trunk/OOPSE-3.0/ChangeLog

2006-05-19 16:45  tim

        * src/io/DumpWriter.cpp: Fix a bug of printing empty line in
        DumpWriter

2006-05-19 11:11  tim

        * make/Makefile.in: change the order of include path and library
        path

2006-05-17 17:51  tim

        * ChangeLog, samples/water/ssd/ssd.md, src/config.h.in,
        src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp,
        src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp,
        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
        src/UseTheForce/doForces_interface.h,
        src/UseTheForce/fForceOptions.h,
        src/UseTheForce/DarkSide/eam_interface.h,
        src/UseTheForce/DarkSide/electrostatic_interface.h,
        src/UseTheForce/DarkSide/gb_interface.h,
        src/UseTheForce/DarkSide/lj_interface.h,
        src/UseTheForce/DarkSide/shapes_interface.h,
        src/UseTheForce/DarkSide/simulation_interface.h,
        src/UseTheForce/DarkSide/sticky_interface.h,
        src/UseTheForce/DarkSide/suttonchen_interface.h,
        src/applications/dynamicProps/CrossTimeCorrFunc.cpp,
        src/applications/dynamicProps/CrossTimeCorrFunc.hpp,
        src/applications/dynamicProps/DipoleCorrFunc.cpp,
        src/applications/dynamicProps/DipoleCorrFunc.hpp,
        src/applications/dynamicProps/LegendreCorrFunc.cpp,
        src/applications/dynamicProps/LegendreCorrFunc.hpp,
        src/applications/dynamicProps/ParticleTimeCorrFunc.cpp,
        src/applications/dynamicProps/ParticleTimeCorrFunc.hpp,
        src/applications/dynamicProps/RCorrFunc.cpp,
        src/applications/dynamicProps/RCorrFunc.hpp,
        src/applications/dynamicProps/TimeCorrFunc.hpp,
        src/applications/dynamicProps/VCorrFunc.cpp,
        src/applications/dynamicProps/VCorrFunc.hpp,
        src/applications/hydrodynamics/Makefile,
        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
        src/applications/randomBuilder/randomBuilder.cpp,
        src/applications/simpleBuilder/randomBuilder.cpp,
        src/applications/staticProps/DensityPlot.cpp,
        src/applications/staticProps/DensityPlot.hpp,
        src/applications/staticProps/GofAngle2.cpp,
        src/applications/staticProps/GofAngle2.hpp,
        src/applications/staticProps/GofR.cpp,
        src/applications/staticProps/GofR.hpp,
        src/applications/staticProps/GofRAngle.cpp,
        src/applications/staticProps/GofRAngle.hpp,
        src/applications/staticProps/GofXyz.cpp,
        src/applications/staticProps/GofXyz.hpp,
        src/applications/staticProps/Hxy.cpp,
        src/applications/staticProps/Hxy.hpp,
        src/applications/staticProps/P2OrderParameter.cpp,
        src/applications/staticProps/P2OrderParameter.hpp,
        src/applications/staticProps/RhoZ.cpp,
        src/applications/staticProps/RhoZ.hpp,
        src/applications/staticProps/SCDOrderParameter.cpp,
        src/applications/staticProps/SCDOrderParameter.hpp,
        src/applications/staticProps/StaticProps.cpp,
        src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp,
        src/brains/DataStorage.hpp, src/brains/ForceManager.cpp,
        src/brains/SimCreator.cpp, src/brains/SimInfo.cpp,
        src/brains/SimInfo.hpp, src/brains/Snapshot.cpp,
        src/brains/Snapshot.hpp, src/brains/Stats.hpp,
        src/brains/Thermo.cpp, src/brains/Thermo.hpp,
        src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp,
        src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp,
        src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp,
        src/constraints/ZconstraintForceManager.cpp,
        src/constraints/ZconstraintForceManager.hpp,
        src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp,
        src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp,
        src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp,
        src/integrators/DLM.hpp, src/integrators/Integrator.hpp,
        src/integrators/LDForceManager.cpp,
        src/integrators/LDForceManager.hpp,
        src/integrators/LangevinDynamics.cpp,
        src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp,
        src/integrators/NPAT.hpp, 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/NPrT.cpp,
        src/integrators/NPrT.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/BendTypesSectionParser.cpp,
        src/io/BondTypesSectionParser.cpp,
        src/io/ChargeAtomTypesSectionParser.cpp,
        src/io/DirectionalAtomTypesSectionParser.cpp,
        src/io/DumpReader.cpp, src/io/DumpWriter.cpp,
        src/io/EAMAtomTypesSectionParser.cpp,
        src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp,
        src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp,
        src/io/RestReader.cpp, src/io/RestReader.hpp,
        src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp,
        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
        src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp,
        src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp,
        src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp,
        src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp,
        src/math/CholeskyDecomposition.hpp,
        src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp,
        src/math/MatVec3.c, src/math/MatVec3.h,
        src/math/MersenneTwister.hpp, src/math/Polynomial.hpp,
        src/math/Quaternion.hpp, src/math/RandNumGen.hpp,
        src/math/RealSphericalHarmonic.cpp,
        src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp,
        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
        src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp,
        src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp,
        src/minimizers/CGFamilyMinimizer.cpp,
        src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp,
        src/minimizers/Minimizer.hpp,
        src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp,
        src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp,
        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
        src/primitives/Bend.cpp, src/primitives/Bend.hpp,
        src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp,
        src/primitives/DirectionalAtom.cpp,
        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
        src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp,
        src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp,
        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
        src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp,
        src/primitives/Torsion.cpp, src/primitives/Torsion.hpp,
        src/primitives/UreyBradleyBend.cpp,
        src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp,
        src/restraints/Restraints.cpp, src/restraints/Restraints.hpp,
        src/restraints/ThermoIntegrationForceManager.hpp,
        src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp,
        src/selection/SelectionEvaluator.cpp,
        src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp,
        src/types/AtomStamp.hpp, src/types/AtomType.cpp,
        src/types/AtomType.hpp, src/types/AtomTypeProperties.h,
        src/types/BendType.hpp, src/types/BondType.hpp,
        src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp,
        src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp,
        src/types/DirectionalAtomType.cpp,
        src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp,
        src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.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/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp,
        src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp,
        src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp,
        src/utils/GenericData.hpp, src/utils/MoLocator.cpp,
        src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp,
        src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp,
        src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp,
        src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h,
        src/utils/residentMem.c, src/utils/residentMem.h,
        src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp:
        Adding single precision capabilities to c++ side

2006-05-17 15:54  gezelter

        * configure, ac-tools/configure.in, make/Makefile.in,
        src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/neighborLists.F90,
        src/UseTheForce/DarkSide/shapes.F90,
        src/UseTheForce/DarkSide/simParallel.F90,
        src/UseTheForce/DarkSide/simulation_interface.F90,
        src/utils/definitions.F90: Adding single precision capabilities to
        the fortran side

2006-05-17 12:10  gezelter

        * configure, ac-tools/configure.in, src/config.h.in: adding
        --enable-single to configure script

2006-05-17 11:37  gezelter

        * ac-tools/aclocal.m4, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/electrostatic_interface.F90,
        src/UseTheForce/DarkSide/gb.F90,
        src/UseTheForce/DarkSide/lj_interface.F90,
        src/UseTheForce/DarkSide/shapes.F90,
        src/UseTheForce/DarkSide/sticky.F90,
        src/UseTheForce/DarkSide/suttonchen.F90,
        src/UseTheForce/DarkSide/suttonchen_interface.F90,
        src/UseTheForce/DarkSide/switcheroo.F90, src/math/derfc.F90,
        src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran
        side prepped for single precision...

2006-05-17 10:03  chrisfen

        * samples/water/ssd-ion/ssdCl.md,
        src/UseTheForce/DarkSide/electrostatic.F90: electrostatic
        refinement

2006-05-16 23:03  gezelter

        * configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes

2006-05-16 16:38  gezelter

        * configure, ac-tools/OOPSE.m4, ac-tools/config.guess,
        ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh,
        ac-tools/missing, ac-tools/mkinstalldirs, make/Makefile.in,
        src/config.h.in, src/applications/staticProps/Hxy.cpp,
        src/applications/staticProps/Hxy.hpp,
        src/applications/staticProps/StaticProps.cpp: Autoconf fixes for
        FFTW.  Multiple FFTW version support.

2006-05-15 22:06  gezelter

        * README, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        make/Makefile.in, src/config.h.in,
        src/applications/hydrodynamics/AnalyticalModel.cpp,
        src/applications/hydrodynamics/AnalyticalModel.hpp,
        src/applications/staticProps/Hxy.cpp,
        src/applications/staticProps/Hxy.hpp,
        src/applications/staticProps/StaticProps.cpp,
        src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp,
        src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp,
        src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp,
        src/integrators/LDForceManager.cpp,
        src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp,
        src/utils/HydroProps.hpp: [no log message]

2006-05-12 17:34  xsun

        * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile,
        StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to
        calculate undulation spectrum

2006-05-09 21:44  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dump2Xyz/Dump2XYZ.ggo,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h,
        applications/hydrodynamics/ApproximationModel.cpp,
        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a
        gay-berne switch to Dump2XYZ

2006-05-05 13:58  gezelter

        * src/UseTheForce/DarkSide/qpole.F90: Adding qpole

2006-05-05 10:34  tim

        * ac-tools/aclocal.m4: finding ifort arguments that won't die under
        two different versions of the intel fortran compiler

2006-05-03 09:15  chrisfen

        * src/applications/randomBuilder/Makefile: missing makefile was
        hanging up 'make clean'

2006-04-25 18:59  chuckv

        * src/applications/randomBuilder/: randomBuilder.cpp,
        randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added
        random builder to cvs.

2006-04-25 18:54  chuckv

        * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
        Change in siminfo used in nanoparticleBuilder.

2006-04-25 18:30  chuckv

        * make/Makefile.in: Added random builder

2006-04-25 18:29  chuckv

        * src/applications/simpleBuilder/: Makefile, randomBuilder.cpp,
        randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a
        random builder to oopse.

2006-04-25 09:35  gezelter

        * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp,
        ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table
        to pick vdw radii for hydrodynamics if the LJ sigma can't be found.

2006-04-24 22:09  gezelter

        * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90,
        src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp,
        src/brains/SimCreator.cpp, src/brains/SimInfo.cpp,
        src/brains/SimInfo.hpp, src/brains/Thermo.cpp,
        src/brains/Thermo.hpp, src/integrators/LDForceManager.cpp,
        src/integrators/LDForceManager.hpp,
        src/integrators/LangevinDynamics.cpp, src/io/Globals.cpp,
        src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding
        spherical boundary conditions to LD integrator

2006-04-24 22:06  gezelter

        * src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp:
        Added EAM atom types to Hydro models

2006-04-21 16:02  chrisfen

        * src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the
        EAM module

2006-04-21 15:32  chrisfen

        * ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape,
        samples/shape/C60.shape, samples/shape/C70.shape,
        samples/shape/Makefile, samples/shape/Shapes.frc,
        samples/shape/cholesterol.shape, samples/shape/ethylBenzene.shape,
        samples/shape/linear.in, samples/shape/linear.md,
        samples/shape/linear.shape, samples/shape/toluene.shape,
        samples/thermoIntegration/liquid/ssde.md,
        samples/thermoIntegration/solid/ssde.md,
        samples/water/spce/spce.md, samples/water/ssd/ssd.md,
        samples/water/ssd-ion/ssdCl.md, samples/water/ssde/ssde.md,
        samples/water/ssdrf/ssdrf.md, samples/water/tip3p_ice/tp3.md,
        samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/LJ.F90: Removed sqrt splines and shape
        stuff (doesn't work, so why was it in there?).  Changed some of the
        water samples to use shifted_force.  Probably should set the
        defaults to use the damped version now that we sped it up.

