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

Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1630 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC

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+-11-04 14:48  tim
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+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
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+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
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+        class
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+-11-04 14:48  tim
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+        * src/brains/Stats.cpp: file Stats.cpp was initially added on
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+        branch new_design.
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+-11-04 14:48  tim
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+        * src/brains/Stats.hpp: file Stats.hpp was initially added on
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+        branch new_design.
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+-11-04 11:22  gezelter
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+        * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
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+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
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+        linearAxis are virtual in StuntDouble, but are implemented by
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+        DirectionalAtom and RigidBody In StuntDouble, they should return
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+        false and "-1" but there should be logic to figure them out in the
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+        other two classes
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+-11-04 11:20  gezelter
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+        * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
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+        remember what I did
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+-11-04 11:20  gezelter
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+        * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
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+-11-04 11:20  gezelter
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+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
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+        in the entry_plug so that it only is set if the atoms really are in
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+        the simulation
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+-11-04 11:20  gezelter
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+        * samples/water/ssd/ssd.md: testing force fields
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+-11-04 11:19  gezelter
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+        * samples/shape/linear.in: testing shapes
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+-11-03 14:56  tim
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+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
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+        added on branch new_design.
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+-11-03 14:56  tim
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+        * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
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+        class(similar as SimSetup)
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+-11-03 14:56  tim
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+        * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
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+        added on branch new_design.
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+-11-03 13:00  tim
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
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+        UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp,
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+        brains/DataStorage.hpp, primitives/Atom.hpp,
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+        primitives/DirectionalAtom.hpp, restraints/Restraints.hpp,
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+        visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
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+        compiled. Still a long way to go ......
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+-11-03 11:08  tim
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+        * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
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+        src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
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+        src/integrators/NPTf.cpp, src/integrators/NPTi.cpp,
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+        src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp,
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+        src/io/ZConsReader.cpp, src/primitives/Bend.cpp,
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+        src/primitives/Bond.cpp, src/primitives/GhostBend.cpp,
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+        src/primitives/Molecule.cpp, src/primitives/Molecule.hpp,
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+        src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp,
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+        src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp,
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+        src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp,
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+        src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
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+        src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
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+-11-02 17:41  tim
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+        * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
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+        initially added on branch new_design.
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+-11-02 17:41  tim
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+        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
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+        branch new_design.
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+-11-02 17:41  tim
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+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
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+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
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+        Need unit test
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+-11-02 11:59  tim
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+        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
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+        SimSnapshotManager.hpp: SimModel in progress
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+-11-02 11:59  tim
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+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
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+        branch new_design.
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+-11-02 10:28  chrisfen
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+        * src/: UseTheForce/DarkSide/shapes.F90,
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+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
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+        looks like it's working
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+-11-02 10:27  tim
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+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
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+        added on branch new_design.
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+-11-02 10:27  tim
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+        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
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+        functions for dealing with memory issue
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+-11-02 10:23  tim
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+        * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
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+        brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
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+        SimModel(something similar as SimInfo)
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+-11-01 17:52  tim
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+        * src/: applications/simpleBuilder/MoLocator.hpp,
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+        applications/simpleBuilder/simpleBuilder.cpp,
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+        brains/DataStorage.hpp, brains/ForceFields.cpp,
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+        brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp,
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+        constraints/ZConstraint.cpp, integrators/Integrator.cpp,
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+        integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp,
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+        math/SquareMatrix3.hpp, math/Vector3.hpp,
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+        minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp,
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+        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
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+        primitives/Molecule.cpp, primitives/Molecule.hpp,
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+        primitives/RigidBody.hpp, primitives/Torsion.hpp,
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+        restraints/Restraints.cpp, types/TorsionType.hpp,
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+        utils/PropertyMap.hpp, utils/StringTokenizer.hpp,
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+        visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp,
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+        visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
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+        RigidBody and StuntDouble classes get compiled
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+-11-01 16:40  tim
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+        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
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+        on branch new_design.
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+-11-01 16:40  tim
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+        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
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+        branch new_design.
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+-11-01 16:40  tim
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+        * src/primitives/Bond.hpp: file Bond.hpp was initially added on
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+        branch new_design.
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+-11-01 16:40  tim
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+        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
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+        version of Bond, Bend and Torsion.
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+-11-01 16:37  tim
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+        * src/types/BendType.hpp: file BendType.hpp was initially added on
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+        branch new_design.
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+-11-01 16:37  tim
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+        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
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+        BondType, BendType, TorsionType
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+-11-01 16:37  tim
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+        * src/types/TorsionType.hpp: file TorsionType.hpp was initially
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+        added on branch new_design.
