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

2004-03-17 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 like a good choice, next commit will seperate SMD and
        ZConstraint

2004-03-16 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

2004-03-02 15:32  tim

        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp,
        StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to
        support large file

2004-03-01 16:17  tim

        * utils/zsub.cpp: Fix a couple of bugs in zsub

2004-03-01 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

2004-02-24 11:36  tim

        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
        libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log
        message]

2004-02-24 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

2004-02-24 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

2004-02-17 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

2004-02-10 16:33  tim

        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
        libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp:
        single version of energy minimization is working.

2004-02-09 15:38  mmeineke

        * staticProps/: AllCorr.cpp, staticProps.cpp:  started a bug fix on
        the massive memory overusage by OOPSE

2004-02-09 09:48  chrisfen

        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the
        hardwired LJ_rcut

2004-02-06 19:14  tim

        * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log
        message]

2004-02-06 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

2004-02-06 14:05  tim

        * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add
        one more file into Makefile.in

2004-02-06 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

2004-02-04 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

2004-02-03 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

2004-02-03 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]

2004-02-03 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

2004-02-03 12:10  tim

        * libmdtools/Functor.hpp: Functor.hpp pass unit test

2004-02-03 10:21  tim

        * ChangeLog, libmdtools/Minimizer1D.cpp,
        libmdtools/Minimizer1D.hpp: begin unit test of minimizer

2004-02-02 15:29  tim

        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
        Adding GoldenSection and Brent LineSearch Method

2004-01-30 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

2004-01-30 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...

2004-01-29 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

2004-01-29 16:44  tim

        * libmdtools/MinimizerParameterSet.hpp: Adding
        MinimizerParameterSet class.

2004-01-28 17:44  tim

        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
        NLModel0 and NLModel1

2004-01-28 15:40  tim

        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
        of NLModel

2004-01-27 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

2004-01-27 15:34  gezelter

        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
        stuff

2004-01-27 14:39  gezelter

        * samples/water/ssd.bass: Longer run time to test SSD water in MPI

2004-01-27 14:39  gezelter

        * samples/metals/Au.bass: Longer run time to test gold in MPI

2004-01-27 14:38  gezelter

        * samples/argon/argon.bass: Longer run time to test argon

2004-01-27 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

2004-01-27 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

2004-01-27 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

2004-01-26 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

2004-01-26 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

2004-01-26 16:52  gezelter

        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians

2004-01-26 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

2004-01-26 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

2004-01-26 13:52  gezelter

        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies

2004-01-22 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

2004-01-21 17:16  tim

        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
        NLOPModel.hpp: constraint class in energy minimization

2004-01-20 15:34  tim

        * libmdtools/MinimizerBase.hpp: Adding energy minimization

2004-01-20 15:32  tim

        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer

2004-01-19 16:17  gezelter

        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
        more user-friendly

2004-01-19 13:51  chrisfen

        * forceFields/DUFF.frc: Updated the default water to SSD/E

2004-01-19 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

2004-01-19 11:10  gezelter

        * third-party/Makefile.in: Added a bunch of dummy targets so make
        won't complain

2004-01-19 11:10  gezelter

        * samples/lipid/5x5.bass: Fixed old bass file

2004-01-19 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

2004-01-19 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

2004-01-16 16:55  tim

        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
        eor file

2004-01-16 16:51  mmeineke

        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
        write eor files

2004-01-16 10:01  mmeineke

        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
        initialization of the AtomStruct

2004-01-15 16:57  chuckv

        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps

2004-01-15 10:51  gezelter

        * ac-tools/aclocal.m4: Changes for altivec

2004-01-15 09:22  gezelter

        * libmdtools/DumpWriter.cpp: Documented the Spud Toss

2004-01-14 23:33  gezelter

        * libmdtools/do_Forces.F90: changes for charge charge interactions

2004-01-14 20:14  gezelter

        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
        notifyCutoffs.F90: More work for adding charges

2004-01-14 17:41  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        src/Makefile.in: autoconf fixes

2004-01-14 11:28  mmeineke

        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug

2004-01-14 10:48  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        src/Makefile.in, third-party/Makefile.in: autoconf compatibility
        changes for icc8

2004-01-13 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)

2004-01-13 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

2004-01-13 17:11  tim

        * Functor.hpp, libmdtools/Functor.hpp: [no log message]

2004-01-13 16:22  tim

        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method

2004-01-13 15:35  tim

        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
        eor file whenever it is used instead of rewinding it

2004-01-13 15:04  tim

        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
        of writeFrame

2004-01-13 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

2004-01-12 17:54  tim

        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
        a bug in copying string

2004-01-12 15:37  tim

        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
        samples/water/ssd.bass: Dumpwriter only write out the atoms on
        master nodes

2004-01-10 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

2004-01-09 21:15  tim

        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub

2004-01-09 15:29  gezelter

        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)

2004-01-08 17:25  chuckv

        * libmdtools/DumpWriter.cpp: A work in progress...