2006-04-20 23:19  chrisfen

        * samples/water/spce/spce.md,
        src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added...

2006-04-20 17:02  chrisfen

        * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90,
        src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky

2006-04-20 14:24  gezelter

        * samples/metals/EAM/Au_bulk_voter.md,
        samples/metals/Sutton-Chen/Au_bulk_SC.md,
        samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp,
        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90,
        src/UseTheForce/DarkSide/eam.F90,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/suttonchen.F90,
        src/UseTheForce/DarkSide/switcheroo.F90,
        src/UseTheForce/DarkSide/switcheroo_interface.F90,
        src/UseTheForce/DarkSide/switcheroo_interface.h,
        src/utils/interpolation.F90: Complete rewrite of spline code and
        everything that uses it.

2006-04-17 17:49  gezelter

        * configure, ac-tools/aclocal.m4, samples/argon/500.md,
        samples/metals/EAM/Au_bulk_voter.md,
        samples/metals/Sutton-Chen/Au_bulk_SC.md,
        samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/interpolation.F90,
        src/UseTheForce/DarkSide/sticky.F90,
        src/UseTheForce/DarkSide/suttonchen.F90,
        src/UseTheForce/DarkSide/switcheroo.F90,
        src/applications/hydrodynamics/Hydro.ggo,
        src/applications/hydrodynamics/HydroCmd.c,
        src/applications/hydrodynamics/HydroCmd.h,
        src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp,
        src/utils/interpolation.F90: Many performance improvements

2006-04-15 22:51  chrisfen

        * configure, samples/argon/500.md, src/UseTheForce/doForces.F90,
        src/UseTheForce/fSwitchingFunction.h,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to
        switcheroo

2006-04-15 17:58  chrisfen

        * src/utils/Makefile.in: Since status.F90 is used by
        interpolation.F90, the former needs to be listed above the later in
        the Makefile.

2006-04-14 17:59  gezelter

        * src/utils/interpolation.F90: changed the interface a bit

2006-04-14 17:49  gezelter

        * src/utils/interpolation.F90: added some logical flags

2006-04-14 17:06  chrisfen

        * src/utils/interpolation.F90: Wiped the spline with derivatives
        and corrected a boundary comparision error by eliminating the
        check.  This algorithm REQUIRES known first derivatives at the
        endpoints.

2006-04-14 16:04  gezelter

        * src/utils/: Makefile.in, interpolation.F90: bug fixes for
        interpolation module

2006-04-14 15:57  gezelter

        * src/utils/interpolation.F90: Heavily modified interpolation
        module, also moved to "utils"

2006-04-12 17:15  chuckv

        * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation
        module.

2006-04-11 11:33  gezelter

        * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c,
        StaticPropsCmd.h: [no log message]

2006-04-03 11:37  chuckv

        * configure, ac-tools/aclocal.m4, make/Makefile.in,
        src/UseTheForce/DarkSide/simParallel.F90: Added status module to
        simParallel for error reporting.

2006-03-31 13:09  tim

        * src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now

2006-03-30 16:08  chuckv

        * src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug
        where SCList capacity was not reset to zero on destruction.

2006-03-30 14:37  chuckv

        * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
        More testing of nanoparticleBuilder.

2006-03-29 17:24  chuckv

        * src/mdParser/SimplePreprocessor.hpp: Added check to make sure md
        file exists.

2006-03-29 14:17  chuckv

        * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp,
        lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed
        latticeOrt in shapedlatice and latticebuilder.

2006-03-29 13:11  tim

        * src/applications/dynamicProps/: DipoleCorrFunc.cpp,
        LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem
        in calculating correlation functions

2006-03-29 13:09  tim

        * src/applications/hydrodynamics/: ApproximationModel.cpp,
        ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo,
        HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1)
        RoughShell Model is working; (20)Adding a new option into Hydro
        which allows user to generate the beads only

2006-03-27 11:21  chuckv

        * src/applications/nanoparticleBuilder/Makefile: Makefile for
        nanoparticle builder.

2006-03-27 11:03  chuckv

        * make/Makefile.in, src/lattice/shapedLattice.cpp,
        src/lattice/shapedLattice.hpp: Added nanoparticle builder to
        makefile

2006-03-24 15:46  chuckv

        * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
        Debugging changes to nanoparticle builder.

2006-03-24 12:29  tim

        * src/applications/dynamicProps/: DynamicProps.cpp,
        DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile,
        RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps

2006-03-24 11:49  tim

        * src/applications/dynamicProps/: DynamicProps.cpp,
        DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile,
        RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation
        function. The command line option for DynamicProps is now changed.
        --rcorr is for position correlation and --rmsd is for mean square
        displacement.

2006-03-23 10:03  tim

        * src/applications/hydrodynamics/: AnalyticalModel.cpp,
        AnalyticalModel.hpp, ApproximationModel.cpp,
        ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads
        method

2006-03-23 10:02  tim

        * src/io/Globals.hpp: remove a unknown method

2006-03-23 10:00  tim

        * src/math/CholeskyDecomposition.hpp: The off diagnal is not set

2006-03-23 09:59  tim

        * src/mdParser/SimplePreprocessor.hpp: Throw exception if the file
        can not be opened for preprocessing

2006-03-22 15:57  chuckv

        * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
        shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added
        shaped lattice.

2006-03-21 10:33  tim

        * src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug
        in calculating hydrodynamics tensor when the radius of beads are
        not the same

2006-03-20 19:26  tim

        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
        applications/hydrodynamics/BeadModel.cpp,
        applications/hydrodynamics/ShapeBuilder.cpp,
        integrators/LDForceManager.cpp: Fix a bug in friction calculation
        for ellipsoid

2006-03-20 14:12  tim

        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
        applications/hydrodynamics/Ellipsoid.cpp,
        applications/hydrodynamics/Ellipsoid.hpp,
        applications/hydrodynamics/ShapeBuilder.cpp,
        integrators/LDForceManager.cpp: Verify the correctness of
        Ellipsoid's hydrodynamics properties

2006-03-17 18:51  tim

        * src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New
        version of Hydro is working now.

2006-03-17 18:20  tim

        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
        applications/hydrodynamics/AnalyticalModel.hpp,
        applications/hydrodynamics/ApproximationModel.cpp,
        applications/hydrodynamics/ApproximationModel.hpp,
        applications/hydrodynamics/BeadModel.hpp,
        applications/hydrodynamics/CompositeShape.cpp,
        applications/hydrodynamics/CompositeShape.hpp,
        applications/hydrodynamics/Ellipsoid.cpp,
        applications/hydrodynamics/Ellipsoid.hpp,
        applications/hydrodynamics/Hydro.cpp,
        applications/hydrodynamics/Hydro.ggo,
        applications/hydrodynamics/HydroCmd.c,
        applications/hydrodynamics/HydroCmd.h,
        applications/hydrodynamics/HydrodynamicsModel.cpp,
        applications/hydrodynamics/HydrodynamicsModel.hpp,
        applications/hydrodynamics/HydrodynamicsModelCreator.hpp,
        applications/hydrodynamics/HydrodynamicsModelFactory.cpp,
        applications/hydrodynamics/HydrodynamicsModelFactory.hpp,
        applications/hydrodynamics/Makefile,
        applications/hydrodynamics/RoughShell.cpp,
        applications/hydrodynamics/RoughShell.hpp,
        applications/hydrodynamics/Shape.hpp,
        applications/hydrodynamics/ShapeBuilder.cpp,
        applications/hydrodynamics/ShapeBuilder.hpp,
        applications/hydrodynamics/Spheric.cpp,
        applications/hydrodynamics/Spheric.hpp,
        applications/hydrodynamics/StuntDoubleShape.cpp,
        applications/hydrodynamics/StuntDoubleShape.hpp,
        integrators/LDForceManager.cpp, integrators/LDForceManager.hpp,
        io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp,
        utils/HydroProps.hpp: refactor Hydrodynamics module.

2006-03-17 11:10  chuckv

        * src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile:
        Generic Shaped Lattice for oopse. Can overload to get spherical or
        nanorod.

2006-03-16 17:50  tim

        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
        integrators/LDForceManager.cpp, math/MersenneTwister.hpp:
        LagevinDynamics is working?

2006-03-16 16:52  gezelter

        * src/applications/hydrodynamics/RoughShell.hpp: fixed a const
        problem

2006-03-15 17:08  tim

        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit
        conversion for diffusion tensor is wrong

2006-03-15 16:28  tim

        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
        utils/NumericConstant.hpp: change the epsilon of numeric_limit

2006-03-15 15:58  tim

        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting
        the unit in HydrodynamicsModel

2006-03-15 12:35  tim

        * src/primitives/RigidBody.cpp: using setFrc in
        RigidBody::calcForcesAndTorques will discard if there are force and
        torque applied in rigid body itself. use addFrc instead.

2006-03-15 10:51  tim

        * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp,
        RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel

2006-03-15 10:50  tim

        * make/Makefile.in, src/applications/hydrodynamics/Makefile: adding
        hydrodynamics module into build system

2006-03-14 18:46  tim

        * src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition

2006-03-13 17:42  tim

        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
        applications/hydrodynamics/HydrodynamicsModel.hpp,
        applications/hydrodynamics/StuntDoubleShape.cpp,
        applications/hydrodynamics/StuntDoubleShape.hpp,
        brains/Register.cpp, integrators/LDForceManager.cpp,
        integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp,
        integrators/LangevinDynamics.hpp, integrators/Makefile,
        io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp,
        math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in
        progress

2006-03-07 11:43  gezelter

        * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a
        double/int bug.  Surprised no one ever noticed before...

2006-02-24 16:17  tim

        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs
        in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out
        product of Rij

2006-02-23 18:16  tim

        * src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo,
        HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp,
        HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp,
        HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp,
        MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp,
        StuntDoubleShape.hpp: Bead Model is working

2006-02-22 15:35  tim

        * src/: applications/hydrodynamics/Hydro.cpp,
        applications/hydrodynamics/Hydro.ggo,
        applications/hydrodynamics/HydroCmd.c,
        applications/hydrodynamics/HydroCmd.h,
        applications/hydrodynamics/HydrodynamicsModel.cpp,
        applications/hydrodynamics/HydrodynamicsModel.hpp,
        applications/hydrodynamics/HydrodynamicsModelCreator.hpp,
        applications/hydrodynamics/HydrodynamicsModelFactory.cpp,
        applications/hydrodynamics/HydrodynamicsModelFactory.hpp,
        applications/hydrodynamics/MoleculeShape.cpp,
        applications/hydrodynamics/MoleculeShape.hpp,
        math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp,
        math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics
        Module

2006-02-16 17:05  gezelter

        * src/brains/Snapshot.cpp: fixed a spelling error

2006-02-16 16:40  gezelter

        * src/: UseTheForce/doForces.F90,
        UseTheForce/DarkSide/simulation.F90, math/Makefile,
        math/linearAlgebra.F90: fixed a problem with cutoff radii being set
        larger than 1/2 the length of the shortest box dimension.  added a
        few fortran utility routines

2006-02-15 15:46  chuckv

        * src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp,
        sphericalNanoparticle.hpp: Changed Names of class files.

