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

Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1603 by tim, Tue Oct 19 21:28:55 2004 UTC vs.
Revision 1681 by tim, Thu Oct 28 22:26:32 2004 UTC

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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
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+        * ChangeLog, src/utils/GenericFactory.hpp,
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+        test/utils/GenericFactoryTestCase.cpp,
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+        test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding
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+        GenericFactory Test Case. GenericFactory now can bed used to creat
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+        ForcefieldFactory and IntegratorFactory etc.
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+-10-24 23:08  tim
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+        * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
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+        brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
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+        brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
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+        get reconstructed
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+-10-24 02:55  tim
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+        * src/utils/GenericFactory.hpp: GenericFactory pass unit test
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+-10-23 18:09  tim
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+        * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
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+        StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
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+        RigidBody.cpp: Refactoring in progress
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+-10-22 18:09  tim
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+        * ChangeLog, src/brains/Snapshot.hpp,
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+        src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
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+        test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
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+        test/brains/StuntDouble.hpp: more work in Snapshot
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+-10-22 17:59  chrisfen
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+        * src/: UseTheForce/LJFF.cpp,
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+        UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
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+        god!  It runs and conserves energy!
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+-10-22 17:54  chrisfen
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+        * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
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+-10-22 17:53  chrisfen
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
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+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
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+        brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
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+        breakey
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+-10-22 17:53  chrisfen
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+        * make/Makefile.in: compiler flags
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+-10-22 16:20  gezelter
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
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+        brains/fSimulation.h, types/AtomType.hpp,
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+        types/DirectionalAtomType.hpp: fixey fixey
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+-10-22 15:22  gezelter
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+        * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
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+        charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
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+        lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
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+        fortran files and c/Fortran interfaces
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+-10-22 15:21  gezelter
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+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
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+        DirectionalAtomType.hpp, Makefile: More on AtomType and
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+        DirectionalAtomType
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+-10-22 09:47  gezelter
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+        * src/types/AtomType.hpp: Adding AtomType
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+-10-21 16:31  tim
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+        * ChangeLog, src/brains/Snapshot.hpp,
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+        src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
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+        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
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+        src/math/Vector.hpp, src/math/Vector3.hpp,
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+        test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
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+        Snapshot and SnapshotManager in progress
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+-10-21 16:30  tim
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+        * test/brains/: BrainsTest.cpp, Makefile,
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+        SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
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+        SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
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+        Snapshot and snapshotManager.
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+-10-21 15:15  gezelter
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
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+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
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+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
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+        UseTheForce/doForces_interface.h, UseTheForce/fForceField.h,
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+        UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h,
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+        brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
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+        Fixey Fixey.
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+-10-21 11:32  tim
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+        * src/utils/GenericData.cpp, src/utils/Makefile,
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+        test/utils/Makefile, test/utils/UtilTest: remove some junk files
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+-10-21 11:24  tim
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+        * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
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+-10-21 11:22  tim
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+        * ChangeLog, src/brains/SimSetup.cpp,
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+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
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+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
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+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
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+        src/integrators/NVT.cpp, src/io/DumpReader.cpp,
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+        src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp,
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+        src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp,
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+        src/utils/GenericData.cpp, src/utils/GenericData.hpp,
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+        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
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+        src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp,
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+        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
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+        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
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+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
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+        src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
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+        GenericData
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+-10-21 10:25  chuckv
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+        * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
-+
+        module.
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+-10-21 10:24  chuckv
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+        * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
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+        fortran lj module.
-+
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+-10-20 17:54  tim
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+        * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
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+        test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
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+        test/utils/PropertyMapTestCase.cpp,
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+        test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
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+        GenericData and PropertyMap  pass unit test.
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+-10-20 16:52  gezelter
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+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
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+        DarkSide/sticky_interface.h: fixed a fortran name problem
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+-10-20 16:38  tim
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+        * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
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+        GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
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+        UtilTest, UtilTest.cpp: adding generic data test case
-+
-+
+-10-20 16:16  chuckv
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+        * configure, ac-tools/aclocal.m4,
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+        src/UseTheForce/DarkSide/Makefile,
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+        src/UseTheForce/DarkSide/mpiSimulation.F90,
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+        src/UseTheForce/DarkSide/mpiSimulation_interface.h,
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+        src/UseTheForce/DarkSide/simParallel.F90,
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+        src/UseTheForce/DarkSide/simParallel_interface.h,
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+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp:
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+        Fortran/C++ interface de-obfuscation project appears to be
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+        complete!  Woo hoo!
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+-10-20 15:47  chuckv
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+        * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
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+        fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
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+        continues
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+-10-20 15:46  chuckv
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+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
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+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
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+        UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp,
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+        UseTheForce/doForces_interface.h,
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+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90,
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+        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
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+        de-obfuscation project (It is a very long story)
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+-10-20 13:07  tim
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+        * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
-+
+        test/math/SquareMatrix3TestCase.cpp,
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+        test/math/SquareMatrixTestCase.cpp,
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+        test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
-+
-+
+-10-20 00:52  tim
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+        * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
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+        SnapshotManager in design phase
-+
-+
+-10-19 23:54  gezelter
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+        * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
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+        problem prevented linking
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-+
+-10-19 23:54  gezelter
-+
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+        * src/UseTheForce/Shapes_FF.cpp: fixed include
-+
-+
+-10-19 23:26  gezelter
-+
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+        * src/utils/: Makefile, definitions.F90, definitions_module.F90,
-+
+        oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
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+        more fortran name mangling
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-+
+-10-19 23:23  gezelter
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+        * src/profiling/timing.F90: yet more fortran renaming
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+-10-19 23:19  gezelter
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+        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
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+        do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
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+        notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
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+        wrappers.F90: Fortran name cleanup continues
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+-10-19 23:12  gezelter
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+        * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
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+        broken fortran stuff
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+-10-19 23:02  gezelter
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+        * 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

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents): Revision 1603 by tim, Tue Oct 19 21:28:55 2004 UTC vs. Revision 1681 by tim, Thu Oct 28 22:26:32 2004 UTC

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1603 by tim, Tue Oct 19 21:28:55 2004 UTC vs.
Revision 1681 by tim, Thu Oct 28 22:26:32 2004 UTC