2004-01-08 13:59  gezelter

        * libmdtools/DumpWriter.cpp: null terminate some strings just in
        case

2004-01-08 13:13  mmeineke

        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
        state bug.

2004-01-08 13:05  gezelter

        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter

2004-01-08 12:57  mmeineke

        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
        exstended state bug

2004-01-08 12:40  gezelter

        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter

2004-01-08 10:44  mmeineke

        * libmdtools/InitializeFromFile.cpp: added support for the ignore
        XS state info  flag

2004-01-07 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

2004-01-06 14:49  chuckv

        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
        performance fixes in the dipole dipole and reaction field code

2004-01-06 13:54  chuckv

        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
        little more sane

2004-01-05 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

2004-01-05 17:18  chuckv

        * libmdtools/do_Forces.F90: mangling forces even further

2004-01-05 17:18  chuckv

        * configure, ac-tools/configure.in: mpich mucking

2004-01-05 17:12  chuckv

        * libmdtools/do_Forces.F90: mangled do_forces...

2004-01-05 16:00  chuckv

        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
        libmdtools/do_Forces.F90: Added bitmask to do_forces property
        lookup

2003-12-29 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.

2003-12-22 16:26  chuckv

        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
        Fixes to profile code.

2003-12-19 15:36  mmeineke

        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
        timing.F90, timing.f90: More profiling fixes.

2003-12-19 15:19  chuckv

        * libmdtools/timing.f90: Another change for MPI in timing.

2003-12-19 15:17  chuckv

        * libmdtools/timing.f90: Small update to timing in MPI

2003-12-19 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

2003-12-19 12:25  mmeineke

        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
        some profiling routines

2003-12-19 10:12  mmeineke

        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
        and GofRomega
        
        additional work on randomBilayer

2003-12-19 10:12  mmeineke

        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
        GofRomega

2003-12-18 16:47  mmeineke

        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
        some profile functionality

2003-12-18 15:46  chuckv

        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
        Added functions for simple profiling in fortran.

2003-12-17 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.

2003-12-16 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.

2003-12-12 10:42  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
        gradients (to do minimizations)

2003-12-12 10:33  mmeineke

        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
        header

2003-12-10 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

2003-11-25 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

2003-11-21 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

2003-11-21 15:07  mmeineke

        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
        ing in the GofR,CosTheta

2003-11-21 14:31  chrisfen

        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
        a bug in SimInfo ordering of radii

2003-11-11 12:20  mmeineke

        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
        a min function.

2003-11-10 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.

2003-11-07 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.:

2003-11-07 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.

2003-11-06 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

2003-11-06 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

2003-11-06 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

2003-11-06 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.

2003-11-05 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

2003-11-03 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.

2003-10-31 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.

2003-10-31 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

2003-10-31 13:28  mmeineke

        * libBASS/Makefile.in: added template stuff to the Maikefile
        template

2003-10-30 13:59  gezelter

        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
        rList problems

2003-10-30 09:11  gezelter

        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
        queried before q0 was allocated.

2003-10-29 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

2003-10-29 15:40  mmeineke

        * libBASS/BASSlex.l: fixed a stdlib.h include error

2003-10-29 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.

2003-10-29 09:28  gezelter

        * configure, ac-tools/configure.in, libBASS/Makefile.in,
        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
        templates

2003-10-28 22:16  gezelter

        * src/Makefile.in: Refixed broken makefile

2003-10-28 22:06  gezelter

        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
        fixes

2003-10-28 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.

2003-10-28 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.

2003-10-28 15:42  gezelter

        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
        Portability fixes

2003-10-28 15:09  gezelter

        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
        src/Makefile.in: Compatibility fixes

2003-10-28 12:08  mmeineke

        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
        started work on template removal

2003-10-28 12:04  gezelter

        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
        trying to understand extern "C" stuff for pointers

2003-10-28 11:20  gezelter

        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility

2003-10-28 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.