2006-02-10 10:45  kdaily

        * src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log
        message]

2006-02-10 10:12  tim

        * src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in
        converting integer to double

2006-02-08 13:21  chrisfen

        * forceFields/DUFF2.frc: added DPD molecule type parameters

2006-02-07 11:39  tim

        * src/applications/dynamicProps/: DipoleCorrFunc.cpp,
        LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of
        trajectory file during analysis

2006-02-02 12:14  tim

        * src/: math/Polynomial.hpp, math/SquareMatrix3.hpp,
        types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug
        in AtomStamp where orientation is not set correctly.

2006-02-02 11:49  gezelter

        * src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that
        contain directional atoms

2006-02-02 10:49  xsun

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor
        for GBlipid atom type

2006-02-01 21:57  gezelter

        * make/Makefile.in: added CXXFLAGS to the LinkOptions to allow
        compilation with icc9 (skipping the gcc-4 std c++ libraries).

2006-02-01 16:06  chrisfen

        * src/brains/SimInfo.cpp: Missing brace caused the last commit not
        to build

2006-02-01 15:54  chrisfen

        * samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to
        cutoff radius setting to a more logical procedure - still may
        change...

2006-02-01 12:26  gezelter

        * src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp:
        Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X

2006-01-30 17:25  tim

        * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
        applications/dynamicProps/DynamicProps.cpp,
        applications/dynamicProps/DynamicProps.ggo,
        applications/dynamicProps/DynamicPropsCmd.c,
        applications/dynamicProps/DynamicPropsCmd.h,
        applications/dynamicProps/LegendreCorrFunc.cpp,
        applications/dynamicProps/LegendreCorrFunc.hpp,
        applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp,
        math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp:
        Adding :LegendrePolynomial

2006-01-19 17:54  chuckv

        * src/applications/nanoparticleBuilder/: Makefile,
        nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to
        nanoparticle builder

2006-01-18 16:08  chuckv

        * src/applications/nanoparticleBuilder/Makefile: Added Makefile for
        nanoparticle builder.

2006-01-17 11:16  gezelter

        * AUTHORS, README: Cleaning up for 3.0.1 release

2006-01-17 10:50  gezelter

        * ChangeLog: Prepping 3.0.1 release

2006-01-17 10:32  gezelter

        * src/config.h.in: new version number

2006-01-17 10:32  gezelter

        * doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html,
        definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png,
        oopseManual.pdf: Updated Documentation

2006-01-16 18:10  gezelter

        * ChangeLog, README: Getting ready for release!

2006-01-16 10:26  gezelter

        * configure: Testing commit

2006-01-13 16:57  chuckv

        * src/: UseTheForce/SC_FF.cpp,
        applications/nanoparticleBuilder/sphericalNanoparticle.cpp,
        io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals.
        Handled by forceField now.

2006-01-13 14:17  chuckv

        * src/io/Globals.cpp: Added NPAT to Globals integrators.

2006-01-13 11:33  gezelter

        * Makefile: [no log message]

2006-01-13 11:26  gezelter

        * Makefile: testing to make sure GNU make is the make that was used
        to build OOPSE

2006-01-13 10:48  gezelter

        * configure, ac-tools/configure.in: changed compiler search order

2006-01-12 19:09  chuckv

        * forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc,
        samples/metals/Sutton-Chen/Au_bulk.in,
        samples/metals/Sutton-Chen/Au_bulk_QSC.md,
        samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen
        units

2006-01-12 16:16  gezelter

        * LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some
        version info and the copyright date

2006-01-12 15:52  gezelter

        * src/config.h.in: added some missing checks for header files
        (particularly zlib.h), used autoheader to help generate config.h.in

2006-01-12 15:51  gezelter

        * configure, ac-tools/configure.in: added some missing checks for
        header files (particularly zlib.h)

2006-01-12 15:19  gezelter

        * make/Makefile.in: fixed a dependency problem for the Executable
        builds

2006-01-12 15:02  gezelter

        * samples/gbljtest/Makefile: Missing Makefile in this sample
        directory

2006-01-12 15:01  gezelter

        * make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile:
        Old makefile.in no longer required

2006-01-12 15:01  gezelter

        * forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff
        needs to be installed

2006-01-12 14:56  chuckv

        * src/io/DumpWriter.cpp: Changed formating.

2006-01-12 11:47  chrisfen

        * samples/water/tip4p/tp4.md,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/electrostatic_interface.F90,
        src/UseTheForce/DarkSide/electrostatic_interface.h,
        src/brains/SimInfo.cpp: unifying function name in electrostatics

2006-01-12 11:04  tim

        * samples/metals/: EAM/nanoparticle/Makefile,
        EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile,
        Sutton-Chen/Makefile: fix make install problem for metals samples

2006-01-12 10:22  tim

        * make/Makefile.in: remove samples/metals from install list.

2006-01-12 09:31  tim

        * src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not
        handle multiple line macro, just convert multiple line macro into
        single line macro.

2006-01-11 23:13  chrisfen

        * src/: UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some
        changes to electrostatics for shifted-potential and shifted-force
        with mono and multipoles

2006-01-11 18:04  gezelter

        * src/config.h.in, src/UseTheForce/doForces_interface.h,
        src/UseTheForce/DarkSide/atype_interface.h,
        src/UseTheForce/DarkSide/eam_interface.h,
        src/UseTheForce/DarkSide/electrostatic_interface.h,
        src/UseTheForce/DarkSide/fForceOptions_interface.h,
        src/UseTheForce/DarkSide/gb_interface.h,
        src/UseTheForce/DarkSide/lj_interface.h,
        src/UseTheForce/DarkSide/shapes_interface.h,
        src/UseTheForce/DarkSide/simParallel_interface.h,
        src/UseTheForce/DarkSide/simulation_interface.h,
        src/UseTheForce/DarkSide/sticky_interface.h,
        src/UseTheForce/DarkSide/suttonchen_interface.h,
        src/UseTheForce/DarkSide/switcheroo_interface.h,
        src/mdParser/MDParser.g, src/profiling/mdProfile.cpp,
        src/utils/fError.c, configure, make/Makefile.in: autoconf
        modernization and cruft removal

2006-01-11 18:04  gezelter

        * ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf
        modernization and cruft-removal

2006-01-11 17:50  tim

        * src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix
        some error messages

2006-01-11 14:01  tim

        * src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp,
        io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp,
        types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp,
        types/TorsionStamp.hpp, utils/OOPSEException.hpp,
        utils/StringUtils.hpp: instead of printing to std::cout, throwing
        an exception when error is found.

2006-01-11 13:41  gezelter

        * src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling
        error

2006-01-10 17:55  chuckv

        * forceFields/SuttonChen.frc: Changed conversion factor.

2006-01-10 16:14  chuckv

        * samples/metals/Sutton-Chen/Au_bulk_SC.md,
        src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be
        working now.

2006-01-09 17:22  chuckv

        * src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC

2006-01-09 17:14  tim

        * src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp,
        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
        StaticPropsCmd.h: fixing RhoZ

2006-01-09 14:26  chuckv

        * forceFields/SuttonChen.frc,
        samples/metals/Sutton-Chen/Au_bulk_SC.md,
        src/io/LennardJonesAtomTypesSectionParser.cpp,
        src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to
        section parsers.

2006-01-09 14:11  tim

        * src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp,
        utils/StringUtils.hpp: replace isType<int> with isInteger

2006-01-06 16:15  tim

        * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra
        forceFieldOptions from SC_FF

2006-01-06 15:27  chuckv

        * forceFields/SuttonChen.frc: Add force file.

2005-12-31 17:42  chuckv

        * src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer
        segfaults or produces 0 potential, but rather produces Inf for the
        potential. Progress....

2005-12-30 18:15  chuckv

        * samples/metals/Sutton-Chen/Au_bulk_SC.md,
        src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp,
        src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More
        Sutton-Chen bug fixes.

2005-12-30 16:25  tim

        * src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range
        potential return from fortran is already accumulated, it should not
        be accumulated again; nGroupTypesCol is not initialized;
        GroupMaxCutoffCol is not allocated;

2005-12-30 10:32  tim

        * make/Makefile.in, src/brains/SimCreator.cpp: In order to compile
        MPI version, we need to cast const char* to void* for
        stringstream.str(); Previous Makefile use bjects of single version
        to make the MPI library;

2005-12-29 19:18  chuckv

        * make/Makefile.in, samples/metals/Makefile,
        src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes.
        Almost there...

2005-12-29 15:19  chuckv

        * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in
        forcefield.

2005-12-29 15:07  chuckv

        * samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile,
        metals.md: added files for sutton-chen

2005-12-29 11:37  chuckv

        * samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile,
        metals.md: More cvs changing.

2005-12-29 11:34  chuckv

        * samples/metals/Au_nanoparticle.in: More moving...

2005-12-29 11:33  chuckv

        * samples/metals/EAM/nanoparticle/:
        Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md,
        Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More
        changes to directory structure.

2005-12-29 11:21  chuckv

        * samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md,
        Au_bulk_voter.md, Makefile, metals.md: More Directory changes...

2005-12-29 11:17  chuckv

        * samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in,
        Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md,
        Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of
        directory structure

2005-12-29 11:03  chuckv

        * src/: UseTheForce/DarkSide/fForceOptions_interface.F90,
        brains/SimCreator.cpp: Fixed issue with symbol naming and added
        call to set force options in SimCreator.

2005-12-28 16:44  chuckv

        * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More
        changes to forcefield options.

2005-12-28 16:42  chuckv

        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options
        passed to fortran.

2005-12-23 18:04  chuckv

        * src/: UseTheForce/DarkSide/fForceOptions_interface.h,
        io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option
        changes.

2005-12-16 16:52  tim

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        src/config.h.in, src/UseTheForce/DarkSide/gb.F90,
        src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp,
        src/openbabel/chains.cpp, src/openbabel/chiral.cpp,
        src/openbabel/data.cpp, src/openbabel/fingerprint.cpp,
        src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp,
        src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp,
        src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp,
        src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp,
        src/openbabel/obbond.cpp, src/openbabel/oberror.cpp,
        src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp,
        src/openbabel/obutil.cpp, src/openbabel/patty.cpp,
        src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp,
        src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp,
        src/openbabel/ring.cpp, src/openbabel/rotor.cpp,
        src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp,
        src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed
        __FUNCTION__ to __func__ to match C99 standard, and then added an
        autoconf test to check for __func__ usability.  Changed some
        default compile flags for the Sun architecture

2005-12-16 14:01  gezelter

        * ac-tools/AC_CXX_HAVE_STL.m4: added the STL check

2005-12-16 13:55  tim

        * src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor
        change to build oopse under solaris

2005-12-16 13:26  tim

        * src/: brains/SimCreator.cpp, io/Globals.cpp,
        types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library
        came with SUN compiler does not have a conforming std::use_facet,
        define a macro to handle it. Adding exception handling to
        SimCreator.

