools/SimSetup.cpp: bugfix in simsetup?
->
->
+-05-27 13:59  gezelter
->
->
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp,
->
+        InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp,
->
+        ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp,
->
+        mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp,
->
+        mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90:
->
+        Cutoff group changes under MPI
->
->
+-05-27 11:20  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for
->
+        xlc++
->
->
+-05-27 10:31  tim
->
->
+        * libmdtools/SimInfo.cpp: groupList new bases on global index of
->
+        atoms
->
->
+-05-27 10:21  gezelter
->
->
+        * src/: oopse.cpp, oose.cpp: Modified the nifty banner
->
->
+-05-27 10:21  gezelter
->
->
+        * libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90:
->
+        Fixed off-by-one error in groupStartRow and groupStartCol
->
->
+-05-26 19:48  tim
->
->
+        * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp,
->
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90,
->
+        libmdtools/calc_charge_charge.F90,
->
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
->
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/force_globals.F90, libmdtools/mdProfile.cpp,
->
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp,
->
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
->
+        libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
->
+        libmdtools/simulation_module.F90: in the progress of fixing MPI
->
+        version of cutoff group
->
->
+-05-26 11:41  gezelter
->
->
+        * libmdtools/do_Forces.F90: Compacted all of the 8 copies of the
->
+        force loop into one.
->
->
+-05-24 17:24  gezelter
->
->
+        * libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes
->
->
+-05-24 16:23  chrisfen
->
->
+        * libmdtools/Restraints.cpp: Removed unnecessary variables and
->
+        changed error messages in Restraints.cpp
->
->
+-05-24 16:03  gezelter
->
->
+        * libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90,
->
+        calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
->
+        calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes
->
+        for stress / pressure tensor by cutoff group
->
->
+-05-22 15:55  chrisfen
->
->
+        * libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp...
->
+        Too many arguements in a function call.
->
->
+-05-22 13:17  chrisfen
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword
->
+        useThermInt.
->
->
+-05-22 13:16  chrisfen
->
->
+        * libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
->
+        ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp,
->
+        Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp,
->
+        SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp,
->
+        StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration
->
+        code.
->
->
+-05-21 10:58  gezelter
->
->
+        * libmdtools/: do_Forces.F90, simulation_module.F90: Major changes
->
+        to skipThisPair for efficiency
->
->
+-05-21 09:22  gezelter
->
->
+        * configure, ac-tools/configure.in, forceFields/LJ.vdw,
->
+        forceFields/amber99.vdw, forceFields/charmm27.vdw,
->
+        forceFields/gaff.vdw, forceFields/oplsaal.vdw,
->
+        samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes
->
+        for SHAPES potential
->
->
+-05-20 15:27  chrisfen
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit
->
+        included the bass keywords
->
->
+-05-20 15:24  chrisfen
->
->
+        * libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp,
->
+        Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp,
->
+        Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several
->
+        additions... Restraints.cpp and .hpp were included for restraining
->
+        particles in thermodynamic integration.  By including these,
->
+        changes were made in Integrator, SimInfo, ForceFeilds, SimSetup,
->
+        StatWriter, and possibly some other files.  Two bass keywords were
->
+        also added for performing thermodynamic integration: a lambda value
->
+        one and a k power one.
