[ViewVC] Annotation of: OpenMD/trunk/ChangeLog

2005-04-15 17:03  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
        UseTheForce/ForceFieldCreator.hpp,
        UseTheForce/ForceFieldFactory.cpp,
        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
        UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90,
        UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h,
        UseTheForce/notifyCutoffs.F90,
        UseTheForce/notifyCutoffs_interface.F90,
        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
        UseTheForce/DarkSide/atype.F90,
        UseTheForce/DarkSide/atype_interface.F90,
        UseTheForce/DarkSide/eam.F90,
        UseTheForce/DarkSide/eam_interface.F90,
        UseTheForce/DarkSide/eam_interface.h,
        UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/electrostatic_interface.F90,
        UseTheForce/DarkSide/electrostatic_interface.h,
        UseTheForce/DarkSide/force_globals.F90,
        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
        UseTheForce/DarkSide/lj_interface.F90,
        UseTheForce/DarkSide/lj_interface.h,
        UseTheForce/DarkSide/neighborLists.F90,
        UseTheForce/DarkSide/reactionField.F90,
        UseTheForce/DarkSide/shapes.F90,
        UseTheForce/DarkSide/shapes_interface.F90,
        UseTheForce/DarkSide/shapes_interface.h,
        UseTheForce/DarkSide/simParallel.F90,
        UseTheForce/DarkSide/simParallel_interface.F90,
        UseTheForce/DarkSide/simParallel_interface.h,
        UseTheForce/DarkSide/simulation.F90,
        UseTheForce/DarkSide/simulation_interface.F90,
        UseTheForce/DarkSide/simulation_interface.h,
        UseTheForce/DarkSide/sticky.F90,
        UseTheForce/DarkSide/sticky_interface.F90,
        UseTheForce/DarkSide/sticky_interface.h,
        UseTheForce/DarkSide/switcheroo.F90,
        applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h,
        applications/dynamicProps/CrossTimeCorrFunc.cpp,
        applications/dynamicProps/CrossTimeCorrFunc.hpp,
        applications/dynamicProps/DipoleCorrFunc.cpp,
        applications/dynamicProps/DipoleCorrFunc.hpp,
        applications/dynamicProps/DynamicProps.cpp,
        applications/dynamicProps/DynamicPropsCmd.c,
        applications/dynamicProps/DynamicPropsCmd.h,
        applications/dynamicProps/FrameTimeCorrFunc.hpp,
        applications/dynamicProps/ParticleTimeCorrFunc.cpp,
        applications/dynamicProps/ParticleTimeCorrFunc.hpp,
        applications/dynamicProps/RCorrFunc.cpp,
        applications/dynamicProps/RCorrFunc.hpp,
        applications/dynamicProps/TimeCorrFunc.cpp,
        applications/dynamicProps/TimeCorrFunc.hpp,
        applications/dynamicProps/VCorrFunc.cpp,
        applications/dynamicProps/VCorrFunc.hpp,
        applications/nanoRodBuilder/GeometryBuilder.cpp,
        applications/nanoRodBuilder/GeometryBuilder.hpp,
        applications/nanoRodBuilder/nanorodBuilder.cpp,
        applications/nanoRodBuilder/nanorodBuilderCmd.c,
        applications/nanoRodBuilder/nanorodBuilderCmd.h,
        applications/oopse/oopse.cpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        applications/simpleBuilder/simpleBuilderCmd.c,
        applications/simpleBuilder/simpleBuilderCmd.h,
        applications/staticProps/GofAngle2.cpp,
        applications/staticProps/GofAngle2.hpp,
        applications/staticProps/GofR.cpp,
        applications/staticProps/GofR.hpp,
        applications/staticProps/GofRAngle.cpp,
        applications/staticProps/GofRAngle.hpp,
        applications/staticProps/GofXyz.cpp,
        applications/staticProps/GofXyz.hpp,
        applications/staticProps/RadialDistrFunc.cpp,
        applications/staticProps/RadialDistrFunc.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
        brains/Exclude.hpp, brains/ForceManager.cpp,
        brains/ForceManager.hpp, brains/MoleculeCreator.cpp,
        brains/MoleculeCreator.hpp, brains/Register.cpp,
        brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
        brains/SimSnapshotManager.hpp, brains/Snapshot.cpp,
        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp,
        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
        brains/fSimulation.h, constraints/ConstraintElem.hpp,
        constraints/ConstraintPair.hpp, constraints/Rattle.cpp,
        constraints/Rattle.hpp, constraints/ZconsStruct.hpp,
        constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
        integrators/DLM.hpp, integrators/Integrator.cpp,
        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
        integrators/NVT.cpp, integrators/NVT.hpp,
        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
        integrators/Velocitizer.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp,
        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
        io/ChargeAtomTypesSectionParser.hpp,
        io/DirectionalAtomTypesSectionParser.cpp,
        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
        io/Globals.cpp, io/Globals.hpp,
        io/LennardJonesAtomTypesSectionParser.cpp,
        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
        io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp,
        io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp,
        io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp,
        io/SectionParser.cpp, io/SectionParser.hpp,
        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
        io/StatWriter.cpp, io/StatWriter.hpp,
        io/StickyAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.hpp,
        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp,
        io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c,
        io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h,
        io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp,
        lattice/CubicLattice.hpp, lattice/FCCLattice.cpp,
        lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
        lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp,
        lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp,
        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
        math/ParallelRandNumGen.hpp, math/Polynomial.hpp,
        math/Quaternion.hpp, math/RandNumGen.hpp,
        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
        math/RectMatrix.hpp, math/SeqRandNumGen.cpp,
        math/SeqRandNumGen.hpp, math/SquareMatrix.hpp,
        math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp,
        minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp,
        minimizers/Minimizer.cpp, minimizers/Minimizer.hpp,
        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
        minimizers/MinimizerFactory.hpp,
        minimizers/MinimizerParameterSet.cpp,
        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
        primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp,
        primitives/Molecule.cpp, primitives/Molecule.hpp,
        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
        primitives/Torsion.cpp, primitives/Torsion.hpp,
        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
        profiling/timing.F90, restraints/Restraints.cpp,
        restraints/Restraints.hpp,
        restraints/ThermoIntegrationForceManager.cpp,
        restraints/ThermoIntegrationForceManager.hpp,
        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
        selection/NameFinder.cpp, selection/NameFinder.hpp,
        selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp,
        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp,
        selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp,
        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
        types/DirectionalAtomType.hpp, types/FixedBondType.hpp,
        types/HarmonicBendType.hpp, types/HarmonicBondType.hpp,
        types/MakeStamps.cpp, types/MakeStamps.hpp,
        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
        types/MorseBondType.hpp, types/OplsTorsionType.hpp,
        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
        types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp,
        types/QuarticBondType.hpp, types/QuarticTorsionType.hpp,
        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
        types/TorsionType.hpp, types/UreyBradleyBendType.hpp,
        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp,
        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
        utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp,
        utils/NumericConstant.hpp, utils/OOPSEConstant.hpp,
        utils/PropertyMap.cpp, utils/PropertyMap.hpp,
        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
        utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp,
        utils/any.hpp, utils/definitions.F90, utils/fError.c,
        utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h,
        utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h,
        utils/residentMem.h, utils/simError.c, utils/simError.h,
        utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp,
        visitors/AtomData.hpp, visitors/AtomVisitor.cpp,
        visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp,
        visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp,
        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp,
        visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp,
        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
        been drafted to perform our indentation services

2005-04-15 17:03  gezelter

        * configure, ac-tools/configure.in: Jedi mind-trick warning
        messages have been added to make users ignore CGAL.

2005-04-15 13:41  tim

        * make/Makefile.in: fix make install

2005-04-15 13:41  tim

        * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
        add  Makefile of samples

2005-04-15 13:33  tim

        * samples/: lipid/Makefile, water/dimer/Makefile,
        water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
        installed correctly

2005-04-14 16:41  gezelter

        * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
        scripts/filepp, scripts/filepp.in: configure now searches for perl
        to use with filepp

2005-04-14 16:20  gezelter

        * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
        MoLocator

2005-04-14 14:12  gezelter

        * LICENSE: [no log message]

2005-04-14 11:10  chuckv

        * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
        nanorodbuilder now exit's when libCGAL is not present.

2005-04-14 10:20  tim

        * src/io/make_nodes.h: fix one more warning message in make_nodes

2005-04-13 18:36  chuckv

        * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
        interface name for SGI Compiler

2005-04-13 18:29  chrisfen

        * samples/water/ssde/ssde.md: oops...  bad sample

2005-04-13 18:00  chuckv

        * src/config.h.in: Change typo in CGAL.

2005-04-13 17:43  tim

        * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
        selection/SelectionCompiler.hpp: fix some warning messages

2005-04-13 17:30  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        make/Makefile.in, src/config.h.in,
        src/applications/nanoRodBuilder/Makefile,
        src/applications/nanoRodBuilder/Makefile.in,
        src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
        checks

2005-04-13 15:36  chuckv

        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
        DarkSide/LJ.F90, DarkSide/electrostatic.F90,
        DarkSide/electrostatic_interface.F90,
        DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90,
        DarkSide/lj_interface.h, DarkSide/sticky.F90,
        DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
        destroy methods for Fortran modules.

2005-04-13 15:17  chuckv

        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
        shapes_interface.h: Added destroy method to clean up memory

2005-04-13 13:41  tim

        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp,
        primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp,
        types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
        fixed

2005-04-12 17:44  chuckv

        * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
        for nanoRodBuilder.

2005-04-12 17:42  tim

        * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
        simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
        and simpleBuilder(forget to delete lattice)

2005-04-12 17:33  tim

        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
        refactory lattice

2005-04-12 17:07  tim

        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
        CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
        Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
        LatticeFactory and LatticeCreator

2005-04-12 16:58  tim

        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
        applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
        brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp,
        lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp,
        lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
        lattice/Makefile: refactory LatticeFactory and LatticeCreator

2005-04-12 16:28  gezelter

        * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
        vector_class.F90: cleaned up vector_class memory leak fix by
        deallocating in reverse order of how we allocated.  Also migrated
        MoLocator into utils directory

2005-04-12 16:27  gezelter

        * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
        Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
        LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
        directory

2005-04-12 16:27  gezelter

        * src/applications/: nanoRodBuilder/BaseLattice.cpp,
        nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
        nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp,
        nanoRodBuilder/LatticeCreator.hpp,
        nanoRodBuilder/LatticeFactory.cpp,
        nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile,
        nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp,
        nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp,
        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile,
        simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp,
        simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
        these files are now redundant

2005-04-12 16:27  gezelter

        * src/UseTheForce/DarkSide/: atype_interface.F90,
        atype_interface.h: cleaned up memory leak fix

2005-04-12 16:26  gezelter

        * make/Makefile.in: added lattice subdirectory

2005-04-12 15:57  chrisfen

        * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
        a space by accident

2005-04-12 15:56  chrisfen

        * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
        quadrupole sample

2005-04-12 15:56  chrisfen

        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
        samples

2005-04-12 13:30  tim

        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
        type in fortran side

2005-04-12 12:45  chuckv

        * src/utils/vector_class.F90: Further changes to vector_class
        destroy function.

2005-04-12 12:39  chuckv

        * src/utils/vector_class.F90: Fixed pointer memory leak in
        vector_class.

2005-04-12 12:12  chuckv

        * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
        DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
        DarkSide/eam.F90, DarkSide/eam_interface.F90,
        DarkSide/eam_interface.h: Updates to deallocate object in fortran.

2005-04-12 09:24  chrisfen

        * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
        output

2005-04-11 19:29  chuckv

        * src/: UseTheForce/DarkSide/atype.F90,
        applications/nanoRodBuilder/Makefile: Changes to delete atypes...

2005-04-11 19:28  chuckv

        * src/utils/vector_class.F90: Added code to delete vector.

2005-04-11 17:03  chuckv

        * samples/metals/nanorod/: Au_nanoparticle.md,
        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
        aren't these here?

2005-04-11 16:58  tim

        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
        basic_ifstrstream

2005-04-11 16:37  chuckv

        * make/Makefile.in,
        src/applications/nanoRodBuilder/BaseLattice.cpp,
        src/applications/nanoRodBuilder/BaseLattice.hpp,
        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
        src/applications/nanoRodBuilder/Lattice.cpp,
        src/applications/nanoRodBuilder/Lattice.hpp,
        src/applications/nanoRodBuilder/LatticeCreator.cpp,
        src/applications/nanoRodBuilder/LatticeCreator.hpp,
        src/applications/nanoRodBuilder/LatticeFactory.cpp,
        src/applications/nanoRodBuilder/LatticeFactory.hpp,
        src/applications/nanoRodBuilder/Makefile,
        src/applications/nanoRodBuilder/MoLocator.cpp,
        src/applications/nanoRodBuilder/MoLocator.hpp,
        src/applications/nanoRodBuilder/nanoBuilder.ggo,
        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
        src/applications/nanoRodBuilder/nanorodBuilder.ggo,
        src/applications/nanoRodBuilder/nanorodBuilderCmd.c,
        src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing
        nanoRodBuilder application (may not work yet).  ((Doesn't work
        yet.)) (((May never work....)))

2005-04-11 15:54  tim

        * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
        prepareVisitor in Dump2XYZ

2005-04-11 15:19  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
        quadrupoles.  look!  it's divide by 3 like stone says!

2005-04-11 15:18  chrisfen

        * forceFields/DUFF2.frc: fixing of the quadrupoles

2005-04-11 15:16  tim

        * src/selection/Token.hpp: change the parameter name in
        constructors

2005-04-11 14:49  gezelter

        * make/Makefile.in: One more bug fix for GNU make versions < 3.80

2005-04-11 14:06  gezelter

        * make/Makefile.in: Fixed the uc and lc functions for GNU make
        versions < 3.80

2005-04-11 11:13  gezelter

        * make/Makefile.in, src/UseTheForce/Makefile,
        src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
        some stuff to clean out module files during "make clean"

2005-04-08 17:13  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
        interactions should be working with a remaining question of
        interaction magnitude

2005-04-08 17:12  chrisfen

        * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
        samples

2005-04-08 13:48  chrisfen

        * samples/water/ssd/ssd.md: oops...  messed up a sample

2005-04-08 09:43  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
        charge-dipole interactions

2005-04-08 09:42  chrisfen

        * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
        ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole

2005-04-08 09:41  chrisfen

        * forceFields/DUFF2.frc: added Cl- and Na+

2005-04-06 18:59  tim

        * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser

2005-04-05 18:09  tim

        * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
        SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
        in atom type name;clean the code a little bit

2005-03-29 16:00  tim

        * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug
        in converting rotation matrix to quaternion

2005-03-28 17:41  tim

        * src/visitors/LipidTransVisitor.cpp: fixed the wrapping

2005-03-28 17:30  tim

        * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do
        the wrapping

2005-03-28 10:54  tim

        * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the
        dimension of histogram

2005-03-22 11:38  tim

        * make/Makefile.in, src/applications/dump2Xyz/Makefile,
        src/applications/dynamicProps/Makefile,
        src/applications/oopse/Makefile,
        src/applications/simpleBuilder/Makefile,
        src/applications/staticProps/Makefile: avoid building parallel
        executable for dump2XYZ, simpleBuilder, staticProps and
        dynamicProps

2005-03-21 17:34  chrisfen

        * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the
        forcefield files

2005-03-21 15:51  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
        DarkSide/reactionField.F90: Make sure electrostatic_module provides
        data for reaction_field

2005-03-21 15:50  chrisfen

        * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff.  HE
        WILL CHANGE THIS BACK, RIGHT?

2005-03-21 14:23  gezelter

        * src/UseTheForce/DarkSide/electrostatic.F90: constant back to
        correct value

2005-03-21 14:22  gezelter

        * make/Makefile.in: fixed an install-related bug. 
        $(InstallCommand) had been set to $(InstallData)

2005-03-15 09:21  gezelter

        * src/integrators/Integrator.cpp: VelocityVerletIntegrator already
        deletes and Nullifies restWriter, so Integrator shouldn't do it.

