--- trunk/OOPSE-2.0/ChangeLog 2004/10/18 23:13:23 1594 +++ trunk/OOPSE-2.0/ChangeLog 2004/11/04 20:55:01 1712 @@ -1,3 +1,856 @@ +2004-11-04 14:48 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, + SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats + class + +2004-11-04 14:48 tim + + * src/brains/Stats.cpp: file Stats.cpp was initially added on + branch new_design. + +2004-11-04 14:48 tim + + * src/brains/Stats.hpp: file Stats.hpp was initially added on + branch new_design. + +2004-11-04 11:22 gezelter + + * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, + RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and + linearAxis are virtual in StuntDouble, but are implemented by + DirectionalAtom and RigidBody In StuntDouble, they should return + false and "-1" but there should be logic to figure them out in the + other two classes + +2004-11-04 11:20 gezelter + + * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't + remember what I did + +2004-11-04 11:20 gezelter + + * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky + +2004-11-04 11:20 gezelter + + * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX + in the entry_plug so that it only is set if the atoms really are in + the simulation + +2004-11-04 11:20 gezelter + + * samples/water/ssd/ssd.md: testing force fields + +2004-11-04 11:19 gezelter + + * samples/shape/linear.in: testing shapes + +2004-11-03 14:56 tim + + * src/brains/SimCreator.cpp: file SimCreator.cpp was initially + added on branch new_design. + +2004-11-03 14:56 tim + + * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator + class(similar as SimSetup) + +2004-11-03 14:56 tim + + * src/brains/SimCreator.hpp: file SimCreator.hpp was initially + added on branch new_design. + +2004-11-03 13:00 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, + UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, + brains/DataStorage.hpp, primitives/Atom.hpp, + primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, + visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get + compiled. Still a long way to go ...... + +2004-11-03 11:08 tim + + * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, + src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, + src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, + src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, + src/io/ZConsReader.cpp, src/primitives/Bend.cpp, + src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, + src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, + src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, + src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, + src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, + src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, + src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... + +2004-11-02 17:41 tim + + * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was + initially added on branch new_design. + +2004-11-02 17:41 tim + + * src/brains/Migrator.hpp: file Migrator.hpp was initially added on + branch new_design. + +2004-11-02 17:41 tim + + * src/: brains/Migrator.hpp, brains/SimModel.cpp, + utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. + Need unit test + +2004-11-02 11:59 tim + + * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: SimModel in progress + +2004-11-02 11:59 tim + + * src/brains/SimModel.cpp: file SimModel.cpp was initially added on + branch new_design. + +2004-11-02 10:28 chrisfen + + * src/: UseTheForce/DarkSide/shapes.F90, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes + looks like it's working + +2004-11-02 10:27 tim + + * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially + added on branch new_design. + +2004-11-02 10:27 tim + + * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some + functions for dealing with memory issue + +2004-11-02 10:23 tim + + * src/: brains/SimModel.hpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding + SimModel(something similar as SimInfo) + +2004-11-01 17:52 tim + + * src/: applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/DataStorage.hpp, brains/ForceFields.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, + constraints/ZConstraint.cpp, integrators/Integrator.cpp, + integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, + math/SquareMatrix3.hpp, math/Vector3.hpp, + minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.hpp, primitives/Torsion.hpp, + restraints/Restraints.cpp, types/TorsionType.hpp, + utils/PropertyMap.hpp, utils/StringTokenizer.hpp, + visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, + visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, + RigidBody and StuntDouble classes get compiled + +2004-11-01 16:40 tim + + * src/primitives/Torsion.hpp: file Torsion.hpp was initially added + on branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/Bend.hpp: file Bend.hpp was initially added on + branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/Bond.hpp: file Bond.hpp was initially added on + branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial + version of Bond, Bend and Torsion. + +2004-11-01 16:37 tim + + * src/types/BendType.hpp: file BendType.hpp was initially added on + branch new_design. + +2004-11-01 16:37 tim + + * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding + BondType, BendType, TorsionType + +2004-11-01 16:37 tim + + * src/types/TorsionType.hpp: file TorsionType.hpp was initially + added on branch new_design. + +2004-11-01 16:37 tim + + * src/types/BondType.hpp: file BondType.hpp was initially added on + branch new_design. + +2004-11-01 15:15 tim + + * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, + CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, + GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, + RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: + break, break and break..... + +2004-11-01 14:57 tim + + * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, + DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, + StuntDouble.hpp: these core classes get compiled + +2004-10-29 17:37 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule + class + +2004-10-29 17:28 chrisfen + + * src/: UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, + types/ShapeAtomType.cpp: still debugging + +2004-10-29 17:28 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: + shapes rcut calculator added + +2004-10-29 17:27 chrisfen + + * samples/shape/linear.md: shorter run + +2004-10-29 15:54 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. + +2004-10-29 11:22 tim + + * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove + some deprecated files + +2004-10-29 11:20 tim + + * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, + DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: + More painful reconstruction is coming !!! + +2004-10-28 17:34 tim + + * src/brains/DataStorage.hpp, src/utils/next_combination.hpp, + test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, + test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, + test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, + DirectionalAtom and RigidBody + +2004-10-28 17:26 tim + + * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/MoLocator.cpp, + src/applications/simpleBuilder/Vector3d.hpp, + src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: + remove old Vector3d.hpp from application/simpleBuilder + +2004-10-28 16:42 tim + + * src/utils/next_combination.hpp: Minor change in next_combination + +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 + SnapshotManager in design phase + +2004-10-19 23:54 gezelter + + * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace + problem prevented linking + +2004-10-19 23:54 gezelter + + * src/UseTheForce/Shapes_FF.cpp: fixed include + +2004-10-19 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 + +2004-10-19 23:23 gezelter + + * src/profiling/timing.F90: yet more fortran renaming + +2004-10-19 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 + +2004-10-19 23:12 gezelter + + * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some + broken fortran stuff + +2004-10-19 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 + +2004-10-19 19:18 tim + + * test/math/SquareMatrix3TestCase.hpp: [no log message] + +2004-10-19 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 + +2004-10-19 17:43 chuckv + + * src/UseTheForce/do_Forces.h: Added correct prototypes for + C-fortran interface functions. + +2004-10-19 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. + +2004-10-19 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 + +2004-10-19 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. + +2004-10-19 15:43 gezelter + + * src/UseTheForce/Makefile: regressing + +2004-10-19 15:40 gezelter + + * src/: UseTheForce/DarkSide/calc_shapes.F90, + UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: + working on shapes for portability + +2004-10-19 15:40 gezelter + + * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes + +2004-10-19 13:21 chrisfen + + * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around + findBegin + +2004-10-18 23:34 tim + + * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs + are fixed in Vector class + +2004-10-18 23:28 tim + + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix + some bugs in RectMatrixTestCase + +2004-10-18 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 + +2004-10-18 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 + +2004-10-18 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 + +2004-10-18 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 + +2004-10-18 11:30 gezelter + + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + Your basic run of the mill real-valued versions of Y_l^m(\theta, + \phi) + +2004-10-18 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 + +2004-10-18 10:21 gezelter + + * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType + +2004-10-18 00:23 tim + + * test/math/VectorTestCase.hpp: adding vector test case + +2004-10-18 00:23 tim + + * src/utils/GenericFactory.hpp: adding generic factory and vector + test case + 2004-10-16 20:19 tim * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, @@ -361,8 +1214,7 @@ 2004-09-29 12:56 gezelter - * make/: Make.conf.in, Makefile.in, _files/style.css: Working on - make stuff + * make/: Make.conf.in, Makefile.in: Working on make stuff 2004-09-29 12:46 tim @@ -628,8 +1480,7 @@ 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, - make/_files/style.css, samples/Makefile.in, + 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, @@ -804,8 +1655,7 @@ 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, - make/_files/style.css, samples/Makefile.in, + 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,