[ViewVC] Diff of: OpenMD/trunk/ChangeLog

Comparing trunk/ChangeLog (file contents):
Revision 208 by chrisfen, Fri Nov 5 21:03:47 2004 UTC vs.
Revision 226 by tim, Wed Nov 24 18:20:15 2004 UTC

-+
+-11-24 12:42  tim
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+        * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
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+        brains/DataStorage.hpp, brains/SimCreator.cpp,
-+
+        brains/SimCreator.hpp, integrators/Integrator.hpp,
-+
+        io/ElectrostaticAtomTypesSectionParser.cpp,
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+        primitives/DirectionalAtom.cpp: add SetForceManager method to
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+        integrator
-+
-+
+-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,
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+        integrators/VelocityVerletIntegrator.hpp,
-+
+        types/UreyBradleyBendType.hpp: refactory NPT integrator
-+
-+
+-11-23 17:50  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
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+        Restraints should work in parallel now
-+
-+
+-11-23 17:48  chrisfen
-+
-+
+        * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
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+        brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
-+
+        integrators/Integrator.cpp, integrators/Integrator.hpp,
-+
+        io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp,
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+        io/RestraintReader.cpp, io/RestraintWriter.cpp,
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+        restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
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+        to restraints
-+
-+
+-11-23 17:47  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
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+        return to the original on next commit
-+
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+-11-23 12:53  tim
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
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+        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
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+        applications/simpleBuilder/simpleBuilder.cpp,
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+        io/ChargeAtomTypesSectionParser.cpp,
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+        io/DirectionalAtomTypesSectionParser.hpp,
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+        io/EAMAtomTypesSectionParser.cpp,
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+        io/ElectrostaticAtomTypesSectionParser.cpp,
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+        io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp,
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+        io/SectionParser.hpp, types/DirectionalAtomType.cpp,
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+        utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
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-+
+-11-23 12:53  tim
-+
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+        * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
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+        ElectrostaticAtomTypesSectionParser.hpp was initially added on
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+        branch new_design.
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-+
+-11-23 12:53  tim
-+
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+        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
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+        ElectrostaticAtomTypesSectionParser.cpp was initially added on
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+        branch new_design.
-+
-+
+-11-23 01:03  tim
-+
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+        * src/: io/EAMAtomTypesSectionParser.cpp,
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+        io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
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+        types/AtomType.hpp, types/DirectionalAtomType.cpp,
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+        types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
-+
-+
+-11-23 01:03  tim
-+
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+        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
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+        was initially added on branch new_design.
-+
-+
+-11-23 01:03  tim
-+
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+        * src/io/EAMAtomTypesSectionParser.hpp: file
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+        EAMAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-23 01:03  tim
-+
-+
+        * src/io/EAMAtomTypesSectionParser.cpp: file
-+
+        EAMAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 23:35  tim
-+
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+        * src/io/TorsionTypesSectionParser.hpp: file
-+
+        TorsionTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 23:35  tim
-+
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+        * src/io/BendTypesSectionParser.hpp: file
-+
+        BendTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 23:35  tim
-+
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+        * src/io/BondTypesSectionParser.hpp: file
-+
+        BondTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 23:35  tim
-+
-+
+        * src/io/BondTypesSectionParser.cpp: file
-+
+        BondTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 23:35  tim
-+
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+        * src/io/TorsionTypesSectionParser.cpp: file
-+
+        TorsionTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
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+-11-22 23:35  tim
-+
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+        * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
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+        BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
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+        TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add
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+        BondTypesSectionParser, BendTypesSectionParser and
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+        TorsionTypeSectionParser
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+-11-22 23:35  tim
-+
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+        * src/io/BendTypesSectionParser.cpp: file
-+
+        BendTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 18:04  tim
-+
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+        * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
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+        DUFF and EAM
-+
-+
+-11-22 18:02  tim
-+
-+
+        * src/io/: DirectionalAtomTypesParser.hpp,
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+        DirectionalAtomTypesSectionParser.hpp: adding section parsers
-+
-+
+-11-22 18:02  tim
-+
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+        * src/io/DirectionalAtomTypesSectionParser.hpp: file
-+
+        DirectionalAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DipoleAtomTypesSectionParser.hpp: file
-+
+        DipoleAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/AtomTypesSectionParser.hpp: file
-+
+        AtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/HarmonicBondTypesSectionParser.hpp: file
-+
+        HarmonicBondTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/StickyAtomTypesSectionParser.cpp: file
-+
+        StickyAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
-+
+        LennardJonesAtomTypesSectionParser.hpp was initially added on
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+        branch new_design.
-+
-+
+-11-22 15:55  tim
-+
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+        * src/io/HarmonicBondTypesSectionParser.cpp: file
-+
+        HarmonicBondTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DirectionalAtomTypesSectionParser.cpp: file
-+
+        DirectionalAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/AtomTypesSectionParser.cpp: file
-+
+        AtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/ChargeAtomTypesSectionParser.cpp: file
-+
+        ChargeAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DipoleAtomTypesSectionParser.cpp: file
-+
+        DipoleAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
-+
+        LennardJonesAtomTypesSectionParser.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/ChargeAtomTypesSectionParser.hpp: file
-+
+        ChargeAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/StickyAtomTypesSectionParser.hpp: file
-+
+        StickyAtomTypesSectionParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-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
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/DirectionalAtomTypesParser.hpp: file
-+
+        DirectionalAtomTypesParser.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-19 17:12  tim
-+
-+
+        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-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
-+
-+
+-11-19 16:47  tim
-+
-+
+        * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
-+
+        integrators/Integrator.cpp, applications/Makedepend: remove more
-+
+        useless files
-+
-+
+-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
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 16:38  tim
-+
-+
+        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-19 16:38  tim
-+
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+        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 15:37  tim
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+        * forceFields/newDUFF.frc: new DUFF forcefield
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
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+        UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
-+
+        utils/TypeContainer.hpp: add EAM
-+
-+
+-11-19 15:23  tim
-+
-+
+        * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-19 13:02  tim
-+
-+
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
-+
+        error checking
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-19 12:56  tim
-+
-+
+        * src/types/FixBondType.hpp: file FixBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-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
-+
-+
+-11-18 19:11  tim
-+
-+
+        * src/UseTheForce/DUFF.cpp: adding DUFF parser
-+
-+
+-11-18 18:26  tim
-+
-+
+        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-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
-+
-+
+-11-18 16:42  tim
-+
-+
+        * forceFields/newDUFF.frc: adding new format DUFF force field
-+
-+
+-11-18 10:57  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
-+
+        slowed down the force loop
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 00:42  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
-+
+        primitives/Bend.cpp, utils/NumericConstant.cpp,
-+
+        utils/NumericConstant.hpp: Adding NumericConstant class
-+
-+
+-11-17 23:16  tim
-+
-+
+        * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
-+
+        UseTheForce/ForceFields.hpp: remove more junk files
-+
-+
+-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
-+
-+
+-11-17 23:07  tim
-+
-+
+        * src/primitives/BendExtensions.cpp: remove some junk files
-+
-+
+-11-17 23:04  tim
-+
-+
+        * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
-+
+        QuadraticBondType.hpp: refine QudraticBond
-+
-+
+-11-17 22:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
-+
-+
+-11-17 22:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 16:47  tim
-+
-+
+        * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-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
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-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
-+
-+
+-11-17 13:58  tim
-+
-+
+        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/PolynomialTorsionType.hpp: file
-+
+        PolynomialTorsionType.hpp was initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-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
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:37  tim
-+
-+
+        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 20:11  tim
-+
-+
+        * src/types/: BendType.hpp, PolynomialBondType.hpp,
-+
+        TorsionType.hpp: add PolynomialBondType
-+
-+
+-11-16 20:11  tim
-+
-+
+        * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 18:20  tim
-+
-+
+        * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-16 18:20  tim
-+
-+
+        * src/math/Polynomial.hpp: Adding Polynomial class
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 17:04  gezelter
-+
-+
+        * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
-+
+        MorseBondType.hpp, TorsionType.hpp: added some new stuff
-+
-+
+-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
-+
-+
+-11-15 21:07  tim
-+
-+
+        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-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
-+
-+
+-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
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 18:00  tim
-+
-+
+        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 13:02  tim
-+
-+
+        * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-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
-+
-+
+-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
-+
-+
+-11-12 17:43  tim
-+
-+
+        * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
-+
+        StringTokenizer.cpp: bug fix in hasMoreTokens
-+
-+
+-11-12 17:28  tim
-+
-+
+        * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-12 17:28  tim
-+
-+
+        * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
-+
+        StringUtils, a c-style strtok like class, need unit test
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-11-11 16:48  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: working sample
-+
-+
+-11-11 16:47  chrisfen
-+
-+
+        * src/restraints/Restraints.cpp: working towards parallel
-+
+        restraints
-+
-+
+-11-11 16:47  chrisfen
-+
-+
+        * src/integrators/Integrator.cpp: Commented out some write
-+
+        statements
-+
-+
+-11-11 16:46  chrisfen
-+
-+
+        * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
-+
+        write statements
-+
-+
+-11-11 16:46  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: Fun with ice
-+
-+
+-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
-+
-+
+-11-11 11:41  tim
-+
-+
+        * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-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
-+
-+
+-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
-+
-+
+-11-10 09:52  tim
-+
-+
+        * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
-+
+        configurable StatWriter
-+
-+
+-11-10 09:52  tim
-+
-+
+        * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-09 21:58  tim
-+
-+
+        * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
-+
+        in progress
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.cpp: file
-+
+        VelocityVerletIntegrator.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-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
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 18:11  tim
-+
-+
+        * src/integrators/NVE.cpp: file NVE.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-08 20:08  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.hpp: file
-+
+        VelocityVerletIntegrator.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-08 20:08  tim
-+
-+
+        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-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
-+
-+
+-11-06 00:21  tim
-+
-+
+        * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-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
-+
-+
+-11-05 18:38  tim
-+
-+
+        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-05 18:38  tim
-+
-+
+        * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-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.
-+
-+
+-11-05 16:45  chrisfen
-+
-+
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
-+
+        linear visitor
-+
-+
+-11-05 16:04  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/shapes.F90: current status of the
-+
+        debugging process
-+
-+
+-11-05 16:04  chrisfen
-+
-+
+        * make/Makefile.in: included visitors and minimizer
-+
-+
+-11-05 16:03  chrisfen
-+
-+
+        * ChangeLog: new changes
-+
+-11-04 21:56  tim
+        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
+-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
+-09-29 12:46  tim
+        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,
+        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,

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Comparing trunk/ChangeLog (file contents): Revision 208 by chrisfen, Fri Nov 5 21:03:47 2004 UTC vs. Revision 226 by tim, Wed Nov 24 18:20:15 2004 UTC

Diff Legend

Comparing trunk/ChangeLog (file contents):
Revision 208 by chrisfen, Fri Nov 5 21:03:47 2004 UTC vs.
Revision 226 by tim, Wed Nov 24 18:20:15 2004 UTC