2005-03-15 09:20  gezelter

        * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos

2005-03-13 02:39  gezelter

        * src/UseTheForce/DarkSide/electrostatic.F90: first run at
        charge-quadrupole interactions

2005-03-12 14:12  chrisfen

        * samples/: Makefile.in, thermoIntegration/liquid/Makefile,
        thermoIntegration/solid/Makefile: forgot a couple of makefiles

2005-03-12 14:05  chrisfen

        * samples/thermoIntegration/liquid/ssde.in,
        samples/thermoIntegration/liquid/ssde.md,
        samples/thermoIntegration/liquid/water.md,
        samples/thermoIntegration/solid/idealCrystal.in,
        samples/thermoIntegration/solid/ssde.in,
        samples/thermoIntegration/solid/ssde.md,
        samples/thermoIntegration/solid/ssde.zang0,
        samples/thermoIntegration/solid/water.md,
        samples/water/tip3p_ice/tp3.md,
        src/UseTheForce/DarkSide/sticky.F90,
        src/restraints/ThermoIntegrationForceManager.cpp: added some
        samples

2005-03-11 12:50  tim

        * src/: brains/SimCreator.cpp,
        io/MultipoleAtomTypesSectionParser.cpp: fix a typo in
        MultipoleAtomTypesSectionParser

2005-03-11 10:55  tim

        * src/brains/SimInfo.cpp: pairs inside cutoff group should not be
        excluded

2005-03-11 10:53  gezelter

        * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for
        quadrupoles

2005-03-11 10:52  gezelter

        * forceFields/DUFF2.frc: quadrupoles for SSD models

2005-03-11 10:00  tim

        * ChangeLog, doc/SelectionExpression.html,
        doc/classoopse_1_1StuntDouble.png, doc/definition.jpg,
        doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png,
        src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp,
        src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp,
        src/selection/TokenMap.cpp: clean up SimInfo; modify the images of
        SelectionExpression.html

2005-03-10 19:43  chrisfen

        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
        MPI restraints

2005-03-10 18:56  tim

        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
        and cutoff group

2005-03-10 17:06  gezelter

        * src/types/MorseBondType.hpp: fixed a doxygen problem

2005-03-10 16:51  gezelter

        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
        the split dipole test cases

2005-03-10 16:51  gezelter

        * doc/SelectionExpression.html: updated some documentation

2005-03-10 15:40  gezelter

        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
        Makefile: LinkedList removal project starts now

2005-03-10 15:28  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
        using map to replace link list

2005-03-10 14:11  tim

        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
        case  of split dipole

2005-03-10 14:10  chrisfen

        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
        src/io/RestWriter.cpp,
        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
        builds...

2005-03-10 13:44  tim

        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
        adding test case for split dipole

2005-03-10 12:54  gezelter

        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
        support for split dipoles

2005-03-10 11:27  chrisfen

        * samples/water/tip3p_ice/tp3.md,
        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
        restraints

2005-03-10 11:15  chrisfen

        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
        src/UseTheForce/ForceFields.hpp,
        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints

2005-03-10 11:14  tim

        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
        src/io/MultipoleAtomTypesSectionParser.cpp,
        src/selection/SelectionEvaluator.cpp: minor change

2005-03-10 10:10  chrisfen

        * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
        src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
        src/integrators/Integrator.cpp, src/integrators/Integrator.hpp,
        src/integrators/VelocityVerletIntegrator.cpp,
        src/integrators/VelocityVerletIntegrator.hpp,
        src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp,
        src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp,
        src/io/RestReader.hpp, src/io/RestWriter.cpp,
        src/io/RestWriter.hpp, src/io/RestraintReader.cpp,
        src/io/RestraintWriter.cpp, src/restraints/Makefile,
        src/restraints/Restraints.cpp, src/restraints/Restraints.hpp,
        src/restraints/ThermoIntegrationForceManager.cpp,
        src/restraints/ThermoIntegrationForceManager.hpp: First commit of
        the new restraints code

2005-03-09 13:48  tim

        * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
        IndexFinder

2005-03-09 13:46  tim

        * src/: applications/dump2Xyz/Dump2XYZ.ggo,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h,
        selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
        fix compilation issue

2005-03-09 12:58  tim

        * forceFields/DUFF2.frc, scripts/filepp,
        src/UseTheForce/EAM_FF.cpp,
        src/io/MultipoleAtomTypesSectionParser.cpp,
        src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
        in SectionParser (lineNo is not updated)

2005-03-09 12:30  tim

        * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dump2Xyz/Dump2XYZ.ggo,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp,
        brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp,
        io/ChargeAtomTypesSectionParser.hpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile,
        io/MultipoleAtomTypesSectionParser.cpp,
        io/MultipoleAtomTypesSectionParser.hpp,
        io/SectionParserManager.cpp, selection/Makefile,
        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
        types/AtomType.cpp, types/DirectionalAtomType.cpp,
        visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp,
        visitors/OtherVisitor.hpp: adding IndexFinder which is used to
        select the molecules; Seperate ElectrostaticAtomTypesSectionParser
        into ChargeAtomTypesSectionParser and
        MultipoleAtomTypesSectionParser;remove print dipole option from
        Dump2XYZ;

2005-03-09 12:28  tim

        * forceFields/DUFF2.frc: change the format of DUFF2

2005-03-09 10:44  gezelter

        * src/UseTheForce/DarkSide/: electrostatic.F90,
        electrostatic_interface.F90, electrostatic_interface.h: new
        electrostatic module

2005-03-09 09:26  gezelter

        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
        DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
        and fixed quadrupole stuff

2005-03-09 09:25  gezelter

        * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
        for outdated charge and dipole interfaces

2005-03-08 16:08  gezelter

        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
        mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
        charge-dipole test cases

2005-03-08 16:07  gezelter

        * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
        OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
        strange icc8 bug (we think).

2005-03-08 16:07  gezelter

        * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!

2005-03-08 16:07  gezelter

        * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
        Unification Project

2005-03-08 16:07  gezelter

        * src/io/Globals.cpp: Dunno

2005-03-08 16:06  gezelter

        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
        OOPSE_itoa and checking a NULL left over from the LinkedList days

2005-03-08 16:06  gezelter

        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
        atype_interface.F90, atype_interface.h, charge.F90,
        charge_interface.F90, charge_interface.h, dipole.F90,
        dipole_interface.F90, dipole_interface.h: electrostatic unification
        project fixed an uninitialized variable in Lennard Jones mixing map

2005-03-08 16:05  gezelter

        * src/UseTheForce/doForces.F90: electrostatic unification project

2005-03-08 16:05  gezelter

        * samples/water/dimer/: two.md, water.md: making some cool test
        cases

2005-03-08 16:05  gezelter

        * forceFields/DUFF2.frc: Added a charge for Chlorine

2005-03-07 17:39  tim

        * src/: brains/SimInfo.cpp, io/DumpReader.cpp,
        math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
        primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
        Fixing a bug in BitSet.cpp

2005-03-04 10:28  gezelter

        * src/config.h.in: Cleaning up config.h.in by adding comments

2005-03-04 10:28  gezelter

        * configure, ac-tools/configure.in, make/Makefile.in,
        src/brains/SimCreator.cpp: SPRNG eradication project

2005-03-03 09:40  tim

        * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
        missing atom type problem)

2005-03-02 11:29  tim

        * src/math/RandNumGen.hpp: adding base class of Random Number
        generator

2005-03-02 11:28  tim

        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
        Velocitizer is not initialized which causes a seg fault

2005-03-02 10:36  tim

        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
        integrators/Velocitizer.hpp, math/Makefile,
        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp,
        math/SeqRandNumGen.hpp: remove default parameter from
        MersenneTwister.hpp which causes all kinds of trouble.  Refactory
        random number generator

2005-03-02 02:32  tim

        * test/math/testRandNumGen.cpp: Adding unit test for random number
        generator

2005-03-01 18:17  tim

        * src/brains/Thermo.hpp: fixed a file inclusion problem

2005-03-01 18:17  tim

        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
        OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
        ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
        RandNumGenTestCase.hpp: fixed compilation problem

2005-03-01 18:02  tim

        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
        integrators/Velocitizer.hpp, math/Makefile,
        math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp,
        math/ParallelRandNumGen.hpp, math/mt19937ar.c,
        math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand

2005-03-01 18:00  tim

        * test/math/: Makefile, ParallelandNumGenTestCase.cpp,
        ParallelandNumGenTestCase.hpp: Change the name of test case

2005-03-01 16:00  tim

        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
        OOPSERandNumGenTestCase.hpp: adding testcase for random number
        generator

2005-03-01 15:10  tim

        * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
        integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
        math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp,
        math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp,
        math/Vector3.hpp, minimizers/MinimizerCreator.hpp,
        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
        utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
        visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4

2005-03-01 14:11  tim

        * src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
        math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
        OOPSERandNumGen

2005-03-01 10:44  gezelter

        * make/Makefile.in: Fixed the damned build problem with the
        libraries not being removed in make clean and make distclean (at
        least we think it is fixed).

2005-03-01 10:26  gezelter

        * src/math/MersenneTwister.hpp: Making small modifications to allow
        for use on MPI machines

2005-03-01 09:45  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
        integrators/Velocitizer.cpp, io/DumpReader.cpp,
        math/MersenneTwister.hpp: adding MersenneTwister random number
        generator

2005-02-28 22:55  tim

        * src/math/MersenneTwister.hpp: Adding a modified version of
        MersenneTwister.hpp

2005-02-28 12:24  tim

        * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
        definition.jpg: selection expression

2005-02-25 16:22  tim

        * src/: UseTheForce/DarkSide/LJ.F90,
        UseTheForce/DarkSide/lj_interface.F90,
        UseTheForce/DarkSide/lj_interface.h,
        io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
        types/AtomType.hpp: adding soft potential to LJ Module

2005-02-25 11:38  tim

        * doc/SelectionExpression.html: adding documentation for selection
        expression

2005-02-24 15:55  tim

        * src/: applications/simpleBuilder/simpleBuilder.cpp,
        integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
        io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp:
        adding basic_teebuf which can operate on multiple stream
        simutaneously.

2005-02-22 14:26  chrisfen

        * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf
        sample

2005-02-22 13:56  tim

        * src/: UseTheForce/DarkSide/reactionField.F90,
        primitives/RigidBody.cpp: reactionfield get fixed

2005-02-21 11:57  tim

        * src/: applications/staticProps/GofRAngle.cpp,
        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
        a bug in GofRAngle

2005-02-21 10:28  tim

        * src/primitives/Molecule.cpp: Fix for compilation on the Sun

2005-02-21 10:22  tim

        * src/utils/next_combination.hpp: fix for compilation on the Sun

2005-02-21 10:21  tim

        * src/utils/GenericData.hpp: fix problem in sun

2005-02-18 18:07  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dump2Xyz/Dump2XYZ.ggo,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h,
        applications/dynamicProps/RCorrFunc.cpp,
        applications/staticProps/GofXyz.cpp,
        applications/staticProps/GofXyz.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticProps.ggo,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
        visitors/Makefile: adding LipidTransVisitor, GofXyz is working now

2005-02-18 10:58  gezelter

        * src/brains/Register.cpp: Corrected filename collision for EAM on
        Mac OS X

2005-02-18 10:58  gezelter

        * src/applications/oopse/oopse.cpp: Updated copyright information

2005-02-18 10:58  gezelter

        * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
        Makefile: corrected filename collision for EAM on operating systems
        which are not case sensitive (aka Mac OS X)

2005-02-17 15:15  tim

        * src/applications/staticProps/GofXyz.cpp: more bug get fixed

2005-02-17 14:50  tim

        * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
        in GofXyz

2005-02-17 14:09  tim

        * src/applications/staticProps/RadialDistrFunc.hpp: make
        processHistogram non-abstrct function

2005-02-17 13:41  tim

        * src/applications/staticProps/GofXyz.cpp: [no log message]

2005-02-17 13:30  tim

        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
        GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
        finish GofXyz

2005-02-17 11:21  tim

        * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
        GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
        distribution function

2005-02-17 10:23  tim

        * src/utils/BitSet.hpp: forget the const correctness for BitSet

2005-02-17 10:18  tim

        * src/: brains/BlockSnapshotManager.cpp,
        selection/DistanceFinder.cpp: The change of interface of BitSet
        cause a bug in SelectionEvaluation

2005-02-16 16:13  tim

        * src/utils/residentMem.c: return residentMem in byte

2005-02-16 16:00  tim

        * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
        a bug in writing out the value of cosang

2005-02-16 15:43  tim

        * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
        estimate avaliable memory

2005-02-16 15:30  tim

        * src/: applications/staticProps/GofAngle2.cpp,
        applications/staticProps/GofAngle2.hpp,
        applications/staticProps/GofR.cpp,
        applications/staticProps/GofR.hpp,
        applications/staticProps/GofRAngle.cpp,
        applications/staticProps/GofRAngle.hpp,
        applications/staticProps/GofXyz.cpp,
        applications/staticProps/GofXyz.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticProps.ggo,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h,
        brains/BlockSnapshotManager.cpp: change the default bin number

2005-02-16 14:36  tim

        * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
        applications/dynamicProps/RCorrFunc.cpp,
        applications/dynamicProps/TimeCorrFunc.cpp,
        applications/dynamicProps/VCorrFunc.cpp,
        applications/staticProps/GofAngle2.cpp,
        applications/staticProps/GofR.cpp,
        applications/staticProps/GofR.hpp,
        applications/staticProps/GofRAngle.cpp,
        applications/staticProps/GofRAngle.hpp,
        applications/staticProps/RadialDistrFunc.cpp,
        applications/staticProps/RadialDistrFunc.hpp,
        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
        utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
        files;fix the problem of counting in staticProps

2005-02-15 14:39  tim

        * src/brains/BlockSnapshotManager.cpp: fix a bug in
        BlockSnapshotManager

2005-02-15 14:36  tim

        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
        applications/staticProps/RadialDistrFunc.cpp,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
        reference counting now

2005-02-15 12:49  tim

        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
        replace std::make_pair by VariablesType::value_type to make Sun
        Compiler happy

2005-02-15 12:35  tim

        * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
        TokenMap, using TokenMapType::value_type instead of std::make_pair
        to make Sun compiler happy

2005-02-15 12:24  tim

        * src/applications/staticProps/: GofRAngle.cpp,
        RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps

2005-02-15 12:11  tim

        * src/: applications/staticProps/GofR.cpp,
        applications/staticProps/RadialDistrFunc.cpp,
        applications/staticProps/RadialDistrFunc.hpp,
        brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding
        #ifdef __RWSTD to make sun compiler happy (2) fix pair density
        calculation problem when two selections intersect with each other

2005-02-15 10:24  gezelter

        * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
        xlc++

2005-02-15 10:17  gezelter

        * configure, ac-tools/configure.in, src/config.h.in,
        src/utils/residentMem.c: [no log message]

2005-02-15 01:17  gezelter

        * src/utils/residentMem.c: bug fix for null termination

2005-02-15 01:11  gezelter

        * configure, ac-tools/configure.in, src/utils/residentMem.c:
        bugfixing residentMem

2005-02-15 00:59  gezelter

        * configure, ac-tools/configure.in, src/config.h.in,
        src/utils/residentMem.c: bugfixes for residentMem on LINUX

2005-02-15 00:08  gezelter

        * src/utils/Makefile.in: added residentMem

2005-02-15 00:05  gezelter

        * configure, ac-tools/configure.in, make/Makefile.in,
        src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
        src/utils/residentMem.h: modifications to estimate memory in use by
        other processes autoconf fixes ps syntax checking config.h file
        cleaning

2005-02-14 18:26  gezelter

        * configure, ac-tools/configure.in, make/Makefile.in: ps niceness

2005-02-14 18:16  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
        strangeness

2005-02-14 14:42  tim

        * src/brains/BlockSnapshotManager.cpp: fix a bug in
        BlockSnapshotManager.hpp

2005-02-14 13:51  tim

        * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
        StaticPropsCmd.c: default length for staticProps is 1/2 smallest
        length of first frame

2005-02-14 13:12  tim

        * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
        VelocityVerletIntegrator : last frame is written twice

2005-02-14 12:57  tim

        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
        brains/SimInfo.cpp, primitives/RigidBody.cpp,
        primitives/StuntDouble.hpp: begin bug fix

2005-02-14 12:35  tim

        * src/applications/dynamicProps/: CorrelationFunction.cpp,
        CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
        CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp,
        DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile,
        ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp,
        RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
        VCorrFunc.hpp: refactory CorrelationFunction

2005-02-14 10:18  gezelter

        * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
        and start of switch for type of correlation function

2005-02-13 16:18  tim

        * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
        calculating  bytes per stuntdouble

2005-02-13 16:03  tim

        * src/applications/dynamicProps/CorrelationFunction.cpp: more fix

2005-02-13 15:57  tim

        * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
        bug in CorrelationFunction

2005-02-13 15:36  tim

        * src/: applications/staticProps/GofR.cpp,
        applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
        bug in SimInfo::getCutoff()

2005-02-13 15:08  tim

        * make/Makefile.in: adding staticProps and dynamicProps into
        Makefile.in

2005-02-13 15:05  tim

        * src/: applications/dynamicProps/CorrelationFunction.cpp,
        applications/dynamicProps/CorrelationFunction.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticProps.ggo,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp,
        brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
        defaults to the cutoff radius

2005-02-13 14:14  tim

        * src/utils/Algorithm.hpp: adding Algorithm.hpp

2005-02-13 14:10  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dynamicProps/CorrelationFunction.cpp,
        applications/dynamicProps/CorrelationFunction.hpp,
        applications/dynamicProps/DynamicProps.cpp,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        integrators/Integrator.cpp, integrators/Integrator.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp,
        io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp,
        utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
        visitors/OtherVisitor.cpp: dynamicProps get built

2005-02-13 10:56  tim

        * src/: applications/dynamicProps/CorrelationFunction.cpp,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
        progress

2005-02-13 03:04  tim

        * src/: applications/dynamicProps/CorrelationFunction.hpp,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
        brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
        work in dynamicProps

2005-02-13 02:25  tim

        * src/applications/dynamicProps/DynamicProps.cpp: adding
        dynamicProps

2005-02-13 02:14  tim

        * src/applications/dynamicProps/: DynamicPropsCmd.c,
        DynamicPropsCmd.h: adding command line option to DynamicProps

2005-02-13 02:13  tim

        * src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
        adding command line option for DynamicProps

2005-02-13 01:57  tim

        * src/: applications/dynamicProps/CorrelationFunction.cpp,
        applications/dynamicProps/CorrelationFunction.hpp,
        applications/dynamicProps/DipoleCorrFunc.cpp,
        applications/dynamicProps/DipoleCorrFunc.hpp,
        applications/dynamicProps/RCorrFunc.cpp,
        applications/dynamicProps/RCorrFunc.hpp,
        applications/dynamicProps/VCorrFunc.cpp,
        applications/dynamicProps/VCorrFunc.hpp,
        applications/staticProps/RadialDistrFunc.cpp,
        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
        brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
        primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
        dynamicProps

2005-02-12 15:09  tim

        * src/selection/SelectionManager.cpp: adding SelectionManager.cpp

2005-02-11 17:41  tim

        * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
        more constructor to Snapshot to create customized DataStorage

2005-02-11 17:39  tim

        * src/selection/: DistanceFinder.hpp, Makefile,
        SelectionManager.hpp: adding beginSelected, nextSelected method to
        SelectionManager

2005-02-11 17:36  tim

        * src/config.h.in, configure: adding support for physmem

2005-02-11 17:35  tim

        * ac-tools/configure.in: adding supprot for physmem

2005-02-11 17:35  tim

        * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
        physmem

2005-02-10 17:37  tim

        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
        GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
        GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
        StaticPropsCmd.h: more work in StaticProps

2005-02-10 13:14  tim

        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
        GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp,
        Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
        StaticPropsCmd.h: change the filenames

2005-02-10 09:15  tim

        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
        GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
        RadialDistrFunc.hpp: adding GofRAngle

2005-02-09 13:21  tim

        * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
        useless files

2005-02-09 13:12  tim

        * src/applications/staticProps/: GofR.cpp, Makefile,
        RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress

2005-02-09 12:08  tim

        * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
        RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR

2005-02-07 17:39  tim

        * src/primitives/Molecule.hpp: add getRigidBodyAt  function into
        Molecule class

2005-02-07 17:38  tim

        * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info

2005-02-07 17:36  tim

        * src/selection/: NameFinder.cpp, NameFinder.hpp,
        SelectionCompiler.cpp: support select internal index selection, for
        example, select DMPC.3

2005-02-07 16:11  tim

        * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
        help info for Dump2XYZ

2005-02-07 15:39  chrisfen

        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
        selection librarys added

2005-02-07 15:31  tim

        * src/selection/Makefile, make/Makefile.in: adding Makefile

2005-02-07 15:20  chrisfen

        * src/utils/wildcards.hpp: issue commented out in wildcards

2005-02-07 15:06  tim

        * src/selection/SelectionEvaluator.cpp: forget to reset the pc
        which cause reevaluate return NULL

2005-02-07 14:14  tim

        * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
        SimSnapshotManager.hpp: fix a bug in determing the global index for
        rigidbodies

2005-02-07 14:13  tim

        * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
        in Bitset

2005-02-07 14:13  tim

        * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
        SelectionCompiler.cpp, SelectionCompiler.hpp,
        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
        TokenMap.cpp: selection library is working

2005-02-04 17:46  tim

        * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor

2005-02-04 17:45  tim

        * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
        and XYZVisitor now use selection library

2005-02-04 17:44  tim

        * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
        adding SelectionManager into SimInfo

2005-02-04 17:43  tim

        * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
        Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
        selection library

2005-02-04 17:42  tim

        * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
        in BitSet

2005-02-04 17:41  tim

        * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
        implementation

2005-02-04 17:39  tim

        * src/selection/: NameFinder.cpp, NameFinder.hpp,
        SelectionCompiler.cpp, SelectionCompiler.hpp,
        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
        SelectionManager.hpp, Token.hpp: half of the selection utility is
        working need to debug within keyword and atomproperty keyword

2005-02-04 00:42  tim

        * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
        get built

2005-02-04 00:42  tim

        * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet

2005-02-04 00:26  tim

        * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
        remove some useless files

2005-02-03 23:57  tim

        * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
        selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
        adding wildcard class; NameFinder is finished

2005-02-03 18:14  tim

        * src/selection/: NameFinder.cpp, NameFinder.hpp,
        SelectionCompiler.cpp, SelectionCompiler.hpp,
        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
        SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
        selection library

2005-02-03 09:04  tim

        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
        selection in progress

2005-02-02 18:13  tim

        * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
        Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
        progress, except SelectionEvaluator, other files are compiled

2005-02-02 18:12  tim

        * src/utils/: Makefile.in, any.hpp: adding boost::any

2005-02-02 07:51  tim

        * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp

2005-02-01 17:49  tim

        * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
        selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
        selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
        selection/Token.hpp: Selection in progress

2005-02-01 01:55  tim

        * src/: selection/SelectionCompiler.hpp,
        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
        selection/SelectionManager.hpp, selection/Token.hpp,
        utils/BitSet.cpp, utils/BitSet.hpp: adding selection library

2005-01-26 10:26  tim

        * src/integrators/: Integrator.cpp, Integrator.hpp,
        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
        to add eorWriter

2005-01-26 10:15  tim

        * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
        (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
        wrong column of electroframe

2005-01-25 16:59  tim

        * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
        SimInfo, use number of cutoff stamp as counter to loop over
        rigidbody stamp

2005-01-25 12:45  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
        integrators/DLM.cpp, io/AtomTypesSectionParser.cpp,
        io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp,
        io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp,
        io/EAMAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp,
        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.cpp,
        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
        math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp,
        primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp,
        primitives/GhostTorsion.hpp, primitives/Makefile,
        primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete
        section parser's error message (2) add GhostTorsion (3) accumulate
        inertial tensor from the directional atoms before calculate
        rigidbody's inertial tensor

2005-01-17 17:17  tim

        * forceFields/DUFF2.frc: forget to set dipole for lipid head group

2005-01-17 11:58  tim

        * src/integrators/NVT.cpp: fix a bug in loading initial extended
        system parameters

2005-01-17 11:05  tim

        * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT

2005-01-14 17:02  tim

        * src/UseTheForce/WATER.cpp: remove WATER.cpp

2005-01-14 16:37  tim

        * forceFields/Makefile: sync Makefile

2005-01-14 16:13  gezelter

        * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
        src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
        src/applications/dump2Xyz/Makefile,
        src/applications/oopse/Makefile,
        src/applications/simpleBuilder/Makefile, src/brains/Makefile,
        src/constraints/Makefile, src/integrators/Makefile,
        src/io/Makefile, src/math/Makefile, src/minimizers/Makefile,
        src/primitives/Makefile, src/profiling/Makefile,
        src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in,
        src/visitors/Makefile: moved Package variable into subdirectory
        makefiles to speed up the building process

2005-01-14 15:48  gezelter

        * src/applications/oopse/oopse.cpp: Fixed publication details in
        banner

2005-01-14 15:48  gezelter

        * src/UseTheForce/DarkSide/: simParallel_interface.F90,
        simParallel_interface.h: added dummy subroutine to avoid empty
        unit, synchronized this dummy routine between C and fortran

2005-01-14 15:31  gezelter

        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
        notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
        DarkSide/Makefile, DarkSide/atype.F90,
        DarkSide/atype_interface.F90, DarkSide/charge.F90,
        DarkSide/charge_interface.F90, DarkSide/dipole.F90,
        DarkSide/dipole_interface.F90, DarkSide/eam.F90,
        DarkSide/eam_interface.F90, DarkSide/gb.F90,
        DarkSide/gb_interface.F90, DarkSide/lj_interface.F90,
        DarkSide/shapes.F90, DarkSide/shapes_interface.F90,
        DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90,
        DarkSide/simulation.F90, DarkSide/simulation_interface.F90,
        DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
        modules and C/Fortran interface subroutines

2005-01-14 15:15  gezelter

        * configure, ac-tools/aclocal.m4: more fixes for gnugetopt

2005-01-14 15:09  gezelter

        * configure, ac-tools/configure.in, src/config.h.in,
        src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt

2005-01-14 11:49  tim

        * src/: io/EAMAtomTypesSectionParser.cpp,
        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
        utils/StringUtils.hpp: using c library to do conversion instead of
        using iostream due to a bug in libstdc++(GCC 3.2)

2005-01-13 21:40  tim

        * src/brains/SimSetup.cpp: no message

2005-01-13 20:56  tim

        * src/primitives/Molecule.hpp: fix a bug in global index

2005-01-13 20:04  tim

        * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
        Integrator.hpp in Minimizer

2005-01-13 17:14  gezelter

        * src/utils/Makefile: compile getopt and getopt1 if we need to

2005-01-13 16:56  gezelter

        * make/Makefile.in: template flags

2005-01-13 16:48  gezelter

        * src/applications/oopse/Makefile: formatting

2005-01-13 16:48  gezelter

        * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
        target

2005-01-13 14:40  tim

        * src/: UseTheForce/fSwitchingFunction.h,
        UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
        math/Makefile, math/RectMatrix.hpp, math/Vector.hpp,
        primitives/RigidBody.cpp, types/AtomTypeProperties.h,
        types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform

2005-01-13 13:26  tim

        * make/Makefile.in: change the order of linking (object file comes
        first and then follow by user built library)

2005-01-12 18:24  tim

        * src/io/DumpWriter.cpp: remove useless debug info

2005-01-12 18:21  tim

        * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix

2005-01-12 18:17  tim

        * make/: Makefile.in, Makefile.in: missing tab

2005-01-12 18:15  tim

        * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
        get fixed

2005-01-12 17:40  gezelter

        * make/Makefile.in, src/UseTheForce/DUFF.cpp,
        src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
        src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp,
        src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp,
        src/UseTheForce/ForceFieldCreator.hpp,
        src/UseTheForce/ForceFieldFactory.cpp,
        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp,
        src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp,
        src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h,
        src/UseTheForce/fSwitchingFunction.h,
        src/UseTheForce/mpiComponentPlan.h,
        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
        src/UseTheForce/notifyCutoffs.F90,
        src/UseTheForce/notifyCutoffs_interface.h,
        src/UseTheForce/DarkSide/LJ.F90,
        src/UseTheForce/DarkSide/atype.F90,
        src/UseTheForce/DarkSide/atype_interface.h,
        src/UseTheForce/DarkSide/charge.F90,
        src/UseTheForce/DarkSide/charge_interface.h,
        src/UseTheForce/DarkSide/dipole.F90,
        src/UseTheForce/DarkSide/dipole_interface.h,
        src/UseTheForce/DarkSide/eam.F90,
        src/UseTheForce/DarkSide/eam_interface.h,
        src/UseTheForce/DarkSide/force_globals.F90,
        src/UseTheForce/DarkSide/gb.F90,
        src/UseTheForce/DarkSide/gb_interface.h,
        src/UseTheForce/DarkSide/lj_interface.h,
        src/UseTheForce/DarkSide/neighborLists.F90,
        src/UseTheForce/DarkSide/reactionField.F90,
        src/UseTheForce/DarkSide/shapes.F90,
        src/UseTheForce/DarkSide/shapes_interface.h,
        src/UseTheForce/DarkSide/simParallel.F90,
        src/UseTheForce/DarkSide/simParallel_interface.h,
        src/UseTheForce/DarkSide/simulation.F90,
        src/UseTheForce/DarkSide/simulation_interface.h,
        src/UseTheForce/DarkSide/sticky.F90,
        src/UseTheForce/DarkSide/sticky_interface.h,
        src/UseTheForce/DarkSide/switcheroo.F90,
        src/applications/Makedepend, src/applications/quickLate.c,
        src/applications/dump2Xyz/Dump2XYZ.cpp,
        src/applications/oopse/oopse.cpp,
        src/applications/simpleBuilder/BaseLattice.cpp,
        src/applications/simpleBuilder/BaseLattice.hpp,
        src/applications/simpleBuilder/Lattice.cpp,
        src/applications/simpleBuilder/Lattice.hpp,
        src/applications/simpleBuilder/LatticeCreator.cpp,
        src/applications/simpleBuilder/LatticeCreator.hpp,
        src/applications/simpleBuilder/LatticeFactory.cpp,
        src/applications/simpleBuilder/LatticeFactory.hpp,
        src/applications/simpleBuilder/MoLocator.cpp,
        src/applications/simpleBuilder/MoLocator.hpp,
        src/applications/simpleBuilder/simpleBuilder.cpp,
        src/brains/DataStorage.cpp, src/brains/DataStorage.hpp,
        src/brains/Exclude.cpp, src/brains/Exclude.hpp,
        src/brains/ForceManager.cpp, src/brains/ForceManager.hpp,
        src/brains/Makefile, src/brains/Migrator.hpp,
        src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp,
        src/brains/Register.cpp, src/brains/Register.hpp,
        src/brains/SimCreator.cpp, src/brains/SimCreator.hpp,
        src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
        src/brains/SimModel.hpp, src/brains/SimSetup.hpp,
        src/brains/SimSnapshotManager.cpp,
        src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp,
        src/brains/SimState.hpp, src/brains/SkipList.cpp,
        src/brains/SkipList.hpp, src/brains/Snapshot.cpp,
        src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp,
        src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp,
        src/brains/Thermo.hpp, src/brains/fSimulation.h,
        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
        src/constraints/AbstractClasses.hpp,
        src/constraints/ConstraintElem.hpp,
        src/constraints/ConstraintPair.hpp, src/constraints/Makefile,
        src/constraints/Rattle.cpp, src/constraints/Rattle.hpp,
        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
        src/constraints/ZconsStruct.hpp,
        src/constraints/ZconstraintForceManager.cpp,
        src/constraints/ZconstraintForceManager.hpp,
        src/integrators/AbstractClasses.hpp,
        src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp,
        src/integrators/DLM.hpp, src/integrators/Integrator.cpp,
        src/integrators/Integrator.hpp,
        src/integrators/IntegratorCreator.hpp,
        src/integrators/IntegratorFactory.cpp,
        src/integrators/IntegratorFactory.hpp, src/integrators/Makefile,
        src/integrators/NPT.cpp, src/integrators/NPT.hpp,
        src/integrators/NPTf.cpp, src/integrators/NPTf.hpp,
        src/integrators/NPTi.cpp, src/integrators/NPTi.hpp,
        src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp,
        src/integrators/NVE.cpp, src/integrators/NVE.hpp,
        src/integrators/NVT.cpp, src/integrators/NVT.hpp,
        src/integrators/RotationAlgorithm.hpp,
        src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp,
        src/integrators/VelocityVerletIntegrator.cpp,
        src/integrators/VelocityVerletIntegrator.hpp,
        src/io/AtomTypesSectionParser.cpp,
        src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp,
        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
        src/io/BendTypesSectionParser.cpp,
        src/io/BendTypesSectionParser.hpp,
        src/io/BondTypesSectionParser.cpp,
        src/io/BondTypesSectionParser.hpp,
        src/io/DirectionalAtomTypesSectionParser.cpp,
        src/io/DirectionalAtomTypesSectionParser.hpp,
        src/io/DumpReader.cpp, src/io/DumpReader.hpp,
        src/io/DumpWriter.cpp, src/io/DumpWriter.hpp,
        src/io/EAMAtomTypesSectionParser.cpp,
        src/io/EAMAtomTypesSectionParser.hpp,
        src/io/ElectrostaticAtomTypesSectionParser.cpp,
        src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp,
        src/io/Globals.hpp, src/io/InitializeFromFile.cpp,
        src/io/LennardJonesAtomTypesSectionParser.cpp,
        src/io/LennardJonesAtomTypesSectionParser.hpp,
        src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp,
        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
        src/io/Makefile, src/io/SectionParser.cpp,
        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
        src/io/SectionParserManager.hpp, src/io/StatWriter.cpp,
        src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp,
        src/io/StickyAtomTypesSectionParser.hpp,
        src/io/TorsionTypesSectionParser.cpp,
        src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp,
        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp,
        src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h,
        src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h,
        src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c,
        src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp,
        src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c,
        src/math/MatVec3.h, src/math/Polynomial.hpp,
        src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp,
        src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp,
        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
        src/math/Vector.hpp, src/math/Vector3.hpp,
        src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp,
        src/minimizers/CGFamilyMinimizer.cpp,
        src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile,
        src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp,
        src/minimizers/MinimizerCreator.hpp,
        src/minimizers/MinimizerFactory.cpp,
        src/minimizers/MinimizerFactory.hpp,
        src/minimizers/MinimizerParameterSet.cpp,
        src/minimizers/MinimizerParameterSet.hpp,
        src/minimizers/OOPSEMinimizer.cpp,
        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
        src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp,
        src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp,
        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
        src/primitives/Bend.cpp, src/primitives/Bend.hpp,
        src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp,
        src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp,
        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
        src/primitives/GhostBend.hpp, src/primitives/Makefile,
        src/primitives/Molecule.cpp, src/primitives/Molecule.hpp,
        src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp,
        src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp,
        src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp,
        src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp,
        src/primitives/UreyBradleyBend.cpp,
        src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp,
        src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp,
        src/types/AtomStamp.hpp, src/types/AtomType.cpp,
        src/types/AtomType.hpp, src/types/AtomTypeProperties.h,
        src/types/BendStamp.cpp, src/types/BendStamp.hpp,
        src/types/BendType.hpp, src/types/BondStamp.cpp,
        src/types/BondStamp.hpp, src/types/BondType.hpp,
        src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp,
        src/types/Component.cpp, src/types/Component.hpp,
        src/types/CubicBendType.hpp, src/types/CubicBondType.hpp,
        src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp,
        src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp,
        src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp,
        src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp,
        src/types/MakeStamps.cpp, src/types/MakeStamps.hpp,
        src/types/Makefile, src/types/MoleculeStamp.cpp,
        src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp,
        src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp,
        src/types/PolynomialBondType.hpp,
        src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp,
        src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp,
        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
        src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp,
        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
        src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp,
        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
        src/utils/GenericData.hpp, src/utils/GenericFactory.hpp,
        src/utils/LocalIndexManager.hpp, src/utils/Makefile,
        src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp,
        src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp,
        src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp,
        src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp,
        src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp,
        src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp,
        src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp,
        src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp,
        src/utils/Utility.cpp, src/utils/Utility.hpp,
        src/utils/definitions.F90, src/utils/fError.c,
        src/utils/next_combination.hpp, src/utils/oopseMPI.F90,
        src/utils/simError.c, src/utils/simError.h, src/utils/status.F90,
        src/utils/vector_class.F90, src/visitors/AtomData.hpp,
        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
        src/visitors/ZconsVisitor.hpp: merging new_design branch into
        OOPSE-2.0