->
->
+-05-13 16:08  gezelter
->
->
+        * libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list
->
->
+-05-12 17:01  tim
->
->
+        * samples/: argon/Makefile, argon/argonEM.bass,
->
+        argon/init_argon.eor, minimizer/argon/Makefile,
->
+        minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor,
->
+        minimizer/water/Makefile, minimizer/water/Makefile.in,
->
+        minimizer/water/WATER.frc, minimizer/water/init_ssd.eor,
->
+        minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass,
->
+        minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add
->
+        minimizer sample
->
->
+-05-12 16:54  gezelter
->
->
+        * libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X
->
+        compilation
->
->
+-05-12 15:54  gezelter
->
->
+        * libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes
->
+        for compilation under Mac OS X with IBM's xl compilers
->
->
+-05-12 15:14  gezelter
->
->
+        * src/: oopse.cpp, oose.cpp: Added a nifty neato banner
->
->
+-05-12 15:14  gezelter
->
->
+        * libmdtools/LJFF.cpp: Removed an extraneous write
->
->
+-05-12 15:13  gezelter
->
->
+        * libBASS/simError.h: Starting to change the error model
->
->
+-05-12 14:45  gezelter
->
->
+        * utils/Dump2XYZ.cpp: const char* fix
->
->
+-05-12 14:44  gezelter
->
->
+        * libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
->
+        src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous
->
+        write statements
->
->
+-05-12 11:38  tim
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp,
->
+        ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
->
+        SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and
->
+        massratio from simState, creat cutoff group forevery atom which
->
+        does not belong to cutoff group defined at mdl file
->
->
+-05-12 10:58  gezelter
->
->
+        * libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in
->
+        CutoffGroup
->
->
+-05-12 10:35  gezelter
->
->
+        * samples/water/water.mdl: Added the cutoff Groups to the default
->
+        water.mdl file
->
->
+-05-12 10:02  tim
->
->
+        * ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp:
->
+        fixed a bug in CutoffGroup::getCOM()
->
->
+-05-12 09:29  gezelter
->
->
+        * libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
->
+        samples/water/ssd.bass: bug fixes for cutoffGroups
->
->
+-05-11 17:28  tim
->
->
+        * utils/Vector3.hpp: adding generic Vector3 class
->
->
+-05-11 16:44  tim
->
->
+        * libmdtools/Integrator.hpp: adding instantiation of
->
+        Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
->
->
+-05-11 16:31  gezelter
->
->
+        * libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90,
->
+        calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90,
->
+        calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90:
->
+        Fortran-side changes for group-based cutoffs
->
->
+-05-11 16:20  tim
->
->
+        * libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp
->
->
+-05-11 16:14  tim
->
->
+        * libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp,
->
+        SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix
->
+        anoter one in CutoffGroup which causes seg fault
->
->
+-05-11 15:33  tim
->
->
+        * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp,
->
+        libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup
->
+        into OOPSE
->
->
+-05-11 15:07  gezelter
->
->
+        * libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup
->
->
+-05-11 11:00  gezelter
->
->
+        * libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
->
+        fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to
->
+        use the simplified cutoff stuff in the BASS library
->
->
+-05-10 23:21  gezelter
->
->
+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y,
->
+        CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp,
->
+        Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
->
+        MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c,
->
+        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
->
+        parse_tree.c: BASS changes for adding CutoffGroups to molecules.
->
+        Also restructured the plethora of cutoff radii into one
->
+        cutoffRadius and one switchingRadius.  Also removed the
->
+        useMolecularCutoffs keyword
->
->
+-05-10 15:28  tim
->
->
+        * ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize
->
+        DumpWriter
->
->
+-05-07 16:36  gezelter
->
->
+        * libmdtools/: fSwitchingFunction.h, switch_module.F90: New module
->
+        for fortran group-based switching function
->
->
+-05-07 16:35  gezelter
->
->
+        * libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp,
->
+        Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp,
->
+        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
->
+        calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90,
->
+        force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h,
->
+        mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90,
->
+        simulation_module.F90: Many changes to get group-based cutoffs to
->
+        work
->
->
+-05-01 13:52  tim
->
->
+        * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90,
->
+        libmdtools/do_Forces.F90, libmdtools/fSimulation.h,
->
+        libmdtools/fortranWrapDefines.hpp,
->
+        libmdtools/simulation_module.F90: C++ pass groupList to fortran
->
->
+-04-29 11:03  tim
->
->
+        * ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in
->
+        calc_charge_charge when using molecular cutoff
->
->
+-04-28 21:11  tim
->
->
+        * libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an
->
+        unmatched c/fortran interface
->
->
+-04-28 18:09  tim
->
->
+        * ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp:
->
+        keep the previous position of cantilever in SMD
->
->
+-04-28 17:34  tim
->
->
+        * ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp,
->
+        libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug
->
+        in Molecule.cpp which initialize massRatio before creat the array.
->
+        fix two bugs in ZconsVisitor
->
->
+-04-28 17:06  gezelter
->
->
+        * libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
->
+        Adding molecular cutoffs
->
->
+-04-28 16:39  gezelter
->
->
+        * libmdtools/: calc_charge_charge.F90, do_Forces.F90,
->
+        fSimulation.h, force_globals.F90, simulation_module.F90: work on
->
+        molecular cutoffs
->
->
+-04-28 16:39  gezelter
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to
->
+        Globals
->
->
+-04-27 11:26  tim
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp,
->
+        ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp,
->
+        fSimulation.h, fortranWrapDefines.hpp: add center of mass of the
->
+        molecule and massRation into atom class
->
->
+-04-26 16:16  mmeineke
->
->
+        * libBASS/Globals.cpp: modified the defaults for the system init
->
+        time and system init state.
->
->
+-04-26 09:29  gezelter
->
->
+        * libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in
->
+        calc_charge_charge.F90
->
->
+-04-23 23:31  tim
->
->
+        * ChangeLog, libmdtools/AtomVisitor.cpp,
->
+        libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add
->
+        reaction field correction to charge-charge interaction
->
->
+-04-22 16:33  tim
->
->
+        * libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp,
->
+        Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the
->
+        calculation of pressure tensor
->
->
+-04-22 09:55  tim
->
->
+        * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed
->
+        another bug in InitFromFile. MPI verion of OOPSE is working again
->
->
+-04-21 22:29  tim
->
->
+        * libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp,
->
+        InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp,
->
+        SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two
->
+        bugs in MPI version of InitfromFile and one unmatch MPI command in
->
+        DumpWriter
->
->
+-04-21 00:32  tim
->
->
+        * libmdtools/Functor.hpp, libmdtools/LinearCons.cpp,
->
+        libmdtools/LinearCons.hpp, utils/CmdlineZsub.c,
->
+        utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some
->
+        useless files
->
->
+-04-20 11:56  tim
->
->
+        * libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp,
->
+        SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel  and
->
+        velocitize at thermo
->
->
+-04-20 00:39  tim
->
->
+        * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp,
->
+        libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
->
+        libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp,
->
+        libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp,
->
+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
->
+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
->
+        utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c,
->
+        utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version
->
->
+-04-19 17:13  gezelter
->
->
+        * libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp,
->
+        Thermo.cpp: Fixed a charge bug
->
->
+-04-19 15:54  tim
->
->
+        * libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp,
->
+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
->
+        libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed
->
+        a bug in CompositeVisitor which cause the double counting problem
->
->
+-04-19 12:44  tim
->
->
+        * libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
->
+        libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp,
->
+        libmdtools/DumpReader.cpp, libmdtools/Make.dep,
->
+        libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp,
->
+        libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in:
->
+        Dump2XYZ is almost working except atoms in rigidbody are double
->
+        counted
->
->
+-04-18 22:52  tim
->
->
+        * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp,
->
+        libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp,
->
+        libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp,
->
+        libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp,
->
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
->
+        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
->
+        libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp,
->
+        libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp,
->
+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
->
+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp,
->
+        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
->
->
+-04-15 17:15  tim
->
->
+        * libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting
->
+        exclude list
->
->
+-04-15 11:18  tim
->
->
+        * ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp,
->
+        libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp,
->
+        libmdtools/Integrator.cpp, libmdtools/Molecule.cpp,
->
+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/Thermo.cpp, libmdtools/WATER.cpp,
->
+        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, minimizer/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,
->
+        samples/minimizer/argon/argon.bass, samples/water/ssd.bass:
->
+        Dumpwriter only write out the atoms on master nodes
->
->
+-01-10 04:46  tim
->
->
+        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
->
+        roll it back fix a bug of copying string to a pointer Still have
->
+        Seg fault, it looks like a random MPI seg fault in totalview
->
->
+-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
->
->
+        * libmdtools/DumpWriter.cpp: A work in progress...
->
->
+-01-08 13:59  gezelter
->
->
+        * libmdtools/DumpWriter.cpp: null terminate some strings just in
->
+        case
->
->
+-01-08 13:13  mmeineke
->
->
+        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
->
+        state bug.
->
->
+-01-08 13:05  gezelter
->
->
+        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
->
->
+-01-08 12:57  mmeineke
->
->
+        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
->
+        exstended state bug
->
->
+-01-08 12:40  gezelter
->
->
+        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
->
->
+-01-08 10:44  mmeineke
->
->
+        * libmdtools/InitializeFromFile.cpp: added support for the ignore
->
+        XS state info  flag
->
->
+-01-07 14:26  tim
->
->
+        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
->
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass,
->
+        samples/water/ssd.bass: Fixed a bug of sending message from master
->
+        node to itself in DumpWriter.cpp and 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
->
+        third-party directory for code not written by us. Also added
->
+        Mersenne Twister random number generator code. This will eventually
->
+        replace sprng as the random number generator used by OOPSE.
->
->
+-12-22 16:26  chuckv
->
->
+        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
->
+        Fixes to profile code.
->
->
+-12-19 15:36  mmeineke
->
->
+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
->
+        timing.F90, timing.f90: More profiling fixes.
->
->
+-12-19 15:19  chuckv
->
->
+        * libmdtools/timing.f90: Another change for MPI in timing.
->
->
+-12-19 15:17  chuckv
->
->
+        * libmdtools/timing.f90: Small update to timing in MPI
->
->
+-12-19 13:53  mmeineke
->
->
+        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
->
+        profiling commands work now. Will start adding PROFILE ifdefs into
->
+        the code
->
->
+-12-19 12:25  mmeineke
->
->
+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
->
+        some profiling routines
->
->
+-12-19 10:12  mmeineke
->
->
+        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
->
+        and GofRomega
-<
+        added identification of identI in matchI.
->
+        additional work on randomBilayer
->
->
+-12-19 10:12  mmeineke
->
->
+        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
->
+        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
->
+        GofRomega
->
->
+-12-18 16:47  mmeineke
->
->
+        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
->
+        some profile functionality
->
->
+-12-18 15:46  chuckv
->
->
+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
->
+        Added functions for simple profiling in fortran.
->
->
+-12-17 15:13  chuckv
->
->
+        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
->
+        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
->
+        rho_col were scattered into the same array. Unfortunately, MPI
->
+        zeros the array between scatters so half of the sum was being lost.
->
+        Fixed by added a temp array for column scatter, then sum loop over
->
+        nlocal.
->
->
+-12-16 15:49  mmeineke
->
->
+        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
->
+        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
->
+        gofRomega. both need to be debugged and tested.
->
->
+-12-12 10:42  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
->
+        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
->
+        gradients (to do minimizations)
->
->
+-12-12 10:33  mmeineke
->
->
+        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
->
+        header
->
->
+-12-10 11:52  mmeineke
->
->
+        * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
->
+        randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
->
+        randomBilayer to the build. Also move the random bilayer builder
->
+        from bilayerSys to randomBilayer
->
->
+-11-25 10:44  mmeineke
->
->
+        * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
->
+        DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
->
+        TB3 in DUFF.frc
->
->
+-11-21 15:09  mmeineke
->
->
+        * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
->
+        utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
->
+        message in SimInfo. Added a more informative error message in
->
+        InitializeFromFile
->
->
+-11-21 15:07  mmeineke
->
->
+        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
->
+        ing in the GofR,CosTheta
->
->
+-11-21 14:31  chrisfen
->
->
+        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
->
+        a bug in SimInfo ordering of radii
->
->
+-11-11 12:20  mmeineke
->
->
+        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
->
+        a min function.