2003-10-28 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

2003-10-28 11:02  gezelter

        * configure, ac-tools/aclocal.m4: mod file fixes and portability
        stuff

2003-10-27 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

2003-10-27 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.

2003-10-27 17:07  mmeineke

        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
        routines for the sysbuilder to work with simSetup

2003-10-27 11:20  gezelter

        * configure, ac-tools/configure.in, samples/water/ssd.bass,
        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild

2003-10-24 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

2003-10-24 12:36  gezelter

        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
        builder

2003-10-24 12:35  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
        merge problem

2003-10-23 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

2003-10-23 14:57  mmeineke

        * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
        to the init
        
        fixed an eam mpi parmeter setup bug

2003-10-23 14:57  mmeineke

        * forceFields/Makefile.in: added eam ForceField files to the init

2003-10-22 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.

2003-10-21 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;

2003-10-17 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.

2003-10-17 16:18  mmeineke

        * ac-tools/configure.in: added the staticProps directory to the
        build list for both configure  and configure.in

2003-10-17 16:17  mmeineke

        * configure: added the staticProps directory to the build list

2003-10-16 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.

2003-10-10 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

2003-10-09 17:09  mmeineke

        * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in
        a position where it will compile and run first runs.

2003-10-04 13:46  chuckv

        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
        samples/metals/Au.bass: Fixed bug in calc_eam.

2003-10-04 13:08  chuckv

        * samples/metals/init_au.in: added Au init file for eam.

2003-10-03 17:11  mmeineke

        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
        entahlpy from the statwriter and thermo.

2003-10-03 17:02  mmeineke

        * libmdtools/SimInfo.hpp: changed the formating ogf the error
        statements in simError
        
        added a function to get the maxCutoff

2003-10-03 17:01  mmeineke

        * libBASS/simError.c: changed the formating ogf the error
        statements in simError

2003-09-30 11:00  mmeineke

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
        f90Flags so they are no longer overwritten by the compiler.

2003-09-29 17:06  mmeineke

        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
        for conifig.in
        
        fixed wrappers to extern "C"

2003-09-29 17:06  mmeineke

        * ac-tools/configure.in: added mpif90 mod check back same for
        conifig.in

2003-09-29 17:05  mmeineke

        * configure: added mpif90 mod check back

2003-09-29 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

2003-09-29 12:38  mmeineke

        * libmdtools/GenericData.hpp: light change in syntax. no
        signifigant change.

2003-09-25 16:17  mmeineke

        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
        additional remarks from icc -w3 (extra verbose output)

2003-09-25 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

2003-09-25 13:54  gezelter

        * configure, ac-tools/configure.in: fixed a bug in configure

2003-09-25 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

2003-09-24 14:34  mmeineke

        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
        that it is called before the first Statistics are written.

2003-09-23 15:36  gezelter

        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
        bunch of Make.dep files to CVS

2003-09-23 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

2003-09-22 18:07  tim

        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
        SimInfo.hpp: fix bug in calculating maxCutoff

2003-09-22 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

2003-09-19 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.

2003-09-19 11:03  mmeineke

        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
        makefile

2003-09-19 11:01  gezelter

        * samples/water/ssd.bass: goofing off to test NPTf and NPTi

2003-09-19 11:01  gezelter

        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
        (nearly) conserved quantities for both NPTi and NPTf

2003-09-19 10:20  mmeineke

        * utils/Makefile.in: fixed a typo in the makefile.

2003-09-19 09:55  gezelter

        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
        samples/water/ssd.bass: [no log message]

2003-09-19 09:22  tim

        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]

2003-09-17 09:22  mmeineke

        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
        work with constraints.

2003-09-16 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.

2003-09-15 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

2003-09-12 11:20  gezelter

        * libmdtools/: Make.dep, Makefile.in: Added integrators to
        Makefile.in

2003-09-12 11:20  gezelter

        * ChangeLog: Entered changes for configure into ChangeLog

2003-09-09 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.

2003-09-09 15:34  mmeineke

        * ChangeLog: updated the ChangeLog

2003-09-05 17:45  gezelter

        * libmdtools/Make.dep: dependency on config.h

2003-09-05 17:36  gezelter

        * configure, ac-tools/aclocal.m4: fixed sprng problem

2003-09-05 16:29  gezelter

        * samples/metals/Makefile.in: New Makefile for metals sample

2003-09-05 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

2003-09-04 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.