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+-11-01 16:37  tim
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+        * src/types/BondType.hpp: file BondType.hpp was initially added on
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+        branch new_design.
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+-11-01 15:15  tim
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+        * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
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+        CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
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+        GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp,
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+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
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+        break, break and break.....
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+-11-01 14:57  tim
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+        * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
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+        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
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+        StuntDouble.hpp: these core classes get compiled
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+-10-29 17:37  tim
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+        * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
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+        class
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+-10-29 17:28  chrisfen
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+        * src/: UseTheForce/DarkSide/atype.F90,
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+        UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
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+        types/ShapeAtomType.cpp: still debugging
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+-10-29 17:28  chrisfen
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+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
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+        shapes rcut calculator added
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+-10-29 17:27  chrisfen
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+        * samples/shape/linear.md: shorter run
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+-10-29 15:54  tim
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+        * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
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+-10-29 11:22  tim
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+        * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
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+        ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
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+        some deprecated files
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+-10-29 11:20  tim
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+        * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
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+        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
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+        More painful reconstruction is coming !!!
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+-10-28 17:34  tim
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+        * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
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+        test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
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+        test/brains/RigidBody.cpp, test/brains/RigidBody.hpp,
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+        test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
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+        DirectionalAtom and RigidBody
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+-10-28 17:26  tim
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+        * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
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+        src/applications/simpleBuilder/MoLocator.cpp,
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+        src/applications/simpleBuilder/Vector3d.hpp,
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+        src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
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+        remove old Vector3d.hpp from application/simpleBuilder
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+-10-28 16:42  tim
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+        * src/utils/next_combination.hpp: Minor change in next_combination
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+-10-28 16:28  tim
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+        * src/utils/next_combination.hpp,
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+        test/utils/NextCombinationTestCase.cpp,
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+        test/utils/ReplaceWildCardTestCase.cpp: Done with combination
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+-10-28 16:11  tim
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+        * src/utils/next_combination.hpp: change documentation of
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+        next_combination.hpp
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+-10-28 15:41  tim
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+        * ChangeLog, src/utils/next_combination.hpp,
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+        test/utils/NextCombinationTestCase.cpp,
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+        test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
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+-10-28 15:01  tim
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+        * src/utils/next_combination.hpp: adding replace wildcard function
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+-10-28 14:33  tim
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+        * src/utils/next_combination.hpp: Minor change
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+-10-28 14:06  tim
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+        * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
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+        src/applications/simpleBuilder/simpleBuilder.cpp,
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+        src/utils/next_combination.hpp, test/utils/Makefile,
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+        test/utils/NextCombinationTestCase.cpp,
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+        test/utils/ReplaceWildCardTestCase.cpp,
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+        test/utils/next_combination.hpp: STL next_permutation like
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+        next_combination is working
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+-10-28 12:22  chrisfen
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+        * src/UseTheForce/WATER.cpp: fix of setDipoles
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+-10-28 12:20  gezelter
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+        * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
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+        shapeFile
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+-10-28 12:20  gezelter
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+        * samples/shape/linear.md: forgot the orientation line
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+-10-28 11:56  gezelter
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
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+        UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
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+        declaration foo
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+-10-28 11:55  gezelter
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+        * samples/lipid/5x5.md: uncommented .in line
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+-10-28 10:42  tim
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+        * test/utils/: Makefile, NextCombinationTestCase.cpp,
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+        NextCombinationTestCase.hpp, next_combination.hpp: next_combination
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+        in progress
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+-10-28 10:15  tim
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+        * test/utils/: NextCombinationTestCase.cpp,
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+        NextCombinationTestCase.hpp: adding next_combination test case
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+-10-28 10:02  tim
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+        * test/utils/next_combination.hpp: STL Compatible combination
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+        sequence generator
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+-10-28 01:23  tim
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+        * test/utils/: GenerateCombination.hpp,
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+        ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
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+-10-28 01:16  tim
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+        * test/utils/GenerateCombination.hpp: a STL next_permutaion like
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+        next_combination function.
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+-10-27 22:27  tim
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+        * test/utils/ReplaceWildCard.hpp: no message
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+-10-27 22:14  tim
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+        * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
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+        ReplaceWildCard(recursive version) is working, need refactoring. An
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+        iterative version is on the way
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+-10-27 21:28  tim
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+        * test/utils/: Makefile, ReplaceWildCard.hpp,
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+        ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
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+-10-27 21:08  tim
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+        * test/utils/: ReplaceWildCardTestCase.cpp,
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+        ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
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+-10-27 18:17  tim
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+        * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
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+        test
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+-10-27 01:25  tim
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+        * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
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+        char matching is on the way
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+-10-27 01:07  tim
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+        * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
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+-10-26 22:00  gezelter
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+        * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
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+-10-26 21:20  gezelter
-+
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+        * src/UseTheForce/ForceFields.hpp: subclass foo
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+-10-26 21:16  gezelter
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+        * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
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+        string conversion
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+-10-26 19:01  gezelter
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
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+        brains/SimSetup.hpp: char* -> string
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+-10-26 17:25  gezelter
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+        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
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+        Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
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+        ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
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+        isXXX
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+-10-26 17:25  gezelter
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+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
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+        define name collision
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+-10-26 17:24  gezelter
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
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+        UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp,
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+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
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+        UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
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+        forcefield refactoring for shapes
-+
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+-10-26 17:24  gezelter
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+        * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
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+        Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
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+        linear.md, linear.shape, toluene.shape: adding sample shape
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+        directory
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+-10-26 17:19  tim
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+        * ChangeLog, src/brains/DataStorage.cpp,
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+        src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
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+        test/brains/DataStorageTestCase.cpp,
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+        test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
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+        DataStorage passes unit test
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+-10-26 13:03  chrisfen
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+        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
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+        Changes to help advance shapes
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+-10-26 13:02  chrisfen
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+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
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+        Shapes force field reader
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+-10-26 12:28  tim
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+        * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
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+        SnapshotTestCase in progress
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+-10-25 17:46  tim
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+        * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
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+        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
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+        src/math/Vector3.hpp, test/brains/StuntDouble.hpp,
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+        test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp,
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+        test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
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+        and Vector classes
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+-10-25 12:03  tim
-+
-+
+        * ChangeLog, src/utils/GenericFactory.hpp,
-+
+        test/utils/GenericFactoryTestCase.cpp,
-+
+        test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding
-+
+        GenericFactory Test Case. GenericFactory now can bed used to creat
-+
+        ForcefieldFactory and IntegratorFactory etc.
-+
-+
+-10-24 23:08  tim
-+
-+
+        * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
-+
+        brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
-+
+        brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
-+
+        get reconstructed
-+
-+
+-10-24 02:55  tim
-+
-+
+        * src/utils/GenericFactory.hpp: GenericFactory pass unit test
-+
-+
+-10-23 18:09  tim
-+
-+
+        * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
-+
+        StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
-+
+        RigidBody.cpp: Refactoring in progress
-+
-+
+-10-22 18:09  tim
-+
-+
+        * ChangeLog, src/brains/Snapshot.hpp,
-+
+        src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
-+
+        test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
-+
+        test/brains/StuntDouble.hpp: more work in Snapshot
-+
-+
+-10-22 17:59  chrisfen
-+
-+
+        * src/: UseTheForce/LJFF.cpp,
-+
+        UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
-+
+        god!  It runs and conserves energy!
-+
-+
+-10-22 17:54  chrisfen
-+
-+
+        * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
-+
-+
+-10-22 17:53  chrisfen
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
-+
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
-+
+        brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
-+
+        breakey
-+
-+
+-10-22 17:53  chrisfen
-+
-+
+        * make/Makefile.in: compiler flags
-+
-+
+-10-22 16:20  gezelter
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
-+
+        brains/fSimulation.h, types/AtomType.hpp,
-+
+        types/DirectionalAtomType.hpp: fixey fixey
-+
-+
+-10-22 15:22  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
-+
+        charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
-+
+        lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
-+
+        fortran files and c/Fortran interfaces
-+
-+
+-10-22 15:21  gezelter
-+
-+
+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
-+
+        DirectionalAtomType.hpp, Makefile: More on AtomType and
-+
+        DirectionalAtomType
-+
-+
+-10-22 09:47  gezelter
-+
-+
+        * src/types/AtomType.hpp: Adding AtomType
-+
-+
+-10-21 16:31  tim
-+
-+
+        * ChangeLog, src/brains/Snapshot.hpp,
-+
+        src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
-+
+        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
-+
+        src/math/Vector.hpp, src/math/Vector3.hpp,
-+
+        test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
-+
+        Snapshot and SnapshotManager in progress
-+
-+
+-10-21 16:30  tim
-+
-+
+        * test/brains/: BrainsTest.cpp, Makefile,
-+
+        SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
-+
+        SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
-+
+        Snapshot and snapshotManager.
-+
+-10-21 15:15  gezelter
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents): Revision 1630 by tim, Thu Oct 21 21:31:39 2004 UTC vs. Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1630 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC