--- trunk/OOPSE-3.0/ChangeLog 2005/03/11 15:00:20 2116 +++ trunk/OOPSE-3.0/ChangeLog 2005/04/15 22:22:10 2205 @@ -1,82 +1,751 @@ -2005-03-11 00:43 chrisfen +2005-04-15 17:03 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.F90, + UseTheForce/DarkSide/eam.F90, + UseTheForce/DarkSide/eam_interface.F90, + UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/CrossTimeCorrFunc.cpp, + applications/dynamicProps/CrossTimeCorrFunc.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/FrameTimeCorrFunc.hpp, + applications/dynamicProps/ParticleTimeCorrFunc.cpp, + applications/dynamicProps/ParticleTimeCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/nanoRodBuilder/GeometryBuilder.cpp, + applications/nanoRodBuilder/GeometryBuilder.hpp, + applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/nanoRodBuilder/nanorodBuilderCmd.c, + applications/nanoRodBuilder/nanorodBuilderCmd.h, + applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + applications/simpleBuilder/simpleBuilderCmd.c, + applications/simpleBuilder/simpleBuilderCmd.h, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/Register.cpp, + brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/fSimulation.h, constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/Rattle.cpp, + constraints/Rattle.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/Globals.cpp, io/Globals.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, + io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, + io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, + io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, + lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, + lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, + lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/Polynomial.hpp, + math/Quaternion.hpp, math/RandNumGen.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, + math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, + minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, + minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + profiling/timing.F90, restraints/Restraints.cpp, + restraints/Restraints.hpp, + restraints/ThermoIntegrationForceManager.cpp, + restraints/ThermoIntegrationForceManager.hpp, + selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, + selection/IndexFinder.cpp, selection/IndexFinder.hpp, + selection/NameFinder.cpp, selection/NameFinder.hpp, + selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, + selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.hpp, types/FixedBondType.hpp, + types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/MorseBondType.hpp, types/OplsTorsionType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, + types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/TorsionType.hpp, types/UreyBradleyBendType.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, + utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, + utils/PropertyMap.cpp, utils/PropertyMap.hpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, + utils/any.hpp, utils/definitions.F90, utils/fError.c, + utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, + utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, + utils/residentMem.h, utils/simError.c, utils/simError.h, + utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, + visitors/AtomData.hpp, visitors/AtomVisitor.cpp, + visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, + visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, + visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has + been drafted to perform our indentation services + +2005-04-15 17:03 gezelter + + * configure, ac-tools/configure.in: Jedi mind-trick warning + messages have been added to make users ignore CGAL. + +2005-04-15 13:41 tim + + * make/Makefile.in: fix make install + +2005-04-15 13:41 tim + + * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: + add Makefile of samples + +2005-04-15 13:33 tim + + * samples/: lipid/Makefile, water/dimer/Makefile, + water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not + installed correctly + +2005-04-14 16:41 gezelter + + * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, + scripts/filepp, scripts/filepp.in: configure now searches for perl + to use with filepp + +2005-04-14 16:20 gezelter + + * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of + MoLocator + +2005-04-14 14:12 gezelter + + * LICENSE: [no log message] + +2005-04-14 11:10 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: + nanorodbuilder now exit's when libCGAL is not present. + +2005-04-14 10:20 tim + + * src/io/make_nodes.h: fix one more warning message in make_nodes + +2005-04-13 18:36 chuckv + + * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed + interface name for SGI Compiler + +2005-04-13 18:29 chrisfen + + * samples/water/ssde/ssde.md: oops... bad sample + +2005-04-13 18:00 chuckv + + * src/config.h.in: Change typo in CGAL. + +2005-04-13 17:43 tim + + * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, + selection/SelectionCompiler.hpp: fix some warning messages + +2005-04-13 17:30 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, src/config.h.in, + src/applications/nanoRodBuilder/Makefile, + src/applications/nanoRodBuilder/Makefile.in, + src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL + checks + +2005-04-13 15:36 chuckv + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, + DarkSide/LJ.F90, DarkSide/electrostatic.F90, + DarkSide/electrostatic_interface.F90, + DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, + DarkSide/lj_interface.h, DarkSide/sticky.F90, + DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added + destroy methods for Fortran modules. + +2005-04-13 15:17 chuckv + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, + shapes_interface.h: Added destroy method to clean up memory + +2005-04-13 13:41 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, + types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are + fixed + +2005-04-12 17:44 chuckv + + * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed + for nanoRodBuilder. + +2005-04-12 17:42 tim + + * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, + simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder + and simpleBuilder(forget to delete lattice) + +2005-04-12 17:33 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: + refactory lattice + +2005-04-12 17:07 tim + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, + CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, + Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory + LatticeFactory and LatticeCreator + +2005-04-12 16:58 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, + brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, + lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, + lattice/Makefile: refactory LatticeFactory and LatticeCreator + +2005-04-12 16:28 gezelter + + * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, + vector_class.F90: cleaned up vector_class memory leak fix by + deallocating in reverse order of how we allocated. Also migrated + MoLocator into utils directory + +2005-04-12 16:27 gezelter + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, + Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, + LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice + directory + +2005-04-12 16:27 gezelter + + * src/applications/: nanoRodBuilder/BaseLattice.cpp, + nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, + nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, + nanoRodBuilder/LatticeCreator.hpp, + nanoRodBuilder/LatticeFactory.cpp, + nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, + nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, + nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, + simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, + simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, + simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, + simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, + simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, + simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of + these files are now redundant + +2005-04-12 16:27 gezelter + + * src/UseTheForce/DarkSide/: atype_interface.F90, + atype_interface.h: cleaned up memory leak fix + +2005-04-12 16:26 gezelter + + * make/Makefile.in: added lattice subdirectory + +2005-04-12 15:57 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added + a space by accident + +2005-04-12 15:56 chrisfen + + * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added + quadrupole sample + +2005-04-12 15:56 chrisfen + + * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating + samples + +2005-04-12 13:30 tim + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom + type in fortran side + +2005-04-12 12:45 chuckv + + * src/utils/vector_class.F90: Further changes to vector_class + destroy function. + +2005-04-12 12:39 chuckv + + * src/utils/vector_class.F90: Fixed pointer memory leak in + vector_class. + +2005-04-12 12:12 chuckv + + * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, + DarkSide/atype_interface.F90, DarkSide/atype_interface.h, + DarkSide/eam.F90, DarkSide/eam_interface.F90, + DarkSide/eam_interface.h: Updates to deallocate object in fortran. + +2005-04-12 09:24 chrisfen + + * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI + output + +2005-04-11 19:29 chuckv + + * src/: UseTheForce/DarkSide/atype.F90, + applications/nanoRodBuilder/Makefile: Changes to delete atypes... + +2005-04-11 19:28 chuckv + + * src/utils/vector_class.F90: Added code to delete vector. + +2005-04-11 17:03 chuckv + + * samples/metals/nanorod/: Au_nanoparticle.md, + Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why + aren't these here? + +2005-04-11 16:58 tim + + * src/io/basic_ifstrstream.hpp: avoid multiple inherit in + basic_ifstrstream + +2005-04-11 16:37 chuckv + + * make/Makefile.in, + src/applications/nanoRodBuilder/BaseLattice.cpp, + src/applications/nanoRodBuilder/BaseLattice.hpp, + src/applications/nanoRodBuilder/GeometryBuilder.cpp, + src/applications/nanoRodBuilder/GeometryBuilder.hpp, + src/applications/nanoRodBuilder/Lattice.cpp, + src/applications/nanoRodBuilder/Lattice.hpp, + src/applications/nanoRodBuilder/LatticeCreator.cpp, + src/applications/nanoRodBuilder/LatticeCreator.hpp, + src/applications/nanoRodBuilder/LatticeFactory.cpp, + src/applications/nanoRodBuilder/LatticeFactory.hpp, + src/applications/nanoRodBuilder/Makefile, + src/applications/nanoRodBuilder/MoLocator.cpp, + src/applications/nanoRodBuilder/MoLocator.hpp, + src/applications/nanoRodBuilder/nanoBuilder.ggo, + src/applications/nanoRodBuilder/nanorodBuilder.cpp, + src/applications/nanoRodBuilder/nanorodBuilder.ggo, + src/applications/nanoRodBuilder/nanorodBuilderCmd.c, + src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing + nanoRodBuilder application (may not work yet). ((Doesn't work + yet.)) (((May never work....))) + +2005-04-11 15:54 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete + prepareVisitor in Dump2XYZ + +2005-04-11 15:19 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the + quadrupoles. look! it's divide by 3 like stone says! + +2005-04-11 15:18 chrisfen + + * forceFields/DUFF2.frc: fixing of the quadrupoles + +2005-04-11 15:16 tim + + * src/selection/Token.hpp: change the parameter name in + constructors + +2005-04-11 14:49 gezelter + + * make/Makefile.in: One more bug fix for GNU make versions < 3.80 + +2005-04-11 14:06 gezelter + + * make/Makefile.in: Fixed the uc and lc functions for GNU make + versions < 3.80 + +2005-04-11 11:13 gezelter + + * make/Makefile.in, src/UseTheForce/Makefile, + src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added + some stuff to clean out module files during "make clean" + +2005-04-08 17:13 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole + interactions should be working with a remaining question of + interaction magnitude + +2005-04-08 17:12 chrisfen + + * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with + samples + +2005-04-08 13:48 chrisfen + + * samples/water/ssd/ssd.md: oops... messed up a sample + +2005-04-08 09:43 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix + charge-dipole interactions + +2005-04-08 09:42 chrisfen + + * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, + ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole + +2005-04-08 09:41 chrisfen + + * forceFields/DUFF2.frc: added Cl- and Na+ + +2005-04-06 18:59 tim + + * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser + +2005-04-05 18:09 tim + + * src/selection/: NameFinder.cpp, SelectionCompiler.cpp, + SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' + in atom type name;clean the code a little bit + +2005-03-29 16:00 tim + + * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug + in converting rotation matrix to quaternion + +2005-03-28 17:41 tim + + * src/visitors/LipidTransVisitor.cpp: fixed the wrapping + +2005-03-28 17:30 tim + + * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do + the wrapping + +2005-03-28 10:54 tim + + * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the + dimension of histogram + +2005-03-22 11:38 tim + + * make/Makefile.in, src/applications/dump2Xyz/Makefile, + src/applications/dynamicProps/Makefile, + src/applications/oopse/Makefile, + src/applications/simpleBuilder/Makefile, + src/applications/staticProps/Makefile: avoid building parallel + executable for dump2XYZ, simpleBuilder, staticProps and + dynamicProps + +2005-03-21 17:34 chrisfen + + * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the + forcefield files +2005-03-21 15:51 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, + DarkSide/reactionField.F90: Make sure electrostatic_module provides + data for reaction_field + +2005-03-21 15:50 chrisfen + + * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE + WILL CHANGE THIS BACK, RIGHT? + +2005-03-21 14:23 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: constant back to + correct value + +2005-03-21 14:22 gezelter + + * make/Makefile.in: fixed an install-related bug. + $(InstallCommand) had been set to $(InstallData) + +2005-03-15 09:21 gezelter + + * src/integrators/Integrator.cpp: VelocityVerletIntegrator already + deletes and Nullifies restWriter, so Integrator shouldn't do it. + +2005-03-15 09:20 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos + +2005-03-13 02:39 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: first run at + charge-quadrupole interactions + +2005-03-12 14:12 chrisfen + + * samples/: Makefile.in, thermoIntegration/liquid/Makefile, + thermoIntegration/solid/Makefile: forgot a couple of makefiles + +2005-03-12 14:05 chrisfen + + * samples/thermoIntegration/liquid/ssde.in, + samples/thermoIntegration/liquid/ssde.md, + samples/thermoIntegration/liquid/water.md, + samples/thermoIntegration/solid/idealCrystal.in, + samples/thermoIntegration/solid/ssde.in, + samples/thermoIntegration/solid/ssde.md, + samples/thermoIntegration/solid/ssde.zang0, + samples/thermoIntegration/solid/water.md, + samples/water/tip3p_ice/tp3.md, + src/UseTheForce/DarkSide/sticky.F90, + src/restraints/ThermoIntegrationForceManager.cpp: added some + samples + +2005-03-11 12:50 tim + + * src/: brains/SimCreator.cpp, + io/MultipoleAtomTypesSectionParser.cpp: fix a typo in + MultipoleAtomTypesSectionParser + +2005-03-11 10:55 tim + + * src/brains/SimInfo.cpp: pairs inside cutoff group should not be + excluded + +2005-03-11 10:53 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for + quadrupoles + +2005-03-11 10:52 gezelter + + * forceFields/DUFF2.frc: quadrupoles for SSD models + +2005-03-11 10:00 tim + + * ChangeLog, doc/SelectionExpression.html, + doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, + doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, + src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, + src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, + src/selection/TokenMap.cpp: clean up SimInfo; modify the images of + SelectionExpression.html + +2005-03-10 19:43 chrisfen + * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, src/restraints/Restraints.cpp, src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in MPI restraints -2005-03-10 23:56 tim +2005-03-10 18:56 tim * doc/SelectionExpression.html, src/brains/SimInfo.cpp, src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody and cutoff group -2005-03-10 22:06 gezelter +2005-03-10 17:06 gezelter * src/types/MorseBondType.hpp: fixed a doxygen problem -2005-03-10 21:51 gezelter +2005-03-10 16:51 gezelter * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with the split dipole test cases -2005-03-10 21:51 gezelter +2005-03-10 16:51 gezelter * doc/SelectionExpression.html: updated some documentation -2005-03-10 20:40 gezelter +2005-03-10 15:40 gezelter * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, Makefile: LinkedList removal project starts now -2005-03-10 20:28 tim +2005-03-10 15:28 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: using map to replace link list -2005-03-10 19:11 tim +2005-03-10 14:11 tim * samples/dipole/: splitInWater.in, splitInWater.md: adding test case of split dipole -2005-03-10 19:10 chrisfen +2005-03-10 14:10 chrisfen * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, src/io/RestWriter.cpp, src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now builds... -2005-03-10 18:44 tim +2005-03-10 13:44 tim * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: adding test case for split dipole -2005-03-10 17:54 gezelter +2005-03-10 12:54 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side support for split dipoles -2005-03-10 16:27 chrisfen +2005-03-10 11:27 chrisfen * samples/water/tip3p_ice/tp3.md, src/restraints/ThermoIntegrationForceManager.cpp: fixes to restraints -2005-03-10 16:15 chrisfen +2005-03-10 11:15 chrisfen * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints -2005-03-10 16:14 tim +2005-03-10 11:14 tim * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, src/io/MultipoleAtomTypesSectionParser.cpp, src/selection/SelectionEvaluator.cpp: minor change -2005-03-10 15:10 chrisfen +2005-03-10 10:10 chrisfen * make/Makefile.in, samples/water/tip3p_ice/tp3.md, src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, @@ -93,12 +762,12 @@ src/restraints/ThermoIntegrationForceManager.hpp: First commit of the new restraints code -2005-03-09 18:48 tim +2005-03-09 13:48 tim * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding IndexFinder -2005-03-09 18:46 tim +2005-03-09 13:46 tim * src/: applications/dump2Xyz/Dump2XYZ.ggo, applications/dump2Xyz/Dump2XYZCmd.c, @@ -106,7 +775,7 @@ selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: fix compilation issue -2005-03-09 17:58 tim +2005-03-09 12:58 tim * forceFields/DUFF2.frc, scripts/filepp, src/UseTheForce/EAM_FF.cpp, @@ -114,7 +783,7 @@ src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug in SectionParser (lineNo is not updated) -2005-03-09 17:30 tim +2005-03-09 12:30 tim * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -136,58 +805,58 @@ MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ; -2005-03-09 17:28 tim +2005-03-09 12:28 tim * forceFields/DUFF2.frc: change the format of DUFF2 -2005-03-09 15:44 gezelter +2005-03-09 10:44 gezelter * src/UseTheForce/DarkSide/: electrostatic.F90, electrostatic_interface.F90, electrostatic_interface.h: new electrostatic module -2005-03-09 14:26 gezelter +2005-03-09 09:26 gezelter * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole and fixed quadrupole stuff -2005-03-09 14:25 gezelter +2005-03-09 09:25 gezelter * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines for outdated charge and dipole interfaces -2005-03-08 21:08 gezelter +2005-03-08 16:08 gezelter * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun charge-dipole test cases -2005-03-08 21:07 gezelter +2005-03-08 16:07 gezelter * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a strange icc8 bug (we think). -2005-03-08 21:07 gezelter +2005-03-08 16:07 gezelter * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! -2005-03-08 21:07 gezelter +2005-03-08 16:07 gezelter * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic Unification Project -2005-03-08 21:07 gezelter +2005-03-08 16:07 gezelter * src/io/Globals.cpp: Dunno -2005-03-08 21:06 gezelter +2005-03-08 16:06 gezelter * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using OOPSE_itoa and checking a NULL left over from the LinkedList days -2005-03-08 21:06 gezelter +2005-03-08 16:06 gezelter * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, atype_interface.F90, atype_interface.h, charge.F90, @@ -195,52 +864,52 @@ dipole_interface.F90, dipole_interface.h: electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map -2005-03-08 21:05 gezelter +2005-03-08 16:05 gezelter * src/UseTheForce/doForces.F90: electrostatic unification project -2005-03-08 21:05 gezelter +2005-03-08 16:05 gezelter * samples/water/dimer/: two.md, water.md: making some cool test cases -2005-03-08 21:05 gezelter +2005-03-08 16:05 gezelter * forceFields/DUFF2.frc: Added a charge for Chlorine -2005-03-07 22:39 tim +2005-03-07 17:39 tim * src/: brains/SimInfo.cpp, io/DumpReader.cpp, math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: Fixing a bug in BitSet.cpp -2005-03-04 15:28 gezelter +2005-03-04 10:28 gezelter * src/config.h.in: Cleaning up config.h.in by adding comments -2005-03-04 15:28 gezelter +2005-03-04 10:28 gezelter * configure, ac-tools/configure.in, make/Makefile.in, src/brains/SimCreator.cpp: SPRNG eradication project -2005-03-03 14:40 tim +2005-03-03 09:40 tim * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the missing atom type problem) -2005-03-02 16:29 tim +2005-03-02 11:29 tim * src/math/RandNumGen.hpp: adding base class of Random Number generator -2005-03-02 16:28 tim +2005-03-02 11:28 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in Velocitizer is not initialized which causes a seg fault -2005-03-02 15:36 tim +2005-03-02 10:36 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/Makefile, @@ -250,23 +919,23 @@ MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator -2005-03-02 07:32 tim +2005-03-02 02:32 tim * test/math/testRandNumGen.cpp: Adding unit test for random number generator -2005-03-01 23:17 tim +2005-03-01 18:17 tim * src/brains/Thermo.hpp: fixed a file inclusion problem -2005-03-01 23:17 tim +2005-03-01 18:17 tim * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, RandNumGenTestCase.hpp: fixed compilation problem -2005-03-01 23:02 tim +2005-03-01 18:02 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/Makefile, @@ -274,18 +943,18 @@ math/ParallelRandNumGen.hpp, math/mt19937ar.c, math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand -2005-03-01 23:00 tim +2005-03-01 18:00 tim * test/math/: Makefile, ParallelandNumGenTestCase.cpp, ParallelandNumGenTestCase.hpp: Change the name of test case -2005-03-01 21:00 tim +2005-03-01 16:00 tim * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, OOPSERandNumGenTestCase.hpp: adding testcase for random number generator -2005-03-01 20:10 tim +2005-03-01 15:10 tim * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, @@ -296,42 +965,42 @@ utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 -2005-03-01 19:11 tim +2005-03-01 14:11 tim * src/: brains/SimCreator.cpp, brains/SimInfo.hpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding OOPSERandNumGen -2005-03-01 15:44 gezelter +2005-03-01 10:44 gezelter * make/Makefile.in: Fixed the damned build problem with the libraries not being removed in make clean and make distclean (at least we think it is fixed). -2005-03-01 15:26 gezelter +2005-03-01 10:26 gezelter * src/math/MersenneTwister.hpp: Making small modifications to allow for use on MPI machines -2005-03-01 14:45 tim +2005-03-01 09:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, integrators/Velocitizer.cpp, io/DumpReader.cpp, math/MersenneTwister.hpp: adding MersenneTwister random number generator -2005-03-01 03:55 tim +2005-02-28 22:55 tim * src/math/MersenneTwister.hpp: Adding a modified version of MersenneTwister.hpp -2005-02-28 17:24 tim +2005-02-28 12:24 tim * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, definition.jpg: selection expression -2005-02-25 21:22 tim +2005-02-25 16:22 tim * src/: UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.F90, @@ -339,12 +1008,12 @@ io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, types/AtomType.hpp: adding soft potential to LJ Module -2005-02-25 16:38 tim +2005-02-25 11:38 tim * doc/SelectionExpression.html: adding documentation for selection expression -2005-02-24 20:55 tim +2005-02-24 15:55 tim * src/: applications/simpleBuilder/simpleBuilder.cpp, integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, @@ -352,30 +1021,35 @@ adding basic_teebuf which can operate on multiple stream simutaneously. -2005-02-22 18:56 tim +2005-02-22 14:26 chrisfen + * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf + sample + +2005-02-22 13:56 tim + * src/: UseTheForce/DarkSide/reactionField.F90, primitives/RigidBody.cpp: reactionfield get fixed -2005-02-21 16:57 tim +2005-02-21 11:57 tim * src/: applications/staticProps/GofRAngle.cpp, visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix a bug in GofRAngle -2005-02-21 15:28 tim +2005-02-21 10:28 tim * src/primitives/Molecule.cpp: Fix for compilation on the Sun -2005-02-21 15:22 tim +2005-02-21 10:22 tim * src/utils/next_combination.hpp: fix for compilation on the Sun -2005-02-21 15:21 tim +2005-02-21 10:21 tim * src/utils/GenericData.hpp: fix problem in sun -2005-02-18 23:07 tim +2005-02-18 18:07 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -392,76 +1066,76 @@ visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, visitors/Makefile: adding LipidTransVisitor, GofXyz is working now -2005-02-18 15:58 gezelter +2005-02-18 10:58 gezelter * src/brains/Register.cpp: Corrected filename collision for EAM on Mac OS X -2005-02-18 15:58 gezelter +2005-02-18 10:58 gezelter * src/applications/oopse/oopse.cpp: Updated copyright information -2005-02-18 15:58 gezelter +2005-02-18 10:58 gezelter * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, Makefile: corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X) -2005-02-17 20:15 tim +2005-02-17 15:15 tim * src/applications/staticProps/GofXyz.cpp: more bug get fixed -2005-02-17 19:50 tim +2005-02-17 14:50 tim * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug in GofXyz -2005-02-17 19:09 tim +2005-02-17 14:09 tim * src/applications/staticProps/RadialDistrFunc.hpp: make processHistogram non-abstrct function -2005-02-17 18:41 tim +2005-02-17 13:41 tim * src/applications/staticProps/GofXyz.cpp: [no log message] -2005-02-17 18:30 tim +2005-02-17 13:30 tim * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: finish GofXyz -2005-02-17 16:21 tim +2005-02-17 11:21 tim * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial distribution function -2005-02-17 15:23 tim +2005-02-17 10:23 tim * src/utils/BitSet.hpp: forget the const correctness for BitSet -2005-02-17 15:18 tim +2005-02-17 10:18 tim * src/: brains/BlockSnapshotManager.cpp, selection/DistanceFinder.cpp: The change of interface of BitSet cause a bug in SelectionEvaluation -2005-02-16 21:13 tim +2005-02-16 16:13 tim * src/utils/residentMem.c: return residentMem in byte -2005-02-16 21:00 tim +2005-02-16 16:00 tim * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix a bug in writing out the value of cosang -2005-02-16 20:43 tim +2005-02-16 15:43 tim * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to estimate avaliable memory -2005-02-16 20:30 tim +2005-02-16 15:30 tim * src/: applications/staticProps/GofAngle2.cpp, applications/staticProps/GofAngle2.hpp, @@ -477,7 +1151,7 @@ applications/staticProps/StaticPropsCmd.h, brains/BlockSnapshotManager.cpp: change the default bin number -2005-02-16 19:36 tim +2005-02-16 14:36 tim * src/: applications/dynamicProps/DipoleCorrFunc.cpp, applications/dynamicProps/RCorrFunc.cpp, @@ -494,12 +1168,12 @@ utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output files;fix the problem of counting in staticProps -2005-02-15 19:39 tim +2005-02-15 14:39 tim * src/brains/BlockSnapshotManager.cpp: fix a bug in BlockSnapshotManager -2005-02-15 19:36 tim +2005-02-15 14:36 tim * src/: applications/dynamicProps/TimeCorrFunc.cpp, applications/staticProps/RadialDistrFunc.cpp, @@ -507,24 +1181,24 @@ selection/SelectionEvaluator.cpp: BlockSnapshotManager is using reference counting now -2005-02-15 17:49 tim +2005-02-15 12:49 tim * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: replace std::make_pair by VariablesType::value_type to make Sun Compiler happy -2005-02-15 17:35 tim +2005-02-15 12:35 tim * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to TokenMap, using TokenMapType::value_type instead of std::make_pair to make Sun compiler happy -2005-02-15 17:24 tim +2005-02-15 12:24 tim * src/applications/staticProps/: GofRAngle.cpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps -2005-02-15 17:11 tim +2005-02-15 12:11 tim * src/: applications/staticProps/GofR.cpp, applications/staticProps/RadialDistrFunc.cpp, @@ -533,35 +1207,35 @@ #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other -2005-02-15 15:24 gezelter +2005-02-15 10:24 gezelter * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy xlc++ -2005-02-15 15:17 gezelter +2005-02-15 10:17 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/residentMem.c: [no log message] -2005-02-15 06:17 gezelter +2005-02-15 01:17 gezelter * src/utils/residentMem.c: bug fix for null termination -2005-02-15 06:11 gezelter +2005-02-15 01:11 gezelter * configure, ac-tools/configure.in, src/utils/residentMem.c: bugfixing residentMem -2005-02-15 05:59 gezelter +2005-02-15 00:59 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/residentMem.c: bugfixes for residentMem on LINUX -2005-02-15 05:08 gezelter +2005-02-15 00:08 gezelter * src/utils/Makefile.in: added residentMem -2005-02-15 05:05 gezelter +2005-02-15 00:05 gezelter * configure, ac-tools/configure.in, make/Makefile.in, src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, @@ -569,38 +1243,38 @@ other processes autoconf fixes ps syntax checking config.h file cleaning -2005-02-14 23:26 gezelter +2005-02-14 18:26 gezelter * configure, ac-tools/configure.in, make/Makefile.in: ps niceness -2005-02-14 23:16 gezelter +2005-02-14 18:16 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps strangeness -2005-02-14 19:42 tim +2005-02-14 14:42 tim * src/brains/BlockSnapshotManager.cpp: fix a bug in BlockSnapshotManager.hpp -2005-02-14 18:51 tim +2005-02-14 13:51 tim * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c: default length for staticProps is 1/2 smallest length of first frame -2005-02-14 18:12 tim +2005-02-14 13:12 tim * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in VelocityVerletIntegrator : last frame is written twice -2005-02-14 17:57 tim +2005-02-14 12:57 tim * src/: applications/dynamicProps/TimeCorrFunc.cpp, brains/SimInfo.cpp, primitives/RigidBody.cpp, primitives/StuntDouble.hpp: begin bug fix -2005-02-14 17:35 tim +2005-02-14 12:35 tim * src/applications/dynamicProps/: CorrelationFunction.cpp, CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, @@ -610,37 +1284,37 @@ RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, VCorrFunc.hpp: refactory CorrelationFunction -2005-02-14 15:18 gezelter +2005-02-14 10:18 gezelter * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix and start of switch for type of correlation function -2005-02-13 21:18 tim +2005-02-13 16:18 tim * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in calculating bytes per stuntdouble -2005-02-13 21:03 tim +2005-02-13 16:03 tim * src/applications/dynamicProps/CorrelationFunction.cpp: more fix -2005-02-13 20:57 tim +2005-02-13 15:57 tim * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a bug in CorrelationFunction -2005-02-13 20:36 tim +2005-02-13 15:36 tim * src/: applications/staticProps/GofR.cpp, applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a bug in SimInfo::getCutoff() -2005-02-13 20:08 tim +2005-02-13 15:08 tim * make/Makefile.in: adding staticProps and dynamicProps into Makefile.in -2005-02-13 20:05 tim +2005-02-13 15:05 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, applications/dynamicProps/CorrelationFunction.hpp, @@ -651,11 +1325,11 @@ brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length defaults to the cutoff radius -2005-02-13 19:14 tim +2005-02-13 14:14 tim * src/utils/Algorithm.hpp: adding Algorithm.hpp -2005-02-13 19:10 tim +2005-02-13 14:10 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dynamicProps/CorrelationFunction.cpp, @@ -669,14 +1343,14 @@ utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, visitors/OtherVisitor.cpp: dynamicProps get built -2005-02-13 15:56 tim +2005-02-13 10:56 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in progress -2005-02-13 08:04 tim +2005-02-13 03:04 tim * src/: applications/dynamicProps/CorrelationFunction.hpp, brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, @@ -684,22 +1358,22 @@ brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more work in dynamicProps -2005-02-13 07:25 tim +2005-02-13 02:25 tim * src/applications/dynamicProps/DynamicProps.cpp: adding dynamicProps -2005-02-13 07:14 tim +2005-02-13 02:14 tim * src/applications/dynamicProps/: DynamicPropsCmd.c, DynamicPropsCmd.h: adding command line option to DynamicProps -2005-02-13 07:13 tim +2005-02-13 02:13 tim * src/applications/dynamicProps/: DynamicProps.ggo, Makefile: adding command line option for DynamicProps -2005-02-13 06:57 tim +2005-02-13 01:57 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, applications/dynamicProps/CorrelationFunction.hpp, @@ -716,35 +1390,35 @@ primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding dynamicProps -2005-02-12 20:09 tim +2005-02-12 15:09 tim * src/selection/SelectionManager.cpp: adding SelectionManager.cpp -2005-02-11 22:41 tim +2005-02-11 17:41 tim * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one more constructor to Snapshot to create customized DataStorage -2005-02-11 22:39 tim +2005-02-11 17:39 tim * src/selection/: DistanceFinder.hpp, Makefile, SelectionManager.hpp: adding beginSelected, nextSelected method to SelectionManager -2005-02-11 22:36 tim +2005-02-11 17:36 tim * src/config.h.in, configure: adding support for physmem -2005-02-11 22:35 tim +2005-02-11 17:35 tim * ac-tools/configure.in: adding supprot for physmem -2005-02-11 22:35 tim +2005-02-11 17:35 tim * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding physmem -2005-02-10 22:37 tim +2005-02-10 17:37 tim * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, @@ -752,7 +1426,7 @@ StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: more work in StaticProps -2005-02-10 18:14 tim +2005-02-10 13:14 tim * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, @@ -761,115 +1435,115 @@ StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: change the filenames -2005-02-10 14:15 tim +2005-02-10 09:15 tim * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofRAngle -2005-02-09 18:21 tim +2005-02-09 13:21 tim * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some useless files -2005-02-09 18:12 tim +2005-02-09 13:12 tim * src/applications/staticProps/: GofR.cpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress -2005-02-09 17:08 tim +2005-02-09 12:08 tim * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR -2005-02-07 22:39 tim +2005-02-07 17:39 tim * src/primitives/Molecule.hpp: add getRigidBodyAt function into Molecule class -2005-02-07 22:38 tim +2005-02-07 17:38 tim * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info -2005-02-07 22:36 tim +2005-02-07 17:36 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp: support select internal index selection, for example, select DMPC.3 -2005-02-07 21:11 tim +2005-02-07 16:11 tim * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update help info for Dump2XYZ -2005-02-07 20:39 chrisfen +2005-02-07 15:39 chrisfen * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: selection librarys added -2005-02-07 20:31 tim +2005-02-07 15:31 tim * src/selection/Makefile, make/Makefile.in: adding Makefile -2005-02-07 20:20 chrisfen +2005-02-07 15:20 chrisfen * src/utils/wildcards.hpp: issue commented out in wildcards -2005-02-07 20:06 tim +2005-02-07 15:06 tim * src/selection/SelectionEvaluator.cpp: forget to reset the pc which cause reevaluate return NULL -2005-02-07 19:14 tim +2005-02-07 14:14 tim * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, SimSnapshotManager.hpp: fix a bug in determing the global index for rigidbodies -2005-02-07 19:13 tim +2005-02-07 14:13 tim * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change in Bitset -2005-02-07 19:13 tim +2005-02-07 14:13 tim * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, TokenMap.cpp: selection library is working -2005-02-04 22:46 tim +2005-02-04 17:46 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor -2005-02-04 22:45 tim +2005-02-04 17:45 tim * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor and XYZVisitor now use selection library -2005-02-04 22:44 tim +2005-02-04 17:44 tim * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: adding SelectionManager into SimInfo -2005-02-04 22:43 tim +2005-02-04 17:43 tim * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of selection library -2005-02-04 22:42 tim +2005-02-04 17:42 tim * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change in BitSet -2005-02-04 22:41 tim +2005-02-04 17:41 tim * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing implementation -2005-02-04 22:39 tim +2005-02-04 17:39 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, @@ -877,27 +1551,27 @@ SelectionManager.hpp, Token.hpp: half of the selection utility is working need to debug within keyword and atomproperty keyword -2005-02-04 05:42 tim +2005-02-04 00:42 tim * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library get built -2005-02-04 05:42 tim +2005-02-04 00:42 tim * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet -2005-02-04 05:26 tim +2005-02-04 00:26 tim * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: remove some useless files -2005-02-04 04:57 tim +2005-02-03 23:57 tim * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: adding wildcard class; NameFinder is finished -2005-02-03 23:14 tim +2005-02-03 18:14 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, @@ -905,59 +1579,59 @@ SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in selection library -2005-02-03 14:04 tim +2005-02-03 09:04 tim * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: selection in progress -2005-02-02 23:13 tim +2005-02-02 18:13 tim * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in progress, except SelectionEvaluator, other files are compiled -2005-02-02 23:12 tim +2005-02-02 18:12 tim * src/utils/: Makefile.in, any.hpp: adding boost::any -2005-02-02 12:51 tim +2005-02-02 07:51 tim * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp -2005-02-01 22:49 tim +2005-02-01 17:49 tim * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, selection/Token.hpp: Selection in progress -2005-02-01 06:55 tim +2005-02-01 01:55 tim * src/: selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, selection/Token.hpp, utils/BitSet.cpp, utils/BitSet.hpp: adding selection library -2005-01-26 15:26 tim +2005-01-26 10:26 tim * src/integrators/: Integrator.cpp, Integrator.hpp, VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget to add eorWriter -2005-01-26 15:15 tim +2005-01-26 10:15 tim * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe -2005-01-25 21:59 tim +2005-01-25 16:59 tim * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp -2005-01-25 17:45 tim +2005-01-25 12:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/MoleculeCreator.cpp, brains/SimCreator.cpp, @@ -977,28 +1651,28 @@ inertial tensor from the directional atoms before calculate rigidbody's inertial tensor -2005-01-17 22:17 tim +2005-01-17 17:17 tim * forceFields/DUFF2.frc: forget to set dipole for lipid head group -2005-01-17 16:58 tim +2005-01-17 11:58 tim * src/integrators/NVT.cpp: fix a bug in loading initial extended system parameters -2005-01-17 16:05 tim +2005-01-17 11:05 tim * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT -2005-01-14 22:02 tim +2005-01-14 17:02 tim * src/UseTheForce/WATER.cpp: remove WATER.cpp -2005-01-14 21:37 tim +2005-01-14 16:37 tim * forceFields/Makefile: sync Makefile -2005-01-14 21:13 gezelter +2005-01-14 16:13 gezelter * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, @@ -1012,18 +1686,18 @@ src/visitors/Makefile: moved Package variable into subdirectory makefiles to speed up the building process -2005-01-14 20:48 gezelter +2005-01-14 15:48 gezelter * src/applications/oopse/oopse.cpp: Fixed publication details in banner -2005-01-14 20:48 gezelter +2005-01-14 15:48 gezelter * src/UseTheForce/DarkSide/: simParallel_interface.F90, simParallel_interface.h: added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran -2005-01-14 20:31 gezelter +2005-01-14 15:31 gezelter * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, @@ -1039,53 +1713,53 @@ DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating modules and C/Fortran interface subroutines -2005-01-14 20:15 gezelter +2005-01-14 15:15 gezelter * configure, ac-tools/aclocal.m4: more fixes for gnugetopt -2005-01-14 20:09 gezelter +2005-01-14 15:09 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt -2005-01-14 16:49 tim +2005-01-14 11:49 tim * src/: io/EAMAtomTypesSectionParser.cpp, utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, utils/StringUtils.hpp: using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2) -2005-01-14 02:40 tim +2005-01-13 21:40 tim * src/brains/SimSetup.cpp: no message -2005-01-14 01:56 tim +2005-01-13 20:56 tim * src/primitives/Molecule.hpp: fix a bug in global index -2005-01-14 01:04 tim +2005-01-13 20:04 tim * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include Integrator.hpp in Minimizer -2005-01-13 22:14 gezelter +2005-01-13 17:14 gezelter * src/utils/Makefile: compile getopt and getopt1 if we need to -2005-01-13 21:56 gezelter +2005-01-13 16:56 gezelter * make/Makefile.in: template flags -2005-01-13 21:48 gezelter +2005-01-13 16:48 gezelter * src/applications/oopse/Makefile: formatting -2005-01-13 21:48 gezelter +2005-01-13 16:48 gezelter * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir target -2005-01-13 19:40 tim +2005-01-13 14:40 tim * src/: UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, @@ -1093,29 +1767,29 @@ primitives/RigidBody.cpp, types/AtomTypeProperties.h, types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform -2005-01-13 18:26 tim +2005-01-13 13:26 tim * make/Makefile.in: change the order of linking (object file comes first and then follow by user built library) -2005-01-12 23:24 tim +2005-01-12 18:24 tim * src/io/DumpWriter.cpp: remove useless debug info -2005-01-12 23:21 tim +2005-01-12 18:21 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix -2005-01-12 23:17 tim +2005-01-12 18:17 tim * make/: Makefile.in, Makefile.in: missing tab -2005-01-12 23:15 tim +2005-01-12 18:15 tim * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor get fixed -2005-01-12 22:40 gezelter +2005-01-12 17:40 gezelter * make/Makefile.in, src/UseTheForce/DUFF.cpp, src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, @@ -1325,18 +1999,18 @@ src/visitors/ZconsVisitor.hpp: merging new_design branch into OOPSE-2.0 -2005-01-12 18:13 tim +2005-01-12 13:13 tim * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, utils/TypeContainer.hpp: forget to include -2005-01-12 17:25 tim +2005-01-12 12:25 tim * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force fields -2005-01-12 17:14 tim +2005-01-12 12:14 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, @@ -1498,12 +2172,12 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: change license -2005-01-12 17:14 tim +2005-01-12 12:14 tim * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on branch new_design. -2005-01-11 21:03 tim +2005-01-11 16:03 tim * src/: constraints/ZconstraintForceManager.cpp, constraints/ZconstraintForceManager.hpp, @@ -1511,73 +2185,73 @@ minimizers/MinimizerParameterSet.hpp: change const static double data member to const double -2005-01-11 20:50 tim +2005-01-11 15:50 tim * src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: -2005-01-11 20:39 tim +2005-01-11 15:39 tim * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: change data type from logical to integer in AtomTypeProperties.h -2005-01-11 16:36 tim +2005-01-11 11:36 tim * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding new format of EAM force field -2005-01-11 16:24 tim +2005-01-11 11:24 tim * src/UseTheForce/DUFF.cpp: change default name of DUFF force field to DUFF2.frc -2005-01-11 16:23 tim +2005-01-11 11:23 tim * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to DUFF2.frc -2005-01-11 16:09 tim +2005-01-11 11:09 tim * make/Makefile.in: adding constraints and minimizers into Makefile.in -2005-01-11 16:03 tim +2005-01-11 11:03 tim * src/io/: ChargeAtomTypesSectionParser.cpp, ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless files -2005-01-11 15:59 tim +2005-01-11 10:59 tim * src/io/ZConsWriter.cpp: [no log message] -2005-01-11 15:53 tim +2005-01-11 10:53 tim * src/UseTheForce/EAM.cpp: minor fix -2005-01-11 15:52 tim +2005-01-11 10:52 tim * src/constraints/Rattle.hpp: file Rattle.hpp was initially added on branch new_design. -2005-01-11 15:52 tim +2005-01-11 10:52 tim * src/constraints/Rattle.cpp: file Rattle.cpp was initially added on branch new_design. -2005-01-11 15:52 tim +2005-01-11 10:52 tim * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm -2005-01-11 15:47 tim +2005-01-11 10:47 tim * make/Makefile.in: forget a '$' sign -2005-01-11 15:46 tim +2005-01-11 10:46 tim * make/Makefile.in: missing tab in rules -2005-01-10 22:04 tim +2005-01-10 17:04 tim * src/: UseTheForce/ForceFieldCreator.cpp, UseTheForce/ForceFieldCreator.hpp, @@ -1596,17 +2270,17 @@ minimizers/MinimizerFactory.hpp: create a register module to register force fields, integrators and minimizers -2005-01-10 22:04 tim +2005-01-10 17:04 tim * src/brains/Register.cpp: file Register.cpp was initially added on branch new_design. -2005-01-10 22:04 tim +2005-01-10 17:04 tim * src/brains/Register.hpp: file Register.hpp was initially added on branch new_design. -2005-01-10 20:52 tim +2005-01-10 15:52 tim * src/: UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, brains/ForceManager.hpp, @@ -1618,7 +2292,7 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint method is working now -2005-01-10 18:05 tim +2005-01-10 13:05 tim * src/: constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, @@ -1628,24 +2302,24 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in zconstraint -2005-01-10 18:05 tim +2005-01-10 13:05 tim * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was initially added on branch new_design. -2005-01-07 21:50 tim +2005-01-07 16:50 tim * src/constraints/ZconstraintForceManager.cpp: file ZconstraintForceManager.cpp was initially added on branch new_design. -2005-01-07 21:50 tim +2005-01-07 16:50 tim * src/constraints/ZconstraintForceManager.hpp: file ZconstraintForceManager.hpp was initially added on branch new_design. -2005-01-07 21:50 tim +2005-01-07 16:50 tim * src/: applications/simpleBuilder/BaseLattice.hpp, applications/simpleBuilder/Lattice.hpp, @@ -1659,12 +2333,12 @@ integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, utils/NumericConstant.hpp: ZConstraintForceManager in progress -2005-01-07 21:50 tim +2005-01-07 16:50 tim * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was initially added on branch new_design. -2005-01-06 22:31 tim +2005-01-06 17:31 tim * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -1673,12 +2347,12 @@ io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: constraint is almost working -2005-01-06 00:36 tim +2005-01-05 19:36 tim * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is working -2005-01-06 00:16 tim +2005-01-05 19:16 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, @@ -1693,17 +2367,17 @@ minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder in progress -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp was initially added on branch new_design. -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially added on branch new_design. -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, @@ -1711,27 +2385,27 @@ OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, SDMinimizer.hpp: minimizer in progress -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp was initially added on branch new_design. -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp was initially added on branch new_design. -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp was initially added on branch new_design. -2005-01-05 17:35 tim +2005-01-05 12:35 tim * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially added on branch new_design. -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, @@ -1742,74 +2416,74 @@ primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in progress -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was initially added on branch new_design. -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/minimizers/MinimizerParameterSet.cpp: file MinimizerParameterSet.cpp was initially added on branch new_design. -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was initially added on branch new_design. -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp was initially added on branch new_design. -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress -2005-01-04 22:18 tim +2005-01-04 17:18 tim * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on branch new_design. -2004-12-20 20:50 chuckv +2004-12-20 15:50 chuckv * make/Makefile.in: Fixed Makefile test bug under OSX and possibly other BSD's, replaced test -f *.mod with ls function since BSD test apparently doesn't support wildcards. -2004-12-20 20:36 tim +2004-12-20 15:36 tim * make/Makefile.in: fix a test command incompatiable problem -2004-12-20 19:49 tim +2004-12-20 14:49 tim * src/integrators/NPTi.cpp: NPT is working now -2004-12-16 19:20 tim +2004-12-16 14:20 tim * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the invalid stamp id -2004-12-16 19:00 tim +2004-12-16 14:00 tim * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: adding new EAM force field files -2004-12-16 18:55 tim +2004-12-16 13:55 tim * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays in EAM parameter file is incorrect -2004-12-16 17:27 tim +2004-12-16 12:27 tim * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM -2004-12-15 22:34 tim +2004-12-15 17:34 tim * src/: applications/simpleBuilder/BaseLattice.cpp, applications/simpleBuilder/BaseLattice.hpp, @@ -1822,33 +2496,33 @@ applications/simpleBuilder/simpleBuilder.cpp, io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream -2004-12-15 21:07 tim +2004-12-15 16:07 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: add EAM Force Field -2004-12-15 19:40 tim +2004-12-15 14:40 tim * src/applications/oopse/oopse.cpp: add more force fields -2004-12-15 16:44 tim +2004-12-15 11:44 tim * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget to call All_reduce in MPI version) -2004-12-15 16:13 tim +2004-12-15 11:13 tim * src/: brains/SimCreator.cpp, brains/SimInfo.cpp, io/DumpReader.cpp: MPI in NVE is working -2004-12-14 21:57 tim +2004-12-14 16:57 tim * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. Master nodes does not brocast the total number of frames -2004-12-14 19:08 tim +2004-12-14 14:08 tim * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, @@ -1857,7 +2531,7 @@ minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, minimizers/SDMinimizer.cpp: more fix in MPI version -2004-12-13 22:30 tim +2004-12-13 17:30 tim * src/: UseTheForce/DarkSide/simParallel.F90, applications/oopse/oopse.cpp, brains/SimCreator.cpp, @@ -1875,62 +2549,62 @@ utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version is built -2004-12-10 18:41 tim +2004-12-10 13:41 tim * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp -2004-12-10 16:14 tim +2004-12-10 11:14 tim * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: forget to zero out the torque. Sticky and Dipole is working now -2004-12-09 23:15 tim +2004-12-09 18:15 tim * src/: UseTheForce/DarkSide/dipole.F90, UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: fix an index problem in eFrame matrix -2004-12-09 23:09 tim +2004-12-09 18:09 tim * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when initializing the new Charge AtomType -2004-12-09 21:15 tim +2004-12-09 16:15 tim * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, types/DirectionalAtomType.cpp: sticky module get compiled -2004-12-09 20:43 gezelter +2004-12-09 15:43 gezelter * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for GB -2004-12-09 20:42 gezelter +2004-12-09 15:42 gezelter * src/UseTheForce/doForces.F90: u_l -> eFrame -2004-12-09 20:27 gezelter +2004-12-09 15:27 gezelter * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky module now has the option for multiple sticky types -2004-12-09 20:27 gezelter +2004-12-09 15:27 gezelter * src/UseTheForce/doForces.F90: sticky -2004-12-09 16:22 tim +2004-12-09 11:22 tim * src/integrators/: NPT.cpp, NVT.cpp: fix an interface inconsistency in lab2Bidy -2004-12-09 15:45 tim +2004-12-09 10:45 tim * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug in calculating torque in rigid body -2004-12-08 20:37 tim +2004-12-08 15:37 tim * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, brains/SnapShot.cpp, brains/Snapshot.hpp, @@ -1938,45 +2612,45 @@ io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: fix a parsing bug in ElectroStaticAtomTypesSectionParser -2004-12-08 17:03 tim +2004-12-08 12:03 tim * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane in NVT is working -2004-12-07 23:08 tim +2004-12-07 18:08 tim * src/: UseTheForce/Makefile, brains/SimInfo.hpp, integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, io/DumpWriter.cpp: NPT in progress -2004-12-07 14:43 tim +2004-12-07 09:43 tim * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log message] -2004-12-07 05:12 tim +2004-12-07 00:12 tim * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in UseInitXSstate -2004-12-07 05:00 tim +2004-12-07 00:00 tim * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message -2004-12-07 04:47 tim +2004-12-06 23:47 tim * src/types/DirectionalAtomType.cpp: [no log message] -2004-12-07 02:18 tim +2004-12-06 21:18 tim * forceFields/newDUFF.frc: merge WATER force field into DUFF -2004-12-07 01:33 tim +2004-12-06 20:33 tim * forceFields/newDUFF.frc: change the force constant of bonds -2004-12-06 23:29 tim +2004-12-06 18:29 tim * src/: UseTheForce/DarkSide/charge.F90, UseTheForce/DarkSide/charge_interface.h, @@ -1984,18 +2658,18 @@ UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: fix atom type ident in Charge and Dipole Module -2004-12-06 22:56 tim +2004-12-06 17:56 tim * src/primitives/Torsion.cpp: butane is working now -2004-12-06 20:15 tim +2004-12-06 15:15 tim * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, primitives/Bond.hpp, primitives/Torsion.cpp: short range interaction for butane is correct.Still something wrong with long range one -2004-12-06 04:49 tim +2004-12-05 23:49 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -2003,44 +2677,44 @@ primitives/Atom.hpp, utils/NumericConstant.hpp, utils/TypeContainer.hpp: fix a bug in Exclude List -2004-12-05 22:21 tim +2004-12-05 17:21 tim * forceFields/newDUFF.frc: minor fix in DUFF -2004-12-05 22:02 tim +2004-12-05 17:02 tim * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: fix a bug in filling MolMembership -2004-12-05 17:12 tim +2004-12-05 12:12 tim * forceFields/newDUFF.frc: minor fix in force field file -2004-12-05 17:09 tim +2004-12-05 12:09 tim * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp -2004-12-04 20:09 tim +2004-12-04 15:09 tim * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, math/Vector3.hpp: NVE is working now, get the same result as OOPSE-1.0 -2004-12-04 19:29 tim +2004-12-04 14:29 tim * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy -2004-12-04 19:24 gezelter +2004-12-04 14:24 gezelter * src/primitives/: Bend.cpp, Torsion.cpp: What? -2004-12-04 19:24 gezelter +2004-12-04 14:24 gezelter * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion -2004-12-04 05:24 tim +2004-12-04 00:24 tim * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, integrators/Integrator.hpp, @@ -2051,7 +2725,7 @@ dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step 4 EAM Step 5 Shape Step 6 Constraint & Restraint -2004-12-04 00:01 tim +2004-12-03 19:01 tim * src/: UseTheForce/DarkSide/LJ.F90, applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, @@ -2060,12 +2734,12 @@ io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, energy of NVE is not conserved -2004-12-03 22:36 tim +2004-12-03 17:36 tim * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running -2004-12-03 21:30 tim +2004-12-03 16:30 tim * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, @@ -2073,12 +2747,12 @@ primitives/Molecule.hpp, primitives/StuntDouble.hpp, primitives/Torsion.hpp: more missing function get implemented -2004-12-03 20:30 tim +2004-12-03 15:30 tim * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo -2004-12-03 17:59 tim +2004-12-03 12:59 tim * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -2087,12 +2761,12 @@ io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, utils/TypeContainer.hpp: begin to fix bugs -2004-12-03 00:26 tim +2004-12-02 19:26 tim * src/utils/Trim.cpp: file Trim.cpp was initially added on branch new_design. -2004-12-03 00:26 tim +2004-12-02 19:26 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceFieldCreator.cpp, @@ -2103,15 +2777,15 @@ utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a bug in countTokens in StringTokenizer -2004-12-03 00:06 tim +2004-12-02 19:06 tim * forceFields/newDUFF.frc: minor fix -2004-12-02 23:15 tim +2004-12-02 18:15 tim * forceFields/newDUFF.frc: new ForceField format -2004-12-02 22:15 tim +2004-12-02 17:15 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceFieldCreator.cpp, @@ -2130,32 +2804,32 @@ types/Makefile: refine factory pattern to make it initialized correctly -2004-12-02 22:15 tim +2004-12-02 17:15 tim * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp was initially added on branch new_design. -2004-12-02 22:15 tim +2004-12-02 17:15 tim * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp was initially added on branch new_design. -2004-12-02 22:15 tim +2004-12-02 17:15 tim * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp was initially added on branch new_design. -2004-12-02 22:15 tim +2004-12-02 17:15 tim * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp was initially added on branch new_design. -2004-12-02 16:53 tim +2004-12-02 11:53 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, types/DirectionalAtomType.cpp, types/Makefile: oopse get built -2004-12-02 16:04 tim +2004-12-02 11:04 tim * src/: applications/simpleBuilder/LatticeCreator.cpp, applications/simpleBuilder/LatticeCreator.hpp, @@ -2179,7 +2853,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still have two linking problem -2004-12-02 05:17 tim +2004-12-02 00:17 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/simpleBuilder/Lattice.cpp, @@ -2191,7 +2865,7 @@ visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, visitors/ZconsVisitor.cpp: change endl to std::endl -2004-12-02 05:14 tim +2004-12-02 00:14 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -2207,12 +2881,12 @@ visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp: minor fix -2004-12-02 05:09 tim +2004-12-02 00:09 tim * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: remove StreamTokenizer -2004-12-02 05:06 tim +2004-12-02 00:06 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, @@ -2221,7 +2895,7 @@ restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using namespace std in .cpp file -2004-12-02 05:04 tim +2004-12-02 00:04 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -2245,7 +2919,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding qulified name prefix std -2004-12-02 04:55 tim +2004-12-01 23:55 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -2261,7 +2935,7 @@ visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp: replace string by std::string -2004-12-02 03:12 tim +2004-12-01 22:12 tim * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, src/applications/simpleBuilder/BaseLattice.hpp, @@ -2282,14 +2956,14 @@ test/brains/RigidBody.cpp: replace misuse of using namespace std in header files -2004-12-02 02:23 tim +2004-12-01 21:23 tim * src/: primitives/Atom.hpp, primitives/RigidBody.hpp, primitives/StuntDouble.hpp, utils/TypeContainer.hpp, utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: begin to fix linking problem -2004-12-02 02:08 tim +2004-12-01 21:08 tim * src/: applications/oopse/oopse.cpp, brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, @@ -2301,22 +2975,22 @@ utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, still has some linking problem -2004-12-02 00:26 tim +2004-12-01 19:26 tim * src/: integrators/NVT.cpp, integrators/NVT.hpp, utils/OOPSEConstant.hpp: NVT get built -2004-12-02 00:09 tim +2004-12-01 19:09 tim * src/integrators/DLM.cpp: file DLM.cpp was initially added on branch new_design. -2004-12-02 00:09 tim +2004-12-01 19:09 tim * src/integrators/DLM.hpp: file DLM.hpp was initially added on branch new_design. -2004-12-02 00:09 tim +2004-12-01 19:09 tim * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, @@ -2328,12 +3002,12 @@ integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE get built -2004-12-02 00:09 tim +2004-12-01 19:09 tim * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp was initially added on branch new_design. -2004-12-01 22:45 tim +2004-12-01 17:45 tim * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, integrators/IntegratorFactory.cpp, @@ -2344,12 +3018,12 @@ io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, io/StatWriter.hpp: rename DumpWrite to DumpWriter -2004-12-01 22:45 tim +2004-12-01 17:45 tim * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on branch new_design. -2004-12-01 20:05 tim +2004-12-01 15:05 tim * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, @@ -2358,11 +3032,11 @@ visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: visitors get built -2004-12-01 19:32 chrisfen +2004-12-01 14:32 chrisfen * samples/water/tip3p_ice/tp3.md: fixed a sample -2004-12-01 19:10 tim +2004-12-01 14:10 tim * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, @@ -2371,7 +3045,7 @@ src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: spell check -2004-12-01 18:42 tim +2004-12-01 13:42 tim * src/: UseTheForce/DarkSide/atype.F90, io/ElectrostaticAtomTypesSectionParser.cpp, @@ -2380,7 +3054,7 @@ primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator and constraint, other directories get built -2004-12-01 17:38 tim +2004-12-01 12:38 tim * src/: brains/DataStorage.cpp, brains/DataStorage.hpp, brains/ForceManager.cpp, brains/MoleculeCreator.cpp, @@ -2393,28 +3067,28 @@ types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: refactory AtomType -2004-12-01 03:11 tim +2004-11-30 22:11 tim * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change -2004-12-01 02:30 tim +2004-11-30 21:30 tim * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change NumericConstant -2004-12-01 02:24 tim +2004-11-30 21:24 tim * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, primitives/RigidBody.cpp: minor fix -2004-11-30 23:14 tim +2004-11-30 18:14 tim * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io get built, next is integrator -2004-11-30 22:43 tim +2004-11-30 17:43 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.hpp, brains/SimCreator.cpp, @@ -2422,14 +3096,14 @@ io/BASS_interface.cpp, primitives/StuntDouble.hpp, utils/StringUtils.hpp: brains get built -2004-11-30 20:50 tim +2004-11-30 15:50 tim * src/: brains/ForceManager.cpp, brains/Makefile, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, primitives/RigidBody.cpp, primitives/RigidBody.hpp, utils/StringUtils.hpp: brains get built, io is next -2004-11-30 19:58 tim +2004-11-30 14:58 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, brains/ForceManager.hpp, @@ -2440,28 +3114,28 @@ brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo -2004-11-30 19:58 tim +2004-11-30 14:58 tim * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially added on branch new_design. -2004-11-30 17:54 tim +2004-11-30 12:54 tim * src/: primitives/Bend.hpp, primitives/Bond.hpp, primitives/StuntDouble.hpp, primitives/Torsion.hpp, utils/LocalIndexManager.hpp: more get fixed -2004-11-30 05:03 tim +2004-11-30 00:03 tim * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was initially added on branch new_design. -2004-11-30 05:03 tim +2004-11-30 00:03 tim * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename LocalndexManager.hpp to LocalIndexManager.hpp -2004-11-30 04:43 tim +2004-11-29 23:43 tim * src/: io/BendTypesSectionParser.cpp, io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, @@ -2470,7 +3144,7 @@ types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp: Section Parsers get compiled -2004-11-30 04:14 tim +2004-11-29 23:14 tim * src/: io/BendTypesSectionParser.cpp, io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, @@ -2478,7 +3152,7 @@ types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor fixed -2004-11-30 03:49 tim +2004-11-29 22:49 tim * src/: io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, @@ -2486,70 +3160,70 @@ types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp: minor fixed -2004-11-30 03:32 tim +2004-11-29 22:32 tim * src/: io/TorsionTypesSectionParser.cpp, types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp: #inlcude statement can not be embedded -2004-11-29 21:42 tim +2004-11-29 16:42 tim * test/math/: Makefile, PolynomialTestCase.cpp, PolynomialTestCase.hpp: add PolynomialTestCase -2004-11-29 21:42 tim +2004-11-29 16:42 tim * src/math/Polynomial.hpp: Polynomial passes unit test -2004-11-29 20:03 tim +2004-11-29 15:03 tim * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename QuarticTorsion.hpp to QuarticTorsionType.hpp -2004-11-29 20:03 tim +2004-11-29 15:03 tim * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was initially added on branch new_design. -2004-11-29 19:56 tim +2004-11-29 14:56 tim * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was initially added on branch new_design. -2004-11-29 19:56 tim +2004-11-29 14:56 tim * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add CubicTorsionType and QuarticTorsionType -2004-11-29 19:56 tim +2004-11-29 14:56 tim * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was initially added on branch new_design. -2004-11-29 18:00 tim +2004-11-29 13:00 tim * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, types/CubicBendType.hpp, types/CubicBondType.hpp, types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get fixed -2004-11-29 17:59 tim +2004-11-29 12:59 tim * src/utils/Trim.hpp: file Trim.hpp was initially added on branch new_design. -2004-11-29 17:59 tim +2004-11-29 12:59 tim * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim Algorithm for std::string -2004-11-29 15:52 tim +2004-11-29 10:52 tim * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove some useless files -2004-11-29 15:50 tim +2004-11-29 10:50 tim * src/io/: BondTypesSectionParser.cpp, ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, @@ -2560,7 +3234,7 @@ SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, StickyAtomTypesSectionParser.hpp: more files get fixed -2004-11-29 15:27 tim +2004-11-29 10:27 tim * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, DirectionalAtomTypesSectionParser.cpp, @@ -2569,28 +3243,28 @@ SectionParserManager.cpp, SectionParserManager.hpp: part of io get built -2004-11-29 14:49 tim +2004-11-29 09:49 tim * src/types/UreyBradleyBendType.hpp: types get built -2004-11-29 14:40 tim +2004-11-29 09:40 tim * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: types get built -2004-11-26 02:13 tim +2004-11-25 21:13 tim * src/: UseTheForce/ForceField.hpp, io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some files -2004-11-25 20:18 tim +2004-11-25 15:18 tim * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was initially added on branch new_design. -2004-11-25 20:18 tim +2004-11-25 15:18 tim * src/: io/AtomTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, @@ -2599,12 +3273,12 @@ types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some files -2004-11-25 20:18 tim +2004-11-25 15:18 tim * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was initially added on branch new_design. -2004-11-24 22:12 tim +2004-11-24 17:12 tim * src/: io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, @@ -2627,13 +3301,13 @@ io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built -2004-11-24 21:33 tim +2004-11-24 16:33 tim * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, LJFF.cpp, Makefile: UseTheForce get built -2004-11-24 20:55 tim +2004-11-24 15:55 tim * src/: math/RectMatrix.hpp, primitives/Bend.cpp, primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, @@ -2643,37 +3317,37 @@ primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp: types and primitives get built -2004-11-24 19:49 tim +2004-11-24 14:49 tim * test/utils/: Makefile, NextCombinationTestCase.cpp, StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint StringTokenizerTestCase -2004-11-24 19:49 tim +2004-11-24 14:49 tim * src/utils/: GenericData.hpp, StringTokenizer.cpp, StringTokenizer.hpp: StringTokenizer passes unit test -2004-11-24 18:20 tim +2004-11-24 13:20 tim * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: change Makefile -2004-11-24 18:06 chrisfen +2004-11-24 13:06 chrisfen * src/io/RestraintReader.cpp: improved restraints - mpi should work fine -2004-11-24 18:06 chrisfen +2004-11-24 13:06 chrisfen * src/integrators/Integrator.cpp: improved restraints -2004-11-24 18:05 chrisfen +2004-11-24 13:05 chrisfen * samples/water/tip3p_ice/tp3.md: oops... -2004-11-24 17:42 tim +2004-11-24 12:42 tim * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, brains/DataStorage.hpp, brains/SimCreator.cpp, @@ -2682,7 +3356,7 @@ primitives/DirectionalAtom.cpp: add SetForceManager method to integrator -2004-11-23 23:12 tim +2004-11-23 18:12 tim * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, @@ -2694,12 +3368,12 @@ integrators/VelocityVerletIntegrator.hpp, types/UreyBradleyBendType.hpp: refactory NPT integrator -2004-11-23 22:50 chrisfen +2004-11-23 17:50 chrisfen * samples/water/tip3p_ice/tp3.md: Back to normal... Oh... Restraints should work in parallel now -2004-11-23 22:48 chrisfen +2004-11-23 17:48 chrisfen * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, @@ -2709,12 +3383,12 @@ restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements to restraints -2004-11-23 22:47 chrisfen +2004-11-23 17:47 chrisfen * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll return to the original on next commit -2004-11-23 17:53 tim +2004-11-23 12:53 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, @@ -2727,73 +3401,73 @@ io/SectionParser.hpp, types/DirectionalAtomType.cpp, utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser -2004-11-23 17:53 tim +2004-11-23 12:53 tim * src/io/ElectrostaticAtomTypesSectionParser.hpp: file ElectrostaticAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 17:53 tim +2004-11-23 12:53 tim * src/io/ElectrostaticAtomTypesSectionParser.cpp: file ElectrostaticAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-23 06:03 tim +2004-11-23 01:03 tim * src/: io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, types/AtomType.hpp, types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: add EAM AtomType Section Parser -2004-11-23 06:03 tim +2004-11-23 01:03 tim * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp was initially added on branch new_design. -2004-11-23 06:03 tim +2004-11-23 01:03 tim * src/io/EAMAtomTypesSectionParser.hpp: file EAMAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 06:03 tim +2004-11-23 01:03 tim * src/io/EAMAtomTypesSectionParser.cpp: file EAMAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/TorsionTypesSectionParser.hpp: file TorsionTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/BendTypesSectionParser.hpp: file BendTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/BondTypesSectionParser.hpp: file BondTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/BondTypesSectionParser.cpp: file BondTypesSectionParser.cpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/TorsionTypesSectionParser.cpp: file TorsionTypesSectionParser.cpp was initially added on branch new_design. -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, @@ -2801,117 +3475,117 @@ BondTypesSectionParser, BendTypesSectionParser and TorsionTypeSectionParser -2004-11-23 04:35 tim +2004-11-22 23:35 tim * src/io/BendTypesSectionParser.cpp: file BendTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 23:04 tim +2004-11-22 18:04 tim * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in DUFF and EAM -2004-11-22 23:02 tim +2004-11-22 18:02 tim * src/io/: DirectionalAtomTypesParser.hpp, DirectionalAtomTypesSectionParser.hpp: adding section parsers -2004-11-22 23:02 tim +2004-11-22 18:02 tim * src/io/DirectionalAtomTypesSectionParser.hpp: file DirectionalAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/DipoleAtomTypesSectionParser.hpp: file DipoleAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/AtomTypesSectionParser.hpp: file AtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/HarmonicBondTypesSectionParser.hpp: file HarmonicBondTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/StickyAtomTypesSectionParser.cpp: file StickyAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/LennardJonesAtomTypesSectionParser.hpp: file LennardJonesAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/HarmonicBondTypesSectionParser.cpp: file HarmonicBondTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/DirectionalAtomTypesSectionParser.cpp: file DirectionalAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/SectionParserManager.cpp: file SectionParserManager.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/AtomTypesSectionParser.cpp: file AtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/ChargeAtomTypesSectionParser.cpp: file ChargeAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/DipoleAtomTypesSectionParser.cpp: file DipoleAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/LennardJonesAtomTypesSectionParser.cpp: file LennardJonesAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/ChargeAtomTypesSectionParser.hpp: file ChargeAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/StickyAtomTypesSectionParser.hpp: file StickyAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/SectionParser.hpp: file SectionParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, @@ -2933,112 +3607,112 @@ types/AtomType.hpp, types/DirectionalAtomType.hpp, utils/GenericData.hpp: adding section parsers -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/DirectionalAtomTypesParser.hpp: file DirectionalAtomTypesParser.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/SectionParserManager.hpp: file SectionParserManager.hpp was initially added on branch new_design. -2004-11-22 20:55 tim +2004-11-22 15:55 tim * src/io/SectionParser.cpp: file SectionParser.cpp was initially added on branch new_design. -2004-11-19 22:12 tim +2004-11-19 17:12 tim * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially added on branch new_design. -2004-11-19 22:12 tim +2004-11-19 17:12 tim * src/: brains/SimState.cpp, brains/SimState.hpp, io/InitializeFromFile.cpp, types/FixBondType.hpp, types/FixedBondType.hpp: remove more useless files -2004-11-19 21:47 tim +2004-11-19 16:47 tim * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, integrators/Integrator.cpp, applications/Makedepend: remove more useless files -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, integrators/NVT.hpp: refactory integrator -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on branch new_design. -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on branch new_design. -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/integrators/NPT.hpp: file NPT.hpp was initially added on branch new_design. -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added on branch new_design. -2004-11-19 21:38 tim +2004-11-19 16:38 tim * src/integrators/NVT.hpp: file NVT.hpp was initially added on branch new_design. -2004-11-19 20:37 tim +2004-11-19 15:37 tim * forceFields/newDUFF.frc: new DUFF forcefield -2004-11-19 20:23 tim +2004-11-19 15:23 tim * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on branch new_design. -2004-11-19 20:23 tim +2004-11-19 15:23 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, utils/TypeContainer.hpp: add EAM -2004-11-19 20:23 tim +2004-11-19 15:23 tim * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on branch new_design. -2004-11-19 18:02 tim +2004-11-19 13:02 tim * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except error checking -2004-11-19 17:56 tim +2004-11-19 12:56 tim * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp was initially added on branch new_design. -2004-11-19 17:56 tim +2004-11-19 12:56 tim * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp was initially added on branch new_design. -2004-11-19 17:56 tim +2004-11-19 12:56 tim * src/types/FixBondType.hpp: file FixBondType.hpp was initially added on branch new_design. -2004-11-19 17:56 tim +2004-11-19 12:56 tim * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, @@ -3049,16 +3723,16 @@ utils/StringTokenizer.cpp: DUFF is almost done except error checking -2004-11-19 00:11 tim +2004-11-18 19:11 tim * src/UseTheForce/DUFF.cpp: adding DUFF parser -2004-11-18 23:26 tim +2004-11-18 18:26 tim * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was initially added on branch new_design. -2004-11-18 23:26 tim +2004-11-18 18:26 tim * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, @@ -3070,37 +3744,37 @@ types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding DUFF parser -2004-11-18 21:42 tim +2004-11-18 16:42 tim * forceFields/newDUFF.frc: adding new format DUFF force field -2004-11-18 15:57 chrisfen +2004-11-18 10:57 chrisfen * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that slowed down the force loop -2004-11-18 05:42 tim +2004-11-18 00:42 tim * src/utils/NumericConstant.cpp: file NumericConstant.cpp was initially added on branch new_design. -2004-11-18 05:42 tim +2004-11-18 00:42 tim * src/utils/NumericConstant.hpp: file NumericConstant.hpp was initially added on branch new_design. -2004-11-18 05:42 tim +2004-11-18 00:42 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, primitives/Bend.cpp, utils/NumericConstant.cpp, utils/NumericConstant.hpp: Adding NumericConstant class -2004-11-18 04:16 tim +2004-11-17 23:16 tim * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp: remove more junk files -2004-11-18 04:12 tim +2004-11-17 23:12 tim * src/: brains/ForceFields.cpp, brains/SimSetup.cpp, brains/SimSetup.hpp, constraints/AbstractClasses.hpp, @@ -3109,60 +3783,60 @@ primitives/BondExtensions.cpp, primitives/SRI.hpp, primitives/TorsionExtensions.cpp: remove some junk files -2004-11-18 04:07 tim +2004-11-17 23:07 tim * src/primitives/BendExtensions.cpp: remove some junk files -2004-11-18 04:04 tim +2004-11-17 23:04 tim * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, QuadraticBondType.hpp: refine QudraticBond -2004-11-18 03:57 tim +2004-11-17 22:57 tim * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp -2004-11-18 03:57 tim +2004-11-17 22:57 tim * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially added on branch new_design. -2004-11-17 21:47 tim +2004-11-17 16:47 tim * src/: math/ChebyshevPolynomials.cpp, math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, @@ -3174,17 +3848,17 @@ types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: UreyBradleyBend and GhostBend -2004-11-17 18:58 tim +2004-11-17 13:58 tim * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp was initially added on branch new_design. -2004-11-17 18:58 tim +2004-11-17 13:58 tim * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp was initially added on branch new_design. -2004-11-17 18:58 tim +2004-11-17 13:58 tim * src/: math/ChebyshevPolynomials.cpp, math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, @@ -3193,22 +3867,22 @@ types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types stuff and Chebyshev Polynomial -2004-11-17 18:58 tim +2004-11-17 13:58 tim * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was initially added on branch new_design. -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/types/PolynomialTorsionType.hpp: file PolynomialTorsionType.hpp was initially added on branch new_design. -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was initially added on branch new_design. -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/: math/Polynomial.hpp, primitives/Bend.cpp, primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, @@ -3222,75 +3896,75 @@ CharmmTorsionType. Need to refine the design and add document for them -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was initially added on branch new_design. -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was initially added on branch new_design. -2004-11-17 06:37 tim +2004-11-17 01:37 tim * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was initially added on branch new_design. -2004-11-17 01:11 tim +2004-11-16 20:11 tim * src/types/: BendType.hpp, PolynomialBondType.hpp, TorsionType.hpp: add PolynomialBondType -2004-11-17 01:11 tim +2004-11-16 20:11 tim * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was initially added on branch new_design. -2004-11-16 23:20 tim +2004-11-16 18:20 tim * src/math/Polynomial.hpp: file Polynomial.hpp was initially added on branch new_design. -2004-11-16 23:20 tim +2004-11-16 18:20 tim * src/math/Polynomial.hpp: Adding Polynomial class -2004-11-16 22:04 gezelter +2004-11-16 17:04 gezelter * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially added on branch new_design. -2004-11-16 22:04 gezelter +2004-11-16 17:04 gezelter * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was initially added on branch new_design. -2004-11-16 22:04 gezelter +2004-11-16 17:04 gezelter * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, MorseBondType.hpp, TorsionType.hpp: added some new stuff -2004-11-16 20:36 tim +2004-11-16 15:36 tim * src/: primitives/Bend.cpp, primitives/Bend.hpp, primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and TorsionType -2004-11-16 02:07 tim +2004-11-15 21:07 tim * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on branch new_design. -2004-11-16 02:07 tim +2004-11-15 21:07 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, utils/StringTokenizer.cpp: adding DUFF class; adding checking statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer -2004-11-15 23:00 tim +2004-11-15 18:00 tim * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, @@ -3298,37 +3972,37 @@ UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, types/AtomType.hpp: adding ForceFieldFactory and LJFF classes -2004-11-15 23:00 tim +2004-11-15 18:00 tim * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp was initially added on branch new_design. -2004-11-15 23:00 tim +2004-11-15 18:00 tim * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp was initially added on branch new_design. -2004-11-15 23:00 tim +2004-11-15 18:00 tim * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on branch new_design. -2004-11-15 18:02 tim +2004-11-15 13:02 tim * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was initially added on branch new_design. -2004-11-15 18:02 tim +2004-11-15 13:02 tim * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on branch new_design. -2004-11-15 18:02 tim +2004-11-15 13:02 tim * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on branch new_design. -2004-11-15 18:02 tim +2004-11-15 13:02 tim * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, @@ -3336,7 +4010,7 @@ io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, DumpWriter.Next Step is LJFF and integrators -2004-11-13 05:08 tim +2004-11-13 00:08 tim * src/: brains/ForceManager.cpp, brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, @@ -3344,34 +4018,34 @@ primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, refactory, refactory -2004-11-12 22:43 tim +2004-11-12 17:43 tim * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, StringTokenizer.cpp: bug fix in hasMoreTokens -2004-11-12 22:28 tim +2004-11-12 17:28 tim * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was initially added on branch new_design. -2004-11-12 22:28 tim +2004-11-12 17:28 tim * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding StringUtils, a c-style strtok like class, need unit test -2004-11-12 17:40 tim +2004-11-12 12:40 tim * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test -2004-11-12 07:05 tim +2004-11-12 02:05 tim * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, primitives/CutoffGroup.hpp, primitives/Molecule.cpp: MoleculeCreator forget to create CutoffGroups for free atoms -2004-11-12 06:19 tim +2004-11-12 01:19 tim * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -3379,30 +4053,30 @@ io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: OOPSE = Object-Obfuscated Parallel Simulation Engine -2004-11-11 21:48 chrisfen +2004-11-11 16:48 chrisfen * samples/water/tip3p_ice/tp3.md: working sample -2004-11-11 21:47 chrisfen +2004-11-11 16:47 chrisfen * src/restraints/Restraints.cpp: working towards parallel restraints -2004-11-11 21:47 chrisfen +2004-11-11 16:47 chrisfen * src/integrators/Integrator.cpp: Commented out some write statements -2004-11-11 21:46 chrisfen +2004-11-11 16:46 chrisfen * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some write statements -2004-11-11 21:46 chrisfen +2004-11-11 16:46 chrisfen * samples/water/tip3p_ice/tp3.md: Fun with ice -2004-11-11 16:41 tim +2004-11-11 11:41 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, @@ -3411,18 +4085,18 @@ io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove useless mpiSimulation -2004-11-11 16:41 tim +2004-11-11 11:41 tim * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on branch new_design. -2004-11-10 22:50 tim +2004-11-10 17:50 tim * src/: brains/ForceManager.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo -2004-11-10 22:01 tim +2004-11-10 17:01 tim * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, @@ -3436,33 +4110,33 @@ BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint -2004-11-10 14:52 tim +2004-11-10 09:52 tim * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a configurable StatWriter -2004-11-10 14:52 tim +2004-11-10 09:52 tim * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on branch new_design. -2004-11-10 02:58 tim +2004-11-09 21:58 tim * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation in progress -2004-11-09 23:11 tim +2004-11-09 18:11 tim * src/brains/ForceManager.cpp: file ForceManager.cpp was initially added on branch new_design. -2004-11-09 23:11 tim +2004-11-09 18:11 tim * src/integrators/VelocityVerletIntegrator.cpp: file VelocityVerletIntegrator.cpp was initially added on branch new_design. -2004-11-09 23:11 tim +2004-11-09 18:11 tim * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -3471,57 +4145,57 @@ integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, integrators/VelocityVerletIntegrator.hpp: adding ForceManager -2004-11-09 23:11 tim +2004-11-09 18:11 tim * src/brains/ForceManager.hpp: file ForceManager.hpp was initially added on branch new_design. -2004-11-09 23:11 tim +2004-11-09 18:11 tim * src/integrators/NVE.cpp: file NVE.cpp was initially added on branch new_design. -2004-11-09 01:08 tim +2004-11-08 20:08 tim * src/integrators/VelocityVerletIntegrator.hpp: file VelocityVerletIntegrator.hpp was initially added on branch new_design. -2004-11-09 01:08 tim +2004-11-08 20:08 tim * src/integrators/NVE.hpp: file NVE.hpp was initially added on branch new_design. -2004-11-09 01:08 tim +2004-11-08 20:08 tim * src/: brains/Exclude.hpp, brains/Stats.hpp, integrators/Integrator.hpp, integrators/NVE.hpp, integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, utils/TypeContainer.hpp: More to break -2004-11-06 05:21 tim +2004-11-06 00:21 tim * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially added on branch new_design. -2004-11-06 05:21 tim +2004-11-06 00:21 tim * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, utils/TypeContainer.hpp, utils/next_combination.hpp: adding ForceField and TypeContainer classes -2004-11-05 23:38 tim +2004-11-05 18:38 tim * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was initially added on branch new_design. -2004-11-05 23:38 tim +2004-11-05 18:38 tim * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was initially added on branch new_design. -2004-11-05 23:38 tim +2004-11-05 18:38 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, @@ -3529,58 +4203,58 @@ brains/SimInfo.hpp, primitives/Molecule.hpp, utils/LocalndexManager.hpp: Fix Exclude class etc. -2004-11-05 21:45 chrisfen +2004-11-05 16:45 chrisfen * src/: applications/dump2Xyz/Dump2XYZ.cpp, visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the linear visitor -2004-11-05 21:04 chrisfen +2004-11-05 16:04 chrisfen * src/UseTheForce/DarkSide/shapes.F90: current status of the debugging process -2004-11-05 21:04 chrisfen +2004-11-05 16:04 chrisfen * make/Makefile.in: included visitors and minimizer -2004-11-05 21:03 chrisfen +2004-11-05 16:03 chrisfen * ChangeLog: new changes -2004-11-05 02:56 tim +2004-11-04 21:56 tim * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, primitives/Molecule.hpp: Pain...... -2004-11-04 20:55 tim +2004-11-04 15:55 tim * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, src/brains/Stats.hpp: time to break SimSetup -2004-11-04 20:51 gezelter +2004-11-04 15:51 gezelter * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new classes in progress -2004-11-04 19:48 tim +2004-11-04 14:48 tim * src/brains/Stats.cpp: file Stats.cpp was initially added on branch new_design. -2004-11-04 19:48 tim +2004-11-04 14:48 tim * src/brains/Stats.hpp: file Stats.hpp was initially added on branch new_design. -2004-11-04 19:48 tim +2004-11-04 14:48 tim * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats class -2004-11-04 16:22 gezelter +2004-11-04 11:22 gezelter * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and @@ -3589,45 +4263,45 @@ false and "-1" but there should be logic to figure them out in the other two classes -2004-11-04 16:20 gezelter +2004-11-04 11:20 gezelter * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't remember what I did -2004-11-04 16:20 gezelter +2004-11-04 11:20 gezelter * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky -2004-11-04 16:20 gezelter +2004-11-04 11:20 gezelter * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation -2004-11-04 16:20 gezelter +2004-11-04 11:20 gezelter * samples/water/ssd/ssd.md: testing force fields -2004-11-04 16:19 gezelter +2004-11-04 11:19 gezelter * samples/shape/linear.in: testing shapes -2004-11-03 19:56 tim +2004-11-03 14:56 tim * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator class(similar as SimSetup) -2004-11-03 19:56 tim +2004-11-03 14:56 tim * src/brains/SimCreator.hpp: file SimCreator.hpp was initially added on branch new_design. -2004-11-03 19:56 tim +2004-11-03 14:56 tim * src/brains/SimCreator.cpp: file SimCreator.cpp was initially added on branch new_design. -2004-11-03 18:00 tim +2004-11-03 13:00 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, @@ -3637,7 +4311,7 @@ visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get compiled. Still a long way to go ...... -2004-11-03 16:08 tim +2004-11-03 11:08 tim * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, @@ -3652,55 +4326,55 @@ src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... -2004-11-02 22:41 tim +2004-11-02 17:41 tim * src/: brains/Migrator.hpp, brains/SimModel.cpp, utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. Need unit test -2004-11-02 22:41 tim +2004-11-02 17:41 tim * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was initially added on branch new_design. -2004-11-02 22:41 tim +2004-11-02 17:41 tim * src/brains/Migrator.hpp: file Migrator.hpp was initially added on branch new_design. -2004-11-02 16:59 tim +2004-11-02 11:59 tim * src/brains/SimModel.cpp: file SimModel.cpp was initially added on branch new_design. -2004-11-02 16:59 tim +2004-11-02 11:59 tim * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, SimSnapshotManager.hpp: SimModel in progress -2004-11-02 15:28 chrisfen +2004-11-02 10:28 chrisfen * src/: UseTheForce/DarkSide/shapes.F90, primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes looks like it's working -2004-11-02 15:27 tim +2004-11-02 10:27 tim * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some functions for dealing with memory issue -2004-11-02 15:27 tim +2004-11-02 10:27 tim * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially added on branch new_design. -2004-11-02 15:23 tim +2004-11-02 10:23 tim * src/: brains/SimModel.hpp, brains/Snapshot.hpp, brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding SimModel(something similar as SimInfo) -2004-11-01 22:52 tim +2004-11-01 17:52 tim * src/: applications/simpleBuilder/MoLocator.hpp, applications/simpleBuilder/simpleBuilder.cpp, @@ -3719,47 +4393,47 @@ visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled -2004-11-01 21:40 tim +2004-11-01 16:40 tim * src/primitives/Torsion.hpp: file Torsion.hpp was initially added on branch new_design. -2004-11-01 21:40 tim +2004-11-01 16:40 tim * src/primitives/Bend.hpp: file Bend.hpp was initially added on branch new_design. -2004-11-01 21:40 tim +2004-11-01 16:40 tim * src/primitives/Bond.hpp: file Bond.hpp was initially added on branch new_design. -2004-11-01 21:40 tim +2004-11-01 16:40 tim * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial version of Bond, Bend and Torsion. -2004-11-01 21:37 tim +2004-11-01 16:37 tim * src/types/BendType.hpp: file BendType.hpp was initially added on branch new_design. -2004-11-01 21:37 tim +2004-11-01 16:37 tim * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding BondType, BendType, TorsionType -2004-11-01 21:37 tim +2004-11-01 16:37 tim * src/types/TorsionType.hpp: file TorsionType.hpp was initially added on branch new_design. -2004-11-01 21:37 tim +2004-11-01 16:37 tim * src/types/BondType.hpp: file BondType.hpp was initially added on branch new_design. -2004-11-01 20:15 tim +2004-11-01 15:15 tim * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, @@ -3767,49 +4441,49 @@ RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: break, break and break..... -2004-11-01 19:57 tim +2004-11-01 14:57 tim * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: these core classes get compiled -2004-10-29 22:37 tim +2004-10-29 17:37 tim * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule class -2004-10-29 22:28 chrisfen +2004-10-29 17:28 chrisfen * src/: UseTheForce/DarkSide/atype.F90, UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, types/ShapeAtomType.cpp: still debugging -2004-10-29 22:28 chrisfen +2004-10-29 17:28 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: shapes rcut calculator added -2004-10-29 22:27 chrisfen +2004-10-29 17:27 chrisfen * samples/shape/linear.md: shorter run -2004-10-29 20:54 tim +2004-10-29 15:54 tim * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. -2004-10-29 16:22 tim +2004-10-29 11:22 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove some deprecated files -2004-10-29 16:20 tim +2004-10-29 11:20 tim * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: More painful reconstruction is coming !!! -2004-10-28 22:34 tim +2004-10-28 17:34 tim * src/brains/DataStorage.hpp, src/utils/next_combination.hpp, test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, @@ -3817,7 +4491,7 @@ test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, DirectionalAtom and RigidBody -2004-10-28 22:26 tim +2004-10-28 17:26 tim * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, src/applications/simpleBuilder/MoLocator.cpp, @@ -3825,36 +4499,36 @@ src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: remove old Vector3d.hpp from application/simpleBuilder -2004-10-28 21:42 tim +2004-10-28 16:42 tim * src/utils/next_combination.hpp: Minor change in next_combination -2004-10-28 21:28 tim +2004-10-28 16:28 tim * src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/ReplaceWildCardTestCase.cpp: Done with combination -2004-10-28 21:11 tim +2004-10-28 16:11 tim * src/utils/next_combination.hpp: change documentation of next_combination.hpp -2004-10-28 20:41 tim +2004-10-28 15:41 tim * ChangeLog, src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working -2004-10-28 20:01 tim +2004-10-28 15:01 tim * src/utils/next_combination.hpp: adding replace wildcard function -2004-10-28 19:33 tim +2004-10-28 14:33 tim * src/utils/next_combination.hpp: Minor change -2004-10-28 19:06 tim +2004-10-28 14:06 tim * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, src/applications/simpleBuilder/simpleBuilder.cpp, @@ -3864,122 +4538,122 @@ test/utils/next_combination.hpp: STL next_permutation like next_combination is working -2004-10-28 17:22 chrisfen +2004-10-28 12:22 chrisfen * src/UseTheForce/WATER.cpp: fix of setDipoles -2004-10-28 17:20 gezelter +2004-10-28 12:20 gezelter * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the shapeFile -2004-10-28 17:20 gezelter +2004-10-28 12:20 gezelter * samples/shape/linear.md: forgot the orientation line -2004-10-28 16:56 gezelter +2004-10-28 11:56 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate declaration foo -2004-10-28 16:55 gezelter +2004-10-28 11:55 gezelter * samples/lipid/5x5.md: uncommented .in line -2004-10-28 15:42 tim +2004-10-28 10:42 tim * test/utils/: Makefile, NextCombinationTestCase.cpp, NextCombinationTestCase.hpp, next_combination.hpp: next_combination in progress -2004-10-28 15:15 tim +2004-10-28 10:15 tim * test/utils/: NextCombinationTestCase.cpp, NextCombinationTestCase.hpp: adding next_combination test case -2004-10-28 15:02 tim +2004-10-28 10:02 tim * test/utils/next_combination.hpp: STL Compatible combination sequence generator -2004-10-28 06:23 tim +2004-10-28 01:23 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp -2004-10-28 06:16 tim +2004-10-28 01:16 tim * test/utils/GenerateCombination.hpp: a STL next_permutaion like next_combination function. -2004-10-28 03:27 tim +2004-10-27 22:27 tim * test/utils/ReplaceWildCard.hpp: no message -2004-10-28 03:14 tim +2004-10-27 22:14 tim * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way -2004-10-28 02:28 tim +2004-10-27 21:28 tim * test/utils/: Makefile, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress -2004-10-28 02:08 tim +2004-10-27 21:08 tim * test/utils/: ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard -2004-10-27 23:17 tim +2004-10-27 18:17 tim * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need test -2004-10-27 06:25 tim +2004-10-27 01:25 tim * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild char matching is on the way -2004-10-27 06:07 tim +2004-10-27 01:07 tim * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 -2004-10-27 03:00 gezelter +2004-10-26 22:00 gezelter * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix -2004-10-27 02:20 gezelter +2004-10-26 21:20 gezelter * src/UseTheForce/ForceFields.hpp: subclass foo -2004-10-27 02:16 gezelter +2004-10-26 21:16 gezelter * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> string conversion -2004-10-27 00:01 gezelter +2004-10-26 19:01 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, brains/SimSetup.hpp: char* -> string -2004-10-26 22:25 gezelter +2004-10-26 17:25 gezelter * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some isXXX -2004-10-26 22:25 gezelter +2004-10-26 17:25 gezelter * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: define name collision -2004-10-26 22:24 gezelter +2004-10-26 17:24 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, @@ -3988,14 +4662,14 @@ UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: forcefield refactoring for shapes -2004-10-26 22:24 gezelter +2004-10-26 17:24 gezelter * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, linear.md, linear.shape, toluene.shape: adding sample shape directory -2004-10-26 22:19 tim +2004-10-26 17:19 tim * ChangeLog, src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, @@ -4003,22 +4677,22 @@ test/brains/DataStorageTestCase.hpp, test/brains/Makefile: DataStorage passes unit test -2004-10-26 18:03 chrisfen +2004-10-26 13:03 chrisfen * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: Changes to help advance shapes -2004-10-26 18:02 chrisfen +2004-10-26 13:02 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to Shapes force field reader -2004-10-26 17:28 tim +2004-10-26 12:28 tim * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and SnapshotTestCase in progress -2004-10-25 22:46 tim +2004-10-25 17:46 tim * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, src/math/Vector.hpp, @@ -4027,7 +4701,7 @@ test/math/VectorTestCase.cpp: add getArray function to RectMatrix and Vector classes -2004-10-25 17:03 tim +2004-10-25 12:03 tim * ChangeLog, src/utils/GenericFactory.hpp, test/utils/GenericFactoryTestCase.cpp, @@ -4035,41 +4709,41 @@ GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc. -2004-10-25 04:08 tim +2004-10-24 23:08 tim * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes get reconstructed -2004-10-24 07:55 tim +2004-10-24 02:55 tim * src/utils/GenericFactory.hpp: GenericFactory pass unit test -2004-10-23 23:09 tim +2004-10-23 18:09 tim * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, RigidBody.cpp: Refactoring in progress -2004-10-22 23:09 tim +2004-10-22 18:09 tim * ChangeLog, src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, test/brains/StuntDouble.hpp: more work in Snapshot -2004-10-22 22:59 chrisfen +2004-10-22 17:59 chrisfen * src/: UseTheForce/LJFF.cpp, UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear god! It runs and conserves energy! -2004-10-22 22:54 chrisfen +2004-10-22 17:54 chrisfen * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY -2004-10-22 22:53 chrisfen +2004-10-22 17:53 chrisfen * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, @@ -4077,35 +4751,35 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey breakey -2004-10-22 22:53 chrisfen +2004-10-22 17:53 chrisfen * make/Makefile.in: compiler flags -2004-10-22 21:20 gezelter +2004-10-22 16:20 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, brains/fSimulation.h, types/AtomType.hpp, types/DirectionalAtomType.hpp: fixey fixey -2004-10-22 20:22 gezelter +2004-10-22 15:22 gezelter * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, lj_interface.h, shapes.F90, simulation.F90: Added un-busticated fortran files and c/Fortran interfaces -2004-10-22 20:21 gezelter +2004-10-22 15:21 gezelter * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, DirectionalAtomType.hpp, Makefile: More on AtomType and DirectionalAtomType -2004-10-22 14:47 gezelter +2004-10-22 09:47 gezelter * src/types/AtomType.hpp: Adding AtomType -2004-10-21 21:31 tim +2004-10-21 16:31 tim * ChangeLog, src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, @@ -4114,14 +4788,14 @@ test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: Snapshot and SnapshotManager in progress -2004-10-21 21:30 tim +2004-10-21 16:30 tim * test/brains/: BrainsTest.cpp, Makefile, SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for Snapshot and snapshotManager. -2004-10-21 20:15 gezelter +2004-10-21 15:15 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -4132,16 +4806,16 @@ brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. Fixey Fixey. -2004-10-21 16:32 tim +2004-10-21 11:32 tim * src/utils/GenericData.cpp, src/utils/Makefile, test/utils/Makefile, test/utils/UtilTest: remove some junk files -2004-10-21 16:24 tim +2004-10-21 11:24 tim * test/utils/GenericData.hpp: remove backup of GenericData.hpp -2004-10-21 16:22 tim +2004-10-21 11:22 tim * ChangeLog, src/brains/SimSetup.cpp, src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, @@ -4159,17 +4833,17 @@ src/visitors/ZconsVisitor.hpp: replace old GebericData with new GenericData -2004-10-21 15:25 chuckv +2004-10-21 10:25 chuckv * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj module. -2004-10-21 15:24 chuckv +2004-10-21 10:24 chuckv * src/UseTheForce/DarkSide/lj_interface.h: Added interface for fortran lj module. -2004-10-20 22:54 tim +2004-10-20 17:54 tim * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, test/utils/GenericDataTestCase.cpp, test/utils/Makefile, @@ -4177,18 +4851,18 @@ test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: GenericData and PropertyMap pass unit test. -2004-10-20 21:52 gezelter +2004-10-20 16:52 gezelter * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, DarkSide/sticky_interface.h: fixed a fortran name problem -2004-10-20 21:38 tim +2004-10-20 16:38 tim * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, UtilTest, UtilTest.cpp: adding generic data test case -2004-10-20 21:16 chuckv +2004-10-20 16:16 chuckv * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/Makefile, @@ -4200,13 +4874,13 @@ Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo! -2004-10-20 20:47 chuckv +2004-10-20 15:47 chuckv * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project continues -2004-10-20 20:46 chuckv +2004-10-20 15:46 chuckv * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -4223,50 +4897,50 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface de-obfuscation project (It is a very long story) -2004-10-20 18:07 tim +2004-10-20 13:07 tim * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp, test/math/SquareMatrixTestCase.cpp, test/math/SquareMatrixTestCase.hpp: Math library pass the unit test -2004-10-20 05:52 tim +2004-10-20 00:52 tim * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and SnapshotManager in design phase -2004-10-20 04:54 gezelter +2004-10-19 23:54 gezelter * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace problem prevented linking -2004-10-20 04:54 gezelter +2004-10-19 23:54 gezelter * src/UseTheForce/Shapes_FF.cpp: fixed include -2004-10-20 04:26 gezelter +2004-10-19 23:26 gezelter * src/utils/: Makefile, definitions.F90, definitions_module.F90, oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: more fortran name mangling -2004-10-20 04:23 gezelter +2004-10-19 23:23 gezelter * src/profiling/timing.F90: yet more fortran renaming -2004-10-20 04:19 gezelter +2004-10-19 23:19 gezelter * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, do_Forces.F90, do_Forces.h, notifyCutoffs.F90, notifyCutoffs_interface.h, notifycutoffs_module_interface.h, wrappers.F90: Fortran name cleanup continues -2004-10-20 04:12 gezelter +2004-10-19 23:12 gezelter * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some broken fortran stuff -2004-10-20 04:02 gezelter +2004-10-19 23:02 gezelter * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, atype_interface.h, atype_module.F90, atype_module_interface.h, @@ -4283,23 +4957,23 @@ sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: name sanity on the fortran side -2004-10-20 00:18 tim +2004-10-19 19:18 tim * test/math/SquareMatrix3TestCase.hpp: [no log message] -2004-10-19 23:01 tim +2004-10-19 18:01 tim * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: except diagonalize(), all of functions in math library pass the test -2004-10-19 22:43 chuckv +2004-10-19 17:43 chuckv * src/UseTheForce/do_Forces.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 22:37 chuckv +2004-10-19 17:37 chuckv * src/UseTheForce/DarkSide/: atype_module_interface.h, eam_module_inteface.h, gb_module_interface.h, @@ -4307,7 +4981,7 @@ sticky_pair_module_interface.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 21:28 tim +2004-10-19 16:28 tim * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/Vector.hpp, @@ -4317,7 +4991,7 @@ test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more bugs get fixed at math library -2004-10-19 20:43 chuckv +2004-10-19 15:43 chuckv * src/UseTheForce/: DarkSide/atype_module_interface.h, DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, @@ -4331,43 +5005,43 @@ notifycutoffs_module_interface.h: Added new files for fortran interface. -2004-10-19 20:43 gezelter +2004-10-19 15:43 gezelter * src/UseTheForce/Makefile: regressing -2004-10-19 20:40 gezelter +2004-10-19 15:40 gezelter * src/: UseTheForce/DarkSide/calc_shapes.F90, UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: working on shapes for portability -2004-10-19 20:40 gezelter +2004-10-19 15:40 gezelter * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes -2004-10-19 18:21 chrisfen +2004-10-19 13:21 chrisfen * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around findBegin -2004-10-19 04:34 tim +2004-10-18 23:34 tim * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs are fixed in Vector class -2004-10-19 04:28 tim +2004-10-18 23:28 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix some bugs in RectMatrixTestCase -2004-10-19 04:21 tim +2004-10-18 23:21 tim * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: implement more test cases -2004-10-18 23:13 tim +2004-10-18 18:13 tim * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, @@ -4376,7 +5050,7 @@ test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more tests on math library -2004-10-18 21:03 tim +2004-10-18 16:03 tim * test/math/: Makefile, QuaternionTestCase.cpp, QuaternionTestCase.hpp, RectMatrixTestCase.cpp, @@ -4384,304 +5058,310 @@ Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding more testing units -2004-10-18 17:07 tim +2004-10-18 12:07 tim * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, utils/GenericFactory.hpp: fix some bugs in Quaternion class -2004-10-18 16:30 gezelter +2004-10-18 11:30 gezelter * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi) -2004-10-18 16:29 gezelter +2004-10-18 11:29 gezelter * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting Shapes into OOPSE -2004-10-18 15:21 gezelter +2004-10-18 10:21 gezelter * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType -2004-10-18 05:23 tim +2004-10-18 00:23 tim * test/math/VectorTestCase.hpp: adding vector test case -2004-10-18 05:23 tim +2004-10-18 00:23 tim * src/utils/GenericFactory.hpp: adding generic factory and vector test case -2004-10-17 01:19 tim +2004-10-16 20:19 tim * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in progress -2004-10-16 01:31 tim +2004-10-15 20:31 tim * src/math/Quaternion.hpp: add quaternion class -2004-10-15 21:11 tim +2004-10-15 16:11 tim * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding test file -2004-10-15 21:10 tim +2004-10-15 16:10 tim * src/io/basic_ifstrstream.hpp: fix a bunch of bugs -2004-10-15 20:42 tim +2004-10-15 15:42 tim * src/io/basic_ifstrstream.hpp: change const_cast to statc_const -2004-10-15 20:35 tim +2004-10-15 15:35 tim * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp -2004-10-15 20:34 tim +2004-10-15 15:34 tim * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use namespace oopse -2004-10-15 19:38 chuckv +2004-10-15 14:38 chuckv * configure, ac-tools/aclocal.m4: Changed optimization flags for XLF and XLC. -2004-10-15 18:28 tim +2004-10-15 13:28 tim * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding ifstrstream test case -2004-10-15 18:20 tim +2004-10-15 13:20 tim * src/io/basic_ifstrstream.hpp: fix include -2004-10-15 18:18 tim +2004-10-15 13:18 tim * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi -2004-10-15 18:17 tim +2004-10-15 13:17 tim * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile -2004-10-15 18:16 tim +2004-10-15 13:16 tim * test/io/: Makefile, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: adding test case for ifstrstream -2004-10-15 15:37 tim +2004-10-15 10:37 tim * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: add ifstrstreamTestCase -2004-10-15 15:20 tim +2004-10-15 10:20 tim * src/io/basic_ifstrstream.hpp: add checkFilename Option -2004-10-15 15:19 tim +2004-10-15 10:19 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add SquareMatrixTestCase class -2004-10-15 07:52 tim +2004-10-15 02:52 tim * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream -2004-10-14 23:28 tim +2004-10-14 18:28 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp: math library in progress -2004-10-14 23:27 tim +2004-10-14 18:27 tim * src/io/FileReader.hpp: FileReader in progress -2004-10-13 23:53 tim +2004-10-13 18:53 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons -2004-10-13 22:28 tim +2004-10-13 17:28 tim * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap class -2004-10-13 22:27 tim +2004-10-13 17:27 tim * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: adding testing unit -2004-10-13 22:24 tim +2004-10-13 17:24 tim * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix -2004-10-13 06:51 tim +2004-10-13 01:51 tim * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: refactory vector and matrix classes -2004-10-13 06:50 tim +2004-10-13 01:50 tim * src/math/Vector3d.hpp: Remove some Makefile.in -2004-10-12 23:57 tim +2004-10-12 18:57 tim * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and Matrix3x3d.hpp -2004-10-12 19:08 tim +2004-10-12 14:08 tim * doc/: cppstyle.html, style.css: adding c++ coding style -2004-10-11 22:15 tim +2004-10-11 17:15 tim * src/: constraints/AbstractClasses.hpp, integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: change #include "mpi.h" to #include in AbstractClasses.hpp -2004-10-11 21:54 tim +2004-10-11 16:54 tim * scripts/filepp: fix a bug in filepp -2004-10-11 21:13 tim +2004-10-11 16:13 tim * make/Makefile.in: using filepp to generate dependencies instead of compilers -2004-10-11 21:10 tim +2004-10-11 16:10 tim * scripts/filepp: filepp can be used to generate dependencies for c/c++ now -2004-10-11 18:40 tim +2004-10-11 13:40 tim * make/Makefile.in: remove -module from F90Options -2004-10-11 18:01 tim +2004-10-11 13:01 tim * make/Makefile.in: adding rules to move fortran 90 module to target directory -2004-10-11 15:43 gezelter +2004-10-11 10:43 gezelter * make/Makefile.in: fixed makefile.in -2004-10-11 14:51 tim +2004-10-11 09:51 tim * scripts/filepp: remove "use bytes" which causes problem in sgi machine -2004-10-11 14:26 tim +2004-10-11 09:26 tim * forceFields/Makefile: add Makefile -2004-10-11 14:23 tim +2004-10-11 09:23 tim * samples/: water/dimer/Makefile, water/spce/Makefile, water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, water/tip4p/Makefile, zcons/Makefile: fix Makefile under water directory -2004-10-09 06:01 tim +2004-10-11 09:23 tim - * samples/: alkane/Makefile.in, lipid/Makefile.in, - metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in + * samples/argon/Makefile: remove argon.dump and argon.eor from + Makefile -2004-10-08 23:15 tim +2004-10-09 01:01 tim + * samples/: alkane/Makefile.in, argon/Makefile.in, + lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: + Remove some Makefile.in + +2004-10-08 18:15 tim + * make/Makefile.in: [no log message] -2004-10-08 22:51 tim +2004-10-08 17:51 tim * make/Makefile.in: fix make install -2004-10-08 22:10 tim +2004-10-08 17:10 tim * make/Makefile.in: adding make install -2004-10-08 22:04 tim +2004-10-08 17:04 tim - * samples/: alkane/Makefile, lipid/Makefile, metals/Makefile, - minimizer/Makefile, water/Makefile.in, water/dimer/Makefile, - water/dimer/Makefile.in, water/spce/Makefile, + * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, + metals/Makefile, minimizer/Makefile, water/Makefile.in, + water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, water/ssde/Makefile, water/ssde/Makefile.in, water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, zcons/Makefile.in: add Makefile to sample directory -2004-10-06 23:03 gezelter +2004-10-06 18:03 gezelter * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt stuff -2004-10-06 23:03 gezelter +2004-10-06 18:03 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Doxyfile, src/applications/getopt.c, src/applications/getopt1.c, src/applications/gnugetopt.h: more build fixes -2004-10-06 22:20 tim +2004-10-06 17:20 tim * make/: Doxyfile, Makefile.in: adding doxygen configuration file -2004-10-06 22:19 tim +2004-10-06 17:19 tim * scripts/filepp: filepp can handle different fortran module case and suffix -2004-10-06 21:27 gezelter +2004-10-06 16:27 gezelter * src/restraints/Restraints.cpp: Chris doesn't know about the OOPSE-2.0 directory structure yet -2004-10-06 21:27 gezelter +2004-10-06 16:27 gezelter * ChangeLog: Yeah yeah, we'lll get around to it later -2004-10-06 21:22 gezelter +2004-10-06 16:22 gezelter * configure, ac-tools/configure.in, ac-tools/fortran90.m4, make/Makefile.in: cleaning up build process -2004-10-06 20:01 chrisfen +2004-10-06 15:01 chrisfen * src/restraints/Restraints.cpp: made the file reading in restraints more intelligent - no longer gives uninformative seg faults -2004-10-06 19:55 gezelter +2004-10-06 14:55 gezelter * src/applications/simpleBuilder/Make.ftemp.old: cleaning up -2004-10-06 19:51 gezelter +2004-10-06 14:51 gezelter * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit -2004-10-06 18:53 tim +2004-10-06 13:53 tim * make/: Makefile, Makefile.in: fix make statistics -2004-10-06 18:18 tim +2004-10-06 13:18 tim * make/: Makefile, Makefile.in: adding GNU make functions to combine all of the static libraries to a big library -2004-10-05 22:57 tim +2004-10-05 17:57 tim * make/: Makefile, Makefile.in: adding shared library flag -2004-10-05 19:37 tim +2004-10-05 14:37 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/mpiSimulation_module.F90, @@ -4689,62 +5369,62 @@ UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move mpiSimulation_module to DarkSide -2004-10-05 19:35 tim +2004-10-05 14:35 tim * make/: Makefile, Makefile.in: building MPI version;using static library instead of shared library -2004-10-05 14:14 tim +2004-10-05 09:14 tim * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 to filepp -2004-10-04 20:56 tim +2004-10-04 15:56 tim * make/: Makefile, Makefile.in: add make cvslog -2004-10-04 16:24 gezelter +2004-10-04 11:24 gezelter * make/: Makefile, Makefile.in: more work on the parallel build -2004-10-04 16:06 gezelter +2004-10-04 11:06 gezelter * make/: Makefile, Makefile.in: changes to backport declare flags -2004-10-04 15:27 gezelter +2004-10-04 10:27 gezelter * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging shapes -2004-10-02 04:40 tim +2004-10-01 23:40 tim * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree -2004-10-02 04:22 tim +2004-10-01 23:22 tim * make/: Makefile, Makefile.in: add oopse_ as library prefix -2004-10-01 21:59 tim +2004-10-01 16:59 tim * make/: Makefile, Makefile.in: fix a space trimming bug in filepp -2004-10-01 21:22 gezelter +2004-10-01 16:22 gezelter * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A few minor build changes -2004-10-01 21:11 tim +2004-10-01 16:11 tim * scripts/filepp: adding fortran90 make dependency tool -2004-09-30 15:41 tim +2004-09-30 10:41 tim * make/: Makefile, Makefile.in: make clean is smart enough to only remove object files belong to current package. turn off silent mode -2004-09-29 21:55 tim +2004-09-29 16:55 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, @@ -4755,45 +5435,44 @@ restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: define DEV_ROOT as relative path -2004-09-29 21:54 tim +2004-09-29 16:54 tim * make/: Makefile, Makefile.in: get the relative path by shell script -2004-09-29 21:32 tim +2004-09-29 16:32 tim * make/Makefile: eliminate DEV_ROOT by relative path -2004-09-29 18:37 tim +2004-09-29 13:37 tim * make/Makefile.in: add PackageLibs; fix dependency rule -2004-09-29 17:57 gezelter +2004-09-29 12:57 gezelter * configure, ac-tools/configure.in: updates -2004-09-29 17:56 gezelter +2004-09-29 12:56 gezelter - * make/: Make.conf.in, Makefile.in, _files/style.css: Working on - make stuff + * make/: Make.conf.in, Makefile.in: Working on make stuff -2004-09-29 17:46 tim +2004-09-29 12:46 tim * Makefile: If makefile does not exist, print error message -2004-09-29 17:12 tim +2004-09-29 12:12 tim * make/: Make.conf.in, Makefile: fix dependencies rule -2004-09-29 15:58 gezelter +2004-09-29 10:58 gezelter * Makefile, make/Makefile: still working on build process -2004-09-29 15:00 tim +2004-09-29 10:00 tim * make/Makefile: add print statment to rules -2004-09-29 14:59 tim +2004-09-29 09:59 tim * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, applications/oopse/Makefile, @@ -4803,12 +5482,12 @@ profiling/Makefile, restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: change Makefile to relative path -2004-09-29 02:55 tim +2004-09-28 21:55 tim * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c which cause headache in bulding libutils -2004-09-28 23:24 tim +2004-09-28 18:24 tim * src/applications/: BaseLattice.cpp, BaseLattice.hpp, Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, @@ -4831,16 +5510,16 @@ change directory structure of application. Every executable file is replaced in seperate directory -2004-09-28 22:15 gezelter +2004-09-28 17:15 gezelter * lib/dummy: Keep that lib around, please. -2004-09-28 22:14 gezelter +2004-09-28 17:14 gezelter * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: starting a configure version -2004-09-28 21:08 tim +2004-09-28 16:08 tim * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/Makefile, @@ -4849,7 +5528,7 @@ brains/Makefile, brains/simulation_module.F90: move fortran files around to solve dependency problem -2004-09-28 20:43 tim +2004-09-28 15:43 tim * Makefile, src/UseTheForce/ForceFields.hpp, src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, @@ -4859,25 +5538,25 @@ src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, src/utils/Makefile: [no log message] -2004-09-28 20:41 tim +2004-09-28 15:41 tim * make/Makefile, scripts/sfmakedepend: fix fortran dependency problem -2004-09-28 16:13 tim +2004-09-28 11:13 tim * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, src/io/Makefile: add yacc and lex rules -2004-09-27 20:24 tim +2004-09-27 15:24 tim * make/Makefile: adding include path to F90Options -2004-09-27 20:13 tim +2004-09-27 15:13 tim * make/Makefile: change suffix from .cc to .cpp -2004-09-24 16:27 tim +2004-09-24 11:27 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -4944,7 +5623,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: change the #include in source files -2004-09-24 04:16 gezelter +2004-09-23 23:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, @@ -5041,8 +5720,7 @@ src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, - src/visitors/ZconsVisitor.hpp, make/Makefile, - make/_files/style.css, samples/Makefile.in, + src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, @@ -5090,6 +5768,10 @@ samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, samples/alkane/Makefile.in, samples/alkane/alkanes.md, samples/alkane/butane.in, samples/alkane/butane.md, + samples/argon/500.in, samples/argon/500.md, + samples/argon/Makefile.in, samples/argon/ar864.in, + samples/argon/ar864.md, samples/argon/argonNVT.in, + samples/argon/argonNVT.md, samples/argon/lj.md, samples/lipid/5x5.in, samples/lipid/5x5.md, samples/lipid/Makefile.in, samples/lipid/lipid.md, samples/lipid/water.md, samples/minimizer/Makefile.in, @@ -5116,7 +5798,7 @@ forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 -2004-09-24 04:16 gezelter +2004-09-23 23:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, @@ -5213,8 +5895,7 @@ src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, - src/visitors/ZconsVisitor.hpp, make/Makefile, - make/_files/style.css, samples/Makefile.in, + src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, @@ -5262,6 +5943,10 @@ samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, samples/alkane/Makefile.in, samples/alkane/alkanes.md, samples/alkane/butane.in, samples/alkane/butane.md, + samples/argon/500.in, samples/argon/500.md, + samples/argon/Makefile.in, samples/argon/ar864.in, + samples/argon/ar864.md, samples/argon/argonNVT.in, + samples/argon/argonNVT.md, samples/argon/lj.md, samples/lipid/5x5.in, samples/lipid/5x5.md, samples/lipid/Makefile.in, samples/lipid/lipid.md, samples/lipid/water.md, samples/minimizer/Makefile.in,