[ViewVC] Diff of: group/trunk/OOPSE-2.0/ChangeLog

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1536 by gezelter, Wed Oct 6 21:27:02 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,
-+
+        UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp,
-+
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
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+        UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
-+
+        forcefield refactoring for shapes
-+
-+
+-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,
-+
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
-+
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
-+
+        UseTheForce/doForces_interface.h, UseTheForce/fForceField.h,
-+
+        UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h,
-+
+        brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
-+
+        Fixey Fixey.
-+
-+
+-10-21 11:32  tim
-+
-+
+        * src/utils/GenericData.cpp, src/utils/Makefile,
-+
+        test/utils/Makefile, test/utils/UtilTest: remove some junk files
-+
-+
+-10-21 11:24  tim
-+
-+
+        * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
-+
-+
+-10-21 11:22  tim
-+
-+
+        * ChangeLog, src/brains/SimSetup.cpp,
-+
+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
-+
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
-+
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
-+
+        src/integrators/NVT.cpp, src/io/DumpReader.cpp,
-+
+        src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp,
-+
+        src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp,
-+
+        src/utils/GenericData.cpp, src/utils/GenericData.hpp,
-+
+        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
-+
+        src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp,
-+
+        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
-+
+        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
-+
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-+
+        src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
-+
+        GenericData
-+
-+
+-10-21 10:25  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
-+
+        module.
-+
-+
+-10-21 10:24  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
-+
+        fortran lj module.
-+
-+
+-10-20 17:54  tim
-+
-+
+        * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
-+
+        test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
-+
+        test/utils/PropertyMapTestCase.cpp,
-+
+        test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
-+
+        GenericData and PropertyMap  pass unit test.
-+
-+
+-10-20 16:52  gezelter
-+
-+
+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
-+
+        DarkSide/sticky_interface.h: fixed a fortran name problem
-+
-+
+-10-20 16:38  tim
-+
-+
+        * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
-+
+        GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
-+
+        UtilTest, UtilTest.cpp: adding generic data test case
-+
-+
+-10-20 16:16  chuckv
-+
-+
+        * configure, ac-tools/aclocal.m4,
-+
+        src/UseTheForce/DarkSide/Makefile,
-+
+        src/UseTheForce/DarkSide/mpiSimulation.F90,
-+
+        src/UseTheForce/DarkSide/mpiSimulation_interface.h,
-+
+        src/UseTheForce/DarkSide/simParallel.F90,
-+
+        src/UseTheForce/DarkSide/simParallel_interface.h,
-+
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp:
-+
+        Fortran/C++ interface de-obfuscation project appears to be
-+
+        complete!  Woo hoo!
-+
-+
+-10-20 15:47  chuckv
-+
-+
+        * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
-+
+        fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
-+
+        continues
-+
-+
+-10-20 15:46  chuckv
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp,
-+
+        UseTheForce/doForces_interface.h,
-+
+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90,
-+
+        UseTheForce/DarkSide/atype_interface.h,
-+
+        UseTheForce/DarkSide/eam_interface.h,
-+
+        UseTheForce/DarkSide/gb_interface.h,
-+
+        UseTheForce/DarkSide/mpiSimulation_interface.h,
-+
+        UseTheForce/DarkSide/shapes_interface.h,
-+
+        UseTheForce/DarkSide/simulation_interface.h,
-+
+        UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp,
-+
+        brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
-+
+        de-obfuscation project (It is a very long story)
-+
-+
+-10-20 13:07  tim
-+
-+
+        * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
-+
+        test/math/SquareMatrix3TestCase.cpp,
-+
+        test/math/SquareMatrixTestCase.cpp,
-+
+        test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
-+
-+
+-10-20 00:52  tim
-+
-+
+        * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
-+
+        SnapshotManager in design phase
-+
-+
+-10-19 23:54  gezelter
-+
-+
+        * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
-+
+        problem prevented linking
-+
-+
+-10-19 23:54  gezelter
-+
-+
+        * src/UseTheForce/Shapes_FF.cpp: fixed include
-+
-+
+-10-19 23:26  gezelter
-+
-+
+        * src/utils/: Makefile, definitions.F90, definitions_module.F90,
-+
+        oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
-+
+        more fortran name mangling
-+
-+
+-10-19 23:23  gezelter
-+
-+
+        * src/profiling/timing.F90: yet more fortran renaming
-+
-+
+-10-19 23:19  gezelter
-+
-+
+        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
-+
+        do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
-+
+        notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
-+
+        wrappers.F90: Fortran name cleanup continues
-+
-+
+-10-19 23:12  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
-+
+        broken fortran stuff
-+
-+
+-10-19 23:02  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
-+
+        atype_interface.h, atype_module.F90, atype_module_interface.h,
-+
+        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
-+
+        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
-+
+        calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90,
-+
+        eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90,
-+
+        gb_interface.h, gb_module_interface.h, mpiSimulation.F90,
-+
+        mpiSimulation_interface.h, mpiSimulation_module.F90,
-+
+        mpisimulation_module_interface.h, reactionField.F90, shapes.F90,
-+
+        shapes_interface.h, shapes_module.h, simulation.F90,
-+
+        simulation_interface.h, simulation_module.F90,
-+
+        simulation_module_interface.h, sticky.F90, sticky_interface.h,
-+
+        sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
-+
+        name sanity on the fortran side
-+
-+
+-10-19 19:18  tim
-+
-+
+        * test/math/SquareMatrix3TestCase.hpp: [no log message]
-+
-+
+-10-19 18:01  tim
-+
-+
+        * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
-+
+        src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
-+
+        except diagonalize(), all of functions in math library pass the
-+
+        test
-+
-+
+-10-19 17:43  chuckv
-+
-+
+        * src/UseTheForce/do_Forces.h: Added correct prototypes for
-+
+        C-fortran interface functions.