2005-12-16 10:53  gezelter

        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
        GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom
        which was living inside the GB particle.  No alien-like ripping out
        of the stomach was required.

2005-12-15 21:57  tim

        * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
        MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
        MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp:
        replace grammar for numerical parsing

2005-12-15 16:43  gezelter

        * src/UseTheForce/doForces.F90: fixed a cutoff bug

2005-12-15 09:48  gezelter

        * src/antlr/: CharScanner.hpp, config.hpp: Removing compiler
        dependencies and replacing them with real autoconf checks

2005-12-15 09:47  gezelter

        * configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4,
        ac-tools/configure.in, src/config.h.in: Adding checks for various
        features used by ANTLR

2005-12-14 13:02  tim

        * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
        MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
        MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a
        nasty negative integer parsing problem by refining the grammar

2005-12-12 14:32  gezelter

        * src/: UseTheForce/doForces_interface.F90,
        UseTheForce/doForces_interface.h,
        UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/electrostatic_interface.F90,
        UseTheForce/DarkSide/electrostatic_interface.h,
        brains/MoleculeCreator.cpp, brains/SimInfo.cpp,
        math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made
        some minor changes to allow compilation with the portland group
        compilers

2005-12-10 11:54  tim

        * src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation
        problem for icc7

2005-12-09 16:18  gezelter

        * src/utils/CaseConversion.hpp: added missing include

2005-12-09 12:11  gezelter

        * configure, ac-tools/aclocal.m4: added some checks for pathscale
        compiler

2005-12-08 17:05  gezelter

        * src/io/ForceFieldOptions.cpp: added copyright

2005-12-08 17:04  gezelter

        * src/UseTheForce/doForces.F90: added info printout

2005-12-08 17:04  gezelter

        * configure, ac-tools/configure.in: added pathscale

2005-12-08 10:38  chuckv

        * src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp,
        UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp,
        UseTheForce/SHAPES_FF.cpp, 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/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
        io/GayBerneAtomTypesSectionParser.cpp,
        io/GayBerneAtomTypesSectionParser.hpp,
        io/MultipoleAtomTypesSectionParser.cpp,
        io/MultipoleAtomTypesSectionParser.hpp,
        io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
        io/ShapeAtomTypesSectionParser.cpp,
        io/ShapeAtomTypesSectionParser.hpp,
        io/StickyAtomTypesSectionParser.cpp,
        io/StickyAtomTypesSectionParser.hpp,
        io/StickyPowerAtomTypesSectionParser.cpp,
        io/StickyPowerAtomTypesSectionParser.hpp,
        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp:
        Wow thats alot o' files. Now passing forceFieldOptions to all of
        the parsers.

2005-12-07 18:10  chuckv

        * src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp,
        SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things....
        Started adding support for ForceOptions to section parsers.

2005-12-07 18:01  gezelter

        * src/UseTheForce/DarkSide/gb_interface.h: [no log message]

2005-12-07 18:00  chuckv

        * src/io/: LennardJonesAtomTypesSectionParser.cpp,
        LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to
        section parser

2005-12-07 14:58  chuckv

        * src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90,
        lj_interface.h, suttonchen.F90, suttonchen_interface.F90,
        suttonchen_interface.h: Removed geometric distance mixing from
        individual modules and now use force options to detemine what the
        deal is.

2005-12-07 14:46  chuckv

        * src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90:
        Further fixes for compiler issues.

2005-12-07 14:44  chuckv

        * src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue.

2005-12-07 14:38  chuckv

        * src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90,
        fForceOptions_interface.F90, fForceOptions_interface.h: Added
        support for fortran force options.

2005-12-06 16:01  tim

        * src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion

2005-12-06 14:26  chuckv

        * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC.

2005-12-06 12:53  chuckv

        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
        GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned
        crystal

2005-12-06 12:52  chuckv

        * src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for
        dumpwriter.

2005-12-06 11:49  tim

        * samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md,
        argon/ar864.md, argon/argonNVT.md, argon/lj.md,
        dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md,
        dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md,
        gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md,
        gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md,
        lipid/5x5.md, lipid/lipid.md, lipid/water.md,
        metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md,
        metals/Au_bulk_voter.md, metals/Au_nanoparticle.md,
        metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md,
        minimizer/water.md, shape/linear.md,
        thermoIntegration/liquid/ssde.md,
        thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md,
        thermoIntegration/solid/water.md, water/dimer/cl.md,
        water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md,
        water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md,
        water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md,
        water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md,
        water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md,
        water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md,
        water/tip3p_ice/tp3.md, water/tip3p_ice/water.md,
        water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md,
        zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated
        keywords from samples

2005-12-05 18:37  tim

        * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp,
        Globals.cpp, Makefile: Fix parsing error in OptionSectionParser

2005-12-05 17:23  gezelter

        * src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp,
        UseTheForce/Makefile, brains/Register.cpp,
        io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding
        handler for CLAY force field

2005-12-05 16:45  chuckv

        * src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug
        in openbabel.

2005-12-05 14:10  tim

        * src/types/MoleculeStamp.cpp: reformat error message

2005-12-05 14:07  gezelter

        * forceFields/CLAYFF.frc: Adding .frc file for CLAYFF

2005-12-05 13:23  tim

        * src/: types/AtomStamp.cpp, types/AtomStamp.hpp,
        types/BendStamp.hpp, types/MoleculeStamp.cpp,
        types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp:
        adding more checking for topology

2005-12-02 17:37  gezelter

        * src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon
        removal

2005-12-02 17:37  gezelter

        * src/config.h.in: We've made big changes.  This isn't 2.0 anymore.

2005-12-02 17:37  gezelter

        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
        GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md,
        traditional.md: removing deprecated nAtoms and nComponents lines

2005-12-02 15:34  tim

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

2005-12-02 15:18  tim

        * src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding
        FragmentStamp

2005-12-02 15:11  gezelter

        * src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no
        longer thrown with consts (fixes compilation bug on the Mac).

2005-12-02 15:10  gezelter

        * src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious
        printing out of timestep

2005-12-02 15:10  gezelter

        * src/brains/ForceManager.cpp: Got rid of spurious printing out of
        junk

2005-12-02 15:10  gezelter

        * make/Makefile.in: Change build process for libOOPSE.a so that the
        libraries aren't unpacked.  libOOPSE.a is now made directly from
        the object files

2005-12-02 15:09  gezelter

        * configure, ac-tools/configure.in: added check for egrep (grep -E)
        needed for new build of libOOPSE.a

2005-12-02 13:43  tim

        * src/types/DataHolder.hpp: adding DataHolder

2005-12-02 12:01  gezelter

        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
        GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test
        case for the cutoff policies

2005-12-02 10:38  tim

        * make/Makefile.in: update Makefile

2005-12-02 10:38  tim

        * src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp,
        antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp,
        antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp,
        antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp,
        antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp,
        antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp,
        antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp,
        antlr/CharScanner.cpp, antlr/CharScanner.hpp,
        antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp,
        antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp,
        antlr/CommonASTWithHiddenTokens.cpp,
        antlr/CommonASTWithHiddenTokens.hpp,
        antlr/CommonHiddenStreamToken.cpp,
        antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp,
        antlr/CommonToken.hpp, antlr/IOException.hpp,
        antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp,
        antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp,
        antlr/Makefile, antlr/MismatchedCharException.cpp,
        antlr/MismatchedCharException.hpp,
        antlr/MismatchedTokenException.cpp,
        antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp,
        antlr/NoViableAltException.hpp,
        antlr/NoViableAltForCharException.cpp,
        antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp,
        antlr/Parser.hpp, antlr/ParserSharedInputState.hpp,
        antlr/RecognitionException.cpp, antlr/RecognitionException.hpp,
        antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp,
        antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp,
        antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp,
        antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp,
        antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp,
        antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp,
        antlr/TokenStreamHiddenTokenFilter.cpp,
        antlr/TokenStreamHiddenTokenFilter.hpp,
        antlr/TokenStreamIOException.hpp,
        antlr/TokenStreamRecognitionException.hpp,
        antlr/TokenStreamRetryException.hpp,
        antlr/TokenStreamRewriteEngine.cpp,
        antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp,
        antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp,
        antlr/TreeParser.cpp, antlr/TreeParser.hpp,
        antlr/TreeParserSharedInputState.hpp, antlr/config.hpp,
        applications/oopse/oopse.cpp, brains/ForceManager.cpp,
        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
        constraints/ZconstraintForceManager.cpp,
        integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp,
        io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
        io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp,
        io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile,
        io/ZConsReader.cpp, 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, mdParser/FilenameObserver.cpp,
        mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp,
        mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g,
        mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp,
        mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g,
        mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp,
        mdParser/Makefile, mdParser/SimplePreprocessor.hpp,
        openbabel/obconversion.cpp, openbabel/oopseformat.cpp,
        openbabel/xyzformat.cpp, primitives/RigidBody.cpp,
        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
        selection/Makefile, selection/NameFinder.cpp,
        selection/NameFinder.hpp, selection/SelectionCompiler.hpp,
        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
        selection/SelectionManager.hpp, selection/SelectionToken.hpp,
        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp,
        types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp,
        types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp,
        types/Component.cpp, types/Component.hpp,
        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
        types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile,
        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
        types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp,
        types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp,
        utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp,
        utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp,
        utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the
        Link --> List Return of the Oject-Oriented replace yacc/lex parser
        with antlr parser

2005-11-30 16:00  chuckv

        * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to
        calculate rho(Z) to calculate density profiles for water slabs.

2005-11-29 17:54  chuckv

        * configure, ac-tools/configure.in: added checks for some functions
        to configure script

2005-11-22 20:05  chuckv

        * src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp,
        obbond.cpp: Changed file names that conflict w/ oopse file name
        object files.

2005-11-21 17:59  gezelter

        * src/utils/residentMem.c: compilation bug

2005-11-21 17:59  gezelter

        * src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp

2005-11-21 17:59  gezelter

        * src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes

2005-11-21 17:59  gezelter

        * src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation
        issue

2005-11-21 17:58  gezelter

        * src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90,
        doForces_interface.F90, doForces_interface.h, fForceOptions.h,
        notifyCutoffs.F90, notifyCutoffs_interface.F90,
        notifyCutoffs_interface.h, DarkSide/LJ.F90,
        DarkSide/electrostatic.F90, DarkSide/gb.F90,
        DarkSide/suttonchen.F90: Cutoff mixing fixes have been made.

2005-11-21 11:22  tim

        * src/io/ParamConstraint.cpp: Adding  ParamConstraint.cpp

2005-11-21 09:59  tim

        * forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt,
        atomtyp.txt, bondtyp.txt, element.txt, extable.txt,
        isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt,
        resdata.txt, torlib.txt, types.txt: adding openbabel data files

2005-11-18 15:17  tim

        * src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp:
        adding support for soft linking

2005-11-18 15:17  tim

        * make/Makefile.in: Adding support for soft linking

2005-11-18 12:50  gezelter

        * make/Makefile.in: Adding linking stuff

2005-11-18 11:38  tim

        * make/Makefile.in, src/applications/atom2mdin/Makefile,
        src/applications/atom2mdin/atom2mdin.cpp,
        src/applications/mdinConverter/Makefile,
        src/applications/mdinConverter/mdinConverter.cpp,
        src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp:
        rename mdinConverter to atom2mdin

2005-11-17 15:44  gezelter

        * src/openbabel/obconversion.cpp: fixed a bug

2005-11-17 15:39  gezelter

        * configure: Adding some config checks for OpenBabel codes we are
        using

2005-11-17 15:39  gezelter

        * ac-tools/configure.in: Adding some checks for OpenBabel code

2005-11-17 15:39  gezelter

        * src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel

2005-11-17 15:38  gezelter

        * src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp,
        bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp,
        fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp,
        obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp,
        patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp,
        residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp:
        Unifying config.h stuff and making sure the OpenBabel codes can
        find our default (and environment variable) Force Field
        directories.

2005-11-17 13:35  tim

        * src/io/ForceFieldOptions.hpp: adding ForceFieldOptions

2005-11-16 18:10  tim

        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
        brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp,
        brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp,
        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
        io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp,
        io/OptionSectionParser.hpp, io/ParamConstraint.hpp,
        io/SectionParser.hpp, io/SectionParserManager.cpp,
        io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp,
        math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp,
        primitives/Bend.hpp, primitives/GhostBend.cpp,
        primitives/GhostBend.hpp, primitives/GhostTorsion.cpp,
        primitives/GhostTorsion.hpp, primitives/Torsion.cpp,
        primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
        primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp,
        types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp,
        types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp,
        types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser
        get compiled

2005-11-16 16:37  chuckv

        * src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp,
        io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp,
        UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField
        optional parameters....

2005-11-16 16:24  tim

        * src/applications/mdinConverter/: Makefile, mdinConverter.cpp:
        adding mdinConverter

2005-11-16 16:22  tim

        * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp,
        fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp,
        gromos96format.cpp, gromos96format.hpp, oopseformat.cpp,
        oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp,
        povrayformat.hpp, smilesformat.cpp, smilesformat.hpp,
        tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp:
        adding more readers/writers

2005-11-16 16:20  tim

        * make/Makefile.in: adding openbabel

2005-11-16 16:20  tim

        * src/brains/: Register.cpp, Register.hpp: register openbabel
        readers/writers

2005-11-16 14:57  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: included shifted
        potential self term

2005-11-16 14:57  chrisfen

        * samples/water/spce/spce.md: just some parameters

2005-11-16 14:42  tim

        * src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp,
        babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp,
        bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp,
        chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp,
        data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp,
        fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp,
        isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp,
        matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp,
        obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp,
        oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp,
        obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp,
        patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp,
        phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp,
        ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp,
        snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp,
        tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp,
        types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp,
        zipstreamimpl.hpp: adding openbabel

2005-11-15 14:42  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary
        commented code

2005-11-15 14:04  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the
        charge-charge interactions a bit...

2005-11-15 14:03  chrisfen

        * samples/water/spce/: spce.md, water.md: just playing

2005-11-15 11:38  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the
        shifted_potential case

2005-11-15 11:37  chrisfen

        * samples/: argon/500.md, water/spce/spce.md, water/spce/water.md:
        just playing around - we need to refresh all the samples sometime
        soon...

2005-11-15 11:18  chuckv

        * src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made
        preforce calc public in suttonchen.

2005-11-15 11:05  chuckv

        * src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to
        SimInfo

2005-11-15 11:01  chuckv

        * src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h,
        DarkSide/simulation.F90: Added Sutton-Chen to force loop...

2005-11-15 10:34  chuckv

        * forceFields/Makefile: Added sutton-chen to makefile.

2005-11-14 17:20  chuckv

        * src/UseTheForce/DarkSide/: suttonchen.F90,
        suttonchen_interface.h: Build Fixes for sutton-chen.

2005-11-14 17:03  chuckv

        * src/io/Makefile: Missed makefile for sutton-chen.

2005-11-14 17:03  chuckv

        * src/UseTheForce/: Makefile, DarkSide/Makefile,
        DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff

2005-11-14 16:29  chuckv

        * src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp,
        io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
        UseTheForce/DarkSide/suttonchen.F90,
        UseTheForce/DarkSide/suttonchen_interface.F90,
        UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp,
        brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp,
        types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to
        fix do_forces to use Sutton-Chen.

2005-11-11 12:21  chrisfen

        * src/UseTheForce/DarkSide/: fSwitchingFunctionType.h,
        switcheroo_interface.F90, switcheroo_interface.h: Forgot to add
        some files

2005-11-11 10:22  chrisfen

        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp,
        io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial
        switching function option

2005-11-11 10:21  chrisfen

        * src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a
        5th order polynomial switching function

2005-11-11 10:21  chrisfen

        * samples/water/ssd/ssd.md: playing with switching functions again

2005-11-11 10:21  chrisfen

        * samples/argon/500.md: playing with switching functions

2005-11-08 19:11  chuckv

        * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force
        files for Sutton-Chen and Quantum Sutton-Chen

2005-11-08 08:32  chrisfen

        * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp,
        DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and
        ability to output forces and torques

2005-11-08 08:32  chrisfen

        * src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for
        output of forces and torques

2005-11-08 08:31  chrisfen

        * src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90:
        Working on shifted_force...

2005-11-08 08:31  chrisfen

        * samples/water/: spce/spce.md, ssde/ssde.md: Just testing...

2005-11-03 18:22  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly
        commented section

2005-11-03 18:12  chrisfen

        * src/: UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/fElectrostaticScreeningMethod.h,
        UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp,
        io/Globals.cpp, io/Globals.hpp: improvements in shifted-force

2005-11-03 18:11  chrisfen

        * samples/water/spce/spce.md: mmm...  damped shifted force...

2005-11-03 18:06  chuckv

        * src/UseTheForce/DarkSide/suttonchen.F90: More work on SC.

2005-11-02 18:50  chuckv

        * src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen.

2005-11-02 16:01  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
        removed some test code

2005-11-02 15:45  chrisfen

        * src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the
        screening method header

2005-11-02 15:36  chrisfen

        * src/brains/SimInfo.cpp: again, changing how we deal with
        summation and screening methods

2005-11-02 15:36  chrisfen

        * src/: UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/electrostatic_interface.F90,
        UseTheForce/DarkSide/electrostatic_interface.h,
        UseTheForce/DarkSide/fElectrostaticSummationMethod.h,
        io/Globals.cpp, io/Globals.hpp: changing how we deal with summation
        and screening methods

2005-11-02 15:35  chrisfen

        * src/UseTheForce/doForces.F90: debug stuff for rf removed

2005-11-01 18:32  chuckv

        * src/: UseTheForce/DarkSide/atype.F90,
        UseTheForce/DarkSide/atype_interface.F90,
        UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp,
        types/AtomTypeProperties.h: Added suppport to atypes for MEAM and
        sutton-chen

2005-11-01 14:24  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
        removed some testing code...

2005-11-01 14:14  chrisfen

        * src/: brains/Register.cpp, brains/SimInfo.cpp,
        brains/fSimulation.h, integrators/IntegratorFactory.hpp,
        io/Globals.cpp: fixed a capitalization problem with NPT integrator
        initialization

2005-11-01 14:13  chrisfen

        * src/applications/oopse/oopse.cpp: nothing

2005-11-01 14:09  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
        DarkSide/simulation.F90: still fixing up wolf...

2005-11-01 13:29  chuckv

        * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In
        process of adding sutton-chen forcefield.

2005-10-26 19:32  chrisfen

        * src/brains/SimInfo.cpp: changed the default switching radius to
        85% of rcut

2005-10-26 19:31  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks
        to be working now - for charges and dipoles alike

2005-10-26 19:31  chrisfen

        * src/UseTheForce/doForces.F90: reaction field looks to be working
        now

2005-10-26 19:30  chrisfen

        * samples/water/ssdrf/water.md: added a test molecule

2005-10-26 19:30  chrisfen

        * forceFields/DUFF2.frc: added a test atom type

2005-10-24 10:06  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole
        reaction field - don't know if it works...

2005-10-23 17:08  chrisfen

        * src/: UseTheForce/doForces.F90,
        UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp:
        streamlined reaction field for dipoles (now a good bit faster) and
        added reaction field for charges - still need to do charge-dipole
        RF

2005-10-23 17:07  chrisfen

        * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction
        field

2005-10-23 17:06  chrisfen

        * samples/water/spce/spce.md: reaction field now works for charges

2005-10-20 16:27  tim

        * src/primitives/Torsion.cpp: Fix the other branch of force
        calculation in Torision.cpp

2005-10-19 15:24  chrisfen

        * src/: UseTheForce/doForces.F90,
        UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp,
        brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals
        toUpper problems - these changes should fix those...

2005-10-19 15:23  chrisfen

        * samples/water/ssdrf/ssdrf.md: nothing

2005-10-19 13:03  gezelter

        * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in
        GayBerne

2005-10-19 12:49  tim

        * src/: UseTheForce/DarkSide/fInteractionMap.h,
        brains/ForceManager.cpp: fix an index mismathcing between c and
        fortran

2005-10-18 19:03  gezelter

        * samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added
        samples for the cutoff methods that Yang Zheng has been working on

2005-10-18 17:13  gezelter

        * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques
        and a rotation matrix bug

2005-10-18 17:13  gezelter

        * samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md,
        gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
        added a few GB test cases

2005-10-18 17:13  gezelter

        * forceFields/DUFF2.frc: Fixing GB parameters

2005-10-18 14:36  kdaily

        * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne
        type

2005-10-18 11:01  chrisfen

        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
        UseTheForce/DarkSide/Makefile,
        UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/electrostatic_interface.F90,
        UseTheForce/DarkSide/electrostatic_interface.h,
        UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged
        reaction field with electrostatics.F90

2005-10-17 19:13  tim

        * src/: brains/ForceManager.cpp, brains/Stats.cpp,
        brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp,
        io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp,
        io/StatWriter.hpp: Customized StatWriter is working

2005-10-17 18:42  kdaily

        * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver
        paper

2005-10-17 17:47  gezelter

        * src/UseTheForce/DarkSide/gb.F90: bugtracking gb

2005-10-17 15:24  tim

        * src/io/ParamConstraint.hpp: Another bug fix

2005-10-17 15:22  tim

        * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace
        issues in Globals

2005-10-17 15:12  gezelter

        * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90,
        UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90,
        UseTheForce/DarkSide/gb_interface.F90,
        UseTheForce/DarkSide/gb_interface.h,
        io/GayBerneAtomTypesSectionParser.cpp,
        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
        changing GB architecture

2005-10-17 15:12  gezelter

        * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in,
        gbRotRoundZ.in: Adding samples for gb tests

2005-10-16 23:06  tim

        * src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy
        a  string to event's err_msg, there are still tons of memory
        leaking problem in Globals

2005-10-16 20:51  tim

        * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change
        error message in Globals

2005-10-14 17:43  tim

        * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for
        parameters are working now

2005-10-14 12:43  gezelter

        * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests

2005-10-14 12:05  gezelter

        * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md,
        gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
        Adding some Gay Berne tests

2005-10-14 12:05  gezelter

        * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some
        cutoff tests

2005-10-14 11:44  kdaily

        * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp,
        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90,
        src/UseTheForce/DarkSide/gb_interface.F90,
        src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne
        LJ

2005-10-14 10:48  tim

        * src/io/ParamConstraint.hpp: Adding Parameter Constraint class

2005-10-14 10:18  chrisfen

        * samples/thermoIntegration/liquid/ssde.md,
        samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp,
        src/restraints/Restraints.cpp: added default restraint spring
        constants into Globals

2005-10-13 18:26  tim

        * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp,
        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp,
        constraints/ZconstraintForceManager.cpp,
        integrators/Integrator.cpp, integrators/NPT.cpp,
        integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp,
        io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp,
        minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp,
        restraints/ThermoIntegrationForceManager.cpp,
        visitors/ZconsVisitor.cpp: rewrite Globals

2005-10-12 17:57  chuckv

        * src/brains/ForceManager.cpp: Fix to forceManager to pass
        potential array to fortran.

2005-10-12 17:00  gezelter

        * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't
        remember what we did

2005-10-12 17:00  gezelter

        * src/UseTheForce/: doForces.F90, doForces_interface.F90,
        DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h,
        DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90,
        DarkSide/sticky.F90: simplifying long range potential array

2005-10-12 17:00  gezelter

        * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new
        cutoff methods

2005-10-12 17:00  gezelter

        * forceFields/DUFF2.frc: Messing with 2-point water models

2005-10-12 16:22  chuckv

        * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran
        interface now expects an array for pot.

2005-10-12 16:18  chuckv

        * src/UseTheForce/: doForces.F90, DarkSide/gb.F90,
        DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for
        calculation of potential.

2005-10-12 15:55  chuckv

        * src/UseTheForce/doForces.F90: More changes to MPI potential
        calculations.

2005-10-12 14:59  chuckv

        * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90,
        DarkSide/eam.F90, DarkSide/electrostatic.F90,
        DarkSide/fInteractionMap.h, DarkSide/force_globals.F90,
        DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky
        Breaky: Add Support for seperating potential contributions.

2005-10-11 18:00  chuckv

        * src/UseTheForce/doForces.F90: Free some variables that weren't
        freed before.

2005-10-11 17:59  chuckv

        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
        GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod
        builder --twinned.

2005-10-11 17:57  chuckv

        * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
        nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c,
        nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp,
        sphericalNanoparticle.hpp: Added code for nanoparticle builder to
        cvs.

2005-10-10 17:34  chuckv

        * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable
        in MPI.

2005-10-10 17:20  chuckv

        * src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column
        indexing of groupToGtype. We now have two seperate maps
        groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer
        that is set to groupToGtypeRow in the single processor version.

2005-10-06 14:44  chrisfen

        * samples/water/: dimer/water.md, spce/water.md, ssd/water.md,
        ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md,
        tip3p_ice/water.md, tip4p/water.md: fixing up the samples

2005-10-05 17:12  tim

        * src/primitives/RigidBody.cpp: There is still something wrong with
        inertia tensor projection

2005-10-05 15:35  tim

        * src/primitives/RigidBody.cpp: erase output of inertia tensor.
        There is still something wrong with current implementation.

2005-10-05 15:34  tim

        * src/brains/MoleculeCreator.cpp: fix a bug in creating
        cutoffGroup. When cutoffGroup is turned off, there is a mismatch
        between group and center of mass array

2005-10-05 15:12  tim

        * src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup.
        When cutoffGroup is turned off, there is a mismatch between group
        and center of mass array

2005-10-04 15:34  chrisfen

        * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying
        mass ratio bug that results in simulation failure with massless
        particles

2005-10-04 15:33  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on
        wolf

2005-10-04 15:32  chrisfen

        * samples/water/dimer/two.md, samples/water/dimer/water.md,
        samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md,
        samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some
        random changes when testing

2005-10-03 11:54  tim

        * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in
        projecting the inertia tensor of directional atom in rigibody into
        rigidbody's body frame (previous commit is wrong)

2005-10-03 10:31  tim

        * src/primitives/RigidBody.cpp: fix a bug in projecting the inertia
        tensor of directional atom in rigibody into rigidbody's body frame

2005-09-28 14:47  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf

2005-09-28 14:46  chrisfen

        * samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md,
        dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md,
        ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md,
        tip4p/tp4.md: fixed some samples

2005-09-28 14:46  chrisfen

        * ChangeLog: updated

2005-09-28 12:55  tim

        * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid
        divergence in rotation matrix to quaternion transformation

2005-09-28 12:32  gezelter

        * src/primitives/RigidBody.cpp: Rotation matrix multiplication
        order error

2005-09-28 12:32  gezelter

        * src/io/DumpReader.cpp: tracking down quaternion bug

2005-09-28 12:32  gezelter

        * forceFields/DUFF2.frc: Added DIP atom types for 2-point water
        model

2005-09-27 16:02  tim

        * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix
        to quaternion

2005-09-26 14:38  chuckv

        * src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc
        7 so derfc is external. Other compilers should treat erfc as
        intrinsic.

2005-09-26 13:07  chuckv

        * src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc
        and declared it to be external to fix issure with ifc7. Hopefully
        this will not cause a problem with other compilers where derfc is
        an intrinsic function.

2005-09-26 12:42  chuckv

        * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype
        in simulation module. We needed a seperate receive buffer.

2005-09-26 11:58  chuckv

        * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added
        support for skinThickness keyword to Globals.

2005-09-26 11:56  tim

        * src/io/DumpReader.cpp: fix a typo in DumpReader

2005-09-26 10:27  chrisfen

        * samples/: minimizer/tip4p_two.md,
        thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md,
        water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md,
        water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md,
        water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md,
        water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md,
        water/tip4p/tp4.md: fixing up some samples

2005-09-24 13:39  chrisfen

        * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now
        roughly the same speed as the old version when using dipoles
        
        energies are now exactly the same between the old version of OOPSE
        and this version

2005-09-24 13:38  chrisfen

        * samples/water/ssdrf/ssdrf.md: turned rf on

2005-09-23 16:31  chuckv

        * src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the
        skin thickness and hardcode listSkin to be 1.0. We now get listskin
        from skin. This will get fixed to where we can manually set skin
        thickness.

2005-09-22 14:50  gezelter

        * src/math/derfc.F90: added error function

2005-09-21 20:08  chuckv

        * src/integrators/Velocitizer.cpp: Removed print statement for
        angular momentum and inertia tensor from velocitizer.

2005-09-21 20:04  chuckv

        * src/integrators/Velocitizer.cpp: Removed print statements for
        remove angular momentum.

2005-09-21 19:45  chuckv

        * src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ
        (say we are using EAM), we probably shouldn't rebuild the LJ mixing
        map.

2005-09-21 16:59  tim

        * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp:
        DumpReader using pure c++ io

2005-09-21 13:20  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a
        defaultCutoff bug (HEMES!)

2005-09-20 18:13  gezelter

        * make/Makefile.in: libz additions

2005-09-20 18:03  gezelter

        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
        src/config.h.in: added check for zlib in configure

2005-09-20 17:22  tim

        * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp,
        gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter

2005-09-20 12:22  tim

        * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding
        testcase for zipstream

2005-09-20 11:41  tim

        * src/io/zipstream.hpp: adding zipstream.hpp

2005-09-20 11:34  chrisfen

        * samples/: dipole/splitInWater.md, dipole/split_SSD.md,
        dipole/twoSplitDipole.md, minimizer/ssdEM.md,
        minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md,
        zcons/zconsMoving.md: fixed up some sample md files

2005-09-19 19:21  chrisfen

        * ChangeLog, samples/water/ssdrf/ssdrf.md,
        src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp,
        src/brains/fSimulation.h: Fixed bugs in reaction field, now it
        appears as though it really is working...

2005-09-18 16:45  chrisfen

        * ChangeLog, samples/water/ssdrf/ssdrf.md,
        src/UseTheForce/doForces.F90,
        src/UseTheForce/doForces_interface.F90,
        src/UseTheForce/doForces_interface.h,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/electrostatic_interface.h,
        src/brains/SimInfo.cpp: reaction field seems to work now, still
        need to do some testing...

2005-09-16 19:04  chuckv

        * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
        dump files.

2005-09-16 17:07  chrisfen

        * src/: UseTheForce/doForces_interface.F90,
        UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
        bug that ifc missed...

2005-09-16 16:36  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
        fixing some summation method issues

2005-09-16 15:35  chrisfen

        * src/brains/SimInfo.cpp: fixed a capitalization error

2005-09-16 15:34  chrisfen

        * src/UseTheForce/: fElectrostaticSummationMethod.h,
        DarkSide/fElectrostaticSummationMethod.h: moved a header file
        around

2005-09-16 15:00  chrisfen

        * src/: UseTheForce/DarkSide/electrostatic_interface.F90,
        brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
        are known issues - particularly with reaction field...

2005-09-16 12:07  chrisfen

        * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
        io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
        (cutting out the old way to do reaction field)

2005-09-15 18:05  gezelter

        * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
        fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
        DarkSide/electrostatic_interface.F90,
        DarkSide/electrostatic_interface.h: Working on adding WOLF

2005-09-15 15:17  tim

        * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
        is called without calling getNFrames

2005-09-15 09:47  chrisfen

        * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header

2005-09-14 22:48  chuckv

        * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
        not initialized after creation. When maxval(gtypeMaxCutoff) was
        called, the largest random garbage value was returned from the
        array.

2005-09-14 20:14  chrisfen

        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
        io/Globals.hpp: changes to include the coulombicCorrection selector

2005-09-14 20:13  chrisfen

        * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
        reactionField.F90: added in the undamped wolf, in the process of
        doing the damped wolf

2005-09-14 20:13  chrisfen

        * src/UseTheForce/: doForces.F90, doForces_interface.F90,
        doForces_interface.h, notifyCutoffs.F90: some changes to activate
        the coulombicCorrection selector

2005-09-14 20:11  chrisfen

        * samples/water/dimer/: cl.in, cl.md, water.md: just some testing

2005-09-14 20:11  chrisfen

        * samples/argon/: 500.in, 500.md: Equilibrated the sample

2005-09-14 20:10  chrisfen

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

2005-09-14 16:31  chuckv

        * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
        eamAtypes instead of assuming a 1-1 correspondence to atypes.

2005-09-14 16:28  gezelter

        * src/UseTheForce/doForces.F90: fix to put back calculation of r in
        do_prepair

2005-09-14 15:02  gezelter

        * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
        createMixingMap routine.  It should now set doShift correctly

2005-09-07 18:44  chuckv

        * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.

2005-09-07 18:23  chuckv

        * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
        logical variables

2005-09-07 18:08  gezelter

        * src/UseTheForce/doForces.F90: bugfix on the grouptype finding
        algorithm

2005-09-07 16:46  gezelter

        * src/: UseTheForce/doForces.F90,
        UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
        UseTheForce/notifyCutoffs_interface.F90,
        UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp,
        io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
        cutoff Policy

2005-09-07 15:18  gezelter

        * src/UseTheForce/doForces.F90: Some bug hunting

2005-09-07 15:18  gezelter

        * samples/argon/argonNVT.md: Just a longer test

2005-09-06 13:32  chuckv

        * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
        etc..

2005-09-01 18:56  gezelter

        * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
        zero

2005-09-01 16:17  gezelter

        * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
        createGtypeCutoffMap

2005-08-30 14:23  chrisfen

        * src/: UseTheForce/doForces.F90,
        UseTheForce/doForces_interface.F90,
        UseTheForce/doForces_interface.h,
        UseTheForce/DarkSide/electrostatic.F90,
        UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp,
        brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
        changes for implementing the wolf potential

2005-08-26 18:39  chrisfen

        * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut

2005-08-26 17:30  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
        DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
        some probably nonfunctional get*cut routines

2005-08-26 16:34  chuckv

        * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.

2005-08-26 12:36  gezelter

        * src/UseTheForce/doForces.F90: fixing some of the problems in the
        interactionHash and gtypeCutoff routines

2005-08-17 11:26  gezelter

        * src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
        DarkSide/simulation.F90: added fCutoffPolicy.h

2005-08-11 17:04  gezelter

        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
        progress

2005-08-10 15:17  gezelter

        * src/primitives/StuntDouble.hpp: putting spaceballs back where
        they belong

2005-08-09 18:33  gezelter

        * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
        Jones module

2005-08-09 18:33  gezelter

        * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky

2005-08-09 15:40  chuckv

        * src/UseTheForce/doForces.F90: In process of re-write for group
        based cutoff....

2005-07-29 15:38  gezelter

        * src/UseTheForce/doForces.F90: fixes in progress

2005-07-29 13:34  tim

        * src/UseTheForce/doForces.F90: fix a bug which does not update
        me_i and me_j correctly

2005-07-28 18:12  chuckv

        * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
        cutoffs... Segfaults nicely now...

2005-07-20 13:04  gezelter

        * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
        error messages from pathscale compiler

2005-07-13 12:48  tim

        * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
        <functional>

2005-07-13 11:54  tim

        * src/: UseTheForce/fSwitchingFunction.h,
        UseTheForce/mpiComponentPlan.h,
        UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h,
        io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
        io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c,
        io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c,
        io/parse_tree.h, math/MatVec3.c, utils/residentMem.c,
        utils/simError.c, utils/simError.h: replace c++ style comment in c
        files

2005-07-03 16:53  chuckv

        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
        UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
        subroutine to set cuttoff for Interaction map and function in
        simulation.F90 to determine if a particular atype is present in a
        simulation.

2005-06-28 09:58  gezelter

        * src/UseTheForce/doForces.F90: [no log message]

2005-06-27 18:21  chuckv

        * src/UseTheForce/doForces.F90: More breaking and destruction of
        force code. Does not build at this point...

2005-06-27 17:01  gezelter

        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
        UseTheForce/DarkSide/fInteractionMap.h,
        UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
        Breaky breaky!

2005-06-20 12:03  gezelter

        * samples/water/ssd/ssd.md,
        src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
        simulation

2005-06-13 14:25  tim

        * src/: applications/staticProps/DensityPlot.cpp,
        applications/staticProps/DensityPlot.hpp,
        applications/staticProps/SCDOrderParameter.cpp,
        applications/staticProps/StaticProps.cpp,
        io/AtomTypesSectionParser.cpp: working version of DensityPlot

2005-05-31 18:31  chuckv

        * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
        remove angular momentum.

2005-05-31 13:34  chuckv

        * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
        typo in nanorodBuilder.

2005-05-30 10:01  chuckv

        * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
        brains/Stats.hpp, integrators/Velocitizer.cpp,
        integrators/Velocitizer.hpp: Added method to remove system angular
        momentum to velocitizer and added method to calculate system
        angular momentum to siminfo.

2005-05-29 17:16  chrisfen

        * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
        balance from the Darkside (files)

2005-05-29 17:15  chrisfen

        * src/UseTheForce/doForces.F90: Removed balance from doForces

2005-05-29 17:15  chrisfen

        * samples/water/tap/: tap.in, tap.md: Updated tap sample

2005-05-29 17:15  chrisfen

        * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
        dimer for testing purposes

2005-05-29 17:14  chrisfen

        * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
        was apparently wiped earlier this month...

2005-05-29 17:13  chrisfen

        * ChangeLog: ran make cvslog

2005-05-28 20:16  tim

        * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
        AtomNameVisitor

2005-05-28 20:09  tim

        * src/integrators/Integrator.cpp: dding resetIntegrator

2005-05-28 20:06  tim

        * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
        NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
        resetIntegrator

2005-05-27 17:11  tim

        * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
        Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
        SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
        StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
        StaticProps

2005-05-27 00:41  tim

        * src/: applications/staticProps/Makefile,
        applications/staticProps/P2OrderParameter.cpp,
        applications/staticProps/P2OrderParameter.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticProps.ggo,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
        utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps

2005-05-26 18:45  tim

        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
        applications/dump2Xyz/Dump2XYZCmd.c,
        applications/dump2Xyz/Dump2XYZCmd.h,
        applications/staticProps/Makefile,
        applications/staticProps/P2OrderParameter.cpp,
        applications/staticProps/P2OrderParameter.hpp,
        applications/staticProps/RadialDistrFunc.cpp,
        applications/staticProps/RadialDistrFunc.hpp,
        applications/staticProps/StaticAnalyser.hpp,
        applications/staticProps/StaticProps.cpp,
        applications/staticProps/StaticProps.ggo,
        applications/staticProps/StaticPropsCmd.c,
        applications/staticProps/StaticPropsCmd.h, visitors/Makefile,
        visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding
        AtomNameVisitor to convert atom name to its base name;
        wrappingvisitor now wrap back to the center of the mass; adding
        P2OrderParameter into StaticProps

2005-05-22 17:36  chuckv

        * src/: applications/nanoRodBuilder/Geometry.cpp,
        applications/nanoRodBuilder/GeometryBuilder.cpp,
        applications/nanoRodBuilder/GeometryFactory.cpp,
        applications/nanoRodBuilder/GeometryFactory.hpp,
        applications/nanoRodBuilder/nanorodBuilder.cpp,
        integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
        tensor.

2005-05-22 17:05  tim

        * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
        io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
        printPressureTensor

2005-05-20 15:27  tim

        * src/integrators/NPrT.cpp: NPrT in progress

2005-05-20 12:01  tim

        * src/: integrators/NPrT.cpp, io/Globals.cpp,
        utils/OOPSEConstant.hpp: NPrT in progress

2005-05-19 17:31  tim

        * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
        integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
        io/Globals.hpp: NPAT is working

2005-05-19 11:49  tim

        * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
        integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT

2005-05-19 00:28  tim

        * src/: brains/Register.cpp, integrators/NPAT.cpp,
        integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
        io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators

2005-05-18 15:06  chrisfen

        * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
        some tap changes

2005-05-18 14:31  chrisfen

        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
        DarkSide/sticky.F90: Modifications to temper the dipolar strength
        in the first solvation shell for tap

2005-05-18 08:35  chrisfen

        * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
        for testing purposes

2005-05-17 18:35  chrisfen

        * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
        samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
        src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/electrostatic.F90,
        src/UseTheForce/DarkSide/electrostatic_interface.F90,
        src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
        correcting changes to the previous merge that were not caught

2005-05-17 00:20  chuckv

        * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
        Fixed merge issues between Kyle and Chris so OOPSE will actually
        build.

2005-05-16 23:46  kdaily

        * src/io/: GayBerneAtomTypesSectionParser.cpp,
        GayBerneAtomTypesSectionParser.hpp, Makefile: help

2005-05-16 22:08  kdaily

        * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
        src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
        src/types/DirectionalAtomType.cpp,
        src/types/DirectionalAtomType.hpp: added gb

2005-05-13 16:36  chrisfen

        * forceFields/DUFF2.frc: Better tap

2005-05-12 15:43  chrisfen

        * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
        samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
        src/applications/dump2Xyz/Dump2XYZ.cpp,
        src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. 
        Need to parametrize.

2005-05-11 19:15  chuckv

        * src/: io/ShapeAtomTypesSectionParser.cpp,
        math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
        build issues under ifc7.

2005-05-09 18:07  chuckv

        * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
        builder changes.

2005-05-05 11:06  chrisfen

        * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
        to TAP

2005-05-05 10:47  chrisfen

        * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
        samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile,
        src/UseTheForce/DarkSide/atype.F90,
        src/UseTheForce/DarkSide/atype_interface.F90,
        src/UseTheForce/DarkSide/simulation.F90,
        src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp,
        src/brains/fSimulation.h, src/io/Makefile,
        src/io/StickyAtomTypesSectionParser.cpp,
        src/io/StickyPowerAtomTypesSectionParser.cpp,
        src/io/StickyPowerAtomTypesSectionParser.hpp,
        src/types/AtomType.cpp, src/types/AtomType.hpp,
        src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp,
        src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
        not parametrized, but OOPSE will now let me run it...

2005-05-03 18:55  chuckv

        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
        GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
        Adding support for generic geometry to nanorodbuilder.

2005-05-03 13:55  chuckv

        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
        nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
        nanorodBuilderCmd.h: More changes to nanoRodBuilder....

2005-04-29 15:16  gezelter

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

2005-04-29 12:26  chrisfen

        * forceFields/DUFF2.frc, samples/water/spce/water.md,
        samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
        samples/water/ssd-ion/water.md, samples/water/ssde/water.md,
        samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
        samples/water/tip4p/water.md: Added TIP4P-Ew

2005-04-27 20:24  chuckv

        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
        GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
        nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
        nanoRodBuilder....

2005-04-27 16:13  chrisfen

        * samples/shape/Shapes.frc, samples/shape/linear.shape,
        src/UseTheForce/DarkSide/atype.F90,
        src/UseTheForce/DarkSide/shapes.F90,
        src/UseTheForce/DarkSide/shapes_interface.F90,
        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
        write statements and am closer to a working shapes

2005-04-22 17:57  chuckv

        * src/utils/Predicate.hpp: Fixed gcc4 bug...

2005-04-22 17:52  tim

        * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
        Trim.hpp: adding CharClassificationFunctor to fix the locale
        problem  of c++

2005-04-21 10:12  chrisfen

        * samples/shape/Shapes.frc, samples/shape/linear.in,
        samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile,
        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90,
        src/UseTheForce/DarkSide/shapes.F90,
        src/UseTheForce/DarkSide/shapes_interface.F90,
        src/UseTheForce/DarkSide/shapes_interface.h,
        src/brains/Register.cpp, src/brains/SimCreator.cpp,
        src/io/Makefile, src/io/SectionParser.cpp,
        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
        src/io/ShapeAtomTypesSectionParser.cpp,
        src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile,
        src/types/AtomType.cpp, src/types/ShapeAtomType.cpp,
        src/types/ShapeAtomType.hpp: Shapes is limping along with a array
        bounds overwrite (I think...). At least the parser loads the
        forcefield fine...

2005-04-18 11:44  chrisfen

        * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
        Mac (capitalization confusion of filenames)

2005-04-17 23:50  chrisfen

        * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
        UseTheForce/Shapes_FF.cpp,
        io/DirectionalAtomTypesSectionParser.cpp,
        io/ShapeAtomTypesSectionParser.cpp,
        io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...

2005-04-15 18:43  gezelter

        * README: gmake in case people forget

2005-04-15 18:40  gezelter

        * src/applications/oopse/oopse.cpp: fixed the spacing on the
        banner.  Vanity.

2005-04-15 18:22  gezelter

        * src/: config.h.in, applications/oopse/oopse.cpp: Version string
        in banner (and version numbers in config.h)

2005-04-15 18:22  gezelter

        * ChangeLog, LICENSE, README: Documentation changes

2005-04-15 18:03  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 18:03  gezelter

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

2005-04-15 14:41  tim

        * make/Makefile.in: fix make install

2005-04-15 14:41  tim

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

2005-04-15 14:33  tim

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

2005-04-14 17:41  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 17:20  gezelter

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

2005-04-14 15:12  gezelter

        * LICENSE: [no log message]

2005-04-14 12:10  chuckv

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

2005-04-14 11:20  tim

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

2005-04-13 19:36  chuckv

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

2005-04-13 19:29  chrisfen

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

2005-04-13 19:00  chuckv

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

2005-04-13 18:43  tim

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

2005-04-13 18:30  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 16:36  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 16:17  chuckv

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

2005-04-13 14:41  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 18:44  chuckv

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

2005-04-12 18:42  tim

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

2005-04-12 18:33  tim

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

2005-04-12 18:07  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 17:58  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 17:28  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 17:27  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 17:27  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 17:27  gezelter

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

2005-04-12 17:26  gezelter

        * make/Makefile.in: added lattice subdirectory

2005-04-12 16:57  chrisfen

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

2005-04-12 16:56  chrisfen

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

2005-04-12 16:56  chrisfen

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

2005-04-12 14:30  tim

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

2005-04-12 13:45  chuckv

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

2005-04-12 13:39  chuckv

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

2005-04-12 13:12  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 10:24  chrisfen

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

2005-04-11 20:29  chuckv

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

2005-04-11 20:28  chuckv

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

2005-04-11 17:58  tim

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

2005-04-11 17:37  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 16:54  tim

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

2005-04-11 16:19  chrisfen

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

2005-04-11 16:18  chrisfen

        * forceFields/DUFF2.frc: fixing of the quadrupoles

2005-04-11 16:16  tim

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

2005-04-11 15:49  gezelter

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

2005-04-11 15:06  gezelter

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

2005-04-11 12:13  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 18:13  chrisfen

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

2005-04-08 18:12  chrisfen

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

2005-04-08 14:48  chrisfen

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

2005-04-08 10:43  chrisfen

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

2005-04-08 10:42  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 10:41  chrisfen

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

2005-04-06 19:59  tim

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

2005-04-05 19:09  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 18:37  tim

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

2004-10-29 18:28  chrisfen

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

2004-10-29 18:28  chrisfen

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

2004-10-29 18:27  chrisfen

        * samples/shape/linear.md: shorter run

2004-10-29 16:54  tim

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

2004-10-29 12:22  tim

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

2004-10-29 12:20  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 18:34  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 18:26  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 17:42  tim

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

2004-10-28 17:28  tim

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

2004-10-28 17:11  tim

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

2004-10-28 16:41  tim

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

2004-10-28 16:01  tim

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

2004-10-28 15:33  tim

        * src/utils/next_combination.hpp: Minor change

2004-10-28 15:06  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 13:22  chrisfen

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

2004-10-28 13:20  gezelter

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

2004-10-28 13:20  gezelter

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

2004-10-28 12:56  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 12:55  gezelter

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

2004-10-28 11:42  tim

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

2004-10-28 11:15  tim

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

2004-10-28 11:02  tim

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

2004-10-28 02:23  tim

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

2004-10-28 02:16  tim

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

2004-10-27 23:27  tim

        * test/utils/ReplaceWildCard.hpp: no message

2004-10-27 23:14  tim

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

2004-10-27 22:28  tim

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

2004-10-27 22:08  tim

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

2004-10-27 19:17  tim

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

2004-10-27 02:25  tim

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

2004-10-27 02:07  tim

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

2004-10-26 23:00  gezelter

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

2004-10-26 22:20  gezelter

        * src/UseTheForce/ForceFields.hpp: subclass foo

2004-10-26 22:16  gezelter

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

2004-10-26 20:01  gezelter

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

2004-10-26 18:25  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 18:25  gezelter

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

2004-10-26 18:24  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 18:24  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 18:19  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 14:03  chrisfen

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

2004-10-26 14:02  chrisfen

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

2004-10-26 13:28  tim

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

2004-10-25 18:46  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 13:03  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.

2004-10-25 00:08  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 03:55  tim

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

2004-10-23 19:09  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 19:09  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 18:59  chrisfen

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

2004-10-22 18:54  chrisfen

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

2004-10-22 18:53  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 18:53  chrisfen

        * make/Makefile.in: compiler flags

2004-10-22 17:20  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 16:22  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 16:21  gezelter

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

2004-10-22 10:47  gezelter

        * src/types/AtomType.hpp: Adding AtomType

2004-10-21 17:31  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 17:30  tim

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

2004-10-21 16:15  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 12:32  tim

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

2004-10-21 12:24  tim

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

2004-10-21 12:22  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 11:25  chuckv

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

2004-10-21 11:24  chuckv

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

2004-10-20 18:54  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 17:52  gezelter

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

2004-10-20 17:38  tim

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

2004-10-20 17:16  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 16:47  chuckv

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

2004-10-20 16:46  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 14:07  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 01:52  tim

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

2004-10-20 00:54  gezelter

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

2004-10-20 00:54  gezelter

        * src/UseTheForce/Shapes_FF.cpp: fixed include

2004-10-20 00:26  gezelter

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

2004-10-20 00:23  gezelter

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

2004-10-20 00:19  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

2004-10-20 00:12  gezelter

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

2004-10-20 00:02  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 20:18  tim

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

2004-10-19 19:01  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 18:43  chuckv

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

2004-10-19 18:37  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 17:28  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 16:43  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 16:43  gezelter

        * src/UseTheForce/Makefile: regressing

2004-10-19 16:40  gezelter

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

2004-10-19 16:40  gezelter

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

2004-10-19 14:21  chrisfen

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

2004-10-19 00:34  tim

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

2004-10-19 00:28  tim

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

2004-10-19 00:21  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 19:13  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 17:03  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 13:07  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 12:30  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 12:29  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 11:21  gezelter

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

2004-10-18 01:23  tim

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

2004-10-18 01:23  tim

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

2004-10-16 21:19  tim

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

2004-10-15 21:31  tim

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

2004-10-15 17:11  tim

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

2004-10-15 17:10  tim

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

2004-10-15 16:42  tim

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

2004-10-15 16:35  tim

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

2004-10-15 16:34  tim

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

2004-10-15 15:38  chuckv

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

2004-10-15 14:28  tim

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

2004-10-15 14:20  tim

        * src/io/basic_ifstrstream.hpp: fix include

2004-10-15 14:18  tim

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

2004-10-15 14:17  tim

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

2004-10-15 14:16  tim

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

2004-10-15 11:37  tim

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

2004-10-15 11:20  tim

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

2004-10-15 11:19  tim

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

2004-10-15 03:52  tim

        * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream

2004-10-14 19:28  tim

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

2004-10-14 19:27  tim

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

2004-10-13 19:53  tim

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

2004-10-13 18:28  tim

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

2004-10-13 18:27  tim

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

2004-10-13 18:24  tim

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

2004-10-13 02:51  tim

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

2004-10-13 02:50  tim

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

2004-10-12 19:57  tim

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

2004-10-12 15:08  tim

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

2004-10-11 18:15  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 17:54  tim

        * scripts/filepp: fix a bug in filepp

2004-10-11 17:13  tim

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

2004-10-11 17:10  tim

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

2004-10-11 14:40  tim

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

2004-10-11 14:01  tim

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

2004-10-11 11:43  gezelter

        * make/Makefile.in: fixed makefile.in

2004-10-11 10:51  tim

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

2004-10-11 10:26  tim

        * forceFields/Makefile: add Makefile

2004-10-11 10:23  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 10:23  tim

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

2004-10-09 02:01  tim

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

2004-10-08 19:15  tim

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

2004-10-08 18:51  tim

        * make/Makefile.in: fix make install

2004-10-08 18:10  tim

        * make/Makefile.in: adding make install

2004-10-08 18:04  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 19:03  gezelter

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

2004-10-06 19:03  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 18:20  tim

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

2004-10-06 18:19  tim

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

2004-10-06 17:27  gezelter

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

2004-10-06 17:27  gezelter

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

2004-10-06 17:22  gezelter

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

2004-10-06 16:01  chrisfen

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

2004-10-06 15:55  gezelter

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

2004-10-06 15:51  gezelter

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

2004-10-06 14:53  tim

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

2004-10-06 14:18  tim

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

2004-10-05 18:57  tim

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

2004-10-05 15:37  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 15:35  tim

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

2004-10-05 10:14  tim

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

2004-10-04 16:56  tim

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

2004-10-04 12:24  gezelter

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

2004-10-04 12:06  gezelter

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

2004-10-04 11:27  gezelter

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

2004-10-02 00:40  tim

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

2004-10-02 00:22  tim

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

2004-10-01 17:59  tim

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

2004-10-01 17:22  gezelter

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

2004-10-01 17:11  tim

        * scripts/filepp: adding fortran90 make dependency tool

2004-09-30 11:41  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 17:55  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 17:54  tim

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

2004-09-29 17:32  tim

        * make/Makefile: eliminate DEV_ROOT by relative path

2004-09-29 14:37  tim

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

2004-09-29 13:57  gezelter

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

2004-09-29 13:56  gezelter

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

2004-09-29 13:46  tim

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

2004-09-29 13:12  tim

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

2004-09-29 11:58  gezelter

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

2004-09-29 11:00  tim

        * make/Makefile: add print statment to rules

2004-09-29 10:59  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 22:55  tim

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

2004-09-28 19:24  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 18:15  gezelter

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

2004-09-28 18:14  gezelter

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

2004-09-28 17:08  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 16:43  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 16:41  tim

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

2004-09-28 12:13  tim

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

2004-09-27 16:24  tim

        * make/Makefile: adding include path to F90Options

2004-09-27 16:13  tim

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

2004-09-24 12:27  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

2004-09-24 00:16  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,
        make/_files/style.css, 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

2004-09-24 00:16  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,
        make/_files/style.css, 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:	2762
Committed:	Fri May 19 21:26:41 2006 UTC (18 years, 1 month ago) by chrisfen
File size:	300617 byte(s)
Log Message:	Last bug showed up in 2 places, fixed the other one.