2003-09-04 16:48  mmeineke

        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
        namespace.

2003-09-02 09:30  tim

        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
        PolicyByMass

2003-08-28 16:09  tim

        * ChangeLog, libmdtools/GenericData.cpp,
        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex

2003-08-27 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

2003-08-27 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.

2003-08-27 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

2003-08-26 15:37  tim

        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
        mpiSimulation.cpp: set default force substraction policy to
        PolicyByMass

2003-08-26 15:29  tim

        * libmdtools/Integrator.cpp: [no log message]

2003-08-26 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

2003-08-26 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

2003-08-26 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

2003-08-26 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)

2003-08-26 13:30  mmeineke

        * Makefile: changed the Makefiel a litle.

2003-08-25 17:17  gezelter

        * utils/sysbuilder/Makefile: More FreeBSD fixes

2003-08-25 16:51  gezelter

        * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
        libmdtools/Makefile, src/Makefile: [no log message]

2003-08-22 15:04  mmeineke

        * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
        frequency of output dumps.

2003-08-20 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

2003-08-20 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)

2003-08-20 14:41  mmeineke

        * libBASS/Globals.hpp: updated the Changelog.
        
        added some bug fixes for setting the random number generator seed
        value.

2003-08-20 14:41  mmeineke

        * ChangeLog: updated the Changelog.

2003-08-20 14:11  tim

        * libBASS/Globals.cpp, libmdtools/DUFF.cpp,
        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
        bend class

2003-08-20 10:13  mmeineke

        * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
        make links. added -f to ln -s.

2003-08-20 09:50  tim

        * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]

2003-08-20 09:34  tim

        * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
        ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
        printing

2003-08-18 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.

2003-08-15 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

2003-08-14 11:16  tim

        * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
        with average force substraction strategy

2003-08-13 16:20  chuckv

        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
        profiling code -DPROFILE.

2003-08-13 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

2003-08-12 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.

2003-08-12 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

2003-08-12 13:40  gezelter

        * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
        and new atypes in LJFF

2003-08-12 13:15  gezelter

        * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
        stuff...

2003-08-12 13:14  chuckv

        * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.

2003-08-12 13:04  chuckv

        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
        Missed del of files before.

2003-08-12 13:03  chuckv

        * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
        message]

2003-08-12 13:01  chuckv

        * utils/sysbuilder/Makefile: commit makefile

2003-08-12 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

2003-08-11 17:31  chuckv

        * utils/Makefile: Changed makefile to only build quicklate.

2003-08-11 17:25  chuckv

        * ac-tools/configure.in: added utils/sysbuilder to be built.

2003-08-11 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.

2003-08-11 14:41  tim

        * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
        moving zconstraint molecules to specified positions

2003-08-11 14:39  tim

        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]

2003-08-11 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.

2003-08-11 13:29  mmeineke

        * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
        degrees of freedom to account for zConstreints

2003-08-08 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.....

2003-08-08 12:48  mmeineke

        * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
        instance of Atom::setZ and Atom::getZ in ZConstaint.

2003-08-07 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

2003-08-06 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...

2003-08-01 11:18  tim

        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of
        Z-Constraint

2003-07-31 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

2003-07-31 10:38  tim

        * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters
        to the globals

2003-07-31 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.

2003-07-30 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.

2003-07-29 11:32  mmeineke

        * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
        working on the props code

2003-07-29 11:32  mmeineke

        * libBASS/Globals.cpp: [no log message]

2003-07-25 15:05  chuckv

        * samples/metals/: Au.bass, metals.mdl: Added bass models for
        metals

2003-07-25 15:00  chuckv

        * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90,
        notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam.

2003-07-24 16:22  chuckv

        * ac-tools/configure.in: Changed configure to look for both upper
        and lower cass .mod files

2003-07-24 14:57  chuckv

        * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for
        eam and do_forces.

2003-07-23 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....

2003-07-22 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.

2003-07-22 15:05  mmeineke

        * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes
        to read dump files

2003-07-22 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]

2003-07-22 11:41  mmeineke

        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp,
        SimSetup.cpp: Fixed a current time initialization bug in
        InitFromFile.

2003-07-21 16:27  mmeineke

        * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp,
        Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and
        friends to accomadate random file access

2003-07-21 11:23  mmeineke

        * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no
        one sets it.

2003-07-21 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.

2003-07-17 16:49  gezelter

        * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp,
        DumpReader.cpp: Started work on a DumpReader

2003-07-17 15:38  gezelter

        * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E

2003-07-17 15:32  gezelter

        * forceFields/DUFF.frc, libmdtools/DUFF.cpp,
        libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp:
        Changes for SSD/E

2003-07-17 14:38  mmeineke

        * libmdtools/do_Forces.F90: commented out an eam line

2003-07-17 14:32  chuckv

        * libmdtools/atype_module.F90: fixed spelling issue

2003-07-17 14:29  chuckv

        * libmdtools/: fInfo.c, status_module.F90: added info module

2003-07-17 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....

2003-07-16 16:49  chuckv

        * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF

2003-07-16 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.

2003-07-16 12:35  gezelter

        * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. 
        quickLate is now somewhat more intelligent about periodic
        boundaries and wrapping.

2003-07-16 11:40  chuckv

        * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists

2003-07-16 10:34  mmeineke

        * scripts/cleanSrc: added a quick wipe-and-update script for quick
        rebuilds on BoB

2003-07-15 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

2003-07-15 17:29  mmeineke

        * libmdtools/simulation_module.F90: removed some debugging print
        statements.

2003-07-15 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.

2003-07-15 16:34  mmeineke

        * libmdtools/: SimInfo.cpp, simulation_module.F90: working on
        fixing ssd bug

2003-07-15 14:56  gezelter

        * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes
        for the NPT ensembles

2003-07-15 13:52  mmeineke

        * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up
        simSetup

2003-07-15 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

2003-07-15 12:25  chuckv

        * utils/sysBuild.ggo: added more command line arguments

2003-07-15 12:11  gezelter

        * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass:
        Fixing force field line

2003-07-15 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

2003-07-15 10:50  gezelter

        * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes

2003-07-15 10:42  gezelter

        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp:
        removed old outdated code

2003-07-15 09:45  gezelter

        * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx

2003-07-15 09:28  gezelter

        * libmdtools/Molecule.cpp: removing get_vx

2003-07-14 22:28  gezelter

        * libmdtools/NPTfm.cpp: Added NPTfm

2003-07-14 22:27  gezelter

        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
        Bugfix in NPTim, fixes for NPTfm

2003-07-14 22:08  gezelter

        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
        Checking in changes for NPTim

2003-07-14 18:06  gezelter

        * utils/Makefile: Broken SysBuilder

2003-07-14 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

2003-07-14 18:06  gezelter

        * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some
        debugging write statements

2003-07-14 17:38  gezelter

        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp,
        NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom

2003-07-14 16:48  mmeineke

        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get
        and set routines to Atom and DirectionalAtom

2003-07-14 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.

2003-07-14 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

2003-07-14 10:04  gezelter

        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on
        NPTim

2003-07-14 09:55  mmeineke

        * forceFields/DUFF.frc: Switched the bond in the force field back
        to constrained, to preserve energy

2003-07-11 17:34  mmeineke

        * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp,
        Integrator.hpp: working on som integrator bugs

2003-07-11 10:26  gezelter

        * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting
        to worry about all the strtok() calls in our code

2003-07-11 09:49  gezelter

        * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness

2003-07-10 20:15  gezelter

        * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and
        eor.

2003-07-10 17:15  mmeineke

        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp,
        SimInfo.cpp, Thermo.cpp: fixed some bugs

2003-07-10 14:53  chuckv

        * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp,
        nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added
        nanoBuilder and a general Lattice builder.

2003-07-10 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

2003-07-09 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.

2003-07-09 10:34  mmeineke

        * libBASS/MoleculeStamp.hpp: starting some work for xlate

2003-07-09 10:33  mmeineke

        * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff

2003-07-09 08:56  gezelter

        * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf

2003-07-09 08:56  gezelter

        * libBASS/Globals.cpp: Removed Qmass

2003-07-08 21:15  gezelter

        * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf
        and NPTi

2003-07-08 20:41  gezelter

        * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf

2003-07-08 16:10  gezelter

        * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message]

2003-07-08 16:06  gezelter

        * libmdtools/NPTi.cpp: fixed box scaling

2003-07-08 15:56  gezelter

        * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp,
        SimInfo.hpp, Thermo.cpp: NPTi

2003-07-03 14:41  mmeineke

        * libBASS/Makefile, libmdtools/Makefile, src/Makefile,
        utils/Makefile, utils/bilayerSys.cpp:  cleaned up the dependecy
        scripts in the makefiles

2003-07-02 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

2003-07-01 17:39  gezelter

        * libmdtools/do_Forces.F90: Fortran flexi-BOX

2003-07-01 17:29  gezelter

        * libmdtools/simulation_module.F90: Fixes for flexi-BOX

2003-07-01 16:33  mmeineke

        * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h,
        fortranWrapDefines.hpp, simulation_module.F90: working on adding
        the box matrix to everything.

2003-06-30 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.

2003-06-25 16:12  mmeineke

        * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds
        to Harmonic bonds in the DUFF frc file
        
        fixed constraints.

2003-06-25 16:11  mmeineke

        * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in
        the DUFF frc file

2003-06-24 17:51  gezelter

        * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT.  Check them!

2003-06-24 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

2003-06-23 16:24  mmeineke

        * libmdtools/Integrator.cpp: Doing some work to debug the
        constraint code.

2003-06-20 15:50  gezelter

        * libmdtools/Integrator.hpp: NPT fix

2003-06-20 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.

2003-06-20 11:49  gezelter

        * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions

2003-06-19 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.

2003-06-19 14:21  mmeineke

        * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp:
        finished the basics of the integrator and SimSetup.cpp

2003-06-19 14:11  mmeineke

        * libmdtools/SimSetup.cpp:  doing some work on SimSetup to clean it
        up / get it to work with the new Integrator.

2003-06-18 17:20  mmeineke

        * libmdtools/Symplectic.cpp: minor changes in an attempt to fix
        output times.

2003-06-17 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)

2003-06-17 16:55  mmeineke

        * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost
        Bend in TraPPE_Ex

2003-06-04 16:06  mmeineke

        * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and
        constrainB to the Symplectic integrator

2003-05-30 16:32  mmeineke

        * utils/bilayerSys.cpp: currently modifiying Symplectic to become
        the basic integrator.
        
        bilayerSys.cpp altered for building tb3.

2003-05-30 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.

2003-05-30 15:19  mmeineke

        * libmdtools/Integrator.hpp: added some member variables for
        position, velocity, etc.

2003-05-30 14:07  mmeineke

        * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT
        is now derived from Integrator

2003-05-20 11:44  mmeineke

        * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug.

2003-05-17 11:57  mmeineke

        * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be
        working

2003-05-16 16:37  mmeineke

        * utils/bilayerSys.cpp: still working on the bilayer code

2003-05-16 09:28  mmeineke

        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some
        work to overhaul sysbuild.

2003-05-13 16:23  mmeineke

        * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop

2003-05-13 15:47  mmeineke

        * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl,
        beadLipid/water.mdl: Added bead lipid model to the sample directory

2003-05-13 15:34  mmeineke

        * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into
        the Trappe extended force field

2003-05-13 12:01  mmeineke

        * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the
        TraPPe_Ex forceField

2003-05-09 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

2003-05-09 14:51  mmeineke

        * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field.
        there were some duplicate entries

2003-05-09 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

2003-05-09 11:55  mmeineke

        * ac-tools/configure.in: added the utils subdirectory to the
        configure script

2003-04-25 11:02  mmeineke

        * utils/bilayerSys.cpp: i quick fix to th distance in the random
        bilayer builder

2003-04-24 21:00  mmeineke

        * libmdtools/f_verlet_constrained.F90: added a new test for
        constraint failure

2003-04-17 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

2003-04-16 16:11  mmeineke

        * utils/: MoLocator.cpp, MoLocator.hpp: almost finished.

2003-04-15 16:47  mmeineke

        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys
        and sysBuild both will build now. woot!

2003-04-15 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

2003-04-15 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...

2003-04-15 11:37  chuckv

        * libmdtools/EAM_FF.cpp: More eam work.

2003-04-14 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

2003-04-14 16:16  chuckv

        * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed
        ordering on NVT calculation in integrators.

2003-04-14 14:51  mmeineke

        * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder,
        obj/placeHolder:  working on a system builder

2003-04-14 14:04  mmeineke

        * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField
        
        added sysBuild to the utils Makefile

2003-04-14 14:03  mmeineke

        * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added
        Ghost bends to the TraPPE_Ex forceField

2003-04-14 13:19  chuckv

        * libmdtools/calc_eam.F90: Added first mangling of EAM.

2003-04-11 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.

2003-04-11 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

2003-04-10 15:08  mmeineke

        * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp:  added a
        globalIndex counter to Molecule

2003-04-10 11:35  gezelter

        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on
        ConstantStress

2003-04-10 11:27  mmeineke

        * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup.
        caused a miscalculation of nLocal.

2003-04-10 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.

2003-04-09 11:20  chuckv

        * samples/alkane/alkanes.mdl: added pentane to the alkane model
        file

2003-04-09 08:59  gezelter

        * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp,
        Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file

2003-04-08 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

2003-04-08 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)...

2003-04-08 16:35  gezelter

        * libBASS/Globals.cpp, libBASS/Globals.hpp,
        libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp,
        libmdtools/SimSetup.cpp: Fixes for NPT / NVT

2003-04-08 12:16  chuckv

        * libmdtools/: do_Forces.F90, neighborLists.F90,
        simulation_module.F90: Moved expand neighborlist to init_FF.

2003-04-08 10:20  chuckv

        * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for
        NVT

2003-04-08 09:39  gezelter

        * libmdtools/Verlet.cpp: fixes for nvt / npt

2003-04-08 09:34  gezelter

        * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp,
        Thermo.cpp, Verlet.cpp: dt/2 fix in nvt

2003-04-08 07:50  gezelter

        * libmdtools/ExtendedSystem.cpp: Fixes for affine transform

2003-04-08 07:44  gezelter

        * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
        Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the
        NVT and NPT ensembles

2003-04-07 16:42  gezelter

        * libBASS/Globals.cpp, libBASS/Globals.hpp,
        libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp,
        libmdtools/SimSetup.cpp: Fixes for NPT and NVT

2003-04-07 16:20  mmeineke

        * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial
        portion of SSD.

2003-04-07 16:16  mmeineke

        * libmdtools/: ForceFields.cpp, Symplectic.cpp: 
        doing some testing in sticky through Symplectic.

2003-04-07 15:51  gezelter

        * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT

2003-04-07 15:50  chuckv

        * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for
        tau and virial.

2003-04-07 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

2003-04-07 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

2003-04-07 09:30  gezelter

        * src/Makefile: Fixed a bug caused by my experimentation

2003-04-07 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

2003-04-07 09:30  gezelter

        * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS

2003-04-04 23:07  gezelter

        * src/Makefile: final mods to try a fortran compiler

2003-04-04 22:39  gezelter

        * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp,
        fortranWrapDefines.hpp: Bug fixes for simulation module rewrites

2003-04-04 21:56  gezelter

        * libmdtools/: Makefile, atype_module.F90, do_Forces.F90,
        fortranWrappers.cpp, wrappers.F90: bug fixes for compilation

2003-04-04 21:45  gezelter

        * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug
        fixes to fortran wrappers

2003-04-04 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...

2003-04-04 14:57  mmeineke

        * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90,
        neighborLists.F90: fixed a memory read bug in neighborlist

2003-04-04 14:47  gezelter

        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
        SimInfo.hpp, Thermo.cpp: Changes for Extended System

2003-04-04 14:16  gezelter

        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
        SimInfo.hpp: Fixes for ExtendedSystem

2003-04-03 20:57  gezelter

        * libmdtools/ExtendedSystem.hpp: Added extended system header

2003-04-03 20:57  gezelter

        * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes
        for extended system code

2003-04-03 18:49  gezelter

        * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to
        extendedsystem

2003-04-03 17:19  mmeineke

        * libmdtools/Molecule.hpp: added some little fixes here and there.

2003-04-03 17:01  mmeineke

        * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before
        initialize bug.

2003-04-03 16:12  mmeineke

        * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just
        little things like deleteing unused variables and such.

2003-04-03 15:57  mmeineke

        * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to
        simError.h also some fixes to Molecule.hpp

2003-04-03 15:57  mmeineke

        * libBASS/simError.h: a few fixes to simError.h

2003-04-03 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

2003-04-03 15:19  gezelter

        * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT

2003-04-03 14:58  gezelter

        * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for
        now)

2003-04-03 08:42  gezelter

        * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c:
        Changed Readme, added some files

2003-04-02 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.

2003-04-02 10:01  mmeineke

        * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting
        the proper atomIdents.

2003-04-01 11:50  chuckv

        * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
        libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
        samples/argon/argon.bass: more bug fixes....

2003-04-01 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

2003-03-31 17:09  chuckv

        * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local
        not zeroed.

2003-03-31 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.

2003-03-28 17:34  chuckv

        * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp

2003-03-28 16:45  chuckv

        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
        libmdtools/InitializeFromFile.cpp: Bug fixes in read-write
        routines.

2003-03-28 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

2003-03-28 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.

2003-03-28 10:28  mmeineke

        * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range
        interactions in Trappe

2003-03-27 18:33  chuckv

        * libmdtools/: SimSetup.cpp, mpiSimulation.cpp,
        mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue.

2003-03-27 17:16  mmeineke

        * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where
        excludes were not being initialized

2003-03-27 16:52  mmeineke

        * src/Makefile: [no log message]

2003-03-27 16:52  mmeineke

        * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug.

2003-03-27 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

2003-03-27 15:48  mmeineke

        * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few
        more bugs.

2003-03-27 15:40  mmeineke

        * libmdtools/Molecule.cpp: added the Molecule.cpp file

2003-03-27 15:39  mmeineke

        * libmdtools/: Makefile, Molecule.hpp:  fixed the makefile

2003-03-27 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

2003-03-27 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.

2003-03-27 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

2003-03-27 12:55  mmeineke

        * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to
        use Molecule

2003-03-27 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.

2003-03-27 10:07  gezelter

        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
        mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom
        numbering in MPI

2003-03-27 09:30  mmeineke

        * libmdtools/mpiSimulation.cpp: little bug fixes here and there.

2003-03-26 20:49  gezelter

        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to
        fileio for MPI

2003-03-26 18:14  gezelter

        * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp,
        mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug
        fixes   many bug fixes

2003-03-26 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.

2003-03-26 17:02  mmeineke

        * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for
        making the molecules is in place. ForceField needs to be updated
        next.

2003-03-26 16:54  mmeineke

        * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of
        the "static" bugs in  Atom and Exclude

2003-03-26 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

2003-03-26 16:24  gezelter

        * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp

2003-03-26 16:23  gezelter

        * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom
        and Exclude list

2003-03-26 16:04  gezelter

        * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and
        delete ranges of atoms

2003-03-26 15:45  mmeineke

        * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class
        with static arrays similar to the Atom class

2003-03-26 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.

2003-03-26 14:34  chuckv

        * libmdtools/mpiSimulation.cpp: Finished globalIndex.

2003-03-26 13:02  gezelter

        * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp,
        mpiSimulation.hpp: MPI stuff for passing out molecules

2003-03-26 11:12  chuckv

        * libmdtools/mpiSimulation.cpp: working on load balancing

2003-03-26 10:37  chuckv

        * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
        samples/argon/argon.bass: Fixes for Parallel thermalization

2003-03-26 09:55  mmeineke

        * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in
        THermo.cpp

2003-03-25 17:54  chuckv

        * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation
        of potential energy and temperature.

2003-03-25 09:29  mmeineke

        * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy,
        src/MPIobj/dummy, src/obj/dummy: [no log message]

2003-03-25 09:29  mmeineke

        * libBASS/MPIobj/dummy: added dummy files to keep the build
        deirectories from being pruned.

2003-03-24 20:07  gezelter

        * samples/Makefile: moving tests to samples

2003-03-24 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

2003-03-24 19:51  gezelter

        * ac-tools/configure.in: Tests are becoming samples

2003-03-24 19:46  gezelter

        * ac-tools/Make.conf.in: Added makefiles in tests directories

2003-03-24 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

2003-03-24 13:33  mmeineke

        * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
        do_Forces.F90: little bug fixes here and there

2003-03-24 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

2003-03-21 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

2003-03-21 16:26  chuckv

        * forceFields/Makefile: added links to the makefile in forceFields

2003-03-21 15:52  gezelter

        * ac-tools/Make.conf.in, ac-tools/configure.in,
        libmdtools/Makefile: Fixed F_MACH_DEP bug

2003-03-21 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

2003-03-21 14:58  gezelter

        * LICENSE: Added license file

2003-03-21 14:55  gezelter

        * forceFields/Makefile: Fixed makefile

2003-03-21 14:49  gezelter

        * forceFields/Makefile: Makefile for forceFields

2003-03-21 14:42  gezelter

        * README: Readme changes

2003-03-21 12:52  mmeineke

        * src/Makefile: [no log message]

2003-03-21 12:52  mmeineke

        * libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends

2003-03-21 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

2003-03-21 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

Revision:	1108
Committed:	Wed Apr 14 15:37:41 2004 UTC (20 years, 2 months ago) by tim
File size:	89876 byte(s)
Log Message:	Change DumpWriter and InitFromFile