[ViewVC] Diff of: group/trunk/OOPSE-3.0/ChangeLog

Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC vs.
Revision 1779 by tim, Wed Nov 24 18:20:15 2004 UTC

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+-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,
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+        brains/SimCreator.hpp, integrators/Integrator.hpp,
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+        io/ElectrostaticAtomTypesSectionParser.cpp,
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+        primitives/DirectionalAtom.cpp: add SetForceManager method to
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+        integrator
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+-11-23 18:12  tim
-+
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+        * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
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+        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
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+        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
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+        integrators/NPTxyz.cpp, integrators/NPTxyz.hpp,
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+        integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp,
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+        integrators/NVT.hpp, integrators/Velocitizer.cpp,
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+        integrators/VelocityVerletIntegrator.cpp,
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+        integrators/VelocityVerletIntegrator.hpp,
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+        types/UreyBradleyBendType.hpp: refactory NPT integrator
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+-11-23 17:50  chrisfen
-+
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+        * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
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+        Restraints should work in parallel now
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+-11-23 17:48  chrisfen
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+        * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
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+        brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
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+        integrators/Integrator.cpp, integrators/Integrator.hpp,
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+        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
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+-11-23 17:47  chrisfen
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+        * 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.
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+-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
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+-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.
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+-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
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+        new_design.
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+-11-23 01:03  tim
-+
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+        * src/io/EAMAtomTypesSectionParser.cpp: file
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+        EAMAtomTypesSectionParser.cpp was initially added on branch
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+        new_design.
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+-11-22 23:35  tim
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+        * src/io/TorsionTypesSectionParser.hpp: file
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+        TorsionTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 23:35  tim
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+        * src/io/BendTypesSectionParser.hpp: file
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+        BendTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 23:35  tim
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+        * src/io/BondTypesSectionParser.hpp: file
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+        BondTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 23:35  tim
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+        * src/io/BondTypesSectionParser.cpp: file
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+        BondTypesSectionParser.cpp was initially added on branch
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+        new_design.
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+-11-22 23:35  tim
-+
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+        * src/io/TorsionTypesSectionParser.cpp: file
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+        TorsionTypesSectionParser.cpp was initially added on branch
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+        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
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+        BendTypesSectionParser.cpp was initially added on branch
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+        new_design.
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+-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
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+-11-22 18:02  tim
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+        * src/io/: DirectionalAtomTypesParser.hpp,
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+        DirectionalAtomTypesSectionParser.hpp: adding section parsers
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+-11-22 18:02  tim
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+        * src/io/DirectionalAtomTypesSectionParser.hpp: file
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+        DirectionalAtomTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
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+        * src/io/DipoleAtomTypesSectionParser.hpp: file
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+        DipoleAtomTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
-+
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+        * src/io/AtomTypesSectionParser.hpp: file
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+        AtomTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
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+        * src/io/HarmonicBondTypesSectionParser.hpp: file
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+        HarmonicBondTypesSectionParser.hpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
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+        * src/io/StickyAtomTypesSectionParser.cpp: file
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+        StickyAtomTypesSectionParser.cpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
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+        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
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+        LennardJonesAtomTypesSectionParser.hpp was initially added on
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+        branch new_design.
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+-11-22 15:55  tim
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+        * src/io/HarmonicBondTypesSectionParser.cpp: file
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+        HarmonicBondTypesSectionParser.cpp was initially added on branch
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+        new_design.
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-+
+-11-22 15:55  tim
-+
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+        * src/io/DirectionalAtomTypesSectionParser.cpp: file
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+        DirectionalAtomTypesSectionParser.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-22 15:55  tim
-+
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+        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
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+        was initially added on branch new_design.
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+-11-22 15:55  tim
-+
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+        * src/io/AtomTypesSectionParser.cpp: file
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+        AtomTypesSectionParser.cpp was initially added on branch
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+        new_design.
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+-11-22 15:55  tim
-+
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+        * src/io/ChargeAtomTypesSectionParser.cpp: file
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+        ChargeAtomTypesSectionParser.cpp was initially added on branch
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+        new_design.
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-+
+-11-22 15:55  tim
-+
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+        * src/io/DipoleAtomTypesSectionParser.cpp: file
-+
+        DipoleAtomTypesSectionParser.cpp was initially added on branch
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+        new_design.
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-+
+-11-22 15:55  tim
-+
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+        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
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+        LennardJonesAtomTypesSectionParser.cpp was initially added on
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+        branch new_design.
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+-11-22 15:55  tim
-+
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+        * src/io/ChargeAtomTypesSectionParser.hpp: file
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+        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
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+        new_design.
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-+
+-11-22 15:55  tim
-+
-+
+        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
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+        added on branch new_design.
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+-11-22 15:55  tim
-+
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
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+        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
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+        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
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+        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
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+        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
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+        io/ChargeAtomTypesSectionParser.hpp,
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+        io/DipoleAtomTypesSectionParser.cpp,
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+        io/DipoleAtomTypesSectionParser.hpp,
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+        io/DirectionalAtomTypesParser.hpp,
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+        io/DirectionalAtomTypesSectionParser.cpp,
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+        io/HarmonicBondTypesSectionParser.cpp,
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+        io/HarmonicBondTypesSectionParser.hpp,
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+        io/LennardJonesAtomTypesSectionParser.cpp,
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+        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
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+        io/SectionParser.hpp, io/SectionParserManager.cpp,
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+        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
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+        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
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+        types/AtomType.hpp, types/DirectionalAtomType.hpp,
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+        utils/GenericData.hpp: adding section parsers
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+-11-22 15:55  tim
-+
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+        * src/io/DirectionalAtomTypesParser.hpp: file
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+        DirectionalAtomTypesParser.hpp was initially added on branch
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+        new_design.
-+
-+
+-11-22 15:55  tim
-+
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+        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
-+
+        was initially added on branch new_design.
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+-11-22 15:55  tim
-+
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+        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
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+        added on branch new_design.
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+-11-19 17:12  tim
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+        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
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+        added on branch new_design.
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+-11-19 17:12  tim
-+
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+        * src/: brains/SimState.cpp, brains/SimState.hpp,
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+        io/InitializeFromFile.cpp, types/FixBondType.hpp,
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+        types/FixedBondType.hpp: remove more useless files
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+-11-19 16:47  tim
-+
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+        * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
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+        integrators/Integrator.cpp, applications/Makedepend: remove more
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+        useless files
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+-11-19 16:38  tim
-+
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
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+        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
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+        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
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+        integrators/NVT.hpp: refactory integrator
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+-11-19 16:38  tim
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+        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
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+        branch new_design.
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+-11-19 16:38  tim
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+        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
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+        branch new_design.
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+-11-19 16:38  tim
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+        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
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+        branch new_design.
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+-11-19 16:38  tim
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+        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
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+        on branch new_design.
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+-11-19 16:38  tim
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+        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
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+        branch new_design.
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+-11-19 15:37  tim
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+        * forceFields/newDUFF.frc: new DUFF forcefield
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+-11-19 15:23  tim
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+        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
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+        branch new_design.
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+-11-19 15:23  tim
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
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+        UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
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+        utils/TypeContainer.hpp: add EAM
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+-11-19 15:23  tim
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+        * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
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+        branch new_design.
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+-11-19 13:02  tim
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+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
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+        error checking
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+-11-19 12:56  tim
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+        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
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+        was initially added on branch new_design.
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-+
+-11-19 12:56  tim
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+        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
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+        was initially added on branch new_design.
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+-11-19 12:56  tim
-+
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+        * src/types/FixBondType.hpp: file FixBondType.hpp was initially
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+        added on branch new_design.
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+-11-19 12:56  tim
-+
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+        * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
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+        UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
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+        UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp,
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+        integrators/IntegratorFactory.cpp,
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+        integrators/IntegratorFactory.hpp, integrators/NVE.hpp,
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+        integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp,
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+        utils/StringTokenizer.cpp: DUFF is almost done except error
-+
+        checking
-+
-+
+-11-18 19:11  tim
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+        * src/UseTheForce/DUFF.cpp: adding DUFF parser
-+
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+-11-18 18:26  tim
-+
-+
+        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
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+        initially added on branch new_design.
-+
-+
+-11-18 18:26  tim
-+
-+
+        * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
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+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
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+        integrators/VelocityVerletIntegrator.cpp,
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+        integrators/VelocityVerletIntegrator.hpp,
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+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
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+        types/CubicBendType.hpp, types/CubicBondType.hpp,
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+        types/HarmonicBondType.hpp, types/QuadraticBendType.hpp,
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+        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
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+        DUFF parser
-+
-+
+-11-18 16:42  tim
-+
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+        * 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
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+        slowed down the force loop
-+
-+
+-11-18 00:42  tim
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-+
+        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-18 00:42  tim
-+
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+        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
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+        initially added on branch new_design.
-+
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+-11-18 00:42  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
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+        primitives/Bend.cpp, utils/NumericConstant.cpp,
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+        utils/NumericConstant.hpp: Adding NumericConstant class
-+
-+
+-11-17 23:16  tim
-+
-+
+        * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
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+        UseTheForce/ForceFields.hpp: remove more junk files
-+
-+
+-11-17 23:12  tim
-+
-+
+        * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
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+        brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
-+
+        integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp,
-+
+        primitives/AbstractClasses.hpp, primitives/Bond.cpp,
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+        primitives/BondExtensions.cpp, primitives/SRI.hpp,
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+        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,
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+        QuadraticBondType.hpp: refine QudraticBond
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-+
+-11-17 22:57  tim
-+
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+        * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
-+
-+
+-11-17 22:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
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+        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
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+        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,
-+
+        primitives/Molecule.hpp: Pain......
-+
-+
+-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
-+
-+
+-11-04 15:51  gezelter
-+
-+
+        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
-+
+        classes in progress
-+
-+
+-11-04 14:48  tim
-+
-+
+        * src/brains/Stats.cpp: file Stats.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-04 14:48  tim
-+
-+
+        * src/brains/Stats.hpp: file Stats.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-04 14:48  tim
-+
-+
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
-+
+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
-+
+        class
-+
-+
+-11-04 11:22  gezelter
-+
-+
+        * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
-+
+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
-+
+        linearAxis are virtual in StuntDouble, but are implemented by
-+
+        DirectionalAtom and RigidBody In StuntDouble, they should return
-+
+        false and "-1" but there should be logic to figure them out in the
-+
+        other two classes
-+
-+
+-11-04 11:20  gezelter
-+
-+
+        * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
-+
+        remember what I did
-+
-+
+-11-04 11:20  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
-+
-+
+-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
-+
-+
+-11-04 11:20  gezelter
-+
-+
+        * samples/water/ssd/ssd.md: testing force fields
-+
-+
+-11-04 11:19  gezelter
-+
-+
+        * samples/shape/linear.in: testing shapes
-+
-+
+-11-03 14:56  tim
-+
-+
+        * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
-+
+        class(similar as SimSetup)
-+
-+
+-11-03 14:56  tim
-+
-+
+        * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-03 14:56  tim
-+
-+
+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-03 13:00  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
-+
+        UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp,
-+
+        brains/DataStorage.hpp, primitives/Atom.hpp,
-+
+        primitives/DirectionalAtom.hpp, restraints/Restraints.hpp,
-+
+        visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
-+
+        compiled. Still a long way to go ......
-+
-+
+-11-03 11:08  tim
-+
-+
+        * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
-+
+        src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
-+
+        src/integrators/NPTf.cpp, src/integrators/NPTi.cpp,
-+
+        src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp,
-+
+        src/io/ZConsReader.cpp, src/primitives/Bend.cpp,
-+
+        src/primitives/Bond.cpp, src/primitives/GhostBend.cpp,
-+
+        src/primitives/Molecule.cpp, src/primitives/Molecule.hpp,
-+
+        src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp,
-+
+        src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp,
-+
+        src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp,
-+
+        src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
-+
+        src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
-+
-+
+-11-02 17:41  tim
-+
-+
+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
-+
+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
-+
+        Need unit test
-+
-+
+-11-02 17:41  tim
-+
-+
+        * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-02 17:41  tim
-+
-+
+        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-02 11:59  tim
-+
-+
+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-02 11:59  tim
-+
-+
+        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
-+
+        SimSnapshotManager.hpp: SimModel in progress
-+
-+
+-11-02 10:28  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/shapes.F90,
-+
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
-+
+        looks like it's working
-+
-+
+-11-02 10:27  tim
-+
-+
+        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
-+
+        functions for dealing with memory issue
-+
-+
+-11-02 10:27  tim
-+
-+
+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-02 10:23  tim
-+
-+
+        * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
-+
+        brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
-+
+        SimModel(something similar as SimInfo)
-+
-+
+-11-01 17:52  tim
-+
-+
+        * src/: applications/simpleBuilder/MoLocator.hpp,
-+
+        applications/simpleBuilder/simpleBuilder.cpp,
-+
+        brains/DataStorage.hpp, brains/ForceFields.cpp,
-+
+        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp,
-+
+        constraints/ZConstraint.cpp, integrators/Integrator.cpp,
-+
+        integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp,
-+
+        math/SquareMatrix3.hpp, math/Vector3.hpp,
-+
+        minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp,
-+
+        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
-+
+        primitives/Molecule.cpp, primitives/Molecule.hpp,
-+
+        primitives/RigidBody.hpp, primitives/Torsion.hpp,
-+
+        restraints/Restraints.cpp, types/TorsionType.hpp,
-+
+        utils/PropertyMap.hpp, utils/StringTokenizer.hpp,
-+
+        visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp,
-+
+        visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
-+
+        RigidBody and StuntDouble classes get compiled
-+
-+
+-11-01 16:40  tim
-+
-+
+        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-01 16:40  tim
-+
-+
+        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-01 16:40  tim
-+
-+
+        * src/primitives/Bond.hpp: file Bond.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-01 16:40  tim
-+
-+
+        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
-+
+        version of Bond, Bend and Torsion.
-+
-+
+-11-01 16:37  tim
-+
-+
+        * src/types/BendType.hpp: file BendType.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-01 16:37  tim
-+
-+
+        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
-+
+        BondType, BendType, TorsionType
-+
-+
+-11-01 16:37  tim
-+
-+
+        * src/types/TorsionType.hpp: file TorsionType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-01 16:37  tim
-+
-+
+        * src/types/BondType.hpp: file BondType.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-01 15:15  tim
-+
-+
+        * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
-+
+        CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
-+
+        GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp,
-+
+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
-+
+        break, break and break.....
-+
-+
+-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
-+
-+
+-10-29 17:37  tim
-+
-+
+        * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
-+
+        class
-+
-+
+-10-29 17:28  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/atype.F90,
-+
+        UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
-+
+        types/ShapeAtomType.cpp: still debugging
-+
-+
+-10-29 17:28  chrisfen
-+
-+
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
-+
+        shapes rcut calculator added
-+
-+
+-10-29 17:27  chrisfen
-+
-+
+        * samples/shape/linear.md: shorter run
-+
-+
+-10-29 15:54  tim
-+
-+
+        * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
-+
-+
+-10-29 11:22  tim
-+
-+
+        * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
-+
+        ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
-+
+        some deprecated files
-+
-+
+-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 !!!
-+
-+
+-10-28 17:34  tim
-+
-+
+        * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
-+
+        test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
-+
+        test/brains/RigidBody.cpp, test/brains/RigidBody.hpp,
-+
+        test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
-+
+        DirectionalAtom and RigidBody
-+
-+
+-10-28 17:26  tim
-+
-+
+        * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
-+
+        src/applications/simpleBuilder/MoLocator.cpp,
-+
+        src/applications/simpleBuilder/Vector3d.hpp,
-+
+        src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
-+
+        remove old Vector3d.hpp from application/simpleBuilder
-+
-+
+-10-28 16:42  tim
-+
-+
+        * src/utils/next_combination.hpp: Minor change in next_combination
-+
-+
+-10-28 16:28  tim
-+
-+
+        * src/utils/next_combination.hpp,
-+
+        test/utils/NextCombinationTestCase.cpp,
-+
+        test/utils/ReplaceWildCardTestCase.cpp: Done with combination
-+
-+
+-10-28 16:11  tim
-+
-+
+        * src/utils/next_combination.hpp: change documentation of
-+
+        next_combination.hpp
-+
-+
+-10-28 15:41  tim
-+
-+
+        * ChangeLog, src/utils/next_combination.hpp,
-+
+        test/utils/NextCombinationTestCase.cpp,
-+
+        test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
-+
-+
+-10-28 15:01  tim
-+
-+
+        * src/utils/next_combination.hpp: adding replace wildcard function
-+
-+
+-10-28 14:33  tim
-+
-+
+        * src/utils/next_combination.hpp: Minor change
-+
-+
+-10-28 14:06  tim
-+
-+
+        * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
-+
+        src/applications/simpleBuilder/simpleBuilder.cpp,
-+
+        src/utils/next_combination.hpp, test/utils/Makefile,
-+
+        test/utils/NextCombinationTestCase.cpp,
-+
+        test/utils/ReplaceWildCardTestCase.cpp,
-+
+        test/utils/next_combination.hpp: STL next_permutation like
-+
+        next_combination is working
-+
-+
+-10-28 12:22  chrisfen
-+
-+
+        * src/UseTheForce/WATER.cpp: fix of setDipoles
-+
-+
+-10-28 12:20  gezelter
-+
-+
+        * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
-+
+        shapeFile
-+
-+
+-10-28 12:20  gezelter
-+
-+
+        * samples/shape/linear.md: forgot the orientation line
-+
-+
+-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
-+
-+
+-10-28 11:55  gezelter
-+
-+
+        * samples/lipid/5x5.md: uncommented .in line
-+
-+
+-10-28 10:42  tim
-+
-+
+        * test/utils/: Makefile, NextCombinationTestCase.cpp,
-+
+        NextCombinationTestCase.hpp, next_combination.hpp: next_combination
-+
+        in progress
-+
-+
+-10-28 10:15  tim
-+
-+
+        * test/utils/: NextCombinationTestCase.cpp,
-+
+        NextCombinationTestCase.hpp: adding next_combination test case
-+
-+
+-10-28 10:02  tim
-+
-+
+        * test/utils/next_combination.hpp: STL Compatible combination
-+
+        sequence generator
-+
-+
+-10-28 01:23  tim
-+
-+
+        * test/utils/: GenerateCombination.hpp,
-+
+        ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
-+
-+
+-10-28 01:16  tim
-+
-+
+        * test/utils/GenerateCombination.hpp: a STL next_permutaion like
-+
+        next_combination function.
-+
-+
+-10-27 22:27  tim
-+
-+
+        * test/utils/ReplaceWildCard.hpp: no message
-+
-+
+-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
-+
-+
+-10-27 21:28  tim
-+
-+
+        * test/utils/: Makefile, ReplaceWildCard.hpp,
-+
+        ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
-+
-+
+-10-27 21:08  tim
-+
-+
+        * test/utils/: ReplaceWildCardTestCase.cpp,
-+
+        ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
-+
-+
+-10-27 18:17  tim
-+
-+
+        * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
-+
+        test
-+
-+
+-10-27 01:25  tim
-+
-+
+        * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
-+
+        char matching is on the way
-+
-+
+-10-27 01:07  tim
-+
-+
+        * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
-+
-+
+-10-26 22:00  gezelter
-+
-+
+        * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
-+
-+
+-10-26 21:20  gezelter
-+
-+
+        * src/UseTheForce/ForceFields.hpp: subclass foo
-+
-+
+-10-26 21:16  gezelter
-+
-+
+        * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
-+
+        string conversion
-+
-+
+-10-26 19:01  gezelter
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
-+
+        brains/SimSetup.hpp: char* -> string
-+
-+
+-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
-+
-+
+-10-26 17:25  gezelter
-+
-+
+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
-+
+        define name collision
-+
-+
+-10-26 17:24  gezelter
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
-+
+        UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp,
-+
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
-+
+        UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
-+
+        forcefield refactoring for shapes
-+
-+
+-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
-+
-+
+-10-26 17:19  tim
-+
-+
+        * ChangeLog, src/brains/DataStorage.cpp,
-+
+        src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
-+
+        test/brains/DataStorageTestCase.cpp,
-+
+        test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
-+
+        DataStorage passes unit test
-+
-+
+-10-26 13:03  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
-+
+        Changes to help advance shapes
-+
-+
+-10-26 13:02  chrisfen
-+
-+
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
-+
+        Shapes force field reader
-+
-+
+-10-26 12:28  tim
-+
-+
+        * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
-+
+        SnapshotTestCase in progress
-+
-+
+-10-25 17:46  tim
-+
-+
+        * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
-+
+        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
-+
+        src/math/Vector3.hpp, test/brains/StuntDouble.hpp,
-+
+        test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp,
-+
+        test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
-+
+        and Vector classes
-+
+-10-25 12:03  tim
+        * ChangeLog, src/utils/GenericFactory.hpp,
+        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
+        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
+        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
-<
+        forceFields/Pt.VC.funcfl: Initial revision
->
+        forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
+-09-23 23:16  gezelter
+        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
+        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
+        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
-<
+        forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
->
+        forceFields/Pt.VC.funcfl: Initial revision

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
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+Changed lines

Comparing trunk/OOPSE-3.0/ChangeLog (file contents): Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC vs. Revision 1779 by tim, Wed Nov 24 18:20:15 2004 UTC

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC vs.
Revision 1779 by tim, Wed Nov 24 18:20:15 2004 UTC