-+
-+
+-10-19 17:37  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: atype_module_interface.h,
-+
+        eam_module_inteface.h, gb_module_interface.h,
-+
+        mpisimulation_module_interface.h, simulation_module_interface.h,
-+
+        sticky_pair_module_interface.h: Added correct prototypes for
-+
+        C-fortran interface functions.
-+
-+
+-10-19 16:28  tim
-+
-+
+        * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
-+
+        src/math/SquareMatrix.hpp, src/math/Vector.hpp,
-+
+        test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp,
-+
+        test/math/RectMatrixTestCase.cpp,
-+
+        test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp,
-+
+        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
-+
+        bugs get fixed at math library
-+
-+
+-10-19 15:43  chuckv
-+
-+
+        * src/UseTheForce/: DarkSide/atype_module_interface.h,
-+
+        DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
-+
+        DarkSide/mpisimulation_module_interface.h,
-+
+        DarkSide/simulation_module_interface.h,
-+
+        DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90,
-+
+        DarkSide/atype_module.F90, DarkSide/calc_gb.F90,
-+
+        DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90,
-+
+        DarkSide/simulation_module.F90, do_Forces.F90,
-+
+        fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90,
-+
+        notifycutoffs_module_interface.h: Added new files for fortran
-+
+        interface.
-+
-+
+-10-19 15:43  gezelter
-+
-+
+        * src/UseTheForce/Makefile: regressing
-+
-+
+-10-19 15:40  gezelter
-+
-+
+        * src/: UseTheForce/DarkSide/calc_shapes.F90,
-+
+        UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
-+
+        working on shapes for portability
-+
-+
+-10-19 15:40  gezelter
-+
-+
+        * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
-+
-+
+-10-19 13:21  chrisfen
-+
-+
+        * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
-+
+        findBegin
-+
-+
+-10-18 23:34  tim
-+
-+
+        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
-+
+        are fixed in Vector class
-+
-+
+-10-18 23:28  tim
-+
-+
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
-+
+        some bugs in RectMatrixTestCase
-+
-+
+-10-18 23:21  tim
-+
-+
+        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
-+
+        test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
-+
+        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
-+
+        test/math/VectorTestCase.hpp: implement more test cases
-+
-+
+-10-18 18:13  tim
-+
-+
+        * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
-+
+        src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
-+
+        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
-+
+        src/utils/StringTokenizer.hpp, test/math/Makefile,
-+
+        test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
-+
+        tests on math library
-+
-+
+-10-18 16:03  tim
-+
-+
+        * test/math/: Makefile, QuaternionTestCase.cpp,
-+
+        QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
-+
+        SquareMatrix3TestCase.cpp, Vector3TestCase.cpp,
-+
+        Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
-+
+        more testing units
-+
-+
+-10-18 12:07  tim
-+
-+
+        * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
-+
+        math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
-+
+        math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
-+
+        utils/GenericFactory.hpp: fix some bugs in Quaternion class
-+
-+
+-10-18 11:30  gezelter
-+
-+
+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
-+
+        Your basic run of the mill real-valued versions of Y_l^m(\theta,
-+
+        \phi)
-+
-+
+-10-18 11:29  gezelter
-+
-+
+        * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
-+
+        types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
-+
+        utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
-+
+        Shapes into OOPSE
-+
-+
+-10-18 10:21  gezelter
-+
-+
+        * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
-+
-+
+-10-18 00:23  tim
-+
-+
+        * test/math/VectorTestCase.hpp: adding  vector test case
-+
-+
+-10-18 00:23  tim
-+
-+
+        * src/utils/GenericFactory.hpp: adding generic factory and vector
-+
+        test case
-+
-+
+-10-16 20:19  tim
-+
-+
+        * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
-+
+        SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
-+
+        progress
-+
-+
+-10-15 20:31  tim
-+
-+
+        * src/math/Quaternion.hpp: add quaternion class
-+
-+
+-10-15 16:11  tim
-+
-+
+        * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
-+
+        IfstrstreamTestCase.hpp: adding test file
-+
-+
+-10-15 16:10  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
-+
-+
+-10-15 15:42  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
-+
-+
+-10-15 15:35  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
-+
-+
+-10-15 15:34  tim
-+
-+
+        * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
-+
+        namespace oopse
-+
-+
+-10-15 14:38  chuckv
-+
-+
+        * configure, ac-tools/aclocal.m4: Changed optimization flags for
-+
+        XLF and XLC.
-+
-+
+-10-15 13:28  tim
-+
-+
+        * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
-+
+        adding ifstrstream test case
-+
-+
+-10-15 13:20  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: fix include
-+
-+
+-10-15 13:18  tim
-+
-+
+        * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
-+
-+
+-10-15 13:17  tim
-+
-+
+        * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
-+
-+
+-10-15 13:16  tim
-+
-+
+        * test/io/: Makefile, ifstrstreamTestCase.cpp,
-+
+        ifstrstreamTestCase.hpp: adding test case for ifstrstream
-+
-+
+-10-15 10:37  tim
-+
-+
+        * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
-+
+        ifstrstreamTestCase.hpp: add ifstrstreamTestCase
-+
-+
+-10-15 10:20  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: add checkFilename Option
-+
-+
+-10-15 10:19  tim
-+
-+
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
-+
+        SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
-+
+        SquareMatrixTestCase class
-+
-+
+-10-15 02:52  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
-+
-+
+-10-14 18:28  tim
-+
-+
+        * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
-+
+        Vector.hpp: math library in progress
-+
-+
+-10-14 18:27  tim
-+
-+
+        * src/io/FileReader.hpp: FileReader in progress
-+
-+
+-10-13 18:53  tim
-+
-+
+        * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
-+
+        test in isOrthogonal of SquareMatrix is failed by some reasons
-+
-+
+-10-13 17:28  tim
-+
-+
+        * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
-+
+        class
-+
-+
+-10-13 17:27  tim
-+
-+
+        * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
-+
+        RectMatrixTestCase.hpp: adding testing unit
-+
-+
+-10-13 17:24  tim
-+
-+
+        * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
-+
-+
+-10-13 01:51  tim
-+
-+
+        * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
-+
+        Vector3.hpp: refactory vector and matrix classes
-+
-+
+-10-13 01:50  tim
-+
-+
+        * src/math/Vector3d.hpp: Remove some Makefile.in
-+
-+
+-10-12 18:57  tim
-+
-+
+        * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
-+
+        Matrix3x3d.hpp
-+
-+
+-10-12 14:08  tim
-+
-+
+        * doc/: cppstyle.html, style.css: adding c++ coding style
-+
-+
+-10-11 17:15  tim
-+
-+
+        * src/: constraints/AbstractClasses.hpp,
-+
+        integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
-+
+        change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
-+
-+
+-10-11 16:54  tim
-+
-+
+        * scripts/filepp: fix a bug in filepp
-+
-+
+-10-11 16:13  tim
-+
-+
+        * make/Makefile.in: using filepp to generate dependencies instead
-+
+        of compilers
-+
-+
+-10-11 16:10  tim
-+
-+
+        * scripts/filepp: filepp can be used to generate dependencies for
-+
+        c/c++ now
-+
-+
+-10-11 13:40  tim
-+
-+
+        * make/Makefile.in: remove -module from F90Options
-+
-+
+-10-11 13:01  tim
-+
-+
+        * make/Makefile.in: adding rules to move fortran 90 module to
-+
+        target directory
-+
-+
+-10-11 10:43  gezelter
-+
-+
+        * make/Makefile.in: fixed makefile.in
-+
-+
+-10-11 09:51  tim
-+
-+
+        * scripts/filepp: remove "use bytes" which causes problem in sgi
-+
+        machine
-+
-+
+-10-11 09:26  tim
-+
-+
+        * forceFields/Makefile: add Makefile
-+
-+
+-10-11 09:23  tim
-+
-+
+        * samples/: water/dimer/Makefile, water/spce/Makefile,
-+
+        water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
-+
+        water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
-+
+        directory
-+
-+
+-10-11 09:23  tim
-+
-+
+        * samples/argon/Makefile: remove argon.dump and argon.eor from
-+
+        Makefile
-+
-+
+-10-09 01:01  tim
-+
-+
+        * samples/: alkane/Makefile.in, argon/Makefile.in,
-+
+        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
-+
+        Remove some Makefile.in
-+
-+
+-10-08 18:15  tim
-+
-+
+        * make/Makefile.in: [no log message]
-+
-+
+-10-08 17:51  tim
-+
-+
+        * make/Makefile.in: fix make install
-+
-+
+-10-08 17:10  tim
-+
-+
+        * make/Makefile.in: adding make install
-+
-+
+-10-08 17:04  tim
-+
-+
+        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
-+
+        metals/Makefile, minimizer/Makefile, water/Makefile.in,
-+
+        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
-+
+        water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
-+
+        water/ssde/Makefile, water/ssde/Makefile.in,
-+
+        water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
-+
+        water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
-+
+        zcons/Makefile.in: add Makefile to sample directory
-+
-+
+-10-06 18:03  gezelter
-+
-+
+        * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
-+
+        stuff
-+
-+
+-10-06 18:03  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        make/Doxyfile, src/applications/getopt.c,
-+
+        src/applications/getopt1.c, src/applications/gnugetopt.h: more
-+
+        build fixes
-+
-+
+-10-06 17:20  tim
-+
-+
+        * make/: Doxyfile, Makefile.in: adding doxygen configuration file
-+
-+
+-10-06 17:19  tim
-+
-+
+        * scripts/filepp: filepp can handle different fortran module case
-+
+        and suffix
-+
-+
+-10-06 16:27  gezelter
-+
-+
+        * src/restraints/Restraints.cpp: Chris doesn't know about the
-+
+        OOPSE-2.0 directory structure yet
-+
-+
+-10-06 16:27  gezelter
-+
-+
+        * ChangeLog: Yeah yeah, we'lll get around to it later
-+
+-10-06 16:22  gezelter
-<
+        * configure, ac-tools/configure.in, ac-tools/fortran90.m4: cleaning
-<
+        up build process
->
+        * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
->
+        make/Makefile.in: cleaning up build process
-+
+-10-06 15:01  chrisfen
-+
-+
+        * src/restraints/Restraints.cpp: made the file reading in
-+
+        restraints more intelligent - no longer gives uninformative seg
-+
+        faults
-+
-+
+-10-06 14:55  gezelter
-+
-+
+        * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
-+
+-10-06 14:51  gezelter
-<
+        * LICENSE, MPIobj/dummy: Cleaning up a bit
->
+        * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
->
+        scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
-+
+-10-06 13:53  tim
-+
-+
+        * make/: Makefile, Makefile.in: fix make statistics
-+
-+
+-10-06 13:18  tim
-+
-+
+        * make/: Makefile, Makefile.in: adding GNU make functions to
-+
+        combine all of the static libraries to a big library
-+
-+
+-10-05 17:57  tim
-+
-+
+        * make/: Makefile, Makefile.in:  adding shared library flag
-+
-+
+-10-05 14:37  tim
-+
-+
+        * src/: Makefile, UseTheForce/Makefile,
-+
+        UseTheForce/mpiSimulation_module.F90,
-+
+        UseTheForce/DarkSide/Makefile,
-+
+        UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
-+
+        mpiSimulation_module to DarkSide
-+
-+
+-10-05 14:35  tim
-+
-+
+        * make/: Makefile, Makefile.in: building MPI version;using static
-+
+        library instead of shared library
-+
-+
+-10-05 09:14  tim
-+
-+
+        * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
-+
+        to filepp
-+
-+
+-10-04 15:56  tim
-+
-+
+        * make/: Makefile, Makefile.in: add make cvslog
-+
-+
+-10-04 11:24  gezelter
-+
-+
+        * make/: Makefile, Makefile.in: more work on the parallel build
-+
-+
+-10-04 11:06  gezelter
-+
-+
+        * make/: Makefile, Makefile.in: changes to backport declare flags
-+
-+
+-10-04 10:27  gezelter
-+
-+
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
-+
+        DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
-+
+        shapes
-+
-+
+-10-01 23:40  tim
-+
-+
+        * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
-+
-+
+-10-01 23:22  tim
-+
-+
+        * make/: Makefile, Makefile.in: add oopse_ as library prefix
-+
-+
+-10-01 16:59  tim
-+
-+
+        * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
-+
+-10-01 16:22  gezelter
-<
+        * Makefile, ac-tools/aclocal.m4: A few minor build changes
->
+        * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
->
+        few minor build changes
-+
+-10-01 16:11  tim
-+
-+
+        * scripts/filepp: adding fortran90 make dependency tool
-+
-+
+-09-30 10:41  tim
-+
-+
+        * make/: Makefile, Makefile.in: make clean is smart enough to only
-+
+        remove object files belong to current package.  turn off silent
-+
+        mode
-+
-+
+-09-29 16:55  tim
-+
-+
+        * src/: Makefile, UseTheForce/Makefile,
-+
+        UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
-+
+        applications/oopse/Makefile, applications/simpleBuilder/Makefile,
-+
+        brains/Makedepend, brains/Makefile, constraints/Makefile,
-+
+        integrators/Makefile, io/Makefile, math/Makefile,
-+
+        minimizers/Makefile, primitives/Makefile, profiling/Makefile,
-+
+        restraints/Makefile, types/Makefile, utils/Makefile,
-+
+        visitors/Makefile: define DEV_ROOT as relative path
-+
-+
+-09-29 16:54  tim
-+
-+
+        * make/: Makefile, Makefile.in: get the relative path by shell
-+
+        script
-+
-+
+-09-29 16:32  tim
-+
-+
+        * make/Makefile: eliminate DEV_ROOT by relative path
-+
-+
+-09-29 13:37  tim
-+
-+
+        * make/Makefile.in: add PackageLibs;  fix dependency rule
-+
+-09-29 12:57  gezelter
+        * configure, ac-tools/configure.in: updates
-+
+-09-29 12:56  gezelter
-+
-+
+        * make/: Make.conf.in, Makefile.in: Working on make stuff
-+
+-09-29 12:46  tim
+        * Makefile: If makefile does not exist, print error message
-+
+-09-29 12:12  tim
-+
-+
+        * make/: Make.conf.in, Makefile: fix dependencies rule
-+
+-09-29 10:58  gezelter
-<
+        * Makefile: still working on build process
->
+        * Makefile, make/Makefile: still working on build process
-+
+-09-29 10:00  tim
-+
-+
+        * make/Makefile: add print statment to rules
-+
-+
+-09-29 09:59  tim
-+
-+
+        * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
-+
+        applications/dump2Xyz/Makefile, applications/oopse/Makefile,
-+
+        applications/simpleBuilder/Makefile, brains/Makefile,
-+
+        constraints/Makefile, integrators/Makefile, io/Makefile,
-+
+        math/Makefile, minimizers/Makefile, primitives/Makefile,
-+
+        profiling/Makefile, restraints/Makefile, types/Makefile,
-+
+        utils/Makefile, visitors/Makefile: change Makefile to relative path
-+
-+
+-09-28 21:55  tim
-+
-+
+        * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
-+
+        which cause headache in bulding libutils
-+
-+
+-09-28 18:24  tim
-+
-+
+        * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
-+
+        Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
-+
+        Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
-+
+        LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp,
-+
+        MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp,
-+
+        nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo,
-+
+        simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp,
-+
+        dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c,
-+
+        dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile,
-+
+        oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp,
-+
+        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
-+
+        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
-+
+        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
-+
+        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old,
-+
+        simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp,
-+
+        simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp,
-+
+        simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo,
-+
+        simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h:
-+
+        change directory structure of application. Every executable file is
-+
+        replaced in seperate directory
-+
-+
+-09-28 17:15  gezelter
-+
-+
+        * lib/dummy: Keep that lib around, please.
-+
+-09-28 17:14  gezelter
-<
+        * Makefile, configure, ac-tools/configure.in: starting a configure
-<
+        version
->
+        * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
->
+        starting a configure version
-+
+-09-28 16:08  tim
-+
-+
+        * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
-+
+        UseTheForce/DarkSide/Makefile,
-+
+        UseTheForce/DarkSide/notifyCutoffs.F90,
-+
+        UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend,
-+
+        brains/Makefile, brains/simulation_module.F90: move fortran files
-+
+        around to solve dependency problem
-+
+-09-28 15:43  tim
-<
+        * Makefile: [no log message]
->
+        * Makefile, src/UseTheForce/ForceFields.hpp,
->
+        src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
->
+        src/applications/Makedepend, src/applications/Makefile,
->
+        src/brains/Makedepend, src/brains/simulation_module.F90,
->
+        src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp,
->
+        src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
->
+        src/utils/Makefile: [no log message]
-+
+-09-28 15:41  tim
-+
-+
+        * make/Makefile, scripts/sfmakedepend: fix fortran dependency
-+
+        problem
-+
-+
+-09-28 11:13  tim
-+
-+
+        * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
-+
+        src/io/Makefile: add yacc and lex rules
-+
-+
+-09-27 15:24  tim
-+
-+
+        * make/Makefile: adding include path to F90Options
-+
-+
+-09-27 15:13  tim
-+
-+
+        * make/Makefile: change suffix from .cc to .cpp
-+
-+
+-09-24 11:27  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
-+
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp,
-+
+        UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp,
-+
+        UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp,
-+
+        UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90,
-+
+        UseTheForce/DarkSide/calc_LJ_FF.F90,
-+
+        UseTheForce/DarkSide/notifyCutoffs.F90,
-+
+        UseTheForce/DarkSide/switch_module.F90,
-+
+        applications/BaseLattice.cpp, applications/Dump2XYZ.cpp,
-+
+        applications/Dump2XYZCmd.c, applications/Lattice.cpp,
-+
+        applications/Lattice.hpp, applications/LatticeCreator.cpp,
-+
+        applications/LatticeCreator.hpp, applications/LatticeFactory.cpp,
-+
+        applications/MoLocator.cpp, applications/MoLocator.hpp,
-+
+        applications/cmdline.c, applications/nanoBuilder.cpp,
-+
+        applications/oopse.cpp, applications/simpleBuilder.cpp,
-+
+        applications/simpleBuilderCmd.c, brains/Exclude.cpp,
-+
+        brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp,
-+
+        brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
-+
+        brains/mpiSimulation.cpp, brains/mpiSimulation.hpp,
-+
+        constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp,
-+
+        integrators/AbstractClasses.hpp, integrators/Integrator.cpp,
-+
+        integrators/Integrator.hpp, integrators/NPT.cpp,
-+
+        integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp,
-+
+        integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c,
-+
+        io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp,
-+
+        io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp,
-+
+        io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp,
-+
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
-+
+        io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c,
-+
+        io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h,
-+
+        io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c,
-+
+        math/MatVec3.h, math/randomSPRNG.cpp,
-+
+        minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp,
-+
+        minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp,
-+
+        minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp,
-+
+        primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp,
-+
+        primitives/BendExtensions.cpp, primitives/Bond.cpp,
-+
+        primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp,
-+
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
-+
+        primitives/GhostBend.cpp, primitives/Molecule.cpp,
-+
+        primitives/Molecule.hpp, primitives/RigidBody.cpp,
-+
+        primitives/RigidBody.hpp, primitives/SRI.hpp,
-+
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
-+
+        primitives/Torsion.cpp, primitives/TorsionExtensions.cpp,
-+
+        profiling/mdProfile.cpp, restraints/Restraints.cpp,
-+
+        restraints/Restraints.hpp, types/AtomStamp.cpp,
-+
+        types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp,
-+
+        types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp,
-+
+        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
-+
+        types/MakeStamps.cpp, types/MakeStamps.hpp,
-+
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
-+
+        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
-+
+        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
-+
+        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp,
-+
+        utils/StreamTokenizer.cpp, utils/StringUtils.c,
-+
+        utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c,
-+
+        utils/simError.c, visitors/AtomVisitor.cpp,
-+
+        visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp,
-+
+        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
-+
+        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
-+
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
-+
+        visitors/ZconsVisitor.hpp: change the #include in source files
-+
+-09-23 23:16  gezelter
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
-+
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
-+
+        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
-+
+        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
-+
+        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
-+
+        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
-+
+        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
-+
+        src/UseTheForce/fForceField.h,
-+
+        src/UseTheForce/fSwitchingFunction.h,
-+
+        src/UseTheForce/fortranWrapDefines.hpp,
-+
+        src/UseTheForce/fortranWrappers.cpp,
-+
+        src/UseTheForce/fortranWrappers.hpp,
-+
+        src/UseTheForce/mpiComponentPlan.h,
-+
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
-+
+        src/UseTheForce/mpiSimulation_module.F90,
-+
+        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
-+
+        src/UseTheForce/DarkSide/atype_module.F90,
-+
+        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
-+
+        src/UseTheForce/DarkSide/calc_charge_charge.F90,
-+
+        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
-+
+        src/UseTheForce/DarkSide/calc_eam.F90,
-+
+        src/UseTheForce/DarkSide/calc_gb.F90,
-+
+        src/UseTheForce/DarkSide/calc_reaction_field.F90,
-+
+        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
-+
+        src/UseTheForce/DarkSide/force_globals.F90,
-+
+        src/UseTheForce/DarkSide/neighborLists.F90,
-+
+        src/UseTheForce/DarkSide/notifyCutoffs.F90,
-+
+        src/UseTheForce/DarkSide/switch_module.F90,
-+
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
-+
+        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
-+
+        src/io/DumpWriter.cpp, src/io/Globals.cpp,
-+
+        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
-+
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
-+
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
-+
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
-+
+        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
-+
+        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
-+
+        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
-+
+        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
-+
+        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
-+
+        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
-+
+        src/types/BondStamp.hpp, src/types/Component.cpp,
-+
+        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
-+
+        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
-+
+        src/types/MakeStamps.hpp, src/types/Makefile,
-+
+        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
-+
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
-+
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
-+
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
-+
+        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
-+
+        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
-+
+        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
-+
+        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
-+
+        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
-+
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
-+
+        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
-+
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
-+
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
-+
+        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
-+
+        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
-+
+        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
-+
+        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
-+
+        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
-+
+        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
-+
+        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
-+
+        src/minimizers/OOPSEMinimizer.cpp,
-+
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
-+
+        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
-+
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
-+
+        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
-+
+        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
-+
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
-+
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
-+
+        src/primitives/Makefile, src/primitives/Molecule.cpp,
-+
+        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
-+
+        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
-+
+        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
-+
+        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
-+
+        src/restraints/Makefile, src/restraints/Restraints.cpp,
-+
+        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
-+
+        src/utils/GenericData.hpp, src/utils/Makefile,
-+
+        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
-+
+        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
-+
+        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
-+
+        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
-+
+        src/utils/Utility.hpp, src/utils/definitions_module.F90,
-+
+        src/utils/fError.c, src/utils/oopseMPI_module.F90,
-+
+        src/utils/simError.c, src/utils/simError.h,
-+
+        src/utils/status_module.F90, src/utils/vector_class.F90,
-+
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
-+
+        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
-+
+        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
-+
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
-+
+        src/visitors/RigidBodyVisitor.cpp,
-+
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-+
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
-+
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
-+
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
-+
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
-+
+        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
-+
+        samples/zcons/Makefile.in, samples/zcons/water.md,
-+
+        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
-+
+        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
-+
+        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
-+
+        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
-+
+        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
-+
+        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
-+
+        src/applications/LatticeCreator.cpp,
-+
+        src/applications/LatticeCreator.hpp,
-+
+        src/applications/LatticeFactory.cpp,
-+
+        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
-+
+        src/applications/Makefile, src/applications/MoLocator.cpp,
-+
+        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
-+
+        src/applications/cmdline.c, src/applications/cmdline.h,
-+
+        src/applications/getopt.c, src/applications/getopt1.c,
-+
+        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
-+
+        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
-+
+        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
-+
+        src/applications/simpleBuilder.ggo,
-+
+        src/applications/simpleBuilderCmd.c,
-+
+        src/integrators/AbstractClasses.hpp,
-+
+        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
-+
+        src/integrators/Integrator.hpp, src/integrators/Makefile,
-+
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
-+
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
-+
+        src/integrators/NVT.cpp, src/profiling/Makefile,
-+
+        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
-+
+        src/profiling/timing.F90, samples/metals/Au_bulk.in,
-+
+        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
-+
+        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
-+
+        samples/water/dimer/two.in, samples/water/dimer/two.md,
-+
+        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
-+
+        samples/water/spce/spce.in, samples/water/spce/spce.md,
-+
+        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
-+
+        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
-+
+        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
-+
+        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
-+
+        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
-+
+        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
-+
+        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
-+
+        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
-+
+        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
-+
+        samples/alkane/butane.in, samples/alkane/butane.md,
-+
+        samples/argon/500.in, samples/argon/500.md,
-+
+        samples/argon/Makefile.in, samples/argon/ar864.in,
-+
+        samples/argon/ar864.md, samples/argon/argonNVT.in,
-+
+        samples/argon/argonNVT.md, samples/argon/lj.md,
-+
+        samples/lipid/5x5.in, samples/lipid/5x5.md,
-+
+        samples/lipid/Makefile.in, samples/lipid/lipid.md,
-+
+        samples/lipid/water.md, samples/minimizer/Makefile.in,
-+
+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
-+
+        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
-+
+        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
-+
+        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
-+
+        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
-+
+        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
-+
+        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
-+
+        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
-+
+        forceFields/EAM.VC.frc, forceFields/EAM.frc,
-+
+        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
-+
+        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
-+
+        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
-+
+        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
-+
+        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
-+
+        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
+        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
-<
+        ac-tools/install-sh, ac-tools/shtool: Import of OOPSE v. 2.0
->
+        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
->
+        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
+-09-23 23:16  gezelter
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
-+
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
-+
+        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
-+
+        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
-+
+        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
-+
+        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
-+
+        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
-+
+        src/UseTheForce/fForceField.h,
-+
+        src/UseTheForce/fSwitchingFunction.h,
-+
+        src/UseTheForce/fortranWrapDefines.hpp,
-+
+        src/UseTheForce/fortranWrappers.cpp,
-+
+        src/UseTheForce/fortranWrappers.hpp,
-+
+        src/UseTheForce/mpiComponentPlan.h,
-+
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
-+
+        src/UseTheForce/mpiSimulation_module.F90,
-+
+        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
-+
+        src/UseTheForce/DarkSide/atype_module.F90,
-+
+        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
-+
+        src/UseTheForce/DarkSide/calc_charge_charge.F90,
-+
+        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
-+
+        src/UseTheForce/DarkSide/calc_eam.F90,
-+
+        src/UseTheForce/DarkSide/calc_gb.F90,
-+
+        src/UseTheForce/DarkSide/calc_reaction_field.F90,
-+
+        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
-+
+        src/UseTheForce/DarkSide/force_globals.F90,
-+
+        src/UseTheForce/DarkSide/neighborLists.F90,
-+
+        src/UseTheForce/DarkSide/notifyCutoffs.F90,
-+
+        src/UseTheForce/DarkSide/switch_module.F90,
-+
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
-+
+        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
-+
+        src/io/DumpWriter.cpp, src/io/Globals.cpp,
-+
+        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
-+
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
-+
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
-+
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
-+
+        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
-+
+        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
-+
+        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
-+
+        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
-+
+        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
-+
+        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
-+
+        src/types/BondStamp.hpp, src/types/Component.cpp,
-+
+        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
-+
+        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
-+
+        src/types/MakeStamps.hpp, src/types/Makefile,
-+
+        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
-+
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
-+
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
-+
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
-+
+        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
-+
+        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
-+
+        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
-+
+        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
-+
+        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
-+
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
-+
+        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
-+
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
-+
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
-+
+        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
-+
+        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
-+
+        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
-+
+        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
-+
+        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
-+
+        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
-+
+        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
-+
+        src/minimizers/OOPSEMinimizer.cpp,
-+
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
-+
+        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
-+
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
-+
+        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
-+
+        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
-+
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
-+
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
-+
+        src/primitives/Makefile, src/primitives/Molecule.cpp,
-+
+        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
-+
+        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
-+
+        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
-+
+        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
-+
+        src/restraints/Makefile, src/restraints/Restraints.cpp,
-+
+        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
-+
+        src/utils/GenericData.hpp, src/utils/Makefile,
-+
+        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
-+
+        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
-+
+        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
-+
+        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
-+
+        src/utils/Utility.hpp, src/utils/definitions_module.F90,
-+
+        src/utils/fError.c, src/utils/oopseMPI_module.F90,
-+
+        src/utils/simError.c, src/utils/simError.h,
-+
+        src/utils/status_module.F90, src/utils/vector_class.F90,
-+
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
-+
+        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
-+
+        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
-+
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
-+
+        src/visitors/RigidBodyVisitor.cpp,
-+
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-+
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
-+
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
-+
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
-+
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
-+
+        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
-+
+        samples/zcons/Makefile.in, samples/zcons/water.md,
-+
+        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
-+
+        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
-+
+        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
-+
+        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
-+
+        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
-+
+        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
-+
+        src/applications/LatticeCreator.cpp,
-+
+        src/applications/LatticeCreator.hpp,
-+
+        src/applications/LatticeFactory.cpp,
-+
+        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
-+
+        src/applications/Makefile, src/applications/MoLocator.cpp,
-+
+        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
-+
+        src/applications/cmdline.c, src/applications/cmdline.h,
-+
+        src/applications/getopt.c, src/applications/getopt1.c,
-+
+        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
-+
+        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
-+
+        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
-+
+        src/applications/simpleBuilder.ggo,
-+
+        src/applications/simpleBuilderCmd.c,
-+
+        src/integrators/AbstractClasses.hpp,
-+
+        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
-+
+        src/integrators/Integrator.hpp, src/integrators/Makefile,
-+
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
-+
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
-+
+        src/integrators/NVT.cpp, src/profiling/Makefile,
-+
+        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
-+
+        src/profiling/timing.F90, samples/metals/Au_bulk.in,
-+
+        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
-+
+        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
-+
+        samples/water/dimer/two.in, samples/water/dimer/two.md,
-+
+        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
-+
+        samples/water/spce/spce.in, samples/water/spce/spce.md,
-+
+        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
-+
+        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
-+
+        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
-+
+        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
-+
+        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
-+
+        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
-+
+        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
-+
+        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
-+
+        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
-+
+        samples/alkane/butane.in, samples/alkane/butane.md,
-+
+        samples/argon/500.in, samples/argon/500.md,
-+
+        samples/argon/Makefile.in, samples/argon/ar864.in,
-+
+        samples/argon/ar864.md, samples/argon/argonNVT.in,
-+
+        samples/argon/argonNVT.md, samples/argon/lj.md,
-+
+        samples/lipid/5x5.in, samples/lipid/5x5.md,
-+
+        samples/lipid/Makefile.in, samples/lipid/lipid.md,
-+
+        samples/lipid/water.md, samples/minimizer/Makefile.in,
-+
+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
-+
+        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
-+
+        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
-+
+        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
-+
+        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
-+
+        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
-+
+        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
-+
+        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
-+
+        forceFields/EAM.VC.frc, forceFields/EAM.frc,
-+
+        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
-+
+        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
-+
+        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
-+
+        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
-+
+        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
-+
+        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
+        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
-<
+        ac-tools/install-sh, ac-tools/shtool: Initial revision
->
+        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
->
+        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

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Comparing trunk/OOPSE-2.0/ChangeLog (file contents): Revision 1536 by gezelter, Wed Oct 6 21:27:02 2004 UTC vs. Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC

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Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1536 by gezelter, Wed Oct 6 21:27:02 2004 UTC vs.
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC