--- trunk/OOPSE-4/ChangeLog 2005/05/29 21:13:23 2246 +++ trunk/OOPSE-4/ChangeLog 2006/04/21 19:32:07 2727 @@ -1,740 +1,3153 @@ -2005-05-28 19:16 tim - - * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding - AtomNameVisitor - -2005-05-28 19:09 tim - - * src/integrators/Integrator.cpp: dding resetIntegrator - -2005-05-28 19:06 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 16:11 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 - -2005-05-26 23:41 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 17:45 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 16:36 chuckv - - * samples/metals/nanorod/Au_nanoparticle_FCC.md, - src/applications/nanoRodBuilder/Geometry.cpp, - src/applications/nanoRodBuilder/GeometryBuilder.cpp, - src/applications/nanoRodBuilder/GeometryFactory.cpp, - src/applications/nanoRodBuilder/GeometryFactory.hpp, - src/applications/nanoRodBuilder/nanorodBuilder.cpp, - src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure - tensor. - -2005-05-22 16:05 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 14:27 tim - - * src/integrators/NPrT.cpp: NPrT in progress - -2005-05-20 11:01 tim - - * src/: integrators/NPrT.cpp, io/Globals.cpp, - utils/OOPSEConstant.hpp: NPrT in progress - -2005-05-19 16:31 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 10:49 tim - - * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, - integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT - -2005-05-18 23:28 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 14:06 chrisfen - - * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just - some tap changes - -2005-05-18 13:31 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 07:35 chrisfen - - * samples/water/tap/: tap.in, tap.md, water.md: added a tap example - for testing purposes - -2005-05-17 17:35 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 - -2005-05-16 23:20 chuckv - - * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: - Fixed merge issues between Kyle and Chris so OOPSE will actually - build. - -2005-05-16 22:46 kdaily - - * src/io/: GayBerneAtomTypesSectionParser.cpp, - GayBerneAtomTypesSectionParser.hpp, Makefile: help - -2005-05-16 21:08 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 15:36 chrisfen - - * forceFields/DUFF2.frc: Better tap - -2005-05-12 14:43 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 18:15 chuckv - - * src/: io/ShapeAtomTypesSectionParser.cpp, - math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed - build issues under ifc7. - -2005-05-09 17:07 chuckv - - * src/applications/nanoRodBuilder/Geometry.hpp: More geometry - builder changes. - -2005-05-05 10:06 chrisfen - - * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED - to TAP - -2005-05-05 09:47 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 17:55 chuckv - - * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, - GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: - Adding support for generic geometry to nanorodbuilder. - -2005-05-03 12:55 chuckv - - * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, - nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, - nanorodBuilderCmd.h: More changes to nanoRodBuilder.... - -2005-04-29 14:16 gezelter - - * make/Makefile.in: [no log message] - -2005-04-29 11:26 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 19:24 chuckv - - * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, - GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, - nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with - nanoRodBuilder.... - -2005-04-27 15:13 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 16:57 chuckv - - * src/utils/Predicate.hpp: Fixed gcc4 bug... - -2005-04-22 16:52 tim - - * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, - Trim.hpp: adding CharClassificationFunctor to fix the locale - problem of c++ - -2005-04-21 09:12 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 10:44 chrisfen - - * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on - Mac (capitalization confusion of filenames) - -2005-04-17 22:50 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 17:43 gezelter - - * README: gmake in case people forget - -2005-04-15 17:40 gezelter - - * src/applications/oopse/oopse.cpp: fixed the spacing on the - banner. Vanity. - -2005-04-15 17:22 gezelter - - * src/: config.h.in, applications/oopse/oopse.cpp: Version string - in banner (and version numbers in config.h) - -2005-04-15 17:22 gezelter - - * ChangeLog, LICENSE, README: Documentation changes - -2005-04-15 17:03 gezelter - - * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, - UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, - UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, - UseTheForce/ForceFieldCreator.hpp, - UseTheForce/ForceFieldFactory.cpp, - UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, - UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, - UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, - UseTheForce/notifyCutoffs.F90, - UseTheForce/notifyCutoffs_interface.F90, - UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, - UseTheForce/DarkSide/atype.F90, - UseTheForce/DarkSide/atype_interface.F90, - UseTheForce/DarkSide/eam.F90, - UseTheForce/DarkSide/eam_interface.F90, - UseTheForce/DarkSide/eam_interface.h, - UseTheForce/DarkSide/electrostatic.F90, - UseTheForce/DarkSide/electrostatic_interface.F90, - UseTheForce/DarkSide/electrostatic_interface.h, - UseTheForce/DarkSide/force_globals.F90, - UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, - UseTheForce/DarkSide/lj_interface.F90, - UseTheForce/DarkSide/lj_interface.h, - UseTheForce/DarkSide/neighborLists.F90, - UseTheForce/DarkSide/reactionField.F90, - UseTheForce/DarkSide/shapes.F90, - UseTheForce/DarkSide/shapes_interface.F90, - UseTheForce/DarkSide/shapes_interface.h, - UseTheForce/DarkSide/simParallel.F90, - UseTheForce/DarkSide/simParallel_interface.F90, - UseTheForce/DarkSide/simParallel_interface.h, - UseTheForce/DarkSide/simulation.F90, - UseTheForce/DarkSide/simulation_interface.F90, - UseTheForce/DarkSide/simulation_interface.h, - UseTheForce/DarkSide/sticky.F90, - UseTheForce/DarkSide/sticky_interface.F90, - UseTheForce/DarkSide/sticky_interface.h, - UseTheForce/DarkSide/switcheroo.F90, - applications/dump2Xyz/Dump2XYZ.cpp, - applications/dump2Xyz/Dump2XYZCmd.c, - applications/dump2Xyz/Dump2XYZCmd.h, - applications/dynamicProps/CrossTimeCorrFunc.cpp, - applications/dynamicProps/CrossTimeCorrFunc.hpp, - applications/dynamicProps/DipoleCorrFunc.cpp, - applications/dynamicProps/DipoleCorrFunc.hpp, - applications/dynamicProps/DynamicProps.cpp, - applications/dynamicProps/DynamicPropsCmd.c, - applications/dynamicProps/DynamicPropsCmd.h, - applications/dynamicProps/FrameTimeCorrFunc.hpp, - applications/dynamicProps/ParticleTimeCorrFunc.cpp, - applications/dynamicProps/ParticleTimeCorrFunc.hpp, - applications/dynamicProps/RCorrFunc.cpp, - applications/dynamicProps/RCorrFunc.hpp, - applications/dynamicProps/TimeCorrFunc.cpp, - applications/dynamicProps/TimeCorrFunc.hpp, - applications/dynamicProps/VCorrFunc.cpp, - applications/dynamicProps/VCorrFunc.hpp, - applications/nanoRodBuilder/GeometryBuilder.cpp, - applications/nanoRodBuilder/GeometryBuilder.hpp, - applications/nanoRodBuilder/nanorodBuilder.cpp, - applications/nanoRodBuilder/nanorodBuilderCmd.c, - applications/nanoRodBuilder/nanorodBuilderCmd.h, - applications/oopse/oopse.cpp, - applications/simpleBuilder/simpleBuilder.cpp, - applications/simpleBuilder/simpleBuilderCmd.c, - applications/simpleBuilder/simpleBuilderCmd.h, - applications/staticProps/GofAngle2.cpp, - applications/staticProps/GofAngle2.hpp, - applications/staticProps/GofR.cpp, - applications/staticProps/GofR.hpp, - applications/staticProps/GofRAngle.cpp, - applications/staticProps/GofRAngle.hpp, - applications/staticProps/GofXyz.cpp, - applications/staticProps/GofXyz.hpp, - applications/staticProps/RadialDistrFunc.cpp, - applications/staticProps/RadialDistrFunc.hpp, - applications/staticProps/StaticProps.cpp, - applications/staticProps/StaticPropsCmd.c, - applications/staticProps/StaticPropsCmd.h, - brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, - brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, - brains/Exclude.hpp, brains/ForceManager.cpp, - brains/ForceManager.hpp, brains/MoleculeCreator.cpp, - brains/MoleculeCreator.hpp, brains/Register.cpp, - brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, - brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, - brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, - brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, - brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, - brains/fSimulation.h, constraints/ConstraintElem.hpp, - constraints/ConstraintPair.hpp, constraints/Rattle.cpp, - constraints/Rattle.hpp, constraints/ZconsStruct.hpp, - constraints/ZconstraintForceManager.cpp, - constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, - integrators/DLM.hpp, integrators/Integrator.cpp, - integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, - integrators/IntegratorFactory.cpp, - integrators/IntegratorFactory.hpp, integrators/NPT.cpp, - integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, - integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, - integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, - integrators/NVT.cpp, integrators/NVT.hpp, - integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, - integrators/Velocitizer.hpp, - integrators/VelocityVerletIntegrator.cpp, - integrators/VelocityVerletIntegrator.hpp, - io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, - io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, - io/BASS_parse.h, io/BendTypesSectionParser.cpp, - io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, - io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, - io/ChargeAtomTypesSectionParser.hpp, - io/DirectionalAtomTypesSectionParser.cpp, - io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, - io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, - io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, - io/Globals.cpp, io/Globals.hpp, - io/LennardJonesAtomTypesSectionParser.cpp, - io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, - io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, - io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, - io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, - io/SectionParser.cpp, io/SectionParser.hpp, - io/SectionParserManager.cpp, io/SectionParserManager.hpp, - io/StatWriter.cpp, io/StatWriter.hpp, - io/StickyAtomTypesSectionParser.cpp, - io/StickyAtomTypesSectionParser.hpp, - io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, - io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, - io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, - io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, - io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, - io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, - lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, - lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, - lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, - lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, - math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, - math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, - math/ParallelRandNumGen.hpp, math/Polynomial.hpp, - math/Quaternion.hpp, math/RandNumGen.hpp, - math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, - math/RectMatrix.hpp, math/SeqRandNumGen.cpp, - math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, - math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, - minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, - minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, - minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, - minimizers/MinimizerFactory.hpp, - minimizers/MinimizerParameterSet.cpp, - minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, - minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, - minimizers/SDMinimizer.hpp, primitives/Atom.cpp, - primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, - primitives/Bond.hpp, primitives/CutoffGroup.hpp, - primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, - primitives/GhostBend.cpp, primitives/GhostBend.hpp, - primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, - primitives/Molecule.cpp, primitives/Molecule.hpp, - primitives/RigidBody.cpp, primitives/RigidBody.hpp, - primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, - primitives/Torsion.cpp, primitives/Torsion.hpp, - primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, - profiling/mdProfile.cpp, profiling/mdProfile.hpp, - profiling/timing.F90, restraints/Restraints.cpp, - restraints/Restraints.hpp, - restraints/ThermoIntegrationForceManager.cpp, - restraints/ThermoIntegrationForceManager.hpp, - selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, - selection/IndexFinder.cpp, selection/IndexFinder.hpp, - selection/NameFinder.cpp, selection/NameFinder.hpp, - selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, - selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, - selection/SelectionManager.cpp, selection/SelectionManager.hpp, - selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, - selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, - types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, - types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, - types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, - types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, - types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, - types/CubicBondType.hpp, types/CubicTorsionType.hpp, - types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, - types/DirectionalAtomType.hpp, types/FixedBondType.hpp, - types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, - types/MakeStamps.cpp, types/MakeStamps.hpp, - types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, - types/MorseBondType.hpp, types/OplsTorsionType.hpp, - types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, - types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, - types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, - types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, - types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, - types/TorsionStamp.cpp, types/TorsionStamp.hpp, - types/TorsionType.hpp, types/UreyBradleyBendType.hpp, - types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, - utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, - utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, - utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, - utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, - utils/PropertyMap.cpp, utils/PropertyMap.hpp, - utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, - utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, - utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, - utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, - utils/any.hpp, utils/definitions.F90, utils/fError.c, - utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, - utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, - utils/residentMem.h, utils/simError.c, utils/simError.h, - utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, - visitors/AtomData.hpp, visitors/AtomVisitor.cpp, - visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, - visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, - visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, - visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, - visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, - visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has - been drafted to perform our indentation services - -2005-04-15 17:03 gezelter - - * configure, ac-tools/configure.in: Jedi mind-trick warning - messages have been added to make users ignore CGAL. - -2005-04-15 13:41 tim - - * make/Makefile.in: fix make install - -2005-04-15 13:41 tim - - * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: - add Makefile of samples - -2005-04-15 13:33 tim - - * samples/: lipid/Makefile, water/dimer/Makefile, - water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not - installed correctly - -2005-04-14 16:41 gezelter - - * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, - make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, - scripts/filepp, scripts/filepp.in: configure now searches for perl - to use with filepp - -2005-04-14 16:20 gezelter - - * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of - MoLocator - -2005-04-14 14:12 gezelter - - * LICENSE: [no log message] - -2005-04-14 11:10 chuckv - - * src/applications/nanoRodBuilder/nanorodBuilder.cpp: - nanorodbuilder now exit's when libCGAL is not present. - -2005-04-14 10:20 tim - - * src/io/make_nodes.h: fix one more warning message in make_nodes - -2005-04-13 18:36 chuckv - - * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed - interface name for SGI Compiler - -2005-04-13 18:29 chrisfen - - * samples/water/ssde/ssde.md: oops... bad sample - -2005-04-13 18:00 chuckv - - * src/config.h.in: Change typo in CGAL. - -2005-04-13 17:43 tim - - * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, - selection/SelectionCompiler.hpp: fix some warning messages - -2005-04-13 17:30 gezelter - - * configure, ac-tools/aclocal.m4, ac-tools/configure.in, - make/Makefile.in, src/config.h.in, - src/applications/nanoRodBuilder/Makefile, - src/applications/nanoRodBuilder/Makefile.in, - src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL - checks - -2005-04-13 15:36 chuckv - - * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, - DarkSide/LJ.F90, DarkSide/electrostatic.F90, - DarkSide/electrostatic_interface.F90, - DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, - DarkSide/lj_interface.h, DarkSide/sticky.F90, - DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added - destroy methods for Fortran modules. - -2005-04-13 15:17 chuckv - - * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, - shapes_interface.h: Added destroy method to clean up memory - -2005-04-13 13:41 tim - - * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, - brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, - io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, - primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, - types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are - fixed - -2005-04-12 17:44 chuckv - - * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed - for nanoRodBuilder. - -2005-04-12 17:42 tim - - * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, - simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder - and simpleBuilder(forget to delete lattice) - -2005-04-12 17:33 tim - - * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, - applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: - refactory lattice - -2005-04-12 17:07 tim - - * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, - CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, - Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory - LatticeFactory and LatticeCreator - -2005-04-12 16:58 tim - - * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, - applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, - brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, - lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, - lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, - lattice/Makefile: refactory LatticeFactory and LatticeCreator - -2005-04-12 16:28 gezelter - - * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, - vector_class.F90: cleaned up vector_class memory leak fix by - deallocating in reverse order of how we allocated. Also migrated - MoLocator into utils directory - -2005-04-12 16:27 gezelter - - * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, - Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, - LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice - directory - -2005-04-12 16:27 gezelter - - * src/applications/: nanoRodBuilder/BaseLattice.cpp, - nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, - nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, - nanoRodBuilder/LatticeCreator.hpp, - nanoRodBuilder/LatticeFactory.cpp, - nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, - nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, - nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, - simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, - simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, - simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, - simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, - simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, - simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of - these files are now redundant - -2005-04-12 16:27 gezelter - - * src/UseTheForce/DarkSide/: atype_interface.F90, - atype_interface.h: cleaned up memory leak fix - -2005-04-12 16:26 gezelter - - * make/Makefile.in: added lattice subdirectory - -2005-04-12 15:57 chrisfen - - * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added - a space by accident - -2005-04-12 15:56 chrisfen - - * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added - quadrupole sample - -2005-04-12 15:56 chrisfen - - * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating - samples - -2005-04-12 13:30 tim - - * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom - type in fortran side - -2005-04-12 12:45 chuckv - - * src/utils/vector_class.F90: Further changes to vector_class - destroy function. - -2005-04-12 12:39 chuckv - - * src/utils/vector_class.F90: Fixed pointer memory leak in - vector_class. - -2005-04-12 12:12 chuckv - - * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, - DarkSide/atype_interface.F90, DarkSide/atype_interface.h, - DarkSide/eam.F90, DarkSide/eam_interface.F90, - DarkSide/eam_interface.h: Updates to deallocate object in fortran. - -2005-04-12 09:24 chrisfen - - * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI - output - -2005-04-11 19:29 chuckv - - * src/: UseTheForce/DarkSide/atype.F90, - applications/nanoRodBuilder/Makefile: Changes to delete atypes... - -2005-04-11 19:28 chuckv - - * src/utils/vector_class.F90: Added code to delete vector. - -2005-04-11 17:03 chuckv - - * samples/metals/nanorod/: Au_nanoparticle.md, - Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why - aren't these here? +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 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 18:32 chrisfen + + * src/brains/SimInfo.cpp: changed the default switching radius to + 85% of rcut + +2005-10-26 18:31 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks + to be working now - for charges and dipoles alike + +2005-10-26 18:31 chrisfen + + * src/UseTheForce/doForces.F90: reaction field looks to be working + now + +2005-10-26 18:30 chrisfen + + * samples/water/ssdrf/water.md: added a test molecule + +2005-10-26 18:30 chrisfen + + * forceFields/DUFF2.frc: added a test atom type + +2005-10-24 09:06 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole + reaction field - don't know if it works... + +2005-10-23 16:08 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 16:07 chrisfen + + * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction + field + +2005-10-23 16:06 chrisfen + + * samples/water/spce/spce.md: reaction field now works for charges + +2005-10-20 15:27 tim + + * src/primitives/Torsion.cpp: Fix the other branch of force + calculation in Torision.cpp + +2005-10-19 14:24 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 14:23 chrisfen + + * samples/water/ssdrf/ssdrf.md: nothing + +2005-10-19 12:03 gezelter + + * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in + GayBerne + +2005-10-19 11:49 tim + + * src/: UseTheForce/DarkSide/fInteractionMap.h, + brains/ForceManager.cpp: fix an index mismathcing between c and + fortran + +2005-10-18 18:03 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 16:13 gezelter + + * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques + and a rotation matrix bug + +2005-10-18 16:13 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 16:13 gezelter + + * forceFields/DUFF2.frc: Fixing GB parameters + +2005-10-18 13:36 kdaily + + * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne + type + +2005-10-18 10:01 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 18:13 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 17:42 kdaily + + * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver + paper + +2005-10-17 16:47 gezelter + + * src/UseTheForce/DarkSide/gb.F90: bugtracking gb + +2005-10-17 14:24 tim + + * src/io/ParamConstraint.hpp: Another bug fix + +2005-10-17 14:22 tim + + * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace + issues in Globals + +2005-10-17 14:12 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 14:12 gezelter + + * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, + gbRotRoundZ.in: Adding samples for gb tests + +2005-10-16 22:06 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 19:51 tim + + * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change + error message in Globals + +2005-10-14 16:43 tim + + * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for + parameters are working now + +2005-10-14 11:43 gezelter + + * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests + +2005-10-14 11:05 gezelter + + * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, + gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: + Adding some Gay Berne tests + +2005-10-14 11:05 gezelter + + * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some + cutoff tests + +2005-10-14 10:44 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 09:48 tim + + * src/io/ParamConstraint.hpp: Adding Parameter Constraint class + +2005-10-14 09:18 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 17:26 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 16:57 chuckv + + * src/brains/ForceManager.cpp: Fix to forceManager to pass + potential array to fortran. + +2005-10-12 16:00 gezelter + + * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't + remember what we did + +2005-10-12 16:00 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 16:00 gezelter + + * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new + cutoff methods + +2005-10-12 16:00 gezelter + + * forceFields/DUFF2.frc: Messing with 2-point water models + +2005-10-12 15:22 chuckv + + * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran + interface now expects an array for pot. + +2005-10-12 15:18 chuckv + + * src/UseTheForce/: doForces.F90, DarkSide/gb.F90, + DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for + calculation of potential. + +2005-10-12 14:55 chuckv + + * src/UseTheForce/doForces.F90: More changes to MPI potential + calculations. + +2005-10-12 13:59 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 17:00 chuckv + + * src/UseTheForce/doForces.F90: Free some variables that weren't + freed before. + +2005-10-11 16:59 chuckv + + * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, + GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod + builder --twinned. + +2005-10-11 16:57 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 16:34 chuckv + + * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable + in MPI. + +2005-10-10 16:20 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 13:44 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 16:12 tim + + * src/primitives/RigidBody.cpp: There is still something wrong with + inertia tensor projection + +2005-10-05 14:35 tim + + * src/primitives/RigidBody.cpp: erase output of inertia tensor. + There is still something wrong with current implementation. + +2005-10-05 14:34 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 14:12 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 14:34 chrisfen + + * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying + mass ratio bug that results in simulation failure with massless + particles + +2005-10-04 14:33 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on + wolf + +2005-10-04 14:32 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 10:54 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 09:31 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 13:47 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf + +2005-09-28 13:46 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 13:46 chrisfen + + * ChangeLog: updated + +2005-09-28 11:55 tim + + * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid + divergence in rotation matrix to quaternion transformation + +2005-09-28 11:32 gezelter + + * src/primitives/RigidBody.cpp: Rotation matrix multiplication + order error + +2005-09-28 11:32 gezelter + + * src/io/DumpReader.cpp: tracking down quaternion bug + +2005-09-28 11:32 gezelter + + * forceFields/DUFF2.frc: Added DIP atom types for 2-point water + model + +2005-09-27 15:02 tim + + * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix + to quaternion + +2005-09-26 13:38 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 12:07 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 11:42 chuckv + + * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype + in simulation module. We needed a seperate receive buffer. + +2005-09-26 10:58 chuckv + + * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added + support for skinThickness keyword to Globals. + +2005-09-26 10:56 tim + + * src/io/DumpReader.cpp: fix a typo in DumpReader + +2005-09-26 09:27 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 12:39 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 12:38 chrisfen + + * samples/water/ssdrf/ssdrf.md: turned rf on + +2005-09-23 15:31 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 13:50 gezelter + + * src/math/derfc.F90: added error function + +2005-09-21 19:08 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statement for + angular momentum and inertia tensor from velocitizer. + +2005-09-21 19:04 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statements for + remove angular momentum. + +2005-09-21 18:45 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 15:59 tim + + * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: + DumpReader using pure c++ io + +2005-09-21 12:20 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a + defaultCutoff bug (HEMES!) + +2005-09-20 17:13 gezelter + + * make/Makefile.in: libz additions + +2005-09-20 17:03 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/config.h.in: added check for zlib in configure + +2005-09-20 16:22 tim + + * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, + gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter + +2005-09-20 11:22 tim + + * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding + testcase for zipstream + +2005-09-20 10:41 tim + + * src/io/zipstream.hpp: adding zipstream.hpp + +2005-09-20 10:34 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 18:21 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 15:45 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 18:04 chuckv + + * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed + dump files. + +2005-09-16 16:07 chrisfen + + * src/: UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a + bug that ifc missed... + +2005-09-16 15:36 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: + fixing some summation method issues + +2005-09-16 14:35 chrisfen + + * src/brains/SimInfo.cpp: fixed a capitalization error + +2005-09-16 14:34 chrisfen + + * src/UseTheForce/: fElectrostaticSummationMethod.h, + DarkSide/fElectrostaticSummationMethod.h: moved a header file + around + +2005-09-16 14:00 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 11:07 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 17:05 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 14:17 tim + + * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame + is called without calling getNFrames + +2005-09-15 08:47 chrisfen + + * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header + +2005-09-14 21:48 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 19:14 chrisfen + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, + io/Globals.hpp: changes to include the coulombicCorrection selector + +2005-09-14 19:13 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 19:13 chrisfen + + * src/UseTheForce/: doForces.F90, doForces_interface.F90, + doForces_interface.h, notifyCutoffs.F90: some changes to activate + the coulombicCorrection selector + +2005-09-14 19:11 chrisfen + + * samples/water/dimer/: cl.in, cl.md, water.md: just some testing + +2005-09-14 19:11 chrisfen + + * samples/argon/: 500.in, 500.md: Equilibrated the sample + +2005-09-14 19:10 chrisfen + + * forceFields/DUFF2.frc: re-added Cl- and Na+ + +2005-09-14 15:31 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 15:28 gezelter + + * src/UseTheForce/doForces.F90: fix to put back calculation of r in + do_prepair + +2005-09-14 14:02 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the + createMixingMap routine. It should now set doShift correctly + +2005-09-07 17:44 chuckv + + * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. + +2005-09-07 17:23 chuckv + + * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi + logical variables + +2005-09-07 17:08 gezelter + + * src/UseTheForce/doForces.F90: bugfix on the grouptype finding + algorithm + +2005-09-07 15:46 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 14:18 gezelter + + * src/UseTheForce/doForces.F90: Some bug hunting + +2005-09-07 14:18 gezelter + + * samples/argon/argonNVT.md: Just a longer test + +2005-09-06 12:32 chuckv + + * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap + etc.. + +2005-09-01 17:56 gezelter + + * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to + zero + +2005-09-01 15:17 gezelter + + * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote + createGtypeCutoffMap + +2005-08-30 13:23 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 17:39 chrisfen + + * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut + +2005-08-26 16:30 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 15:34 chuckv + + * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. + +2005-08-26 11:36 gezelter + + * src/UseTheForce/doForces.F90: fixing some of the problems in the + interactionHash and gtypeCutoff routines + +2005-08-17 10:26 gezelter + + * src/UseTheForce/: doForces.F90, fCutoffPolicy.h, + DarkSide/simulation.F90: added fCutoffPolicy.h + +2005-08-11 16:04 gezelter + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in + progress + +2005-08-10 14:17 gezelter + + * src/primitives/StuntDouble.hpp: putting spaceballs back where + they belong + +2005-08-09 17:33 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard + Jones module + +2005-08-09 17:33 gezelter + + * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky + +2005-08-09 14:40 chuckv + + * src/UseTheForce/doForces.F90: In process of re-write for group + based cutoff.... + +2005-07-29 14:38 gezelter + + * src/UseTheForce/doForces.F90: fixes in progress + +2005-07-29 12:34 tim + + * src/UseTheForce/doForces.F90: fix a bug which does not update + me_i and me_j correctly + +2005-07-28 17:12 chuckv + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed + cutoffs... Segfaults nicely now... + +2005-07-20 12:04 gezelter + + * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text + error messages from pathscale compiler + +2005-07-13 11:48 tim + + * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in + + +2005-07-13 10:54 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 15:53 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 08:58 gezelter + + * src/UseTheForce/doForces.F90: [no log message] + +2005-06-27 17:21 chuckv + + * src/UseTheForce/doForces.F90: More breaking and destruction of + force code. Does not build at this point... + +2005-06-27 16:01 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 11:03 gezelter + + * samples/water/ssd/ssd.md, + src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a + simulation + +2005-06-13 13:25 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 17:31 chuckv + + * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to + remove angular momentum. + +2005-05-31 12:34 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in + typo in nanorodBuilder. + +2005-05-30 09:01 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 16:16 chrisfen + + * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed + balance from the Darkside (files) + +2005-05-29 16:15 chrisfen + + * src/UseTheForce/doForces.F90: Removed balance from doForces + +2005-05-29 16:15 chrisfen + + * samples/water/tap/: tap.in, tap.md: Updated tap sample + +2005-05-29 16:15 chrisfen + + * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap + dimer for testing purposes + +2005-05-29 16:14 chrisfen + + * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It + was apparently wiped earlier this month... + +2005-05-29 16:13 chrisfen + + * ChangeLog: ran make cvslog + +2005-05-28 19:16 tim + + * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding + AtomNameVisitor + +2005-05-28 19:09 tim + + * src/integrators/Integrator.cpp: dding resetIntegrator + +2005-05-28 19:06 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 16:11 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 + +2005-05-26 23:41 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 17:45 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 16:36 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 16:05 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 14:27 tim + + * src/integrators/NPrT.cpp: NPrT in progress + +2005-05-20 11:01 tim + + * src/: integrators/NPrT.cpp, io/Globals.cpp, + utils/OOPSEConstant.hpp: NPrT in progress + +2005-05-19 16:31 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 10:49 tim + + * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, + integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT + +2005-05-18 23:28 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 14:06 chrisfen + + * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just + some tap changes + +2005-05-18 13:31 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 07:35 chrisfen + + * samples/water/tap/: tap.in, tap.md, water.md: added a tap example + for testing purposes + +2005-05-17 17:35 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 + +2005-05-16 23:20 chuckv + + * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: + Fixed merge issues between Kyle and Chris so OOPSE will actually + build. + +2005-05-16 22:46 kdaily + + * src/io/: GayBerneAtomTypesSectionParser.cpp, + GayBerneAtomTypesSectionParser.hpp, Makefile: help + +2005-05-16 21:08 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 15:36 chrisfen + + * forceFields/DUFF2.frc: Better tap + +2005-05-12 14:43 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 18:15 chuckv + + * src/: io/ShapeAtomTypesSectionParser.cpp, + math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed + build issues under ifc7. + +2005-05-09 17:07 chuckv + + * src/applications/nanoRodBuilder/Geometry.hpp: More geometry + builder changes. + +2005-05-05 10:06 chrisfen + + * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED + to TAP + +2005-05-05 09:47 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 17:55 chuckv + + * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, + GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: + Adding support for generic geometry to nanorodbuilder. + +2005-05-03 12:55 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, + nanorodBuilderCmd.h: More changes to nanoRodBuilder.... + +2005-04-29 14:16 gezelter + + * make/Makefile.in: [no log message] + +2005-04-29 11:26 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 19:24 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, + nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with + nanoRodBuilder.... + +2005-04-27 15:13 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 16:57 chuckv + + * src/utils/Predicate.hpp: Fixed gcc4 bug... + +2005-04-22 16:52 tim + + * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, + Trim.hpp: adding CharClassificationFunctor to fix the locale + problem of c++ + +2005-04-21 09:12 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 10:44 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on + Mac (capitalization confusion of filenames) + +2005-04-17 22:50 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 17:43 gezelter + + * README: gmake in case people forget + +2005-04-15 17:40 gezelter + + * src/applications/oopse/oopse.cpp: fixed the spacing on the + banner. Vanity. + +2005-04-15 17:22 gezelter + + * src/: config.h.in, applications/oopse/oopse.cpp: Version string + in banner (and version numbers in config.h) + +2005-04-15 17:22 gezelter + + * ChangeLog, LICENSE, README: Documentation changes + +2005-04-15 17:03 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.F90, + UseTheForce/DarkSide/eam.F90, + UseTheForce/DarkSide/eam_interface.F90, + UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/CrossTimeCorrFunc.cpp, + applications/dynamicProps/CrossTimeCorrFunc.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/FrameTimeCorrFunc.hpp, + applications/dynamicProps/ParticleTimeCorrFunc.cpp, + applications/dynamicProps/ParticleTimeCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/nanoRodBuilder/GeometryBuilder.cpp, + applications/nanoRodBuilder/GeometryBuilder.hpp, + applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/nanoRodBuilder/nanorodBuilderCmd.c, + applications/nanoRodBuilder/nanorodBuilderCmd.h, + applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + applications/simpleBuilder/simpleBuilderCmd.c, + applications/simpleBuilder/simpleBuilderCmd.h, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/Register.cpp, + brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/fSimulation.h, constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/Rattle.cpp, + constraints/Rattle.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/Globals.cpp, io/Globals.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, + io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, + io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, + io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, + lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, + lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, + lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/Polynomial.hpp, + math/Quaternion.hpp, math/RandNumGen.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, + math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, + minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, + minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + profiling/timing.F90, restraints/Restraints.cpp, + restraints/Restraints.hpp, + restraints/ThermoIntegrationForceManager.cpp, + restraints/ThermoIntegrationForceManager.hpp, + selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, + selection/IndexFinder.cpp, selection/IndexFinder.hpp, + selection/NameFinder.cpp, selection/NameFinder.hpp, + selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, + selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.hpp, types/FixedBondType.hpp, + types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/MorseBondType.hpp, types/OplsTorsionType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, + types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/TorsionType.hpp, types/UreyBradleyBendType.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, + utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, + utils/PropertyMap.cpp, utils/PropertyMap.hpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, + utils/any.hpp, utils/definitions.F90, utils/fError.c, + utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, + utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, + utils/residentMem.h, utils/simError.c, utils/simError.h, + utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, + visitors/AtomData.hpp, visitors/AtomVisitor.cpp, + visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, + visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, + visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has + been drafted to perform our indentation services + +2005-04-15 17:03 gezelter + + * configure, ac-tools/configure.in: Jedi mind-trick warning + messages have been added to make users ignore CGAL. + +2005-04-15 13:41 tim + + * make/Makefile.in: fix make install + +2005-04-15 13:41 tim + + * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: + add Makefile of samples + +2005-04-15 13:33 tim + + * samples/: lipid/Makefile, water/dimer/Makefile, + water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not + installed correctly + +2005-04-14 16:41 gezelter + + * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, + scripts/filepp, scripts/filepp.in: configure now searches for perl + to use with filepp + +2005-04-14 16:20 gezelter + + * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of + MoLocator + +2005-04-14 14:12 gezelter + + * LICENSE: [no log message] + +2005-04-14 11:10 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: + nanorodbuilder now exit's when libCGAL is not present. + +2005-04-14 10:20 tim + + * src/io/make_nodes.h: fix one more warning message in make_nodes + +2005-04-13 18:36 chuckv + + * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed + interface name for SGI Compiler + +2005-04-13 18:29 chrisfen + + * samples/water/ssde/ssde.md: oops... bad sample + +2005-04-13 18:00 chuckv + + * src/config.h.in: Change typo in CGAL. + +2005-04-13 17:43 tim + + * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, + selection/SelectionCompiler.hpp: fix some warning messages + +2005-04-13 17:30 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, src/config.h.in, + src/applications/nanoRodBuilder/Makefile, + src/applications/nanoRodBuilder/Makefile.in, + src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL + checks + +2005-04-13 15:36 chuckv + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, + DarkSide/LJ.F90, DarkSide/electrostatic.F90, + DarkSide/electrostatic_interface.F90, + DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, + DarkSide/lj_interface.h, DarkSide/sticky.F90, + DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added + destroy methods for Fortran modules. + +2005-04-13 15:17 chuckv + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, + shapes_interface.h: Added destroy method to clean up memory + +2005-04-13 13:41 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, + types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are + fixed + +2005-04-12 17:44 chuckv + + * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed + for nanoRodBuilder. + +2005-04-12 17:42 tim + + * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, + simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder + and simpleBuilder(forget to delete lattice) + +2005-04-12 17:33 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: + refactory lattice + +2005-04-12 17:07 tim + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, + CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, + Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory + LatticeFactory and LatticeCreator + +2005-04-12 16:58 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, + brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, + lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, + lattice/Makefile: refactory LatticeFactory and LatticeCreator + +2005-04-12 16:28 gezelter + + * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, + vector_class.F90: cleaned up vector_class memory leak fix by + deallocating in reverse order of how we allocated. Also migrated + MoLocator into utils directory + +2005-04-12 16:27 gezelter + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, + Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, + LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice + directory + +2005-04-12 16:27 gezelter + + * src/applications/: nanoRodBuilder/BaseLattice.cpp, + nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, + nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, + nanoRodBuilder/LatticeCreator.hpp, + nanoRodBuilder/LatticeFactory.cpp, + nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, + nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, + nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, + simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, + simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, + simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, + simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, + simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, + simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of + these files are now redundant + +2005-04-12 16:27 gezelter + + * src/UseTheForce/DarkSide/: atype_interface.F90, + atype_interface.h: cleaned up memory leak fix + +2005-04-12 16:26 gezelter + + * make/Makefile.in: added lattice subdirectory + +2005-04-12 15:57 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added + a space by accident + +2005-04-12 15:56 chrisfen + + * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added + quadrupole sample + +2005-04-12 15:56 chrisfen + + * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating + samples + +2005-04-12 13:30 tim + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom + type in fortran side + +2005-04-12 12:45 chuckv + + * src/utils/vector_class.F90: Further changes to vector_class + destroy function. + +2005-04-12 12:39 chuckv + + * src/utils/vector_class.F90: Fixed pointer memory leak in + vector_class. + +2005-04-12 12:12 chuckv + + * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, + DarkSide/atype_interface.F90, DarkSide/atype_interface.h, + DarkSide/eam.F90, DarkSide/eam_interface.F90, + DarkSide/eam_interface.h: Updates to deallocate object in fortran. + +2005-04-12 09:24 chrisfen + + * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI + output + +2005-04-11 19:29 chuckv + + * src/: UseTheForce/DarkSide/atype.F90, + applications/nanoRodBuilder/Makefile: Changes to delete atypes... + +2005-04-11 19:28 chuckv + + * src/utils/vector_class.F90: Added code to delete vector. 2005-04-11 16:58 tim