->
->
+-11-10 16:50  mmeineke
->
->
+        * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
->
+        reordered the rcut/ecr/boxSize initialization
->
->
+        removed the rcut/ecr shrink and grow algorithm. the simulation will
->
+        now exit when it runs into rcut or ecr.
->
->
+-11-07 16:46  chuckv
->
->
+        * libmdtools/: Makefile.in, mpiSimulation_module.F90,
->
+        oopseMPI_module.F90: Added support for compiling fortran without
->
+        use of mpich modules. We use mpif.h instead.:
->
->
+-11-07 12:09  mmeineke
->
->
+        * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
->
+        NPTxyz.cpp: moved the velocity scale matrix calculation outside of
->
+        the atom loop in the NPT family of integrators.
->
->
+-11-06 17:01  mmeineke
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
->
+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
->
+        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
->
+        utils/sysbuilder/latticeBilayer.cpp: added the following parameters
->
+        to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance
->
+          * useIntiTime => useInitialTime
->
->
+-11-06 14:24  mmeineke
->
->
+        * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
->
+        make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
->
+        parse_tree.h: fixed the includes in the Make.dep
->
->
+-11-06 14:11  mmeineke
->
->
+        * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
->
+        NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the
->
+        new-templateless branch to the main trunk.
->
->
+        bug Fixes include:   * fixed the switching function from ortho to
->
+        non-ortho box.           !!!!! THis was responsible for all of the
->
+        sudden deaths we saw.    * some formating in the string when we
->
+        write out the extended system state.    * added NPT.cpp to the
->
+        makefile.in
->
->
+-11-06 13:20  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
->
+        SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
->
+        bug.    The box was not switching between orthorhombic and
->
+        non-orthorhombic wrapping correctly.         we added a fabs() to
->
+        the check.which should fix it.
->
->
+-11-05 14:16  mmeineke
->
->
+        * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
->
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
->
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
->
+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
->
+        libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
->
+        utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
->
+        some work on trying to find the compression bug
->
->
+-11-03 17:07  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
->
+        InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
->
+        NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
->
+        SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
->
+        most of standard template library from OOPSE.
->
->
+-10-31 16:06  mmeineke
->
->
+        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
->
+        Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
->
+        SimSetup.cpp: started work on template removal.
->
->
+-10-31 13:28  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
->
+        added template stuff to the Maikefile template
->
->
+        little changes to some printf format statements
->
->
+-10-31 13:28  mmeineke
->
->
+        * libBASS/Makefile.in: added template stuff to the Maikefile
->
+        template
->
->
+-10-30 13:59  gezelter
->
->
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
->
+        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
->
+        rList problems
->
->
+-10-30 09:11  gezelter
->
->
+        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
->
+        queried before q0 was allocated.
->
->
+-10-29 15:41  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
->
+        SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
->
+        calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error
->
+        in bass.l
->
->
+        fixed a little bug in the first time step, regarding the setting of
->
+        ecr and est in fortran
->
->
+-10-29 15:40  mmeineke
->
->
+        * libBASS/BASSlex.l: fixed a stdlib.h include error
->
->
+-10-29 12:55  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
->
+        SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
->
+        rcut is setup, as well as additional debugging comments.
->
->
+-10-29 09:28  gezelter
->
->
+        * configure, ac-tools/configure.in, libBASS/Makefile.in,
->
+        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
->
+        templates
->
->
+-10-28 22:16  gezelter
->
->
+        * src/Makefile.in: Refixed broken makefile
->
->
+-10-28 22:06  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
->
+        fixes
->
->
+-10-28 19:19  tim
->
->
+        * ChangeLog, libmdtools/AbstractClasses.hpp,
->
+        libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
->
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
->
+        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
->
+        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
->
+        samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi
->
+        and eta to the comment line of dump file.
->
->
+-10-28 17:25  mmeineke
->
->
+        * libmdtools/: ForceFields.hpp, SimInfo.hpp,
->
+        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
->
+        mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
->
+        how c calls fortran. All function pointers and fortran calls are
->
+        rigidly typecast now.
->
->
+-10-28 15:42  gezelter
->
->
+        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
->
+        Portability fixes
->
->
+-10-28 15:09  gezelter
->
->
+        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
->
+        src/Makefile.in: Compatibility fixes
->
->
+-10-28 12:08  mmeineke
->
->
+        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
->
+        started work on template removal
->
->
+-10-28 12:04  gezelter
->
->
+        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
->
+        trying to understand extern "C" stuff for pointers
->
->
+-10-28 11:20  gezelter
->
->
+        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
->
+        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
->
->
+-10-28 11:03  gezelter
->
->
+        * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
->
+        DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
->
+        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
->
+        ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
->
+        Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
->
+        ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
->
+        StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
->
+        calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
->
+        mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with
->
+        more portable c header stuff Also, mod file fixes and portability
->
+        changes Some fortran changes will need to be reversed.
->
->
+-10-28 11:03  gezelter
->
->
+        * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
->
+        Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
->
+        Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
->
+        portable c header stuff Also, mod file fixes and portability
->
+        changes
->
->
+-10-28 11:02  gezelter
->
->
+        * configure, ac-tools/aclocal.m4: mod file fixes and portability
->
+        stuff
->
->
+-10-27 18:00  gezelter
->
->
+        * Makefile.in, configure, ac-tools/aclocal.m4,
->
+        ac-tools/configure.in, ac-tools/fortran90.m4,
->
+        libmdtools/Makefile.in: Stuff for MOD support in other compilers
->
->
+-10-27 17:08  mmeineke
->
->
+        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
->
+        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
->
+        added routines for the sysbuilder to work with simSetup
->
->
+        remved the QuickBass routines, and had all parsing go through
->
+        SimSetup.  LatticeBilayer is in complete working order now.
->
->
+-10-27 17:07  mmeineke
->
->
+        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
->
+        routines for the sysbuilder to work with simSetup
->
->
+-10-27 11:20  gezelter
->
->
+        * configure, ac-tools/configure.in, samples/water/ssd.bass,
->
+        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
->
->
+-10-24 17:17  mmeineke
->
->
+        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
->
+        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
->
+        latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
->
+        QuickBass, MoLocator, and latticeBuilder into a Builder Library
->
+        overhauled latticeBilayer into its own program. Removed sysBuild
->
+        from the Makefile
->
->
+-10-24 12:36  gezelter
->
->
+        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
->
+        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
->
+        builder
->
->
+-10-24 12:35  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
->
+        merge problem
->
->
+-10-23 14:57  mmeineke
->
->
+        * samples/metals/Makefile.in: added eam ForceField files to the
->
+        init
->
->
+        fixed an eam mpi parmeter setup bug
->
->
+        added the init file to the makefile
->
->
+-10-23 14:57  mmeineke
->
->
+        * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
->
+        to the init
->
->
+        fixed an eam mpi parmeter setup bug
->
->
+-10-23 14:57  mmeineke
->
->
+        * forceFields/Makefile.in: added eam ForceField files to the init
->
->
+-10-22 16:17  mmeineke
->
->
+        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
->
+        NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
->
+        integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
->
+        no box skew allowed.
->
->
+-10-21 14:33  mmeineke
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
->
+        staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax.
->
+            * useInitTime = false: sets the origin time to 0.0 regardless
->
+        of the time stamp in the .init file     * default=> useInitTime =
->
+        true;
->
->
+-10-17 16:19  mmeineke
->
->
+        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
->
+        Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
->
+        staticProps.cpp, obj/placeholder: added the staticProps directory
->
+        to the build list for both configure  and configure.in
->
->
+        fixed a number of bugs in the staticProps code. gofr is now
->
+        working.
->
->
+-10-17 16:18  mmeineke
->
->
+        * ac-tools/configure.in: added the staticProps directory to the
->
+        build list for both configure  and configure.in
->
->
+-10-17 16:17  mmeineke
->
->
+        * configure: added the staticProps directory to the build list
->
->
+-10-16 14:16  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
->
+        Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to
->
+        use linked lists instead of a vector.
->
->
+        Fixed the makefile to build DumpReader.cpp
->
->
+        Removed a comment output in Exclude.cpp
->
->
+        Modified DumpWriter and Integrator to write an eor file every time
->
+        a frame is written.  This lets the .eor file represent the last
->
+        written frame of a simulation.
->
->
+-10-10 12:10  mmeineke
->
->
+        * 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: Contiuned work on staticProps. should be in
->
+        a position where it will compile and run first runs.
->
->
+-10-04 13:46  chuckv
->
->
+        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
->
+        samples/metals/Au.bass: Fixed bug in calc_eam.
->
->
+-10-04 13:08  chuckv
->
->
+        * samples/metals/init_au.in: added Au init file for eam.
->
->
+-10-03 17:11  mmeineke
->
->
+        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
->
+        entahlpy from the statwriter and thermo.
->
->
+-10-03 17:02  mmeineke
->
->
+        * libmdtools/SimInfo.hpp: changed the formating ogf the error
->
+        statements in simError
->
->
+        added a function to get the maxCutoff
->
->
+-10-03 17:01  mmeineke
->
->
+        * libBASS/simError.c: changed the formating ogf the error
->
+        statements in simError
->
->
+-09-30 11:00  mmeineke
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
->
+        f90Flags so they are no longer overwritten by the compiler.
->
->
+-09-29 17:06  mmeineke
->
->
+        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
->
+        for conifig.in
->
->
+        fixed wrappers to extern "C"
->
->
+-09-29 17:06  mmeineke
->
->
+        * ac-tools/configure.in: added mpif90 mod check back same for
->
+        conifig.in
->
->
+-09-29 17:05  mmeineke
->
->
+        * configure: added mpif90 mod check back
->
->
+-09-29 16:16  mmeineke
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
->
+        libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
->
+        libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp,
->
+        libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp,
->
+        libBASS/ZconStamp.cpp, libBASS/simError.c,
->
+        libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90,
->
+        libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
->
+        found with SUN's SUNWspro.s1s7
->
->
+-09-29 12:38  mmeineke
->
->
+        * libmdtools/GenericData.hpp: light change in syntax. no
->
+        signifigant change.
->
->
+-09-25 16:17  mmeineke
->
->
+        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
->
+        additional remarks from icc -w3 (extra verbose output)
->
->
+-09-25 14:27  mmeineke
->
->
+        * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
->
+        libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
->
+        libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp,
->
+        libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp,
->
+        libmdtools/Integrator.cpp, libmdtools/LJFF.cpp,
->
+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
->
+        libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp,
->
+        libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
->
+        gcc -Wall and g++ -Wall
->
->
+-09-25 13:54  gezelter
->
->
+        * configure, ac-tools/configure.in: fixed a bug in configure
->
->
+-09-25 11:42  gezelter
->
->
+        * Makefile.in, configure, ac-tools/aclocal.m4,
->
+        ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
->
+        src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
->
+        fixes for configure
->
->
+-09-24 14:34  mmeineke
->
->
+        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
->
+        that it is called before the first Statistics are written.
->
->
+-09-23 15:36  gezelter
->
->
+        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
->
+        bunch of Make.dep files to CVS
->
->
+-09-23 15:34  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
->
+        SimSetup.cpp: Removed NPTfm from Integrator.hpp.
->
->
+        Some small syntax cleaning in NPTfm and SimSetup
->
->
+-09-22 18:07  tim
->
->
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
->
+        SimInfo.hpp: fix bug in calculating maxCutoff
->
->
+-09-22 16:23  mmeineke
->
->
+        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
->
+        Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
->
+        Converted NPTf to work with the NPT base class.
->
->
+        Removed NPTfm and NPTim from cvs
->
->
+-09-19 15:00  mmeineke
->
->
+        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
->
+        NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
->
+        class. NPTi is up to date. NPTf is not.
->
->
+-09-19 11:03  mmeineke
->
->
+        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
->
+        makefile
->
->
+-09-19 11:01  gezelter
->
->
+        * samples/water/ssd.bass: goofing off to test NPTf and NPTi
->
->
+-09-19 11:01  gezelter
->
->
+        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
->
+        (nearly) conserved quantities for both NPTi and NPTf
->
->
+-09-19 10:20  mmeineke
->
->
+        * utils/Makefile.in: fixed a typo in the makefile.
->
->
+-09-19 09:55  gezelter
->
->
+        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
->
+        samples/water/ssd.bass: [no log message]
->
->
+-09-19 09:22  tim
->
->
+        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
->
->
+-09-17 09:22  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
->
+        work with constraints.
->
->
+-09-16 15:02  tim
->
->
+        * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
->
+        SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
->
->
+        fixed conserved quantity in NPT (Still some small bug)
->
->
+        NPTi appears very stable.
->
->
+-09-15 11:52  tim
-+
+        * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
-+
+        libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp,
-+
+        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp,
-+
+        libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp,
-+
+        utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
-+
+        statWriter fix bug of vector wrapping at NPTi
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * libmdtools/: Make.dep, Makefile.in: Added integrators to
-+
+        Makefile.in
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * ChangeLog: Entered changes for configure into ChangeLog
-+
+-09-09 15:35  mmeineke
+        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
+        samples/Makefile.in, samples/alkane/Makefile,
+        samples/alkane/Makefile.in, samples/argon/Makefile,
+        samples/argon/Makefile.in, samples/argon/argon.bass,
-<
+        samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
-<
+        samples/lipid/Makefile, samples/lipid/Makefile.in,
-<
+        samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
-<
+        src/Makefile.in, utils/Makefile, utils/Makefile.in,
-<
+        utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
-<
+        autoconf / configure method of configuring OOPSE
->
+        samples/minimizer/argon/Makefile,
->
+        samples/minimizer/argon/Makefile.in,
->
+        samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile,
->
+        samples/beadLipid/Makefile.in, samples/lipid/Makefile,
->
+        samples/lipid/Makefile.in, samples/water/Makefile,
->
+        samples/water/Makefile.in, src/Makefile, src/Makefile.in,
->
+        utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile,
->
+        utils/sysbuilder/Makefile.in: Changes to autoconf / configure
->
+        method of configuring OOPSE
+-09-04 16:48  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
+        libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
+        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
+-07-14 18:06  gezelter
+        * samples/: alkane/init_butane.eor, argon/argon.bass,
-<
+        argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes
-<
+        for samples
->
+        argon/init_argon.eor, minimizer/argon/argon.bass,
->
+        minimizer/argon/init_argon.eor, lipid/init_5x5.eor,
->
+        water/init_ssd.eor: Fixes for samples
+-07-14 18:06  gezelter
+        * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
+        libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
-<
+        samples/argon/argon.bass: more bug fixes....
->
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more
->
+        bug fixes....
+-04-01 11:49  mmeineke
+-03-26 10:37  chuckv
+        * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
-<
+        samples/argon/argon.bass: Fixes for Parallel thermalization
->
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes
->
+        for Parallel thermalization
+-03-26 09:55  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, minimizer/argon/Makefile,
->
+        minimizer/argon/argon.bass, minimizer/argon/init_argon.eor,
->
+        minimizer/argon/lj.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

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/OOPSE/ChangeLog (file contents): Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC vs. Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

Diff Legend

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC