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

Comparing:
branches/mmeineke/OOPSE/ChangeLog (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/ChangeLog (file contents), Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC

-<
+/19/2003 - finished porting the packge into autoconf and automake. Incremented version to 0.6
-<
-<
+/13/2003 - Starting to port the package into the OOPSE distribution
->
+-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: 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/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/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
->
->
+        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/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,
->
+        NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog
->
->
+        added two new NPT integrators, they still need work.
->
->
+-09-09 15:34  mmeineke
->
->
+        * ChangeLog: updated the ChangeLog
->
->
+-09-05 17:45  gezelter
->
->
+        * libmdtools/Make.dep: dependency on config.h
->
->
+-09-05 17:36  gezelter
->
->
+        * configure, ac-tools/aclocal.m4: fixed sprng problem
->
->
+-09-05 16:29  gezelter
->
->
+        * samples/metals/Makefile.in: New Makefile for metals sample
->
->
+-09-05 16:27  gezelter
->
->
+        * Makefile, Makefile.in, ac-tools/aclocal.m4,
->
+        ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile,
->
+        forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
->
+        libBASS/Makefile.in, libmdtools/Integrator.hpp,
->
+        libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep,
->
+        libmdtools/Makefile, libmdtools/Makefile.in,
->
+        libmdtools/calc_eam.F90, libmdtools/config.h.in,
->
+        libmdtools/definitions_module.F90, libmdtools/fInfo.c,
->
+        libmdtools/fortranWrappers.cpp,
->
+        libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90,
->
+        libmdtools/simulation_module.F90, samples/Makefile,
->
+        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
->
->
+-09-04 16:48  mmeineke
->
->
+        * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
->
+        libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp,
->
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile:
->
+        added resetTime to the Global namespace.
->
->
+        added ability to reset the integrators in the NVT and NPT family.
->
->
+-09-04 16:48  mmeineke
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
->
+        namespace.
->
->
+-09-02 09:30  tim
->
->
+        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
->
+        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
->
+        PolicyByMass
->
->
+-08-28 16:09  tim
->
->
+        * ChangeLog, libmdtools/GenericData.cpp,
->
+        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
->
->
+-08-27 14:23  tim
->
->
+        * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
->
+        bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to
->
+        MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we
->
+        turn on the optimization flag, it causes a seg fault
->
->
+-08-27 11:25  gezelter
->
->
+        * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
->
+        calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for
->
+        stress tensor parallel bug.
->
->
+-08-27 11:16  tim
->
->
+        * ChangeLog, libmdtools/DUFF.cpp,
->
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90:
->
+        fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90
->
+        molMembershipList use global index instead of local index
->
->
+-08-26 15:37  tim
->
->
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
->
+        mpiSimulation.cpp: set default force substraction policy to
->
+        PolicyByMass
->
->
+-08-26 15:29  tim
->
->
+        * libmdtools/Integrator.cpp: [no log message]
->
->
+-08-26 15:13  mmeineke
->
->
+        * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to
->
+        Statwriter and Dumpwriter to handle files larger than 2 gb.
->
->
+        commented out some print statements in Zconstraint
->
->
+        hard coding some system init into bilayer.sys
->
->
+-08-26 15:12  mmeineke
->
->
+        * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp:
->
+        added define statemewnt to Statwriter and Dumpwriter to handle
->
+        files larger than 2 gb.
->
->
+        commented out some print statements in Zconstraint
->
->
+-08-26 15:02  tim
->
->
+        * libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed
->
+        and check the seed which is specified by user at least contains 9
->
+        digits
->
->
+-08-26 13:32  mmeineke
->
->
+        * libmdtools/DUFF.cpp: changed the Makefiel a litle.
->
->
+        Fixed a bug in MPI_DUFF. The atom block type was not being properly
->
+        constucted in MPI. (The MPI struct had 6 doubles declared versus
->
+        the actual 11)
->
->
+-08-26 13:30  mmeineke
->
->
+        * Makefile: changed the Makefiel a litle.
->
->
+-08-25 17:17  gezelter
->
->
+        * utils/sysbuilder/Makefile: More FreeBSD fixes
->
->
+-08-25 16:51  gezelter
->
->
+        * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
->
+        libmdtools/Makefile, src/Makefile: [no log message]
->
->
+-08-22 15:04  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
->
+        frequency of output dumps.
->
->
+-08-20 17:23  tim
->
->
+        * libBASS/Globals.hpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
->
+        libmdtools/mpiSimulation.cpp: user can setup seed in bass file now,
->
+        if he does not specify any value for seed, oopse will take the
->
+        value of seconds of system time as seed
->
->
+-08-20 14:42  mmeineke
->
->
+        * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
->
+        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/SimState.cpp,
->
+        utils/sysbuilder/bilayerSys.cpp: updated the Changelog.
->
->
+        added some bug fixes for setting the random number generator seed
->
+        value.
->
->
+        fixed a bug where ghostbend atom b was not being set. ( recent bug
->
+        from SimState conversion)
->
->
+-08-20 14:41  mmeineke
->
->
+        * libBASS/Globals.hpp: updated the Changelog.
->
->
+        added some bug fixes for setting the random number generator seed
->
+        value.
->
->
+-08-20 14:41  mmeineke
->
->
+        * ChangeLog: updated the Changelog.
->
->
+-08-20 14:11  tim
->
->
+        * libBASS/Globals.cpp, libmdtools/DUFF.cpp,
->
+        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
->
+        bend class
->
->
+-08-20 10:13  mmeineke
->
->
+        * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
->
+        make links. added -f to ln -s.
->
->
+-08-20 09:50  tim
->
->
+        * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]
->
->
+-08-20 09:34  tim
->
->
+        * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
->
+        ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
->
+        printing
->
->
+-08-18 15:59  chuckv
->
->
+        * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
->
+        latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp,
->
+        sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works.
->
+        Nanobuilder still broke.
->
->
+-08-15 14:24  tim
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/GenericData.hpp, libmdtools/Integrator.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp,
->
+        libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint
->
+        Method
->
->
+-08-14 11:16  tim
->
->
+        * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
->
+        with average force substraction strategy
->
->
+-08-13 16:20  chuckv
->
->
+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
->
+        profiling code -DPROFILE.
->
->
+-08-13 14:21  tim
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic
->
+        potential & z-contraint method
->
->
+-08-12 16:44  mmeineke
->
->
+        * libBASS/BASS_interface.cpp, libBASS/Globals.hpp,
->
+        libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
->
+        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really
->
+        annoying bug in Directional Atom, where mu was getting written to
->
+        pseudorandom memory location.
->
->
+-08-12 14:56  tim
->
->
+        * libBASS/BASS_interface.cpp, libBASS/Globals.cpp,
->
+        libBASS/Globals.hpp, libmdtools/Atom.hpp,
->
+        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
->
+        libmdtools/SimSetup.cpp: debugging globals
->
->
+-08-12 13:40  gezelter
->
->
+        * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
->
+        and new atypes in LJFF
->
->
+-08-12 13:15  gezelter
->
->
+        * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
->
+        stuff...
->
->
+-08-12 13:14  chuckv
->
->
+        * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.
->
->
+-08-12 13:04  chuckv
->
->
+        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
->
+        Missed del of files before.
->
->
+-08-12 13:03  chuckv
->
->
+        * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
->
+        message]
->
->
+-08-12 13:01  chuckv
->
->
+        * utils/sysbuilder/Makefile: commit makefile
->
->
+-08-12 12:51  tim
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
->
+        libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added
->
+        harmonical potential to z-constraint method
->
->
+-08-11 17:31  chuckv
->
->
+        * utils/Makefile: Changed makefile to only build quicklate.
->
->
+-08-11 17:25  chuckv
->
->
+        * ac-tools/configure.in: added utils/sysbuilder to be built.
->
->
+-08-11 17:12  chuckv
->
->
+        * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
->
+        bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp,
->
+        sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp,
->
+        sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp,
->
+        sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c,
->
+        sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp,
->
+        sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp,
->
+        sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp,
->
+        sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged
->
+        sysbuilder into a subdirectory. Fixed some of sysbuilder to work
->
+        with new atom allocation in libmdtools.
->
->
+-08-11 14:41  tim
->
->
+        * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
->
+        moving zconstraint molecules to specified positions
->
->
+-08-11 14:39  tim
->
->
+        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]
->
->
+-08-11 14:38  mmeineke
->
->
+        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
->
+        libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp,
->
+        libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp,
->
+        libBASS/ZconStamp.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/SimInfo.hpp: Added zConstraint
->
+        into the BASS language syntax.
->
->
+-08-11 13:29  mmeineke
->
->
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
->
+        degrees of freedom to account for zConstreints
->
->
+-08-08 16:22  chuckv
->
->
+        * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90,
->
+        libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
->
+        samples/metals/Au.bass: EAM works...... Neighbor list also
->
+        works.....
->
->
+-08-08 12:48  mmeineke
->
->
+        * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
->
+        instance of Atom::setZ and Atom::getZ in ZConstaint.
->
->
+-08-07 16:47  mmeineke
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
->
+        DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp,
->
+        GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp,
->
+        SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp,
->
+        SimState.hpp, Torsion.cpp: switched SimInfo to use a system
->
+        configuration from SimState rather than arrays from Atom
->
->
+-08-06 19:47  chuckv
->
->
+        * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90,
->
+        libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
->
+        samples/metals/Au.bass: Bug fixes for eam...
->
->
+-08-01 11:18  tim
->
->
+        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of
->
+        Z-Constraint
->
->
+-07-31 14:59  tim
->
->
+        * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
->
+        libmdtools/ZConstraint.cpp: add index range checking into
->
+        ZConstraint
->
->
+-07-31 10:38  tim
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters
->
+        to the globals
->
->
+-07-31 10:35  tim
->
->
+        * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp,
->
+        Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp,
->
+        NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
->
+        SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp:
->
+        Added Z constraint.
->
->
+-07-30 16:17  chuckv
->
->
+        * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp,
->
+        libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90,
->
+        libmdtools/do_Forces.F90, libmdtools/wrappers.F90,
->
+        samples/metals/Au.bass: More bug fixes for eam.
->
->
+-07-29 11:32  mmeineke
->
->
+        * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
->
+        working on the props code
->
->
+-07-29 11:32  mmeineke
->
->
+        * libBASS/Globals.cpp: [no log message]
->
->
+-07-25 15:05  chuckv
->
->
+        * samples/metals/: Au.bass, metals.mdl: Added bass models for
->
+        metals
->
->
+-07-25 15:00  chuckv
->
->
+        * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90,
->
+        notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam.
->
->
+-07-24 16:22  chuckv
->
->
+        * ac-tools/configure.in: Changed configure to look for both upper
->
+        and lower cass .mod files
->
->
+-07-24 14:57  chuckv
->
->
+        * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for
->
+        eam and do_forces.
->
->
+-07-23 17:13  chuckv
->
->
+        * libmdtools/: Makefile, calc_eam.F90, do_Forces.F90,
->
+        force_globals.F90, simulation_module.F90, status_module.F90:
->
+        Finished most code for eam....
->
->
+-07-22 16:49  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan
->
+        function to the DumpReader. It should now save the start of each
->
+        frame in a vector.
->
->
+-07-22 15:05  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes
->
+        to read dump files
->
->
+-07-22 14:54  tim
->
->
+        * libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp,
->
+        Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp,
->
+        NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log
->
+        message]
->
->
+-07-22 11:41  mmeineke
->
->
+        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp,
->
+        SimSetup.cpp: Fixed a current time initialization bug in
->
+        InitFromFile.
->
->
+-07-21 16:27  mmeineke
->
->
+        * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp,
->
+        Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and
->
+        friends to accomadate random file access
->
->
+-07-21 11:23  mmeineke
->
->
+        * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no
->
+        one sets it.
->
->
+-07-21 11:23  mmeineke
->
->
+        * libmdtools/: InitializeFromFile.cpp, Integrator.cpp,
->
+        ReadWrite.hpp: fixed Initializefrom file to start the simulation
->
+        from the time specified in the init file.
->
->
+-07-17 16:49  gezelter
->
->
+        * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp,
->
+        DumpReader.cpp: Started work on a DumpReader
->
->
+-07-17 15:38  gezelter
->
->
+        * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E
->
->
+-07-17 15:32  gezelter
->
->
+        * forceFields/DUFF.frc, libmdtools/DUFF.cpp,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp:
->
+        Changes for SSD/E
->
->
+-07-17 14:38  mmeineke
->
->
+        * libmdtools/do_Forces.F90: commented out an eam line
->
->
+-07-17 14:32  chuckv
->
->
+        * libmdtools/atype_module.F90: fixed spelling issue
->
->
+-07-17 14:29  chuckv
->
->
+        * libmdtools/: fInfo.c, status_module.F90: added info module
->
->
+-07-17 14:25  chuckv
->
->
+        * libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile,
->
+        atype_module.F90, calc_eam.F90, do_Forces.F90,
->
+        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
->
+        mpiSimulation_module.F90: Added massive changes for eam....
->
->
+-07-16 16:49  chuckv
->
->
+        * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF
->
->
+-07-16 16:30  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp,
->
+        SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90,
->
+        calc_reaction_field.F90, do_Forces.F90, fSimulation.h,
->
+        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
->
+        neighborLists.F90, notifyCutoffs.F90, simulation_module.F90,
->
+        wrappers.F90: Changed how cutoffs were handled from C. Now
->
+        notifyCutoffs in Fortran notifies those who need the information of
->
+        any changes to cutoffs.
->
->
+-07-16 12:35  gezelter
->
->
+        * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat.
->
+        quickLate is now somewhat more intelligent about periodic
->
+        boundaries and wrapping.
->
->
+-07-16 11:40  chuckv
->
->
+        * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists
->
->
+-07-16 10:34  mmeineke
->
->
+        * scripts/cleanSrc: added a quick wipe-and-update script for quick
->
+        rebuilds on BoB
->
->
+-07-15 21:11  gezelter
->
->
+        * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp,
->
+        SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more
->
+        fixes for box changes
->
->
+-07-15 17:29  mmeineke
->
->
+        * libmdtools/simulation_module.F90: removed some debugging print
->
+        statements.
->
->
+-07-15 17:22  mmeineke
->
->
+        * libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90,
->
+        do_Forces.F90, simulation_module.F90: fixed a long lived bug in
->
+        do_forces. Rrf was not being used in the neighborlist correctly.
->
+        rcut was conssistently being set lowere than Rrf causing the dipole
->
+        cutoff region to be to small. Also led to the removal of the taper
->
+        region to buffer the dipole cutoff.
->
->
+-07-15 16:34  mmeineke
->
->
+        * libmdtools/: SimInfo.cpp, simulation_module.F90: working on
->
+        fixing ssd bug
->
->
+-07-15 14:56  gezelter
->
->
+        * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes
->
+        for the NPT ensembles
->
->
+-07-15 13:52  mmeineke
->
->
+        * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up
->
+        simSetup
->
->
+-07-15 12:57  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp,
->
+        SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90:
->
+        fixed some bugs, Changed entry_plug to info where appropriate
->
->
+-07-15 12:25  chuckv
->
->
+        * utils/sysBuild.ggo: added more command line arguments
->
->
+-07-15 12:11  gezelter
->
->
+        * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass:
->
+        Fixing force field line
->
->
+-07-15 12:10  gezelter
->
->
+        * libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp,
->
+        calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90,
->
+        calc_reaction_field.F90, calc_sticky_pair.F90: Fixing  pressure
->
+        tensor
->
->
+-07-15 10:50  gezelter
->
->
+        * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes
->
->
+-07-15 10:42  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp:
->
+        removed old outdated code
->
->
+-07-15 09:45  gezelter
->
->
+        * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx
->
->
+-07-15 09:28  gezelter
->
->
+        * libmdtools/Molecule.cpp: removing get_vx
->
->
+-07-14 22:28  gezelter
->
->
+        * libmdtools/NPTfm.cpp: Added NPTfm
->
->
+-07-14 22:27  gezelter
->
->
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
->
+        Bugfix in NPTim, fixes for NPTfm
->
->
+-07-14 22:08  gezelter
->
->
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
->
+        Checking in changes for NPTim
->
->
+-07-14 18:06  gezelter
->
->
+        * utils/Makefile: Broken SysBuilder
->
->
+-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
->
->
+-07-14 18:06  gezelter
->
->
+        * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some
->
+        debugging write statements
->
->
+-07-14 17:38  gezelter
->
->
+        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp,
->
+        NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom
->
->
+-07-14 16:48  mmeineke
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get
->
+        and set routines to Atom and DirectionalAtom
->
->
+-07-14 16:35  chuckv
->
->
+        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp,
->
+        sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder
->
+        that takes different cmd line arguments.
->
->
+-07-14 16:28  mmeineke
->
->
+        * libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp,
->
+        ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile,
->
+        SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors
->
+        were not being updated
->
->
+-07-14 10:04  gezelter
->
->
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on
->
+        NPTim
->
->
+-07-14 09:55  mmeineke
->
->
+        * forceFields/DUFF.frc: Switched the bond in the force field back
->
+        to constrained, to preserve energy
->
->
+-07-11 17:34  mmeineke
->
->
+        * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp,
->
+        Integrator.hpp: working on som integrator bugs
->
->
+-07-11 10:26  gezelter
->
->
+        * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting
->
+        to worry about all the strtok() calls in our code
->
->
+-07-11 09:49  gezelter
->
->
+        * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness
->
->
+-07-10 20:15  gezelter
->
->
+        * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and
->
+        eor.
->
->
+-07-10 17:15  mmeineke
->
->
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp,
->
+        SimInfo.cpp, Thermo.cpp: fixed some bugs
->
->
+-07-10 14:53  chuckv
->
->
+        * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp,
->
+        nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added
->
+        nanoBuilder and a general Lattice builder.
->
->
+-07-10 12:10  gezelter
->
->
+        * libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp,
->
+        Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff
->
->
+-07-09 17:14  mmeineke
->
->
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
->
+        Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp,
->
+        SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the
->
+        caclulation of HmatInverse.
->
->
+-07-09 10:34  mmeineke
->
->
+        * libBASS/MoleculeStamp.hpp: starting some work for xlate
->
->
+-07-09 10:33  mmeineke
->
->
+        * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff
->
->
+-07-09 08:56  gezelter
->
->
+        * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf
->
->
+-07-09 08:56  gezelter
->
->
+        * libBASS/Globals.cpp: Removed Qmass
->
->
+-07-08 21:15  gezelter
->
->
+        * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf
->
+        and NPTi
->
->
+-07-08 20:41  gezelter
->
->
+        * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf
->
->
+-07-08 16:10  gezelter
->
->
+        * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message]
->
->
+-07-08 16:06  gezelter
->
->
+        * libmdtools/NPTi.cpp: fixed box scaling
->
->
+-07-08 15:56  gezelter
->
->
+        * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp,
->
+        SimInfo.hpp, Thermo.cpp: NPTi
->
->
+-07-03 14:41  mmeineke
->
->
+        * libBASS/Makefile, libmdtools/Makefile, src/Makefile,
->
+        utils/Makefile, utils/bilayerSys.cpp:  cleaned up the dependecy
->
+        scripts in the makefiles
->
->
+-07-02 16:26  mmeineke
->
->
+        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
->
+        libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/Makefile, libmdtools/ReadWrite.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
->
+        libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile,
->
+        utils/Makefile: fixed the bugs introduced by switching the periodic
->
+        box to a matrix
->
->
+-07-01 17:39  gezelter
->
->
+        * libmdtools/do_Forces.F90: Fortran flexi-BOX
->
->
+-07-01 17:29  gezelter
->
->
+        * libmdtools/simulation_module.F90: Fixes for flexi-BOX
->
->
+-07-01 16:33  mmeineke
->
->
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h,
->
+        fortranWrapDefines.hpp, simulation_module.F90: working on adding
->
+        the box matrix to everything.
->
->
+-06-30 17:03  mmeineke
->
->
+        * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        src/oopse.cpp:
->
+        Updated the ChangeLog, and Converted most of the SImInfo to use
->
+        non-Isotropic boxes. wrapVector needs to be finished.
->
->
+-06-25 16:12  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds
->
+        to Harmonic bonds in the DUFF frc file
->
->
+        fixed constraints.
->
->
+-06-25 16:11  mmeineke
->
->
+        * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in
->
+        the DUFF frc file
->
->
+-06-24 17:51  gezelter
->
->
+        * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT.  Check them!
->
->
+-06-24 14:57  mmeineke
->
->
+        * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp,
->
+        libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into
->
+        the DUFF forcefield and BondExtensions.cpp
->
->
+-06-23 16:24  mmeineke
->
->
+        * libmdtools/Integrator.cpp: Doing some work to debug the
->
+        constraint code.
->
->
+-06-20 15:50  gezelter
->
->
+        * libmdtools/Integrator.hpp: NPT fix
->
->
+-06-20 15:29  mmeineke
->
->
+        * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
->
+        libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
->
+        libmdtools/Integrator.hpp, libmdtools/LJFF.cpp,
->
+        libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the
->
+        integrator and NVT seem to be working now.
->
->
+-06-20 11:49  gezelter
->
->
+        * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions
->
->
+-06-19 17:02  mmeineke
->
->
+        * forceFields/DUFF.frc, forceFields/LJFF.frc,
->
+        forceFields/LJ_FF.frc, forceFields/Makefile,
->
+        forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc,
->
+        libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp,
->
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile,
->
+        libmdtools/TraPPEFF.cpp: slowly converting to new integrator and
->
+        forcefield names.
->
->
+-06-19 14:21  mmeineke
->
->
+        * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp:
->
+        finished the basics of the integrator and SimSetup.cpp
->
->
+-06-19 14:11  mmeineke
->
->
+        * libmdtools/SimSetup.cpp:  doing some work on SimSetup to clean it
->
+        up / get it to work with the new Integrator.
->
->
+-06-18 17:20  mmeineke
->
->
+        * libmdtools/Symplectic.cpp: minor changes in an attempt to fix
->
+        output times.
->
->
+-06-17 16:56  mmeineke
->
->
+        * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters
->
+        fro the ghost Bend in TraPPE_Ex
->
->
+        some work on the integrator. ( incomplete)
->
->
+-06-17 16:55  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost
->
+        Bend in TraPPE_Ex
->
->
+-06-04 16:06  mmeineke
->
->
+        * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and
->
+        constrainB to the Symplectic integrator
->
->
+-05-30 16:32  mmeineke
->
->
+        * utils/bilayerSys.cpp: currently modifiying Symplectic to become
->
+        the basic integrator.
->
->
+        bilayerSys.cpp altered for building tb3.
->
->
+-05-30 16:31  mmeineke
->
->
+        * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp,
->
+        TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently
->
+        modifiying Symplectic to become the basic integrator.
->
->
+-05-30 15:19  mmeineke
->
->
+        * libmdtools/Integrator.hpp: added some member variables for
->
+        position, velocity, etc.
->
->
+-05-30 14:07  mmeineke
->
->
+        * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT
->
+        is now derived from Integrator
->
->
+-05-20 11:44  mmeineke
->
->
+        * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug.
->
->
+-05-17 11:57  mmeineke
->
->
+        * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be
->
+        working
->
->
+-05-16 16:37  mmeineke
->
->
+        * utils/bilayerSys.cpp: still working on the bilayer code
->
->
+-05-16 09:28  mmeineke
->
->
+        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some
->
+        work to overhaul sysbuild.
->
->
+-05-13 16:23  mmeineke
->
->
+        * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop
->
->
+-05-13 15:47  mmeineke
->
->
+        * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl,
->
+        beadLipid/water.mdl: Added bead lipid model to the sample directory
->
->
+-05-13 15:34  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into
->
+        the Trappe extended force field
->
->
+-05-13 12:01  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the
->
+        TraPPe_Ex forceField
->
->
+-05-09 14:51  mmeineke
->
->
+        * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field.
->
+        there were some duplicate entries
->
->
+        added a two chain lipid to the lipid.mdl in sample
->
->
+-05-09 14:51  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field.
->
+        there were some duplicate entries
->
->
+-05-09 11:56  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the
->
+        configure script
->
->
+        added the CH branching group to the TraPPE_Ex fource field
->
->
+-05-09 11:55  mmeineke
->
->
+        * ac-tools/configure.in: added the utils subdirectory to the
->
+        configure script
->
->
+-04-25 11:02  mmeineke
->
->
+        * utils/bilayerSys.cpp: i quick fix to th distance in the random
->
+        bilayer builder
->
->
+-04-24 21:00  mmeineke
->
->
+        * libmdtools/f_verlet_constrained.F90: added a new test for
->
+        constraint failure
->
->
+-04-17 16:54  mmeineke
->
->
+        * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp,
->
+        utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp,
->
+        utils/bilayerSys.cpp: fixed up sysBuild to where it should now
->
+        build our systems
->
->
+-04-16 16:11  mmeineke
->
->
+        * utils/: MoLocator.cpp, MoLocator.hpp: almost finished.
->
->
+-04-15 16:47  mmeineke
->
->
+        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys
->
+        and sysBuild both will build now. woot!
->
->
+-04-15 16:20  mmeineke
->
->
+        * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
->
+        bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp
->
->
+        sysBuild still need to write the bass file.
->
->
+        MoLocator.cpp is currently empty
->
->
+-04-15 15:40  chuckv
->
->
+        * forceFields/EAM_FF.frc, forceFields/agu3.eam,
->
+        forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam,
->
+        forceFields/pdu3.eam, forceFields/ptu3.eam,
->
+        libmdtools/ForceFields.hpp: Added eam force files...
->
->
+-04-15 11:37  chuckv
->
->
+        * libmdtools/EAM_FF.cpp: More eam work.
->
->
+-04-14 16:22  mmeineke
->
->
+        * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp,
->
+        utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp:
->
+        working on the system builder
->
->
+-04-14 16:16  chuckv
->
->
+        * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed
->
+        ordering on NVT calculation in integrators.
->
->
+-04-14 14:51  mmeineke
->
->
+        * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder,
->
+        obj/placeHolder:  working on a system builder
->
->
+-04-14 14:04  mmeineke
->
->
+        * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField
->
->
+        added sysBuild to the utils Makefile
->
->
+-04-14 14:03  mmeineke
->
->
+        * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added
->
+        Ghost bends to the TraPPE_Ex forceField
->
->
+-04-14 13:19  chuckv
->
->
+        * libmdtools/calc_eam.F90: Added first mangling of EAM.
->
->
+-04-11 13:46  mmeineke
->
->
+        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90,
->
+        simulation_module.F90: fixed a memory bug in Fortran, where
->
+        molMembershipArray was declared nLocal instead of nGlobal.
->
->
+-04-11 10:16  gezelter
->
->
+        * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp,
->
+        SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90,
->
+        fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress
->
+        for NPT
->
->
+-04-10 15:08  mmeineke
->
->
+        * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp:  added a
->
+        globalIndex counter to Molecule
->
->
+-04-10 11:35  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on
->
+        ConstantStress
->
->
+-04-10 11:27  mmeineke
->
->
+        * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup.
->
+        caused a miscalculation of nLocal.
->
->
+-04-10 11:21  mmeineke
->
->
+        * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90,
->
+        do_Forces.F90: fixed a bug in symplectic, where presure was only
->
+        being calculated the first time through.
->
->
+-04-09 11:20  chuckv
->
->
+        * samples/alkane/alkanes.mdl: added pentane to the alkane model
->
+        file
->
->
+-04-09 08:59  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp,
->
+        Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file
->
->
+-04-08 23:06  gezelter
->
->
+        * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp,
->
+        ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
->
+        SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp,
->
+        Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90,
->
+        calc_reaction_field.F90, calc_sticky_pair.F90,
->
+        fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and
->
+        NVT
->
->
+-04-08 17:38  chuckv
->
->
+        * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp,
->
+        libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/simulation_module.F90, samples/water/ssd.bass: It works
->
+        (kinda)...
->
->
+-04-08 16:35  gezelter
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp,
->
+        libmdtools/SimSetup.cpp: Fixes for NPT / NVT
->
->
+-04-08 12:16  chuckv
->
->
+        * libmdtools/: do_Forces.F90, neighborLists.F90,
->
+        simulation_module.F90: Moved expand neighborlist to init_FF.
->
->
+-04-08 10:20  chuckv
->
->
+        * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for
->
+        NVT
->
->
+-04-08 09:39  gezelter
->
->
+        * libmdtools/Verlet.cpp: fixes for nvt / npt
->
->
+-04-08 09:34  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp,
->
+        Thermo.cpp, Verlet.cpp: dt/2 fix in nvt
->
->
+-04-08 07:50  gezelter
->
->
+        * libmdtools/ExtendedSystem.cpp: Fixes for affine transform
->
->
+-04-08 07:44  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
->
+        Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the
->
+        NVT and NPT ensembles
->
->
+-04-07 16:42  gezelter
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
->
+        libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimSetup.cpp: Fixes for NPT and NVT
->
->
+-04-07 16:20  mmeineke
->
->
+        * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial
->
+        portion of SSD.
->
->
+-04-07 16:16  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, Symplectic.cpp:
->
+        doing some testing in sticky through Symplectic.
->
->
+-04-07 15:51  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT
->
->
+-04-07 15:50  chuckv
->
->
+        * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for
->
+        tau and virial.
->
->
+-04-07 15:06  mmeineke
->
->
+        * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp,
->
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90,
->
+        src/Makefile: bug fixes
->
->
+-04-07 11:56  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
->
+        StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp:
->
+        Many fixes to add extended system
->
->
+-04-07 09:30  gezelter
->
->
+        * src/Makefile: Fixed a bug caused by my experimentation
->
->
+-04-07 09:30  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp,
->
+        Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp:
->
+        Added ExtendedSystem infrastructure for NPT and NVT calculations
->
->
+-04-07 09:30  gezelter
->
->
+        * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS
->
->
+-04-04 23:07  gezelter
->
->
+        * src/Makefile: final mods to try a fortran compiler
->
->
+-04-04 22:39  gezelter
->
->
+        * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp,
->
+        fortranWrapDefines.hpp: Bug fixes for simulation module rewrites
->
->
+-04-04 21:56  gezelter
->
->
+        * libmdtools/: Makefile, atype_module.F90, do_Forces.F90,
->
+        fortranWrappers.cpp, wrappers.F90: bug fixes for compilation
->
->
+-04-04 21:45  gezelter
->
->
+        * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug
->
+        fixes to fortran wrappers
->
->
+-04-04 17:22  chuckv
->
->
+        * libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90,
->
+        calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90,
->
+        do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp,
->
+        simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets
->
+        smarter, fortran gets dumber...
->
->
+-04-04 14:57  mmeineke
->
->
+        * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90,
->
+        neighborLists.F90: fixed a memory read bug in neighborlist
->
->
+-04-04 14:47  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
->
+        SimInfo.hpp, Thermo.cpp: Changes for Extended System
->
->
+-04-04 14:16  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
->
+        SimInfo.hpp: Fixes for ExtendedSystem
->
->
+-04-03 20:57  gezelter
->
->
+        * libmdtools/ExtendedSystem.hpp: Added extended system header
->
->
+-04-03 20:57  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes
->
+        for extended system code
->
->
+-04-03 18:49  gezelter
->
->
+        * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to
->
+        extendedsystem
->
->
+-04-03 17:19  mmeineke
->
->
+        * libmdtools/Molecule.hpp: added some little fixes here and there.
->
->
+-04-03 17:01  mmeineke
->
->
+        * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before
->
+        initialize bug.
->
->
+-04-03 16:12  mmeineke
->
->
+        * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just
->
+        little things like deleteing unused variables and such.
->
->
+-04-03 15:57  mmeineke
->
->
+        * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to
->
+        simError.h also some fixes to Molecule.hpp
->
->
+-04-03 15:57  mmeineke
->
->
+        * libBASS/simError.h: a few fixes to simError.h
->
->
+-04-03 15:21  mmeineke
->
->
+        * libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c,
->
+        libBASS/simError.h, libmdtools/DumpWriter.cpp,
->
+        libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp,
->
+        libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp,
->
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp,
->
+        src/Makefile, src/oopse.cpp: fixed some small things with
->
+        simError.h
->
->
+-04-03 15:19  gezelter
->
->
+        * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT
->
->
+-04-03 14:58  gezelter
->
->
+        * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for
->
+        now)
->
->
+-04-03 08:42  gezelter
->
->
+        * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c:
->
+        Changed Readme, added some files
->
->
+-04-02 17:19  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp,
->
+        Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90:
->
+        dipoles mostly work, but there is a memory leak somewhere.
->
->
+-04-02 10:01  mmeineke
->
->
+        * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting
->
+        the proper atomIdents.
->
->
+-04-01 11:50  chuckv
->
->
+        * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
->
+        libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
->
+        samples/argon/argon.bass: more bug fixes....
->
->
+-04-01 11:49  mmeineke
->
->
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed
->
+        DumpWriter to be more robust to errors. also added a little
->
+        namespace to InitFromFile to wrap it's helper functions in MPI
->
->
+-03-31 17:09  chuckv
->
->
+        * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local
->
+        not zeroed.
->
->
+-03-31 16:50  chuckv
->
->
+        * libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp,
->
+        libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp,
->
+        libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
->
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90,
->
+        samples/alkane/butane.bass: Fixes in MPI force calc and in
->
+        Trappe_Ex parsing.
->
->
+-03-28 17:34  chuckv
->
->
+        * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp
->
->
+-03-28 16:45  chuckv
->
->
+        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
->
+        libmdtools/InitializeFromFile.cpp: Bug fixes in read-write
->
+        routines.
->
->
+-03-28 14:33  mmeineke
->
->
+        * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp,
->
+        Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a
->
+        bug where the Excludes were not being created properly
->
->
+-03-28 14:30  chuckv
->
->
+        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
->
+        libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes
->
+        and debugging mpi read write from file.
->
->
+-03-28 10:28  mmeineke
->
->
+        * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range
->
+        interactions in Trappe
->
->
+-03-27 18:33  chuckv
->
->
+        * libmdtools/: SimSetup.cpp, mpiSimulation.cpp,
->
+        mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue.
->
->
+-03-27 17:16  mmeineke
->
->
+        * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where
->
+        excludes were not being initialized
->
->
+-03-27 16:52  mmeineke
->
->
+        * src/Makefile: [no log message]
->
->
+-03-27 16:52  mmeineke
->
->
+        * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug.
->
->
+-03-27 16:07  mmeineke
->
->
+        * libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp,
->
+        Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp,
->
+        Verlet.cpp: fixed the compile time bugs, Source builds and links
->
->
+-03-27 15:48  mmeineke
->
->
+        * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few
->
+        more bugs.
->
->
+-03-27 15:40  mmeineke
->
->
+        * libmdtools/Molecule.cpp: added the Molecule.cpp file
->
->
+-03-27 15:39  mmeineke
->
->
+        * libmdtools/: Makefile, Molecule.hpp:  fixed the makefile
->
->
+-03-27 15:36  mmeineke
->
->
+        * libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
->
+        ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp,
->
+        SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs
->
->
+-03-27 15:12  mmeineke
->
->
+        * libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
->
+        Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp,
->
+        Verlet.cpp: I have implemeted Molecules everywhere I could remember
->
+        to.  will now attempt to compile.
->
->
+-03-27 14:21  mmeineke
->
->
+        * libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp,
->
+        SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished
->
+        updating SimSetup to initialize and use the new MPI division of
->
+        labour, and Molecule class
->
->
+-03-27 12:55  mmeineke
->
->
+        * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to
->
+        use Molecule
->
->
+-03-27 12:32  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp,
->
+        SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been
->
+        converted to the new Molecule model. TraPPE_Ex is currently being
->
+        updated.  SimSetups routines are writtten, but not yet called.
->
->
+-03-27 10:07  gezelter
->
->
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
->
+        mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom
->
+        numbering in MPI
->
->
+-03-27 09:30  mmeineke
->
->
+        * libmdtools/mpiSimulation.cpp: little bug fixes here and there.
->
->
+-03-26 20:49  gezelter
->
->
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to
->
+        fileio for MPI
->
->
+-03-26 18:14  gezelter
->
->
+        * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp,
->
+        mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug
->
+        fixes   many bug fixes
->
->
+-03-26 17:24  gezelter
->
->
+        * libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on
->
+        sequence of atoms on the other processors.  Node 0 now fires
->
+        potatoes at other processors to get them to send french fries back.
->
->
+-03-26 17:02  mmeineke
->
->
+        * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for
->
+        making the molecules is in place. ForceField needs to be updated
->
+        next.
->
->
+-03-26 16:54  mmeineke
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of
->
+        the "static" bugs in  Atom and Exclude
->
->
+-03-26 16:50  mmeineke
->
->
+        * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp,
->
+        SimSetup.cpp: still working on the SimSetup routine. also fixed
->
+        some things in Exclude.hpp
->
->
+-03-26 16:24  gezelter
->
->
+        * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp
->
->
+-03-26 16:23  gezelter
->
->
+        * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom
->
+        and Exclude list
->
->
+-03-26 16:04  gezelter
->
->
+        * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and
->
+        delete ranges of atoms
->
->
+-03-26 15:45  mmeineke
->
->
+        * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class
->
+        with static arrays similar to the Atom class
->
->
+-03-26 15:22  mmeineke
->
->
+        * libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm
->
+        overhauling the molecule class to contain it's own bonds, bends,
->
+        and torsions.
->
->
+        may god have mercy on my soul.
->
->
+-03-26 14:34  chuckv
->
->
+        * libmdtools/mpiSimulation.cpp: Finished globalIndex.
->
->
+-03-26 13:02  gezelter
->
->
+        * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp,
->
+        mpiSimulation.hpp: MPI stuff for passing out molecules
->
->
+-03-26 11:12  chuckv
->
->
+        * libmdtools/mpiSimulation.cpp: working on load balancing
->
->
+-03-26 10:37  chuckv
->
->
+        * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
->
+        samples/argon/argon.bass: Fixes for Parallel thermalization
->
->
+-03-26 09:55  mmeineke
->
->
+        * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in
->
+        THermo.cpp
->
->
+-03-25 17:54  chuckv
->
->
+        * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation
->
+        of potential energy and temperature.
->
->
+-03-25 09:29  mmeineke
->
->
+        * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy,
->
+        src/MPIobj/dummy, src/obj/dummy: [no log message]
->
->
+-03-25 09:29  mmeineke
->
->
+        * libBASS/MPIobj/dummy: added dummy files to keep the build
->
+        deirectories from being pruned.
->
->
+-03-24 20:07  gezelter
->
->
+        * samples/Makefile: moving tests to samples
->
->
+-03-24 20:06  gezelter
->
->
+        * 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
->
->
+        * ac-tools/configure.in: Tests are becoming samples
->
->
+-03-24 19:46  gezelter
->
->
+        * ac-tools/Make.conf.in: Added makefiles in tests directories
->
->
+-03-24 16:55  gezelter
->
->
+        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp,
->
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp,
->
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90,
->
+        libmdtools/calc_reaction_field.F90,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/simulation_module.F90: electrostatic changes for dipole
->
+        / RF separation
->
->
+-03-24 13:33  mmeineke
->
->
+        * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
->
+        do_Forces.F90: little bug fixes here and there
->
->
+-03-24 10:26  mmeineke
->
->
+        * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
->
+        where short range interactions were not being calculated.
->
->
+        removed some debug print statements
->
->
+-03-21 17:11  chuckv
->
->
+        * libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90,
->
+        do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90:
->
+        various write statements for debugging
->
->
+-03-21 16:26  chuckv
->
->
+        * forceFields/Makefile: added links to the makefile in forceFields
->
->
+-03-21 15:52  gezelter
->
->
+        * ac-tools/Make.conf.in, ac-tools/configure.in,
->
+        libmdtools/Makefile: Fixed F_MACH_DEP bug
->
->
+-03-21 15:37  gezelter
->
->
+        * ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in,
->
+        ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile,
->
+        libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend,
->
+        src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org,
->
+        autoconf fixes
->
->
+-03-21 14:58  gezelter
->
->
+        * LICENSE: Added license file
->
->
+-03-21 14:55  gezelter
->
->
+        * forceFields/Makefile: Fixed makefile
->
->
+-03-21 14:49  gezelter
->
->
+        * forceFields/Makefile: Makefile for forceFields
->
->
+-03-21 14:42  gezelter
->
->
+        * README: Readme changes
->
->
+-03-21 12:52  mmeineke
->
->
+        * src/Makefile: [no log message]
->
->
+-03-21 12:52  mmeineke
->
->
+        * libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends
->
->
+-03-21 12:42  mmeineke
->
->
+        * AUTHORS, ChangeLog, NEWS, Makefile, README,
->
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
->
+        ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in,
->
+        ac-tools/install-sh, forceFields/DipoleTest.frc,
->
+        forceFields/LJ_FF.frc, forceFields/TraPPE.frc,
->
+        forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp,
->
+        libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
->
+        libBASS/BASS_interface.h, libBASS/BASS_parse.c,
->
+        libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
->
+        libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
->
+        libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
->
+        libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp,
->
+        libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
->
+        libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
->
+        libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp,
->
+        libBASS/MakeStamps.hpp, libBASS/Makefile,
->
+        libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp,
->
+        libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.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_me.h,
->
+        libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
->
+        libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp,
->
+        utils/sfmakedepend, ac-tools/shtool,
->
+        libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp,
->
+        libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
->
+        libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
->
+        libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp,
->
+        libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp,
->
+        libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp,
->
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90,
->
+        libmdtools/Makefile, libmdtools/Molecule.hpp,
->
+        libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
->
+        libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp,
->
+        libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
->
+        libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp,
->
+        libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp,
->
+        libmdtools/Verlet.cpp, libmdtools/atype_module.F90,
->
+        libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
->
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/fForceField.h, libmdtools/fSimulation.h,
->
+        libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp,
->
+        libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
->
+        libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
->
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
->
+        libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
->
+        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
->
->
+-03-21 12:42  mmeineke
->
->
+        * AUTHORS, ChangeLog, NEWS, Makefile, README,
->
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
->
+        ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in,
->
+        ac-tools/install-sh, forceFields/DipoleTest.frc,
->
+        forceFields/LJ_FF.frc, forceFields/TraPPE.frc,
->
+        forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp,
->
+        libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
->
+        libBASS/BASS_interface.h, libBASS/BASS_parse.c,
->
+        libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
->
+        libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
->
+        libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
->
+        libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp,
->
+        libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
->
+        libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
->
+        libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp,
->
+        libBASS/MakeStamps.hpp, libBASS/Makefile,
->
+        libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp,
->
+        libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.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_me.h,
->
+        libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
->
+        libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp,
->
+        utils/sfmakedepend, ac-tools/shtool,
->
+        libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp,
->
+        libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
->
+        libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
->
+        libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp,
->
+        libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp,
->
+        libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp,
->
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp,
->
+        libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90,
->
+        libmdtools/Makefile, libmdtools/Molecule.hpp,
->
+        libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp,
->
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
->
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
->
+        libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp,
->
+        libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
->
+        libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp,
->
+        libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp,
->
+        libmdtools/Verlet.cpp, libmdtools/atype_module.F90,
->
+        libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
->
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
->
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
->
+        libmdtools/fForceField.h, libmdtools/fSimulation.h,
->
+        libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp,
->
+        libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
->
+        libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
->
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
->
+        libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
->
+        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
->

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Comparing: branches/mmeineke/OOPSE/ChangeLog (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs. trunk/OOPSE/ChangeLog (file contents), Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC

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Comparing:
branches/mmeineke/OOPSE/ChangeLog (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/ChangeLog (file contents), Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC