--- trunk/OOPSE-3.0/ChangeLog 2004/10/20 18:07:08 1616 +++ trunk/OOPSE-3.0/ChangeLog 2004/10/28 22:26:32 1681 @@ -1,3 +1,404 @@ +2004-10-28 16:28 tim + + * src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/ReplaceWildCardTestCase.cpp: Done with combination + +2004-10-28 16:11 tim + + * src/utils/next_combination.hpp: change documentation of + next_combination.hpp + +2004-10-28 15:41 tim + + * ChangeLog, src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working + +2004-10-28 15:01 tim + + * src/utils/next_combination.hpp: adding replace wildcard function + +2004-10-28 14:33 tim + + * src/utils/next_combination.hpp: Minor change + +2004-10-28 14:06 tim + + * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, + src/applications/simpleBuilder/simpleBuilder.cpp, + src/utils/next_combination.hpp, test/utils/Makefile, + test/utils/NextCombinationTestCase.cpp, + test/utils/ReplaceWildCardTestCase.cpp, + test/utils/next_combination.hpp: STL next_permutation like + next_combination is working + +2004-10-28 12:22 chrisfen + + * src/UseTheForce/WATER.cpp: fix of setDipoles + +2004-10-28 12:20 gezelter + + * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the + shapeFile + +2004-10-28 12:20 gezelter + + * samples/shape/linear.md: forgot the orientation line + +2004-10-28 11:56 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, + UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate + declaration foo + +2004-10-28 11:55 gezelter + + * samples/lipid/5x5.md: uncommented .in line + +2004-10-28 10:42 tim + + * test/utils/: Makefile, NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp, next_combination.hpp: next_combination + in progress + +2004-10-28 10:15 tim + + * test/utils/: NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp: adding next_combination test case + +2004-10-28 10:02 tim + + * test/utils/next_combination.hpp: STL Compatible combination + sequence generator + +2004-10-28 01:23 tim + + * test/utils/: GenerateCombination.hpp, + ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp + +2004-10-28 01:16 tim + + * test/utils/GenerateCombination.hpp: a STL next_permutaion like + next_combination function. + +2004-10-27 22:27 tim + + * test/utils/ReplaceWildCard.hpp: no message + +2004-10-27 22:14 tim + + * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: + ReplaceWildCard(recursive version) is working, need refactoring. An + iterative version is on the way + +2004-10-27 21:28 tim + + * test/utils/: Makefile, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress + +2004-10-27 21:08 tim + + * test/utils/: ReplaceWildCardTestCase.cpp, + ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard + +2004-10-27 18:17 tim + + * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need + test + +2004-10-27 01:25 tim + + * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild + char matching is on the way + +2004-10-27 01:07 tim + + * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 + +2004-10-26 22:00 gezelter + + * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix + +2004-10-26 21:20 gezelter + + * src/UseTheForce/ForceFields.hpp: subclass foo + +2004-10-26 21:16 gezelter + + * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> + string conversion + +2004-10-26 19:01 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, + brains/SimSetup.hpp: char* -> string + +2004-10-26 17:25 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, + Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, + ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some + isXXX + +2004-10-26 17:25 gezelter + + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + define name collision + +2004-10-26 17:24 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, + UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, + UseTheForce/WATER.cpp, UseTheForce/doForces.F90, + UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: + forcefield refactoring for shapes + +2004-10-26 17:24 gezelter + + * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, + Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, + linear.md, linear.shape, toluene.shape: adding sample shape + directory + +2004-10-26 17:19 tim + + * ChangeLog, src/brains/DataStorage.cpp, + src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, + test/brains/DataStorageTestCase.cpp, + test/brains/DataStorageTestCase.hpp, test/brains/Makefile: + DataStorage passes unit test + +2004-10-26 13:03 chrisfen + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: + Changes to help advance shapes + +2004-10-26 13:02 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to + Shapes force field reader + +2004-10-26 12:28 tim + + * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and + SnapshotTestCase in progress + +2004-10-25 17:46 tim + + * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, + src/math/SquareMatrix3.hpp, src/math/Vector.hpp, + src/math/Vector3.hpp, test/brains/StuntDouble.hpp, + test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, + test/math/VectorTestCase.cpp: add getArray function to RectMatrix + and Vector classes + +2004-10-25 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. + +2004-10-24 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 + +2004-10-24 02:55 tim + + * src/utils/GenericFactory.hpp: GenericFactory pass unit test + +2004-10-23 18:09 tim + + * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, + StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, + RigidBody.cpp: Refactoring in progress + +2004-10-22 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 + +2004-10-22 17:59 chrisfen + + * src/: UseTheForce/LJFF.cpp, + UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear + god! It runs and conserves energy! + +2004-10-22 17:54 chrisfen + + * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY + +2004-10-22 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 + +2004-10-22 17:53 chrisfen + + * make/Makefile.in: compiler flags + +2004-10-22 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 + +2004-10-22 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 + +2004-10-22 15:21 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.hpp, Makefile: More on AtomType and + DirectionalAtomType + +2004-10-22 09:47 gezelter + + * src/types/AtomType.hpp: Adding AtomType + +2004-10-21 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 + +2004-10-21 16:30 tim + + * test/brains/: BrainsTest.cpp, Makefile, + SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, + SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for + Snapshot and snapshotManager. + +2004-10-21 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. + +2004-10-21 11:32 tim + + * src/utils/GenericData.cpp, src/utils/Makefile, + test/utils/Makefile, test/utils/UtilTest: remove some junk files + +2004-10-21 11:24 tim + + * test/utils/GenericData.hpp: remove backup of GenericData.hpp + +2004-10-21 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 + +2004-10-21 10:25 chuckv + + * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj + module. + +2004-10-21 10:24 chuckv + + * src/UseTheForce/DarkSide/lj_interface.h: Added interface for + fortran lj module. + +2004-10-20 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. + +2004-10-20 16:52 gezelter + + * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, + DarkSide/sticky_interface.h: fixed a fortran name problem + +2004-10-20 16:38 tim + + * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, + GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, + UtilTest, UtilTest.cpp: adding generic data test case + +2004-10-20 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! + +2004-10-20 15:47 chuckv + + * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, + fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project + continues + +2004-10-20 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) + +2004-10-20 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 + 2004-10-20 00:52 tim * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and