2005-01-12 13:13  tim

        * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
        utils/TypeContainer.hpp: forget to include <algorithm>

2005-01-12 12:25  tim

        * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
        newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
        fields

2005-01-12 12:14  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
        UseTheForce/ForceFieldCreator.hpp,
        UseTheForce/ForceFieldFactory.cpp,
        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
        UseTheForce/doForces.F90, UseTheForce/doForces_interface.h,
        UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h,
        UseTheForce/notifyCutoffs.F90,
        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
        UseTheForce/DarkSide/atype.F90,
        UseTheForce/DarkSide/atype_interface.h,
        UseTheForce/DarkSide/charge.F90,
        UseTheForce/DarkSide/charge_interface.h,
        UseTheForce/DarkSide/dipole.F90,
        UseTheForce/DarkSide/dipole_interface.h,
        UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h,
        UseTheForce/DarkSide/force_globals.F90,
        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
        UseTheForce/DarkSide/lj_interface.h,
        UseTheForce/DarkSide/neighborLists.F90,
        UseTheForce/DarkSide/reactionField.F90,
        UseTheForce/DarkSide/shapes.F90,
        UseTheForce/DarkSide/shapes_interface.h,
        UseTheForce/DarkSide/simParallel.F90,
        UseTheForce/DarkSide/simParallel_interface.h,
        UseTheForce/DarkSide/simulation.F90,
        UseTheForce/DarkSide/simulation_interface.h,
        UseTheForce/DarkSide/sticky.F90,
        UseTheForce/DarkSide/sticky_interface.h,
        UseTheForce/DarkSide/switcheroo.F90,
        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
        applications/simpleBuilder/BaseLattice.cpp,
        applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.cpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeCreator.cpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/MoLocator.cpp,
        applications/simpleBuilder/MoLocator.hpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
        brains/Exclude.hpp, brains/ForceManager.cpp,
        brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp,
        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
        brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
        brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp,
        brains/Snapshot.cpp, brains/Snapshot.hpp,
        brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp,
        brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h,
        constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp,
        constraints/Rattle.cpp, constraints/Rattle.hpp,
        constraints/ZconsStruct.hpp,
        constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
        integrators/DLM.hpp, integrators/Integrator.cpp,
        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
        integrators/NVT.cpp, integrators/NVT.hpp,
        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
        integrators/Velocitizer.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp,
        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
        io/BondTypesSectionParser.hpp,
        io/DirectionalAtomTypesSectionParser.cpp,
        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp,
        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
        io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp,
        io/SectionParser.cpp, io/SectionParser.hpp,
        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
        io/StatWriter.cpp, io/StatWriter.hpp,
        io/StickyAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.hpp,
        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c,
        io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h,
        io/node_list.h, io/parse_interface.h, io/parse_me.h,
        io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp,
        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
        math/Polynomial.hpp, math/Quaternion.hpp,
        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
        math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp,
        math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp,
        math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp,
        minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp,
        minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp,
        minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp,
        minimizers/MinimizerParameterSet.cpp,
        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
        primitives/Molecule.cpp, primitives/Molecule.hpp,
        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
        primitives/Torsion.cpp, primitives/Torsion.hpp,
        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
        restraints/Restraints.cpp, restraints/Restraints.hpp,
        types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp,
        types/AtomType.hpp, types/AtomTypeProperties.h,
        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp,
        types/FixedBondType.hpp, types/HarmonicBendType.hpp,
        types/HarmonicBondType.hpp, types/MakeStamps.cpp,
        types/MakeStamps.hpp, types/MoleculeStamp.cpp,
        types/MoleculeStamp.hpp, types/MorseBondType.hpp,
        types/OplsTorsionType.hpp, types/PolynomialBendType.hpp,
        types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
        types/QuarticBendType.hpp, types/QuarticBondType.hpp,
        types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp,
        types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp,
        types/ShapeAtomType.hpp, types/TorsionStamp.cpp,
        types/TorsionStamp.hpp, types/TorsionType.hpp,
        types/UreyBradleyBendType.hpp, types/ZconStamp.cpp,
        types/ZconStamp.hpp, utils/GenericData.hpp,
        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
        utils/MemoryUtils.hpp, utils/NumericConstant.hpp,
        utils/OOPSEConstant.hpp, utils/PropertyMap.cpp,
        utils/PropertyMap.hpp, utils/StringTokenizer.cpp,
        utils/StringTokenizer.hpp, utils/StringUtils.cpp,
        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
        utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90,
        utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90,
        utils/simError.c, utils/simError.h, utils/status.F90,
        utils/vector_class.F90, visitors/AtomData.hpp,
        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp,
        visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
        visitors/ZconsVisitor.hpp: change license

2005-01-12 12:14  tim

        * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
        branch new_design.

2005-01-11 16:03  tim

        * src/: constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp,
        minimizers/MinimizerParameterSet.cpp,
        minimizers/MinimizerParameterSet.hpp: change const static double
        data member to const double

2005-01-11 15:50  tim

        * src/io/basic_ifstrstream.hpp: forget namespace qualifier std::

2005-01-11 15:39  tim

        * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
        change data type from logical to integer in AtomTypeProperties.h

2005-01-11 11:36  tim

        * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
        new format of EAM force field

2005-01-11 11:24  tim

        * src/UseTheForce/DUFF.cpp: change default name of DUFF force field
        to DUFF2.frc

2005-01-11 11:23  tim

        * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
        DUFF2.frc

2005-01-11 11:09  tim

        * make/Makefile.in: adding constraints and minimizers into
        Makefile.in

2005-01-11 11:03  tim

        * src/io/: ChargeAtomTypesSectionParser.cpp,
        ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
        DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
        files

2005-01-11 10:59  tim

        * src/io/ZConsWriter.cpp: [no log message]

2005-01-11 10:53  tim

        * src/UseTheForce/EAM.cpp: minor fix

2005-01-11 10:52  tim

        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
        on branch new_design.

2005-01-11 10:52  tim

        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
        on branch new_design.

2005-01-11 10:52  tim

        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm

2005-01-11 10:47  tim

        * make/Makefile.in: forget a '$' sign

2005-01-11 10:46  tim

        * make/Makefile.in: missing tab in rules

2005-01-10 17:04  tim

        * src/: UseTheForce/ForceFieldCreator.cpp,
        UseTheForce/ForceFieldCreator.hpp,
        UseTheForce/ForceFieldFactory.cpp,
        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
        applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile,
        brains/Register.cpp, brains/Register.hpp,
        integrators/IntegratorCreator.cpp,
        integrators/IntegratorCreator.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/Makefile,
        integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp,
        minimizers/Makefile, minimizers/MinimizerCreator.cpp,
        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
        minimizers/MinimizerFactory.hpp: create a register module to
        register force fields, integrators and minimizers

2005-01-10 17:04  tim

        * src/brains/Register.cpp: file Register.cpp was initially added on
        branch new_design.

2005-01-10 17:04  tim

        * src/brains/Register.hpp: file Register.hpp was initially added on
        branch new_design.

2005-01-10 15:52  tim

        * src/: UseTheForce/ForceFieldFactory.cpp,
        applications/oopse/oopse.cpp, brains/ForceManager.hpp,
        constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp,
        io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp,
        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
        method is working now

2005-01-10 13:05  tim

        * src/: constraints/ConstraintElem.hpp,
        constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
        constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp,
        io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp,
        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
        zconstraint

2005-01-10 13:05  tim

        * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
        initially added on branch new_design.

2005-01-07 16:50  tim

        * src/constraints/ZconstraintForceManager.cpp: file
        ZconstraintForceManager.cpp was initially added on branch
        new_design.

2005-01-07 16:50  tim

        * src/constraints/ZconstraintForceManager.hpp: file
        ZconstraintForceManager.hpp was initially added on branch
        new_design.

2005-01-07 16:50  tim

        * src/: applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp,
        constraints/ConstraintElem.hpp, constraints/Makefile,
        constraints/ZConstraint.cpp, constraints/ZconsData.hpp,
        constraints/ZconstraintForceManager.cpp,
        constraints/ZconstraintForceManager.hpp,
        integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
        utils/NumericConstant.hpp: ZConstraintForceManager in progress

2005-01-07 16:50  tim

        * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
        initially added on branch new_design.

2005-01-06 17:31  tim

        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        constraints/ConstraintPair.hpp, integrators/Integrator.cpp,
        integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp,
        io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
        constraint is almost working

2005-01-05 19:36  tim

        * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
        working

2005-01-05 19:16  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/oopse/oopse.cpp,
        applications/simpleBuilder/BaseLattice.cpp,
        applications/simpleBuilder/Lattice.cpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/MoLocator.cpp,
        applications/simpleBuilder/MoLocator.hpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp,
        minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
        in progress

2005-01-05 12:35  tim

        * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
        was initially added on branch new_design.

2005-01-05 12:35  tim

        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
        added on branch new_design.

2005-01-05 12:35  tim

        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
        Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
        MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
        SDMinimizer.hpp: minimizer in progress

2005-01-05 12:35  tim

        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
        was initially added on branch new_design.

2005-01-05 12:35  tim

        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
        was initially added on branch new_design.

2005-01-05 12:35  tim

        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
        was initially added on branch new_design.

2005-01-05 12:35  tim

        * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
        added on branch new_design.

2005-01-04 17:18  tim

        * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
        brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
        brains/Thermo.cpp, constraints/ConstraintPair.hpp,
        constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp,
        integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp,
        primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
        progress

2005-01-04 17:18  tim

        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
        initially added on branch new_design.

2005-01-04 17:18  tim

        * src/minimizers/MinimizerParameterSet.cpp: file
        MinimizerParameterSet.cpp was initially added on branch new_design.

2005-01-04 17:18  tim

        * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
        initially added on branch new_design.

2005-01-04 17:18  tim

        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
        was initially added on branch new_design.

2005-01-04 17:18  tim

        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress

2005-01-04 17:18  tim

        * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
        branch new_design.

2004-12-20 15:50  chuckv

        * make/Makefile.in: Fixed Makefile test bug under OSX and possibly
        other BSD's, replaced test -f *.mod with ls function since BSD test
        apparently doesn't support wildcards.

2004-12-20 15:36  tim

        * make/Makefile.in: fix a test command incompatiable problem

2004-12-20 14:49  tim

        * src/integrators/NPTi.cpp: NPT is working now

2004-12-16 14:20  tim

        * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
        invalid stamp id

2004-12-16 14:00  tim

        * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
        newEAM.u6.frc: adding new EAM force field files

2004-12-16 13:55  tim

        * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
        in  EAM parameter file is incorrect

2004-12-16 12:27  tim

        * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
        brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
        utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM

2004-12-15 17:34  tim

        * src/: applications/simpleBuilder/BaseLattice.cpp,
        applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.cpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeCreator.cpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream

2004-12-15 16:07  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
        add EAM Force Field

2004-12-15 14:40  tim

        * src/applications/oopse/oopse.cpp: add more force fields

2004-12-15 11:44  tim

        * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
        to call All_reduce in MPI version)

2004-12-15 11:13  tim

        * src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
        io/DumpReader.cpp: MPI in NVE is working

2004-12-14 16:57  tim

        * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
        Master nodes does not brocast the total number of frames

2004-12-14 14:08  tim

        * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
        integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
        minimizers/CGFamilyMinimizer.cpp,
        minimizers/MinimizerParameterSet.hpp,
        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
        minimizers/SDMinimizer.cpp: more fix in MPI version

2004-12-13 17:30  tim

        * src/: UseTheForce/DarkSide/simParallel.F90,
        applications/oopse/oopse.cpp, brains/SimCreator.cpp,
        brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp,
        integrators/DLM.cpp, integrators/Integrator.cpp,
        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
        integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp,
        io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp,
        io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp,
        math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp,
        primitives/RigidBody.cpp, primitives/StuntDouble.cpp,
        primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp,
        utils/LocalIndexManager.hpp, utils/PropertyMap.cpp,
        utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
        is built

2004-12-10 13:41  tim

        * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp

2004-12-10 11:14  tim

        * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
        primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
        and Dipole is working now

2004-12-09 18:15  tim

        * src/: UseTheForce/DarkSide/dipole.F90,
        UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
        fix an index problem in eFrame matrix

2004-12-09 18:09  tim

        * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
        initializing the new Charge AtomType

2004-12-09 16:15  tim

        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
        types/DirectionalAtomType.cpp: sticky module get compiled

2004-12-09 15:43  gezelter

        * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
        reactionField.F90: u_l -> eFrame  for electrostatics u_l -> A for
        GB

2004-12-09 15:42  gezelter

        * src/UseTheForce/doForces.F90: u_l -> eFrame

2004-12-09 15:27  gezelter

        * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
        module now has the option for multiple sticky types

2004-12-09 15:27  gezelter

        * src/UseTheForce/doForces.F90: sticky

2004-12-09 11:22  tim

        * src/integrators/: NPT.cpp, NVT.cpp: fix an interface
        inconsistency in lab2Bidy

2004-12-09 10:45  tim

        * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
        in calculating torque in rigid body

2004-12-08 15:37  tim

        * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
        brains/SnapShot.cpp, brains/Snapshot.hpp,
        integrators/Integrator.cpp,
        io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
        fix a parsing bug in ElectroStaticAtomTypesSectionParser

2004-12-08 12:03  tim

        * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
        in  NVT is working

2004-12-07 18:08  tim

        * src/: UseTheForce/Makefile, brains/SimInfo.hpp,
        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
        integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
        io/DumpWriter.cpp: NPT in progress

2004-12-07 09:43  tim

        * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
        message]

2004-12-07 00:12  tim

        * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
        UseInitXSstate

2004-12-07 00:00  tim

        * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message

2004-12-06 23:47  tim

        * src/types/DirectionalAtomType.cpp: [no log message]

2004-12-06 21:18  tim

        * forceFields/newDUFF.frc: merge WATER force field into DUFF

2004-12-06 20:33  tim

        * forceFields/newDUFF.frc: change the force constant of bonds

2004-12-06 18:29  tim

        * src/: UseTheForce/DarkSide/charge.F90,
        UseTheForce/DarkSide/charge_interface.h,
        UseTheForce/DarkSide/dipole.F90,
        UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
        fix atom type ident in Charge and Dipole Module

2004-12-06 17:56  tim

        * src/primitives/Torsion.cpp: butane is working now

2004-12-06 15:15  tim

        * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
        primitives/Bond.hpp, primitives/Torsion.cpp: short range
        interaction for butane is correct.Still something wrong with long
        range one

2004-12-05 23:49  tim

        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        io/BendTypesSectionParser.cpp, math/Polynomial.hpp,
        primitives/Atom.hpp, utils/NumericConstant.hpp,
        utils/TypeContainer.hpp: fix a bug in Exclude List

2004-12-05 17:21  tim

        * forceFields/newDUFF.frc: minor fix in DUFF

2004-12-05 17:02  tim

        * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
        utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
        fix a bug in filling MolMembership

2004-12-05 12:12  tim

        * forceFields/newDUFF.frc: minor fix in force field file

2004-12-05 12:09  tim

        * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
        integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp

2004-12-04 15:09  tim

        * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
        math/Vector3.hpp: NVE is working now, get the same result as
        OOPSE-1.0

2004-12-04 14:29  tim

        * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy

2004-12-04 14:24  gezelter

        * src/primitives/: Bend.cpp, Torsion.cpp: What?

2004-12-04 14:24  gezelter

        * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion

2004-12-04 00:24  tim

        * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
        integrators/Integrator.hpp,
        integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp,
        utils/TypeContainer.hpp: NVE conserved energy, however, potential
        is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf
        and NPTxyz to test integrator Step 2 SSD in NVE to test DLM,
        dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
        4 EAM Step 5 Shape Step 6 Constraint & Restraint

2004-12-03 19:01  tim

        * src/: UseTheForce/DarkSide/LJ.F90,
        applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
        io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
        energy of NVE is not conserved

2004-12-03 17:36  tim

        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
        primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running

2004-12-03 16:30  tim

        * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
        integrators/NVE.cpp, primitives/Molecule.cpp,
        primitives/Molecule.hpp, primitives/StuntDouble.hpp,
        primitives/Torsion.hpp: more missing function get implemented

2004-12-03 15:30  tim

        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
        SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo

2004-12-03 12:59  tim

        * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp,
        io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
        io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
        utils/TypeContainer.hpp: begin to fix bugs

2004-12-02 19:26  tim

        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
        new_design.

2004-12-02 19:26  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/ForceFieldCreator.cpp,
        UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
        integrators/IntegratorCreator.cpp,
        integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp,
        io/SectionParserManager.hpp, utils/Makefile,
        utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
        bug in countTokens in StringTokenizer

2004-12-02 19:06  tim

        * forceFields/newDUFF.frc: minor fix

2004-12-02 18:15  tim

        * forceFields/newDUFF.frc: new ForceField format

2004-12-02 17:15  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/ForceFieldCreator.cpp,
        UseTheForce/ForceFieldCreator.hpp,
        UseTheForce/ForceFieldFactory.cpp,
        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
        applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp,
        integrators/IntegratorCreator.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/Makefile,
        integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp,
        integrators/NPTi.hpp, integrators/NPTxyz.cpp,
        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
        integrators/NVT.cpp, integrators/NVT.hpp,
        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
        types/Makefile: refine factory pattern to make it initialized
        correctly

2004-12-02 17:15  tim

        * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
        was initially added on branch new_design.

2004-12-02 17:15  tim

        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
        was initially added on branch new_design.

2004-12-02 17:15  tim

        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
        was initially added on branch new_design.

2004-12-02 17:15  tim

        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
        was initially added on branch new_design.

2004-12-02 11:53  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
        types/DirectionalAtomType.cpp, types/Makefile: oopse get built

2004-12-02 11:04  tim

        * src/: applications/simpleBuilder/LatticeCreator.cpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp,
        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
        brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
        brains/SnapshotManager.hpp, brains/Stats.cpp,
        constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp,
        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp,
        io/basic_ifstrstream.hpp, primitives/Bend.hpp,
        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
        types/OplsTorsionType.hpp, types/ShapeAtomType.hpp,
        utils/PropertyMap.hpp, utils/TypeContainer.hpp,
        visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
        have two linking problem

2004-12-02 00:17  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/simpleBuilder/Lattice.cpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp,
        io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp,
        minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp,
        restraints/Restraints.cpp, visitors/AtomVisitor.cpp,
        visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
        visitors/ZconsVisitor.cpp: change endl to std::endl

2004-12-02 00:14  tim

        * src/: UseTheForce/Shapes_FF.cpp,
        applications/dump2Xyz/Dump2XYZ.cpp,
        applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp: minor fix

2004-12-02 00:09  tim

        * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
        remove StreamTokenizer

2004-12-02 00:06  tim

        * src/: UseTheForce/Shapes_FF.cpp,
        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
        applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp,
        io/ZConsWriter.cpp, math/randomSPRNG.cpp,
        restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
        namespace std in .cpp file

2004-12-02 00:04  tim

        * src/: UseTheForce/Shapes_FF.cpp,
        applications/dump2Xyz/Dump2XYZ.cpp,
        applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.cpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/MoLocator.cpp,
        applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp,
        brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp,
        io/ZConsWriter.cpp, io/ZConsWriter.hpp,
        minimizers/MinimizerParameterSet.hpp,
        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
        minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp,
        restraints/Restraints.cpp, restraints/Restraints.hpp,
        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
        utils/GenericData.hpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
        qulified name prefix std

2004-12-01 23:55  tim

        * src/: UseTheForce/Shapes_FF.cpp,
        applications/dump2Xyz/Dump2XYZ.cpp,
        applications/simpleBuilder/BaseLattice.hpp,
        applications/simpleBuilder/Lattice.hpp,
        applications/simpleBuilder/LatticeCreator.hpp,
        applications/simpleBuilder/LatticeFactory.cpp,
        applications/simpleBuilder/LatticeFactory.hpp,
        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp: replace string by std::string

2004-12-01 22:12  tim

        * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
        src/applications/simpleBuilder/BaseLattice.hpp,
        src/applications/simpleBuilder/Lattice.hpp,
        src/applications/simpleBuilder/LatticeCreator.hpp,
        src/applications/simpleBuilder/LatticeFactory.hpp,
        src/applications/simpleBuilder/MoLocator.hpp,
        src/brains/SimInfo.cpp, src/brains/SkipList.hpp,
        src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp,
        src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp,
        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp,
        src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp,
        src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp,
        src/utils/Makefile, src/utils/StringUtils.cpp,
        src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp,
        src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp,
        src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp,
        test/brains/RigidBody.cpp: replace misuse of using namespace std in
        header files

2004-12-01 21:23  tim

        * src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
        primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
        utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
        begin to fix linking problem

2004-12-01 21:08  tim

        * src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
        brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
        integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp,
        math/SquareMatrix3.hpp, primitives/Atom.hpp,
        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
        utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
        still has some linking problem

2004-12-01 19:26  tim

        * src/: integrators/NVT.cpp, integrators/NVT.hpp,
        utils/OOPSEConstant.hpp: NVT get built

2004-12-01 19:09  tim

        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
        branch new_design.

2004-12-01 19:09  tim

        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
        branch new_design.

2004-12-01 19:09  tim

        * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
        brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
        brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
        integrators/Integrator.hpp, integrators/Makefile,
        integrators/NVE.cpp, integrators/NVE.hpp,
        integrators/RotationAlgorithm.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
        get built

2004-12-01 19:09  tim

        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
        was initially added on branch new_design.

2004-12-01 17:45  tim

        * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/Makefile,
        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp,
        io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
        io/StatWriter.hpp: rename DumpWrite to DumpWriter

2004-12-01 17:45  tim

        * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
        branch new_design.

2004-12-01 15:05  tim

        * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
        io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
        utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp,
        visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp,
        visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
        visitors/ZconsVisitor.hpp: visitors get built

2004-12-01 14:32  chrisfen

        * samples/water/tip3p_ice/tp3.md: fixed a sample

2004-12-01 14:10  tim

        * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
        src/types/AtomType.hpp, src/utils/Utility.hpp,
        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
        src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
        spell check

2004-12-01 13:42  tim

        * src/: UseTheForce/DarkSide/atype.F90,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp,
        primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp,
        primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
        and constraint, other directories get built

2004-12-01 12:38  tim

        * src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
        brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp,
        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
        primitives/GhostBend.cpp, primitives/RigidBody.cpp,
        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
        refactory AtomType

2004-11-30 22:11  tim

        * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change

2004-11-30 21:30  tim

        * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
        NumericConstant

2004-11-30 21:24  tim

        * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
        primitives/RigidBody.cpp: minor fix

2004-11-30 18:14  tim

        * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
        io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
        io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
        get built, next is integrator

2004-11-30 17:43  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        io/BASS_interface.cpp, primitives/StuntDouble.hpp,
        utils/StringUtils.hpp: brains get built

2004-11-30 15:50  tim

        * src/: brains/ForceManager.cpp, brains/Makefile,
        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
        utils/StringUtils.hpp: brains get built, io is next

2004-11-30 14:58  tim

        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
        brains/ForceManager.cpp, brains/ForceManager.hpp,
        brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
        brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
        brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp,
        brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
        math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo

2004-11-30 14:58  tim

        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
        added on branch new_design.

2004-11-30 12:54  tim

        * src/: primitives/Bend.hpp, primitives/Bond.hpp,
        primitives/StuntDouble.hpp, primitives/Torsion.hpp,
        utils/LocalIndexManager.hpp: more get fixed

2004-11-30 00:03  tim

        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
        initially added on branch new_design.

2004-11-30 00:03  tim

        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
        LocalndexManager.hpp to LocalIndexManager.hpp

2004-11-29 23:43  tim

        * src/: io/BendTypesSectionParser.cpp,
        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
        io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp,
        io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp,
        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
        types/PolynomialTorsionType.hpp: Section Parsers get compiled

2004-11-29 23:14  tim

        * src/: io/BendTypesSectionParser.cpp,
        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
        io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp,
        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
        fixed

2004-11-29 22:49  tim

        * src/: io/TorsionTypesSectionParser.cpp,
        io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
        types/CubicTorsionType.hpp, types/PolynomialBendType.hpp,
        types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
        types/QuarticTorsionType.hpp: minor fixed

2004-11-29 22:32  tim

        * src/: io/TorsionTypesSectionParser.cpp,
        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
        types/PolynomialTorsionType.hpp: #inlcude statement can not be
        embedded

2004-11-29 16:42  tim

        * test/math/: Makefile, PolynomialTestCase.cpp,
        PolynomialTestCase.hpp: add PolynomialTestCase

2004-11-29 16:42  tim

        * src/math/Polynomial.hpp: Polynomial passes unit test

2004-11-29 15:03  tim

        * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
        QuarticTorsion.hpp to QuarticTorsionType.hpp

2004-11-29 15:03  tim

        * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
        initially added on branch new_design.

2004-11-29 14:56  tim

        * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
        initially added on branch new_design.

2004-11-29 14:56  tim

        * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
        CubicTorsionType and QuarticTorsionType

2004-11-29 14:56  tim

        * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
        initially added on branch new_design.

2004-11-29 13:00  tim

        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
        types/CubicBendType.hpp, types/CubicBondType.hpp,
        types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
        fixed

2004-11-29 12:59  tim

        * src/utils/Trim.hpp: file Trim.hpp was initially added on branch
        new_design.

2004-11-29 12:59  tim

        * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
        Algorithm for std::string

2004-11-29 10:52  tim

        * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
        some useless files

2004-11-29 10:50  tim

        * src/io/: BondTypesSectionParser.cpp,
        ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
        ElectrostaticAtomTypesSectionParser.cpp,
        HarmonicBondTypesSectionParser.cpp,
        HarmonicBondTypesSectionParser.hpp,
        LennardJonesAtomTypesSectionParser.cpp, Makefile,
        SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
        StickyAtomTypesSectionParser.hpp: more files get fixed

2004-11-29 10:27  tim

        * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
        DirectionalAtomTypesSectionParser.cpp,
        EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp,
        Makefile, SectionParser.cpp, SectionParser.hpp,
        SectionParserManager.cpp, SectionParserManager.hpp: part of io get
        built

2004-11-29 09:49  tim

        * src/types/UreyBradleyBendType.hpp: types get built

2004-11-29 09:40  tim

        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
        types  get built

2004-11-25 21:13  tim

        * src/: UseTheForce/ForceField.hpp,
        io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
        types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
        files

2004-11-25 15:18  tim

        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
        initially added on branch new_design.

2004-11-25 15:18  tim

        * src/: io/AtomTypesSectionParser.cpp,
        io/BondTypesSectionParser.cpp,
        io/DirectionalAtomTypesSectionParser.cpp,
        types/QuadraticBendType.hpp, types/QuadraticBondType.hpp,
        types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
        files

2004-11-25 15:18  tim

        * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
        initially added on branch new_design.

2004-11-24 17:12  tim

        * src/: io/AtomTypesSectionParser.cpp,
        io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
        io/ChargeAtomTypesSectionParser.hpp,
        io/DipoleAtomTypesSectionParser.cpp,
        io/DipoleAtomTypesSectionParser.hpp,
        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
        io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp,
        io/EAMAtomTypesSectionParser.hpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp,
        io/HarmonicBondTypesSectionParser.hpp,
        io/LennardJonesAtomTypesSectionParser.cpp,
        io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile,
        io/SectionParser.hpp, io/SectionParserManager.hpp,
        io/StickyAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.hpp,
        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
        utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built

2004-11-24 16:33  tim

        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
        ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
        LJFF.cpp, Makefile: UseTheForce get built

2004-11-24 15:55  tim

        * src/: math/RectMatrix.hpp, primitives/Bend.cpp,
        primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
        primitives/Makefile, primitives/Molecule.cpp,
        primitives/Molecule.hpp, primitives/RigidBody.cpp,
        primitives/StuntDouble.hpp, primitives/Torsion.cpp,
        primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
        primitives/UreyBradleyBend.hpp: types and primitives get built

2004-11-24 14:49  tim

        * test/utils/: Makefile, NextCombinationTestCase.cpp,
        StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
        StringTokenizerTestCase

2004-11-24 14:49  tim

        * src/utils/: GenericData.hpp, StringTokenizer.cpp,
        StringTokenizer.hpp: StringTokenizer passes unit test

2004-11-24 13:20  tim

        * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
        src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
        change Makefile

2004-11-24 13:06  chrisfen

        * src/io/RestraintReader.cpp: improved restraints - mpi should work
        fine

2004-11-24 13:06  chrisfen

        * src/integrators/Integrator.cpp: improved restraints

2004-11-24 13:05  chrisfen

        * samples/water/tip3p_ice/tp3.md: oops...

2004-11-24 12:42  tim

        * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
        brains/DataStorage.hpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, integrators/Integrator.hpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        primitives/DirectionalAtom.cpp: add SetForceManager method to
        integrator

2004-11-23 18:12  tim

        * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
        integrators/NPTxyz.cpp, integrators/NPTxyz.hpp,
        integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp,
        integrators/NVT.hpp, integrators/Velocitizer.cpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp,
        types/UreyBradleyBendType.hpp: refactory NPT integrator

2004-11-23 17:50  chrisfen

        * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
        Restraints should work in parallel now

2004-11-23 17:48  chrisfen

        * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
        brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
        integrators/Integrator.cpp, integrators/Integrator.hpp,
        io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp,
        io/RestraintReader.cpp, io/RestraintWriter.cpp,
        restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
        to restraints

2004-11-23 17:47  chrisfen

        * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
        return to the original on next commit

2004-11-23 12:53  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        io/ChargeAtomTypesSectionParser.cpp,
        io/DirectionalAtomTypesSectionParser.hpp,
        io/EAMAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.cpp,
        io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp,
        io/SectionParser.hpp, types/DirectionalAtomType.cpp,
        utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser

2004-11-23 12:53  tim

        * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
        ElectrostaticAtomTypesSectionParser.hpp was initially added on
        branch new_design.

2004-11-23 12:53  tim

        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
        ElectrostaticAtomTypesSectionParser.cpp was initially added on
        branch new_design.

2004-11-23 01:03  tim

        * src/: io/EAMAtomTypesSectionParser.cpp,
        io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
        types/AtomType.hpp, types/DirectionalAtomType.cpp,
        types/DirectionalAtomType.hpp: add EAM AtomType Section Parser

2004-11-23 01:03  tim

        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
        was initially added on branch new_design.

2004-11-23 01:03  tim

        * src/io/EAMAtomTypesSectionParser.hpp: file
        EAMAtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-23 01:03  tim

        * src/io/EAMAtomTypesSectionParser.cpp: file
        EAMAtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/TorsionTypesSectionParser.hpp: file
        TorsionTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/BendTypesSectionParser.hpp: file
        BendTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/BondTypesSectionParser.hpp: file
        BondTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/BondTypesSectionParser.cpp: file
        BondTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/TorsionTypesSectionParser.cpp: file
        TorsionTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 23:35  tim

        * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
        BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
        TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add
        BondTypesSectionParser, BendTypesSectionParser and
        TorsionTypeSectionParser

2004-11-22 23:35  tim

        * src/io/BendTypesSectionParser.cpp: file
        BendTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 18:04  tim

        * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
        DUFF and EAM

2004-11-22 18:02  tim

        * src/io/: DirectionalAtomTypesParser.hpp,
        DirectionalAtomTypesSectionParser.hpp: adding section parsers

2004-11-22 18:02  tim

        * src/io/DirectionalAtomTypesSectionParser.hpp: file
        DirectionalAtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/DipoleAtomTypesSectionParser.hpp: file
        DipoleAtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/AtomTypesSectionParser.hpp: file
        AtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/HarmonicBondTypesSectionParser.hpp: file
        HarmonicBondTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/StickyAtomTypesSectionParser.cpp: file
        StickyAtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
        LennardJonesAtomTypesSectionParser.hpp was initially added on
        branch new_design.

2004-11-22 15:55  tim

        * src/io/HarmonicBondTypesSectionParser.cpp: file
        HarmonicBondTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/DirectionalAtomTypesSectionParser.cpp: file
        DirectionalAtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
        was initially added on branch new_design.

2004-11-22 15:55  tim

        * src/io/AtomTypesSectionParser.cpp: file
        AtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/ChargeAtomTypesSectionParser.cpp: file
        ChargeAtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/DipoleAtomTypesSectionParser.cpp: file
        DipoleAtomTypesSectionParser.cpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
        LennardJonesAtomTypesSectionParser.cpp was initially added on
        branch new_design.

2004-11-22 15:55  tim

        * src/io/ChargeAtomTypesSectionParser.hpp: file
        ChargeAtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/StickyAtomTypesSectionParser.hpp: file
        StickyAtomTypesSectionParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
        added on branch new_design.

2004-11-22 15:55  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
        io/ChargeAtomTypesSectionParser.hpp,
        io/DipoleAtomTypesSectionParser.cpp,
        io/DipoleAtomTypesSectionParser.hpp,
        io/DirectionalAtomTypesParser.hpp,
        io/DirectionalAtomTypesSectionParser.cpp,
        io/HarmonicBondTypesSectionParser.cpp,
        io/HarmonicBondTypesSectionParser.hpp,
        io/LennardJonesAtomTypesSectionParser.cpp,
        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
        io/SectionParser.hpp, io/SectionParserManager.cpp,
        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
        types/AtomType.hpp, types/DirectionalAtomType.hpp,
        utils/GenericData.hpp: adding section parsers

2004-11-22 15:55  tim

        * src/io/DirectionalAtomTypesParser.hpp: file
        DirectionalAtomTypesParser.hpp was initially added on branch
        new_design.

2004-11-22 15:55  tim

        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
        was initially added on branch new_design.

2004-11-22 15:55  tim

        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
        added on branch new_design.

2004-11-19 17:12  tim

        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
        added on branch new_design.

2004-11-19 17:12  tim

        * src/: brains/SimState.cpp, brains/SimState.hpp,
        io/InitializeFromFile.cpp, types/FixBondType.hpp,
        types/FixedBondType.hpp: remove more useless files

2004-11-19 16:47  tim

        * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
        integrators/Integrator.cpp, applications/Makedepend: remove more
        useless files

2004-11-19 16:38  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
        integrators/NVT.hpp: refactory integrator

2004-11-19 16:38  tim

        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
        branch new_design.

2004-11-19 16:38  tim

        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
        branch new_design.

2004-11-19 16:38  tim

        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
        branch new_design.

2004-11-19 16:38  tim

        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
        on branch new_design.

2004-11-19 16:38  tim

        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
        branch new_design.

2004-11-19 15:37  tim

        * forceFields/newDUFF.frc: new DUFF forcefield

2004-11-19 15:23  tim

        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
        branch new_design.

2004-11-19 15:23  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
        UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
        utils/TypeContainer.hpp: add EAM

2004-11-19 15:23  tim

        * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
        branch new_design.

2004-11-19 13:02  tim

        * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
        error checking

2004-11-19 12:56  tim

        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
        was initially added on branch new_design.

2004-11-19 12:56  tim

        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
        was initially added on branch new_design.

2004-11-19 12:56  tim

        * src/types/FixBondType.hpp: file FixBondType.hpp was initially
        added on branch new_design.

2004-11-19 12:56  tim

        * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
        UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
        UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp,
        integrators/IntegratorFactory.cpp,
        integrators/IntegratorFactory.hpp, integrators/NVE.hpp,
        integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp,
        utils/StringTokenizer.cpp: DUFF is almost done except error
        checking

2004-11-18 19:11  tim

        * src/UseTheForce/DUFF.cpp: adding DUFF parser

2004-11-18 18:26  tim

        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
        initially added on branch new_design.

2004-11-18 18:26  tim

        * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
        integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp,
        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
        types/CubicBendType.hpp, types/CubicBondType.hpp,
        types/HarmonicBondType.hpp, types/QuadraticBendType.hpp,
        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
        DUFF parser

2004-11-18 16:42  tim

        * forceFields/newDUFF.frc: adding new format DUFF force field

2004-11-18 10:57  chrisfen

        * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
        slowed down the force loop

2004-11-18 00:42  tim

        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
        initially added on branch new_design.

2004-11-18 00:42  tim

        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
        initially added on branch new_design.

2004-11-18 00:42  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
        primitives/Bend.cpp, utils/NumericConstant.cpp,
        utils/NumericConstant.hpp: Adding NumericConstant class

2004-11-17 23:16  tim

        * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
        UseTheForce/ForceFields.hpp: remove more junk files

2004-11-17 23:12  tim

        * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
        brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
        integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp,
        primitives/AbstractClasses.hpp, primitives/Bond.cpp,
        primitives/BondExtensions.cpp, primitives/SRI.hpp,
        primitives/TorsionExtensions.cpp: remove some junk files

2004-11-17 23:07  tim

        * src/primitives/BendExtensions.cpp: remove some junk files

2004-11-17 23:04  tim

        * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
        QuadraticBondType.hpp: refine QudraticBond

2004-11-17 22:57  tim

        * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp

2004-11-17 22:57  tim

        * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
        initially added on branch new_design.

2004-11-17 16:47  tim

        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
        was initially added on branch new_design.

2004-11-17 16:47  tim

        * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
        added on branch new_design.

2004-11-17 16:47  tim

        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
        added on branch new_design.

2004-11-17 16:47  tim

        * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
        initially added on branch new_design.

2004-11-17 16:47  tim

        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
        initially added on branch new_design.

2004-11-17 16:47  tim

        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
        initially added on branch new_design.

2004-11-17 16:47  tim

        * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
        added on branch new_design.

2004-11-17 16:47  tim

        * src/: math/ChebyshevPolynomials.cpp,
        math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
        primitives/Bend.hpp, primitives/GhostBend.cpp,
        primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp,
        primitives/UreyBradleyBend.hpp, types/BondType.hpp,
        types/CubicBendType.hpp, types/CubicBondType.hpp,
        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
        UreyBradleyBend and GhostBend

2004-11-17 13:58  tim

        * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
        was initially added on branch new_design.

2004-11-17 13:58  tim

        * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
        was initially added on branch new_design.

2004-11-17 13:58  tim

        * src/: math/ChebyshevPolynomials.cpp,
        math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
        primitives/Bond.hpp, types/CharmmTorsionType.hpp,
        types/OplsTorsionType.hpp, types/PolynomialBondType.hpp,
        types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
        stuff and Chebyshev Polynomial

2004-11-17 13:58  tim

        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
        initially added on branch new_design.

2004-11-17 01:37  tim

        * src/types/PolynomialTorsionType.hpp: file
        PolynomialTorsionType.hpp was initially added on branch new_design.

2004-11-17 01:37  tim

        * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
        initially added on branch new_design.

2004-11-17 01:37  tim

        * src/: math/Polynomial.hpp, primitives/Bend.cpp,
        primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
        types/BondType.hpp, types/CharmmTorsionType.cpp,
        types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp,
        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
        types/PolynomialTorsionType.hpp, types/TorsionType.hpp,
        utils/StringTokenizer.hpp: add  PolynomialBondType,
        PolynomialBendType, PolynomialTorsionType, HarmonicBendType and
        CharmmTorsionType. Need to refine the design and add document for
        them

2004-11-17 01:37  tim

        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
        initially added on branch new_design.

2004-11-17 01:37  tim

        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
        initially added on branch new_design.

2004-11-17 01:37  tim

        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
        initially added on branch new_design.

2004-11-16 20:11  tim

        * src/types/: BendType.hpp, PolynomialBondType.hpp,
        TorsionType.hpp: add PolynomialBondType

2004-11-16 20:11  tim

        * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
        initially added on branch new_design.

2004-11-16 18:20  tim

        * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
        on branch new_design.

2004-11-16 18:20  tim

        * src/math/Polynomial.hpp: Adding Polynomial class

2004-11-16 17:04  gezelter

        * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
        added on branch new_design.

2004-11-16 17:04  gezelter

        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
        initially added on branch new_design.

2004-11-16 17:04  gezelter

        * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
        MorseBondType.hpp, TorsionType.hpp: added some new stuff

2004-11-16 15:36  tim

        * src/: primitives/Bend.cpp, primitives/Bend.hpp,
        primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
        types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
        TorsionType

2004-11-15 21:07  tim

        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
        branch new_design.

2004-11-15 21:07  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
        UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
        utils/StringTokenizer.cpp: adding DUFF class; adding checking
        statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer

2004-11-15 18:00  tim

        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
        UseTheForce/ForceFieldFactory.cpp,
        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes

2004-11-15 18:00  tim

        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
        was initially added on branch new_design.

2004-11-15 18:00  tim

        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
        was initially added on branch new_design.

2004-11-15 18:00  tim

        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
        branch new_design.

2004-11-15 13:02  tim

        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
        initially added on branch new_design.

2004-11-15 13:02  tim

        * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
        branch new_design.

2004-11-15 13:02  tim

        * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
        branch new_design.

2004-11-15 13:02  tim

        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
        integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
        io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
        DumpWriter.Next Step is LJFF and integrators

2004-11-13 00:08  tim

        * src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp, primitives/Molecule.cpp,
        primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
        refactory, refactory

2004-11-12 17:43  tim

        * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
        StringTokenizer.cpp: bug fix in hasMoreTokens

2004-11-12 17:28  tim

        * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
        initially added on branch new_design.

2004-11-12 17:28  tim

        * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
        StringUtils, a c-style strtok like class, need unit test

2004-11-12 12:40  tim

        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp: SimCreator and SimInfo are  ready for unit test

2004-11-12 02:05  tim

        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
        primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
        MoleculeCreator forget to create CutoffGroups for free atoms

2004-11-12 01:19  tim

        * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
        io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
        OOPSE = Object-Obfuscated Parallel Simulation Engine

2004-11-11 16:48  chrisfen

        * samples/water/tip3p_ice/tp3.md: working sample

2004-11-11 16:47  chrisfen

        * src/restraints/Restraints.cpp: working towards parallel
        restraints

2004-11-11 16:47  chrisfen

        * src/integrators/Integrator.cpp: Commented out some write
        statements

2004-11-11 16:46  chrisfen

        * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
        write statements

2004-11-11 16:46  chrisfen

        * samples/water/tip3p_ice/tp3.md: Fun with ice

2004-11-11 11:41  tim

        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
        brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h,
        brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp,
        io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
        useless mpiSimulation

2004-11-11 11:41  tim

        * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
        branch new_design.

2004-11-10 17:50  tim

        * src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
        integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo

2004-11-10 17:01  tim

        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
        brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
        brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
        io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp,
        visitors/AtomVisitor.cpp: another painful day (1) SimCreator,
        SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom
        File will be removed) (3) ForceField (at least LJ) and BondType,
        BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
        Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint

2004-11-10 09:52  tim

        * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
        configurable StatWriter

2004-11-10 09:52  tim

        * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
        branch new_design.

2004-11-09 21:58  tim

        * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
        in progress

2004-11-09 18:11  tim

        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
        added on branch new_design.

2004-11-09 18:11  tim

        * src/integrators/VelocityVerletIntegrator.cpp: file
        VelocityVerletIntegrator.cpp was initially added on branch
        new_design.

2004-11-09 18:11  tim

        * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
        brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
        brains/mpiSimulation.hpp, integrators/Integrator.hpp,
        integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
        integrators/VelocityVerletIntegrator.hpp: adding ForceManager

2004-11-09 18:11  tim

        * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
        added on branch new_design.

2004-11-09 18:11  tim

        * src/integrators/NVE.cpp: file NVE.cpp was initially added on
        branch new_design.

2004-11-08 20:08  tim

        * src/integrators/VelocityVerletIntegrator.hpp: file
        VelocityVerletIntegrator.hpp was initially added on branch
        new_design.

2004-11-08 20:08  tim

        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
        branch new_design.

2004-11-08 20:08  tim

        * src/: brains/Exclude.hpp, brains/Stats.hpp,
        integrators/Integrator.hpp, integrators/NVE.hpp,
        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
        utils/TypeContainer.hpp: More to break

2004-11-06 00:21  tim

        * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
        added on branch new_design.

2004-11-06 00:21  tim

        * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
        UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
        utils/TypeContainer.hpp, utils/next_combination.hpp: adding
        ForceField and TypeContainer classes

2004-11-05 18:38  tim

        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
        initially added on branch new_design.

2004-11-05 18:38  tim

        * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
        initially added on branch new_design.

2004-11-05 18:38  tim

        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
        brains/SimInfo.hpp, primitives/Molecule.hpp,
        utils/LocalndexManager.hpp: Fix Exclude class etc.

2004-11-05 16:45  chrisfen

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
        linear visitor

2004-11-05 16:04  chrisfen

        * src/UseTheForce/DarkSide/shapes.F90: current status of the
        debugging process

2004-11-05 16:04  chrisfen

        * make/Makefile.in: included visitors and minimizer

2004-11-05 16:03  chrisfen

        * ChangeLog: new changes

2004-11-04 21:56  tim

        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
        primitives/Molecule.hpp: Pain......

2004-11-04 15:55  tim

        * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
        src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
        src/brains/Stats.hpp: time to break SimSetup

2004-11-04 15:51  gezelter

        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
        classes in progress

2004-11-04 14:48  tim

        * src/brains/Stats.cpp: file Stats.cpp was initially added on
        branch new_design.

2004-11-04 14:48  tim

        * src/brains/Stats.hpp: file Stats.hpp was initially added on
        branch new_design.

2004-11-04 14:48  tim

        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
        class

2004-11-04 11:22  gezelter

        * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
        linearAxis are virtual in StuntDouble, but are implemented by
        DirectionalAtom and RigidBody In StuntDouble, they should return
        false and "-1" but there should be logic to figure them out in the
        other two classes

2004-11-04 11:20  gezelter

        * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
        remember what I did

2004-11-04 11:20  gezelter

        * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky

2004-11-04 11:20  gezelter

        * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
        in the entry_plug so that it only is set if the atoms really are in
        the simulation

2004-11-04 11:20  gezelter

        * samples/water/ssd/ssd.md: testing force fields

2004-11-04 11:19  gezelter

        * samples/shape/linear.in: testing shapes

2004-11-03 14:56  tim

        * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
        class(similar as SimSetup)

2004-11-03 14:56  tim

        * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
        added on branch new_design.

2004-11-03 14:56  tim

        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
        added on branch new_design.

2004-11-03 13:00  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
        UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp,
        brains/DataStorage.hpp, primitives/Atom.hpp,
        primitives/DirectionalAtom.hpp, restraints/Restraints.hpp,
        visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
        compiled. Still a long way to go ......

2004-11-03 11:08  tim

        * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
        src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
        src/integrators/NPTf.cpp, src/integrators/NPTi.cpp,
        src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp,
        src/io/ZConsReader.cpp, src/primitives/Bend.cpp,
        src/primitives/Bond.cpp, src/primitives/GhostBend.cpp,
        src/primitives/Molecule.cpp, src/primitives/Molecule.hpp,
        src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp,
        src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp,
        src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp,
        src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
        src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......

2004-11-02 17:41  tim

        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
        Need unit test

2004-11-02 17:41  tim

        * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
        initially added on branch new_design.

2004-11-02 17:41  tim

        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
        branch new_design.

2004-11-02 11:59  tim

        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
        branch new_design.

2004-11-02 11:59  tim

        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
        SimSnapshotManager.hpp: SimModel in progress

2004-11-02 10:28  chrisfen

        * src/: UseTheForce/DarkSide/shapes.F90,
        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
        looks like it's working

2004-11-02 10:27  tim

        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
        functions for dealing with memory issue

2004-11-02 10:27  tim

        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
        added on branch new_design.

2004-11-02 10:23  tim

        * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
        brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
        SimModel(something similar as SimInfo)

2004-11-01 17:52  tim

        * src/: applications/simpleBuilder/MoLocator.hpp,
        applications/simpleBuilder/simpleBuilder.cpp,
        brains/DataStorage.hpp, brains/ForceFields.cpp,
        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp,
        constraints/ZConstraint.cpp, integrators/Integrator.cpp,
        integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp,
        math/SquareMatrix3.hpp, math/Vector3.hpp,
        minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp,
        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
        primitives/Molecule.cpp, primitives/Molecule.hpp,
        primitives/RigidBody.hpp, primitives/Torsion.hpp,
        restraints/Restraints.cpp, types/TorsionType.hpp,
        utils/PropertyMap.hpp, utils/StringTokenizer.hpp,
        visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp,
        visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
        RigidBody and StuntDouble classes get compiled

2004-11-01 16:40  tim

        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
        on branch new_design.

2004-11-01 16:40  tim

        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
        branch new_design.

2004-11-01 16:40  tim

        * src/primitives/Bond.hpp: file Bond.hpp was initially added on
        branch new_design.

2004-11-01 16:40  tim

        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
        version of Bond, Bend and Torsion.

2004-11-01 16:37  tim

        * src/types/BendType.hpp: file BendType.hpp was initially added on
        branch new_design.

2004-11-01 16:37  tim

        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
        BondType, BendType, TorsionType

2004-11-01 16:37  tim

        * src/types/TorsionType.hpp: file TorsionType.hpp was initially
        added on branch new_design.

2004-11-01 16:37  tim

        * src/types/BondType.hpp: file BondType.hpp was initially added on
        branch new_design.

2004-11-01 15:15  tim

        * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
        CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
        GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp,
        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
        break, break and break.....

2004-11-01 14:57  tim

        * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
        StuntDouble.hpp: these core classes get compiled

2004-10-29 17:37  tim

        * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
        class

2004-10-29 17:28  chrisfen

        * src/: UseTheForce/DarkSide/atype.F90,
        UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
        types/ShapeAtomType.cpp: still debugging

2004-10-29 17:28  chrisfen

        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
        shapes rcut calculator added

2004-10-29 17:27  chrisfen

        * samples/shape/linear.md: shorter run

2004-10-29 15:54  tim

        * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.

2004-10-29 11:22  tim

        * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
        ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
        some deprecated files

2004-10-29 11:20  tim

        * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
        More painful reconstruction is coming !!!

2004-10-28 17:34  tim

        * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
        test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
        test/brains/RigidBody.cpp, test/brains/RigidBody.hpp,
        test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
        DirectionalAtom and RigidBody

2004-10-28 17:26  tim

        * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
        src/applications/simpleBuilder/MoLocator.cpp,
        src/applications/simpleBuilder/Vector3d.hpp,
        src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
        remove old Vector3d.hpp from application/simpleBuilder

2004-10-28 16:42  tim

        * src/utils/next_combination.hpp: Minor change in next_combination

2004-10-28 16:28  tim

        * src/utils/next_combination.hpp,
        test/utils/NextCombinationTestCase.cpp,
        test/utils/ReplaceWildCardTestCase.cpp: Done with combination

2004-10-28 16:11  tim

        * src/utils/next_combination.hpp: change documentation of
        next_combination.hpp

2004-10-28 15:41  tim

        * ChangeLog, src/utils/next_combination.hpp,
        test/utils/NextCombinationTestCase.cpp,
        test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working

2004-10-28 15:01  tim

        * src/utils/next_combination.hpp: adding replace wildcard function

2004-10-28 14:33  tim

        * src/utils/next_combination.hpp: Minor change

2004-10-28 14:06  tim

        * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
        src/applications/simpleBuilder/simpleBuilder.cpp,
        src/utils/next_combination.hpp, test/utils/Makefile,
        test/utils/NextCombinationTestCase.cpp,
        test/utils/ReplaceWildCardTestCase.cpp,
        test/utils/next_combination.hpp: STL next_permutation like
        next_combination is working

2004-10-28 12:22  chrisfen

        * src/UseTheForce/WATER.cpp: fix of setDipoles

2004-10-28 12:20  gezelter

        * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
        shapeFile

2004-10-28 12:20  gezelter

        * samples/shape/linear.md: forgot the orientation line

2004-10-28 11:56  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
        UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
        declaration foo

2004-10-28 11:55  gezelter

        * samples/lipid/5x5.md: uncommented .in line

2004-10-28 10:42  tim

        * test/utils/: Makefile, NextCombinationTestCase.cpp,
        NextCombinationTestCase.hpp, next_combination.hpp: next_combination
        in progress

2004-10-28 10:15  tim

        * test/utils/: NextCombinationTestCase.cpp,
        NextCombinationTestCase.hpp: adding next_combination test case

2004-10-28 10:02  tim

        * test/utils/next_combination.hpp: STL Compatible combination
        sequence generator

2004-10-28 01:23  tim

        * test/utils/: GenerateCombination.hpp,
        ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp

2004-10-28 01:16  tim

        * test/utils/GenerateCombination.hpp: a STL next_permutaion like
        next_combination function.

2004-10-27 22:27  tim

        * test/utils/ReplaceWildCard.hpp: no message

2004-10-27 22:14  tim

        * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
        ReplaceWildCard(recursive version) is working, need refactoring. An
        iterative version is on the way

2004-10-27 21:28  tim

        * test/utils/: Makefile, ReplaceWildCard.hpp,
        ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress

2004-10-27 21:08  tim

        * test/utils/: ReplaceWildCardTestCase.cpp,
        ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard

2004-10-27 18:17  tim

        * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
        test

2004-10-27 01:25  tim

        * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
        char matching is on the way

2004-10-27 01:07  tim

        * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4

2004-10-26 22:00  gezelter

        * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix

2004-10-26 21:20  gezelter

        * src/UseTheForce/ForceFields.hpp: subclass foo

2004-10-26 21:16  gezelter

        * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
        string conversion

2004-10-26 19:01  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
        brains/SimSetup.hpp: char* -> string

2004-10-26 17:25  gezelter

        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
        Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
        ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
        isXXX

2004-10-26 17:25  gezelter

        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
        define name collision

2004-10-26 17:24  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
        UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp,
        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
        UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
        forcefield refactoring for shapes

2004-10-26 17:24  gezelter

        * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
        Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
        linear.md, linear.shape, toluene.shape: adding sample shape
        directory

2004-10-26 17:19  tim

        * ChangeLog, src/brains/DataStorage.cpp,
        src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
        test/brains/DataStorageTestCase.cpp,
        test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
        DataStorage passes unit test

2004-10-26 13:03  chrisfen

        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
        Changes to help advance shapes

2004-10-26 13:02  chrisfen

        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
        Shapes force field reader

2004-10-26 12:28  tim

        * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
        SnapshotTestCase in progress

2004-10-25 17:46  tim

        * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
        src/math/Vector3.hpp, test/brains/StuntDouble.hpp,
        test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp,
        test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
        and Vector classes

2004-10-25 12:03  tim

        * ChangeLog, src/utils/GenericFactory.hpp,
        test/utils/GenericFactoryTestCase.cpp,
        test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding
        GenericFactory Test Case. GenericFactory now can bed used to creat
        ForcefieldFactory and IntegratorFactory etc.

2004-10-24 23:08  tim

        * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
        brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
        brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
        get reconstructed

2004-10-24 02:55  tim

        * src/utils/GenericFactory.hpp: GenericFactory pass unit test

2004-10-23 18:09  tim

        * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
        StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
        RigidBody.cpp: Refactoring in progress

2004-10-22 18:09  tim

        * ChangeLog, src/brains/Snapshot.hpp,
        src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
        test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
        test/brains/StuntDouble.hpp: more work in Snapshot

2004-10-22 17:59  chrisfen

        * src/: UseTheForce/LJFF.cpp,
        UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
        god!  It runs and conserves energy!

2004-10-22 17:54  chrisfen

        * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY

2004-10-22 17:53  chrisfen

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
        brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
        breakey

2004-10-22 17:53  chrisfen

        * make/Makefile.in: compiler flags

2004-10-22 16:20  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
        brains/fSimulation.h, types/AtomType.hpp,
        types/DirectionalAtomType.hpp: fixey fixey

2004-10-22 15:22  gezelter

        * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
        charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
        lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
        fortran files and c/Fortran interfaces

2004-10-22 15:21  gezelter

        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
        DirectionalAtomType.hpp, Makefile: More on AtomType and
        DirectionalAtomType

2004-10-22 09:47  gezelter

        * src/types/AtomType.hpp: Adding AtomType

2004-10-21 16:31  tim

        * ChangeLog, src/brains/Snapshot.hpp,
        src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
        src/math/Vector.hpp, src/math/Vector3.hpp,
        test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
        Snapshot and SnapshotManager in progress

2004-10-21 16:30  tim

        * test/brains/: BrainsTest.cpp, Makefile,
        SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
        SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
        Snapshot and snapshotManager.

2004-10-21 15:15  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
        UseTheForce/doForces_interface.h, UseTheForce/fForceField.h,
        UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h,
        brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.  
        Fixey Fixey.

2004-10-21 11:32  tim

        * src/utils/GenericData.cpp, src/utils/Makefile,
        test/utils/Makefile, test/utils/UtilTest: remove some junk files

2004-10-21 11:24  tim

        * test/utils/GenericData.hpp: remove backup of  GenericData.hpp

2004-10-21 11:22  tim

        * ChangeLog, src/brains/SimSetup.cpp,
        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
        src/integrators/NVT.cpp, src/io/DumpReader.cpp,
        src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp,
        src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp,
        src/utils/GenericData.cpp, src/utils/GenericData.hpp,
        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
        src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp,
        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
        src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
        GenericData

2004-10-21 10:25  chuckv

        * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
        module.

2004-10-21 10:24  chuckv

        * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
        fortran lj module.

2004-10-20 17:54  tim

        * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
        test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
        test/utils/PropertyMapTestCase.cpp,
        test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
        GenericData and PropertyMap  pass unit test.

2004-10-20 16:52  gezelter

        * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
        DarkSide/sticky_interface.h: fixed a fortran name problem

2004-10-20 16:38  tim

        * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
        GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
        UtilTest, UtilTest.cpp: adding generic data test case

2004-10-20 16:16  chuckv

        * configure, ac-tools/aclocal.m4,
        src/UseTheForce/DarkSide/Makefile,
        src/UseTheForce/DarkSide/mpiSimulation.F90,
        src/UseTheForce/DarkSide/mpiSimulation_interface.h,
        src/UseTheForce/DarkSide/simParallel.F90,
        src/UseTheForce/DarkSide/simParallel_interface.h,
        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp:
        Fortran/C++ interface de-obfuscation project appears to be
        complete!  Woo hoo!

2004-10-20 15:47  chuckv

        * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
        fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
        continues

2004-10-20 15:46  chuckv

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
        UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp,
        UseTheForce/doForces_interface.h,
        UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90,
        UseTheForce/DarkSide/atype_interface.h,
        UseTheForce/DarkSide/eam_interface.h,
        UseTheForce/DarkSide/gb_interface.h,
        UseTheForce/DarkSide/mpiSimulation_interface.h,
        UseTheForce/DarkSide/shapes_interface.h,
        UseTheForce/DarkSide/simulation_interface.h,
        UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp,
        brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
        de-obfuscation project (It is a very long story)

2004-10-20 13:07  tim

        * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
        test/math/SquareMatrix3TestCase.cpp,
        test/math/SquareMatrixTestCase.cpp,
        test/math/SquareMatrixTestCase.hpp: Math library pass the unit test

2004-10-20 00:52  tim

        * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
        SnapshotManager in design phase

2004-10-19 23:54  gezelter

        * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
        problem prevented linking

2004-10-19 23:54  gezelter

        * src/UseTheForce/Shapes_FF.cpp: fixed include

2004-10-19 23:26  gezelter

        * src/utils/: Makefile, definitions.F90, definitions_module.F90,
        oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
        more fortran name mangling

2004-10-19 23:23  gezelter

        * src/profiling/timing.F90: yet more fortran renaming

2004-10-19 23:19  gezelter

        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
        do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
        notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
        wrappers.F90: Fortran name cleanup continues

2004-10-19 23:12  gezelter

        * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
        broken fortran stuff

2004-10-19 23:02  gezelter

        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
        atype_interface.h, atype_module.F90, atype_module_interface.h,
        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
        calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90,
        eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90,
        gb_interface.h, gb_module_interface.h, mpiSimulation.F90,
        mpiSimulation_interface.h, mpiSimulation_module.F90,
        mpisimulation_module_interface.h, reactionField.F90, shapes.F90,
        shapes_interface.h, shapes_module.h, simulation.F90,
        simulation_interface.h, simulation_module.F90,
        simulation_module_interface.h, sticky.F90, sticky_interface.h,
        sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
        name sanity on the fortran side

2004-10-19 19:18  tim

        * test/math/SquareMatrix3TestCase.hpp: [no log message]

2004-10-19 18:01  tim

        * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
        src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
        except diagonalize(), all of functions in math library pass the
        test

2004-10-19 17:43  chuckv

        * src/UseTheForce/do_Forces.h: Added correct prototypes for
        C-fortran interface functions.

2004-10-19 17:37  chuckv

        * src/UseTheForce/DarkSide/: atype_module_interface.h,
        eam_module_inteface.h, gb_module_interface.h,
        mpisimulation_module_interface.h, simulation_module_interface.h,
        sticky_pair_module_interface.h: Added correct prototypes for
        C-fortran interface functions.

2004-10-19 16:28  tim

        * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
        src/math/SquareMatrix.hpp, src/math/Vector.hpp,
        test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp,
        test/math/RectMatrixTestCase.cpp,
        test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp,
        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
        bugs get fixed at math library

2004-10-19 15:43  chuckv

        * src/UseTheForce/: DarkSide/atype_module_interface.h,
        DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
        DarkSide/mpisimulation_module_interface.h,
        DarkSide/simulation_module_interface.h,
        DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90,
        DarkSide/atype_module.F90, DarkSide/calc_gb.F90,
        DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90,
        DarkSide/simulation_module.F90, do_Forces.F90,
        fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90,
        notifycutoffs_module_interface.h: Added new files for fortran
        interface.

2004-10-19 15:43  gezelter

        * src/UseTheForce/Makefile: regressing

2004-10-19 15:40  gezelter

        * src/: UseTheForce/DarkSide/calc_shapes.F90,
        UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
        working on shapes for portability

2004-10-19 15:40  gezelter

        * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes

2004-10-19 13:21  chrisfen

        * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
        findBegin

2004-10-18 23:34  tim

        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
        are fixed in Vector class

2004-10-18 23:28  tim

        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
        some bugs in RectMatrixTestCase

2004-10-18 23:21  tim

        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
        test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
        test/math/VectorTestCase.hpp: implement more test cases

2004-10-18 18:13  tim

        * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
        src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
        src/utils/StringTokenizer.hpp, test/math/Makefile,
        test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
        tests on math library

2004-10-18 16:03  tim

        * test/math/: Makefile, QuaternionTestCase.cpp,
        QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
        SquareMatrix3TestCase.cpp, Vector3TestCase.cpp,
        Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
        more testing units

2004-10-18 12:07  tim

        * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
        math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
        math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
        utils/GenericFactory.hpp: fix some bugs in Quaternion class

2004-10-18 11:30  gezelter

        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
        Your basic run of the mill real-valued versions of Y_l^m(\theta,
        \phi)

2004-10-18 11:29  gezelter

        * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
        types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
        utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
        Shapes into OOPSE

2004-10-18 10:21  gezelter

        * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType

2004-10-18 00:23  tim

        * test/math/VectorTestCase.hpp: adding  vector test case

2004-10-18 00:23  tim

        * src/utils/GenericFactory.hpp: adding generic factory and vector
        test case

2004-10-16 20:19  tim

        * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
        SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
        progress

2004-10-15 20:31  tim

        * src/math/Quaternion.hpp: add quaternion class

2004-10-15 16:11  tim

        * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
        IfstrstreamTestCase.hpp: adding test file

2004-10-15 16:10  tim

        * src/io/basic_ifstrstream.hpp: fix a bunch of bugs

2004-10-15 15:42  tim

        * src/io/basic_ifstrstream.hpp: change const_cast to statc_const

2004-10-15 15:35  tim

        * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp

2004-10-15 15:34  tim

        * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
        namespace oopse

2004-10-15 14:38  chuckv

        * configure, ac-tools/aclocal.m4: Changed optimization flags for
        XLF and XLC.

2004-10-15 13:28  tim

        * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
        adding ifstrstream test case

2004-10-15 13:20  tim

        * src/io/basic_ifstrstream.hpp: fix include

2004-10-15 13:18  tim

        * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi

2004-10-15 13:17  tim

        * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile

2004-10-15 13:16  tim

        * test/io/: Makefile, ifstrstreamTestCase.cpp,
        ifstrstreamTestCase.hpp: adding test case for ifstrstream

2004-10-15 10:37  tim

        * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
        ifstrstreamTestCase.hpp: add ifstrstreamTestCase

2004-10-15 10:20  tim

        * src/io/basic_ifstrstream.hpp: add checkFilename Option

2004-10-15 10:19  tim

        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
        SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
        SquareMatrixTestCase class

2004-10-15 02:52  tim

        * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream

2004-10-14 18:28  tim

        * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
        Vector.hpp: math library in progress

2004-10-14 18:27  tim

        * src/io/FileReader.hpp: FileReader in progress

2004-10-13 18:53  tim

        * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
        test in isOrthogonal of SquareMatrix is failed by some reasons

2004-10-13 17:28  tim

        * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
        class

2004-10-13 17:27  tim

        * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
        RectMatrixTestCase.hpp: adding testing unit

2004-10-13 17:24  tim

        * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix

2004-10-13 01:51  tim

        * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
        Vector3.hpp: refactory vector and matrix classes

2004-10-13 01:50  tim

        * src/math/Vector3d.hpp: Remove some Makefile.in

2004-10-12 18:57  tim

        * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and 
        Matrix3x3d.hpp

2004-10-12 14:08  tim

        * doc/: cppstyle.html, style.css: adding c++ coding style

2004-10-11 17:15  tim

        * src/: constraints/AbstractClasses.hpp,
        integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
        change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp

2004-10-11 16:54  tim

        * scripts/filepp: fix a bug in filepp

2004-10-11 16:13  tim

        * make/Makefile.in: using filepp to generate dependencies instead
        of compilers

2004-10-11 16:10  tim

        * scripts/filepp: filepp can be used to generate dependencies for
        c/c++ now

2004-10-11 13:40  tim

        * make/Makefile.in: remove -module from F90Options

2004-10-11 13:01  tim

        * make/Makefile.in: adding rules to move fortran 90 module to
        target directory

2004-10-11 10:43  gezelter

        * make/Makefile.in: fixed makefile.in

2004-10-11 09:51  tim

        * scripts/filepp: remove "use bytes" which causes problem in sgi
        machine

2004-10-11 09:26  tim

        * forceFields/Makefile: add Makefile

2004-10-11 09:23  tim

        * samples/: water/dimer/Makefile, water/spce/Makefile,
        water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
        water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
        directory

2004-10-11 09:23  tim

        * samples/argon/Makefile: remove argon.dump and argon.eor from
        Makefile

2004-10-09 01:01  tim

        * samples/: alkane/Makefile.in, argon/Makefile.in,
        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
        Remove some Makefile.in

2004-10-08 18:15  tim

        * make/Makefile.in: [no log message]

2004-10-08 17:51  tim

        * make/Makefile.in: fix make install

2004-10-08 17:10  tim

        * make/Makefile.in: adding make install

2004-10-08 17:04  tim

        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
        metals/Makefile, minimizer/Makefile, water/Makefile.in,
        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
        water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
        water/ssde/Makefile, water/ssde/Makefile.in,
        water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
        water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
        zcons/Makefile.in: add Makefile to sample directory

2004-10-06 18:03  gezelter

        * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
        stuff

2004-10-06 18:03  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        make/Doxyfile, src/applications/getopt.c,
        src/applications/getopt1.c, src/applications/gnugetopt.h: more
        build fixes

2004-10-06 17:20  tim

        * make/: Doxyfile, Makefile.in: adding doxygen configuration file

2004-10-06 17:19  tim

        * scripts/filepp: filepp can handle different fortran module case
        and suffix

2004-10-06 16:27  gezelter

        * src/restraints/Restraints.cpp: Chris doesn't know about the
        OOPSE-2.0 directory structure yet

2004-10-06 16:27  gezelter

        * ChangeLog: Yeah yeah, we'lll get around to it later

2004-10-06 16:22  gezelter

        * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
        make/Makefile.in: cleaning up build process

2004-10-06 15:01  chrisfen

        * src/restraints/Restraints.cpp: made the file reading in
        restraints more intelligent - no longer gives uninformative seg
        faults

2004-10-06 14:55  gezelter

        * src/applications/simpleBuilder/Make.ftemp.old: cleaning up

2004-10-06 14:51  gezelter

        * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
        scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit

2004-10-06 13:53  tim

        * make/: Makefile, Makefile.in: fix make statistics

2004-10-06 13:18  tim

        * make/: Makefile, Makefile.in: adding GNU make functions to
        combine all of the static libraries to a big library

2004-10-05 17:57  tim

        * make/: Makefile, Makefile.in:  adding shared library flag

2004-10-05 14:37  tim

        * src/: Makefile, UseTheForce/Makefile,
        UseTheForce/mpiSimulation_module.F90,
        UseTheForce/DarkSide/Makefile,
        UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
        mpiSimulation_module to DarkSide

2004-10-05 14:35  tim

        * make/: Makefile, Makefile.in: building MPI version;using static
        library instead of shared library

2004-10-05 09:14  tim

        * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
        to filepp

2004-10-04 15:56  tim

        * make/: Makefile, Makefile.in: add make cvslog

2004-10-04 11:24  gezelter

        * make/: Makefile, Makefile.in: more work on the parallel build

2004-10-04 11:06  gezelter

        * make/: Makefile, Makefile.in: changes to backport declare flags

2004-10-04 10:27  gezelter

        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
        DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
        shapes

2004-10-01 23:40  tim

        * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree

2004-10-01 23:22  tim

        * make/: Makefile, Makefile.in: add oopse_ as library prefix

2004-10-01 16:59  tim

        * make/: Makefile, Makefile.in: fix a space trimming bug in filepp

2004-10-01 16:22  gezelter

        * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
        few minor build changes

2004-10-01 16:11  tim

        * scripts/filepp: adding fortran90 make dependency tool

2004-09-30 10:41  tim

        * make/: Makefile, Makefile.in: make clean is smart enough to only
        remove object files belong to current package.  turn off silent
        mode

2004-09-29 16:55  tim

        * src/: Makefile, UseTheForce/Makefile,
        UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
        applications/oopse/Makefile, applications/simpleBuilder/Makefile,
        brains/Makedepend, brains/Makefile, constraints/Makefile,
        integrators/Makefile, io/Makefile, math/Makefile,
        minimizers/Makefile, primitives/Makefile, profiling/Makefile,
        restraints/Makefile, types/Makefile, utils/Makefile,
        visitors/Makefile: define DEV_ROOT as relative path

2004-09-29 16:54  tim

        * make/: Makefile, Makefile.in: get the relative path by shell
        script

2004-09-29 16:32  tim

        * make/Makefile: eliminate DEV_ROOT by relative path

2004-09-29 13:37  tim

        * make/Makefile.in: add PackageLibs;  fix dependency rule

2004-09-29 12:57  gezelter

        * configure, ac-tools/configure.in: updates

2004-09-29 12:56  gezelter

        * make/: Make.conf.in, Makefile.in: Working on make stuff

2004-09-29 12:46  tim

        * Makefile: If makefile does not exist, print error message

2004-09-29 12:12  tim

        * make/: Make.conf.in, Makefile: fix dependencies rule

2004-09-29 10:58  gezelter

        * Makefile, make/Makefile: still working on build process

2004-09-29 10:00  tim

        * make/Makefile: add print statment to rules

2004-09-29 09:59  tim

        * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
        applications/dump2Xyz/Makefile, applications/oopse/Makefile,
        applications/simpleBuilder/Makefile, brains/Makefile,
        constraints/Makefile, integrators/Makefile, io/Makefile,
        math/Makefile, minimizers/Makefile, primitives/Makefile,
        profiling/Makefile, restraints/Makefile, types/Makefile,
        utils/Makefile, visitors/Makefile: change Makefile to relative path

2004-09-28 21:55  tim

        * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
        which cause headache in bulding libutils

2004-09-28 18:24  tim

        * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
        Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
        Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
        LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp,
        MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp,
        nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo,
        simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp,
        dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c,
        dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile,
        oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp,
        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old,
        simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp,
        simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp,
        simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo,
        simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h:
        change directory structure of application. Every executable file is
        replaced in seperate directory

2004-09-28 17:15  gezelter

        * lib/dummy: Keep that lib around, please.

2004-09-28 17:14  gezelter

        * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
        starting a configure version

2004-09-28 16:08  tim

        * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
        UseTheForce/DarkSide/Makefile,
        UseTheForce/DarkSide/notifyCutoffs.F90,
        UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend,
        brains/Makefile, brains/simulation_module.F90: move fortran files
        around to solve dependency problem

2004-09-28 15:43  tim

        * Makefile, src/UseTheForce/ForceFields.hpp,
        src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
        src/applications/Makedepend, src/applications/Makefile,
        src/brains/Makedepend, src/brains/simulation_module.F90,
        src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp,
        src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
        src/utils/Makefile: [no log message]

2004-09-28 15:41  tim

        * make/Makefile, scripts/sfmakedepend: fix fortran dependency
        problem

2004-09-28 11:13  tim

        * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
        src/io/Makefile: add yacc and lex rules

2004-09-27 15:24  tim

        * make/Makefile: adding include path to F90Options

2004-09-27 15:13  tim

        * make/Makefile: change suffix from .cc to .cpp

2004-09-24 11:27  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
        UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp,
        UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp,
        UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp,
        UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90,
        UseTheForce/DarkSide/calc_LJ_FF.F90,
        UseTheForce/DarkSide/notifyCutoffs.F90,
        UseTheForce/DarkSide/switch_module.F90,
        applications/BaseLattice.cpp, applications/Dump2XYZ.cpp,
        applications/Dump2XYZCmd.c, applications/Lattice.cpp,
        applications/Lattice.hpp, applications/LatticeCreator.cpp,
        applications/LatticeCreator.hpp, applications/LatticeFactory.cpp,
        applications/MoLocator.cpp, applications/MoLocator.hpp,
        applications/cmdline.c, applications/nanoBuilder.cpp,
        applications/oopse.cpp, applications/simpleBuilder.cpp,
        applications/simpleBuilderCmd.c, brains/Exclude.cpp,
        brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp,
        brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
        brains/mpiSimulation.cpp, brains/mpiSimulation.hpp,
        constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp,
        integrators/AbstractClasses.hpp, integrators/Integrator.cpp,
        integrators/Integrator.hpp, integrators/NPT.cpp,
        integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp,
        integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c,
        io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp,
        io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp,
        io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp,
        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
        io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c,
        io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h,
        io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c,
        math/MatVec3.h, math/randomSPRNG.cpp,
        minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp,
        minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp,
        minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp,
        primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp,
        primitives/BendExtensions.cpp, primitives/Bond.cpp,
        primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp,
        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
        primitives/GhostBend.cpp, primitives/Molecule.cpp,
        primitives/Molecule.hpp, primitives/RigidBody.cpp,
        primitives/RigidBody.hpp, primitives/SRI.hpp,
        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
        primitives/Torsion.cpp, primitives/TorsionExtensions.cpp,
        profiling/mdProfile.cpp, restraints/Restraints.cpp,
        restraints/Restraints.hpp, types/AtomStamp.cpp,
        types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp,
        types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp,
        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
        types/MakeStamps.cpp, types/MakeStamps.hpp,
        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp,
        utils/StreamTokenizer.cpp, utils/StringUtils.c,
        utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c,
        utils/simError.c, visitors/AtomVisitor.cpp,
        visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp,
        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
        visitors/ZconsVisitor.hpp: change the #include in source files

2004-09-23 23:16  gezelter

        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
        src/UseTheForce/fForceField.h,
        src/UseTheForce/fSwitchingFunction.h,
        src/UseTheForce/fortranWrapDefines.hpp,
        src/UseTheForce/fortranWrappers.cpp,
        src/UseTheForce/fortranWrappers.hpp,
        src/UseTheForce/mpiComponentPlan.h,
        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
        src/UseTheForce/mpiSimulation_module.F90,
        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
        src/UseTheForce/DarkSide/atype_module.F90,
        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
        src/UseTheForce/DarkSide/calc_charge_charge.F90,
        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
        src/UseTheForce/DarkSide/calc_eam.F90,
        src/UseTheForce/DarkSide/calc_gb.F90,
        src/UseTheForce/DarkSide/calc_reaction_field.F90,
        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
        src/UseTheForce/DarkSide/force_globals.F90,
        src/UseTheForce/DarkSide/neighborLists.F90,
        src/UseTheForce/DarkSide/notifyCutoffs.F90,
        src/UseTheForce/DarkSide/switch_module.F90,
        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
        src/io/DumpWriter.cpp, src/io/Globals.cpp,
        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
        src/types/BondStamp.hpp, src/types/Component.cpp,
        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
        src/types/MakeStamps.hpp, src/types/Makefile,
        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
        src/brains/SimState.hpp, src/brains/SkipList.cpp,
        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
        src/brains/Thermo.hpp, src/brains/fSimulation.h,
        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
        src/minimizers/OOPSEMinimizer.cpp,
        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
        src/primitives/Makefile, src/primitives/Molecule.cpp,
        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
        src/restraints/Makefile, src/restraints/Restraints.cpp,
        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
        src/utils/GenericData.hpp, src/utils/Makefile,
        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
        src/utils/Utility.hpp, src/utils/definitions_module.F90,
        src/utils/fError.c, src/utils/oopseMPI_module.F90,
        src/utils/simError.c, src/utils/simError.h,
        src/utils/status_module.F90, src/utils/vector_class.F90,
        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
        src/visitors/RigidBodyVisitor.cpp,
        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
        samples/zcons/Makefile.in, samples/zcons/water.md,
        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
        src/applications/LatticeCreator.cpp,
        src/applications/LatticeCreator.hpp,
        src/applications/LatticeFactory.cpp,
        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
        src/applications/Makefile, src/applications/MoLocator.cpp,
        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
        src/applications/cmdline.c, src/applications/cmdline.h,
        src/applications/getopt.c, src/applications/getopt1.c,
        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
        src/applications/simpleBuilder.ggo,
        src/applications/simpleBuilderCmd.c,
        src/integrators/AbstractClasses.hpp,
        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
        src/integrators/Integrator.hpp, src/integrators/Makefile,
        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
        src/integrators/NVT.cpp, src/profiling/Makefile,
        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
        src/profiling/timing.F90, samples/metals/Au_bulk.in,
        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
        samples/water/dimer/two.in, samples/water/dimer/two.md,
        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
        samples/water/spce/spce.in, samples/water/spce/spce.md,
        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
        samples/alkane/butane.in, samples/alkane/butane.md,
        samples/argon/500.in, samples/argon/500.md,
        samples/argon/Makefile.in, samples/argon/ar864.in,
        samples/argon/ar864.md, samples/argon/argonNVT.in,
        samples/argon/argonNVT.md, samples/argon/lj.md,
        samples/lipid/5x5.in, samples/lipid/5x5.md,
        samples/lipid/Makefile.in, samples/lipid/lipid.md,
        samples/lipid/water.md, samples/minimizer/Makefile.in,
        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
        forceFields/EAM.VC.frc, forceFields/EAM.frc,
        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
        forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0

2004-09-23 23:16  gezelter

        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
        src/UseTheForce/fForceField.h,
        src/UseTheForce/fSwitchingFunction.h,
        src/UseTheForce/fortranWrapDefines.hpp,
        src/UseTheForce/fortranWrappers.cpp,
        src/UseTheForce/fortranWrappers.hpp,
        src/UseTheForce/mpiComponentPlan.h,
        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
        src/UseTheForce/mpiSimulation_module.F90,
        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
        src/UseTheForce/DarkSide/atype_module.F90,
        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
        src/UseTheForce/DarkSide/calc_charge_charge.F90,
        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
        src/UseTheForce/DarkSide/calc_eam.F90,
        src/UseTheForce/DarkSide/calc_gb.F90,
        src/UseTheForce/DarkSide/calc_reaction_field.F90,
        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
        src/UseTheForce/DarkSide/force_globals.F90,
        src/UseTheForce/DarkSide/neighborLists.F90,
        src/UseTheForce/DarkSide/notifyCutoffs.F90,
        src/UseTheForce/DarkSide/switch_module.F90,
        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
        src/io/DumpWriter.cpp, src/io/Globals.cpp,
        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
        src/types/BondStamp.hpp, src/types/Component.cpp,
        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
        src/types/MakeStamps.hpp, src/types/Makefile,
        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
        src/brains/SimState.hpp, src/brains/SkipList.cpp,
        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
        src/brains/Thermo.hpp, src/brains/fSimulation.h,
        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
        src/minimizers/OOPSEMinimizer.cpp,
        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
        src/primitives/Makefile, src/primitives/Molecule.cpp,
        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
        src/restraints/Makefile, src/restraints/Restraints.cpp,
        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
        src/utils/GenericData.hpp, src/utils/Makefile,
        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
        src/utils/Utility.hpp, src/utils/definitions_module.F90,
        src/utils/fError.c, src/utils/oopseMPI_module.F90,
        src/utils/simError.c, src/utils/simError.h,
        src/utils/status_module.F90, src/utils/vector_class.F90,
        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
        src/visitors/RigidBodyVisitor.cpp,
        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
        samples/zcons/Makefile.in, samples/zcons/water.md,
        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
        src/applications/LatticeCreator.cpp,
        src/applications/LatticeCreator.hpp,
        src/applications/LatticeFactory.cpp,
        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
        src/applications/Makefile, src/applications/MoLocator.cpp,
        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
        src/applications/cmdline.c, src/applications/cmdline.h,
        src/applications/getopt.c, src/applications/getopt1.c,
        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
        src/applications/simpleBuilder.ggo,
        src/applications/simpleBuilderCmd.c,
        src/integrators/AbstractClasses.hpp,
        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
        src/integrators/Integrator.hpp, src/integrators/Makefile,
        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
        src/integrators/NVT.cpp, src/profiling/Makefile,
        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
        src/profiling/timing.F90, samples/metals/Au_bulk.in,
        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
        samples/water/dimer/two.in, samples/water/dimer/two.md,
        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
        samples/water/spce/spce.in, samples/water/spce/spce.md,
        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
        samples/alkane/butane.in, samples/alkane/butane.md,
        samples/argon/500.in, samples/argon/500.md,
        samples/argon/Makefile.in, samples/argon/ar864.in,
        samples/argon/ar864.md, samples/argon/argonNVT.in,
        samples/argon/argonNVT.md, samples/argon/lj.md,
        samples/lipid/5x5.in, samples/lipid/5x5.md,
        samples/lipid/Makefile.in, samples/lipid/lipid.md,
        samples/lipid/water.md, samples/minimizer/Makefile.in,
        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
        forceFields/EAM.VC.frc, forceFields/EAM.frc,
        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
        forceFields/Pt.VC.funcfl: Initial revision

Revision:	508
Committed:	Fri Apr 15 22:22:10 2005 UTC (20 years, 7 months ago) by gezelter
File size:	202816 byte(s)
Log Message:	Documentation changes