--- trunk/OOPSE-3.0/ChangeLog 2004/11/04 20:55:01 1712 +++ trunk/OOPSE-3.0/ChangeLog 2004/11/24 18:20:15 1779 @@ -1,9 +1,894 @@ -2004-11-04 14:48 tim +2004-11-24 12:42 tim - * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, - SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats - class + * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, + brains/DataStorage.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, integrators/Integrator.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + primitives/DirectionalAtom.cpp: add SetForceManager method to + integrator +2004-11-23 18:12 tim + + * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, + integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, + integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, + integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, + integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, + integrators/NVT.hpp, integrators/Velocitizer.cpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/UreyBradleyBendType.hpp: refactory NPT integrator + +2004-11-23 17:50 chrisfen + + * samples/water/tip3p_ice/tp3.md: Back to normal... Oh... + Restraints should work in parallel now + +2004-11-23 17:48 chrisfen + + * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + integrators/Integrator.cpp, integrators/Integrator.hpp, + io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, + io/RestraintReader.cpp, io/RestraintWriter.cpp, + restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements + to restraints + +2004-11-23 17:47 chrisfen + + * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll + return to the original on next commit + +2004-11-23 12:53 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + io/ChargeAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, + io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, types/DirectionalAtomType.cpp, + utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser + +2004-11-23 12:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.hpp: file + ElectrostaticAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-23 12:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.cpp: file + ElectrostaticAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-23 01:03 tim + + * src/: io/EAMAtomTypesSectionParser.cpp, + io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, + types/AtomType.hpp, types/DirectionalAtomType.cpp, + types/DirectionalAtomType.hpp: add EAM AtomType Section Parser + +2004-11-23 01:03 tim + + * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp + was initially added on branch new_design. + +2004-11-23 01:03 tim + + * src/io/EAMAtomTypesSectionParser.hpp: file + EAMAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 01:03 tim + + * src/io/EAMAtomTypesSectionParser.cpp: file + EAMAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/TorsionTypesSectionParser.hpp: file + TorsionTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BendTypesSectionParser.hpp: file + BendTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BondTypesSectionParser.hpp: file + BondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BondTypesSectionParser.cpp: file + BondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/TorsionTypesSectionParser.cpp: file + TorsionTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, + BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, + TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add + BondTypesSectionParser, BendTypesSectionParser and + TorsionTypeSectionParser + +2004-11-22 23:35 tim + + * src/io/BendTypesSectionParser.cpp: file + BendTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 18:04 tim + + * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in + DUFF and EAM + +2004-11-22 18:02 tim + + * src/io/: DirectionalAtomTypesParser.hpp, + DirectionalAtomTypesSectionParser.hpp: adding section parsers + +2004-11-22 18:02 tim + + * src/io/DirectionalAtomTypesSectionParser.hpp: file + DirectionalAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DipoleAtomTypesSectionParser.hpp: file + DipoleAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/AtomTypesSectionParser.hpp: file + AtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/HarmonicBondTypesSectionParser.hpp: file + HarmonicBondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/StickyAtomTypesSectionParser.cpp: file + StickyAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.hpp: file + LennardJonesAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-22 15:55 tim + + * src/io/HarmonicBondTypesSectionParser.cpp: file + HarmonicBondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DirectionalAtomTypesSectionParser.cpp: file + DirectionalAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParserManager.cpp: file SectionParserManager.cpp + was initially added on branch new_design. + +2004-11-22 15:55 tim + + * src/io/AtomTypesSectionParser.cpp: file + AtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/ChargeAtomTypesSectionParser.cpp: file + ChargeAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DipoleAtomTypesSectionParser.cpp: file + DipoleAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.cpp: file + LennardJonesAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-22 15:55 tim + + * src/io/ChargeAtomTypesSectionParser.hpp: file + ChargeAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/StickyAtomTypesSectionParser.hpp: file + StickyAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParser.hpp: file SectionParser.hpp was initially + added on branch new_design. + +2004-11-22 15:55 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, + brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, + brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, + integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, + io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DipoleAtomTypesSectionParser.cpp, + io/DipoleAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, + types/AtomType.hpp, types/DirectionalAtomType.hpp, + utils/GenericData.hpp: adding section parsers + +2004-11-22 15:55 tim + + * src/io/DirectionalAtomTypesParser.hpp: file + DirectionalAtomTypesParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParserManager.hpp: file SectionParserManager.hpp + was initially added on branch new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParser.cpp: file SectionParser.cpp was initially + added on branch new_design. + +2004-11-19 17:12 tim + + * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially + added on branch new_design. + +2004-11-19 17:12 tim + + * src/: brains/SimState.cpp, brains/SimState.hpp, + io/InitializeFromFile.cpp, types/FixBondType.hpp, + types/FixedBondType.hpp: remove more useless files + +2004-11-19 16:47 tim + + * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, + integrators/Integrator.cpp, applications/Makedepend: remove more + useless files + +2004-11-19 16:38 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, + integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, + integrators/NVT.hpp: refactory integrator + +2004-11-19 16:38 tim + + * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPT.hpp: file NPT.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added + on branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NVT.hpp: file NVT.hpp was initially added on + branch new_design. + +2004-11-19 15:37 tim + + * forceFields/newDUFF.frc: new DUFF forcefield + +2004-11-19 15:23 tim + + * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on + branch new_design. + +2004-11-19 15:23 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, + UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, + utils/TypeContainer.hpp: add EAM + +2004-11-19 15:23 tim + + * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on + branch new_design. + +2004-11-19 13:02 tim + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except + error checking + +2004-11-19 12:56 tim + + * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp + was initially added on branch new_design. + +2004-11-19 12:56 tim + + * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp + was initially added on branch new_design. + +2004-11-19 12:56 tim + + * src/types/FixBondType.hpp: file FixBondType.hpp was initially + added on branch new_design. + +2004-11-19 12:56 tim + + * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, + UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, + utils/StringTokenizer.cpp: DUFF is almost done except error + checking + +2004-11-18 19:11 tim + + * src/UseTheForce/DUFF.cpp: adding DUFF parser + +2004-11-18 18:26 tim + + * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was + initially added on branch new_design. + +2004-11-18 18:26 tim + + * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding + DUFF parser + +2004-11-18 16:42 tim + + * forceFields/newDUFF.frc: adding new format DUFF force field + +2004-11-18 10:57 chrisfen + + * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that + slowed down the force loop + +2004-11-18 00:42 tim + + * src/utils/NumericConstant.cpp: file NumericConstant.cpp was + initially added on branch new_design. + +2004-11-18 00:42 tim + + * src/utils/NumericConstant.hpp: file NumericConstant.hpp was + initially added on branch new_design. + +2004-11-18 00:42 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, + primitives/Bend.cpp, utils/NumericConstant.cpp, + utils/NumericConstant.hpp: Adding NumericConstant class + +2004-11-17 23:16 tim + + * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, + UseTheForce/ForceFields.hpp: remove more junk files + +2004-11-17 23:12 tim + + * src/: brains/ForceFields.cpp, brains/SimSetup.cpp, + brains/SimSetup.hpp, constraints/AbstractClasses.hpp, + integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, + primitives/AbstractClasses.hpp, primitives/Bond.cpp, + primitives/BondExtensions.cpp, primitives/SRI.hpp, + primitives/TorsionExtensions.cpp: remove some junk files + +2004-11-17 23:07 tim + + * src/primitives/BendExtensions.cpp: remove some junk files + +2004-11-17 23:04 tim + + * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, + QuadraticBondType.hpp: refine QudraticBond + +2004-11-17 22:57 tim + + * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp + +2004-11-17 22:57 tim + + * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp + was initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/GhostBend.cpp, + primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp, types/BondType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: + UreyBradleyBend and GhostBend + +2004-11-17 13:58 tim + + * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp + was initially added on branch new_design. + +2004-11-17 13:58 tim + + * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp + was initially added on branch new_design. + +2004-11-17 13:58 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, + primitives/Bond.hpp, types/CharmmTorsionType.hpp, + types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types + stuff and Chebyshev Polynomial + +2004-11-17 13:58 tim + + * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/PolynomialTorsionType.hpp: file + PolynomialTorsionType.hpp was initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/: math/Polynomial.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, + types/BondType.hpp, types/CharmmTorsionType.cpp, + types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp, + utils/StringTokenizer.hpp: add PolynomialBondType, + PolynomialBendType, PolynomialTorsionType, HarmonicBendType and + CharmmTorsionType. Need to refine the design and add document for + them + +2004-11-17 01:37 tim + + * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was + initially added on branch new_design. + +2004-11-16 20:11 tim + + * src/types/: BendType.hpp, PolynomialBondType.hpp, + TorsionType.hpp: add PolynomialBondType + +2004-11-16 20:11 tim + + * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was + initially added on branch new_design. + +2004-11-16 18:20 tim + + * src/math/Polynomial.hpp: file Polynomial.hpp was initially added + on branch new_design. + +2004-11-16 18:20 tim + + * src/math/Polynomial.hpp: Adding Polynomial class + +2004-11-16 17:04 gezelter + + * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially + added on branch new_design. + +2004-11-16 17:04 gezelter + + * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was + initially added on branch new_design. + +2004-11-16 17:04 gezelter + + * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, + MorseBondType.hpp, TorsionType.hpp: added some new stuff + +2004-11-16 15:36 tim + + * src/: primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, + types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and + TorsionType + +2004-11-15 21:07 tim + + * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on + branch new_design. + +2004-11-15 21:07 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, + utils/StringTokenizer.cpp: adding DUFF class; adding checking + statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer + +2004-11-15 18:00 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, + UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, + types/AtomType.hpp: adding ForceFieldFactory and LJFF classes + +2004-11-15 18:00 tim + + * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp + was initially added on branch new_design. + +2004-11-15 18:00 tim + + * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp + was initially added on branch new_design. + +2004-11-15 18:00 tim + + * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was + initially added on branch new_design. + +2004-11-15 13:02 tim + + * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, + integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, + io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, + DumpWriter.Next Step is LJFF and integrators + +2004-11-13 00:08 tim + + * src/: brains/ForceManager.cpp, brains/ForceManager.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, + refactory, refactory + +2004-11-12 17:43 tim + + * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, + StringTokenizer.cpp: bug fix in hasMoreTokens + +2004-11-12 17:28 tim + + * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was + initially added on branch new_design. + +2004-11-12 17:28 tim + + * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding + StringUtils, a c-style strtok like class, need unit test + +2004-11-12 12:40 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test + +2004-11-12 02:05 tim + + * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + primitives/CutoffGroup.hpp, primitives/Molecule.cpp: + MoleculeCreator forget to create CutoffGroups for free atoms + +2004-11-12 01:19 tim + + * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: + OOPSE = Object-Obfuscated Parallel Simulation Engine + +2004-11-11 16:48 chrisfen + + * samples/water/tip3p_ice/tp3.md: working sample + +2004-11-11 16:47 chrisfen + + * src/restraints/Restraints.cpp: working towards parallel + restraints + +2004-11-11 16:47 chrisfen + + * src/integrators/Integrator.cpp: Commented out some write + statements + +2004-11-11 16:46 chrisfen + + * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some + write statements + +2004-11-11 16:46 chrisfen + + * samples/water/tip3p_ice/tp3.md: Fun with ice + +2004-11-11 11:41 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, + brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, + io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove + useless mpiSimulation + +2004-11-11 11:41 tim + + * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on + branch new_design. + +2004-11-10 17:50 tim + + * src/: brains/ForceManager.cpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, + integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo + +2004-11-10 17:01 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, + visitors/AtomVisitor.cpp: another painful day (1) SimCreator, + SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom + File will be removed) (3) ForceField (at least LJ) and BondType, + BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & + Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint + +2004-11-10 09:52 tim + + * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a + configurable StatWriter + +2004-11-10 09:52 tim + + * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on + branch new_design. + +2004-11-09 21:58 tim + + * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation + in progress + +2004-11-09 18:11 tim + + * src/brains/ForceManager.cpp: file ForceManager.cpp was initially + added on branch new_design. + +2004-11-09 18:11 tim + + * src/integrators/VelocityVerletIntegrator.cpp: file + VelocityVerletIntegrator.cpp was initially added on branch + new_design. + +2004-11-09 18:11 tim + + * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, + brains/mpiSimulation.hpp, integrators/Integrator.hpp, + integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp: adding ForceManager + +2004-11-09 18:11 tim + + * src/brains/ForceManager.hpp: file ForceManager.hpp was initially + added on branch new_design. + +2004-11-09 18:11 tim + + * src/integrators/NVE.cpp: file NVE.cpp was initially added on + branch new_design. + +2004-11-08 20:08 tim + + * src/integrators/VelocityVerletIntegrator.hpp: file + VelocityVerletIntegrator.hpp was initially added on branch + new_design. + +2004-11-08 20:08 tim + + * src/integrators/NVE.hpp: file NVE.hpp was initially added on + branch new_design. + +2004-11-08 20:08 tim + + * src/: brains/Exclude.hpp, brains/Stats.hpp, + integrators/Integrator.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + utils/TypeContainer.hpp: More to break + +2004-11-06 00:21 tim + + * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially + added on branch new_design. + +2004-11-06 00:21 tim + + * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, + utils/TypeContainer.hpp, utils/next_combination.hpp: adding + ForceField and TypeContainer classes + +2004-11-05 18:38 tim + + * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was + initially added on branch new_design. + +2004-11-05 18:38 tim + + * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was + initially added on branch new_design. + +2004-11-05 18:38 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.hpp, + utils/LocalndexManager.hpp: Fix Exclude class etc. + +2004-11-05 16:45 chrisfen + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the + linear visitor + +2004-11-05 16:04 chrisfen + + * src/UseTheForce/DarkSide/shapes.F90: current status of the + debugging process + +2004-11-05 16:04 chrisfen + + * make/Makefile.in: included visitors and minimizer + +2004-11-05 16:03 chrisfen + + * ChangeLog: new changes + +2004-11-04 21:56 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + primitives/Molecule.hpp: Pain...... + +2004-11-04 15:55 tim + + * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, + src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, + src/brains/Stats.hpp: time to break SimSetup + +2004-11-04 15:51 gezelter + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new + classes in progress + 2004-11-04 14:48 tim * src/brains/Stats.cpp: file Stats.cpp was initially added on @@ -14,6 +899,12 @@ * src/brains/Stats.hpp: file Stats.hpp was initially added on branch new_design. +2004-11-04 14:48 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, + SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats + class + 2004-11-04 11:22 gezelter * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, @@ -48,11 +939,6 @@ 2004-11-03 14:56 tim - * src/brains/SimCreator.cpp: file SimCreator.cpp was initially - added on branch new_design. - -2004-11-03 14:56 tim - * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator class(similar as SimSetup) @@ -61,6 +947,11 @@ * src/brains/SimCreator.hpp: file SimCreator.hpp was initially added on branch new_design. +2004-11-03 14:56 tim + + * src/brains/SimCreator.cpp: file SimCreator.cpp was initially + added on branch new_design. + 2004-11-03 13:00 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, @@ -88,6 +979,12 @@ 2004-11-02 17:41 tim + * src/: brains/Migrator.hpp, brains/SimModel.cpp, + utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. + Need unit test + +2004-11-02 17:41 tim + * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was initially added on branch new_design. @@ -96,22 +993,16 @@ * src/brains/Migrator.hpp: file Migrator.hpp was initially added on branch new_design. -2004-11-02 17:41 tim +2004-11-02 11:59 tim - * src/: brains/Migrator.hpp, brains/SimModel.cpp, - utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. - Need unit test + * src/brains/SimModel.cpp: file SimModel.cpp was initially added on + branch new_design. 2004-11-02 11:59 tim * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, SimSnapshotManager.hpp: SimModel in progress -2004-11-02 11:59 tim - - * src/brains/SimModel.cpp: file SimModel.cpp was initially added on - branch new_design. - 2004-11-02 10:28 chrisfen * src/: UseTheForce/DarkSide/shapes.F90, @@ -120,13 +1011,13 @@ 2004-11-02 10:27 tim - * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially - added on branch new_design. + * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some + functions for dealing with memory issue 2004-11-02 10:27 tim - * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some - functions for dealing with memory issue + * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially + added on branch new_design. 2004-11-02 10:23 tim