--- trunk/OOPSE-2.0/ChangeLog 2004/10/26 22:19:22 1648 +++ trunk/OOPSE-2.0/ChangeLog 2004/11/05 21:03:47 1714 @@ -1,3 +1,473 @@ +2004-11-04 21:56 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + primitives/Molecule.hpp: Pain...... + +2004-11-04 15:55 tim + + * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, + src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, + src/brains/Stats.hpp: time to break SimSetup + +2004-11-04 15:51 gezelter + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new + classes in progress + +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 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 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, 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 14:56 tim + + * src/brains/SimCreator.cpp: file SimCreator.cpp 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/: brains/Migrator.hpp, brains/SimModel.cpp, + utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. + Need unit test + +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 11:59 tim + + * src/brains/SimModel.cpp: file SimModel.cpp was initially added on + branch new_design. + +2004-11-02 11:59 tim + + * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: SimModel in progress + +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: adding MemoryUtils which provide some + functions for dealing with memory issue + +2004-11-02 10:27 tim + + * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially + added on branch new_design. + +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, @@ -760,7 +1230,8 @@ 2004-09-29 12:56 gezelter - * make/: Make.conf.in, Makefile.in: Working on make stuff + * make/: Make.conf.in, Makefile.in, _files/style.css: Working on + make stuff 2004-09-29 12:46 tim @@ -1026,7 +1497,8 @@ 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, + src/visitors/ZconsVisitor.hpp, make/Makefile, + make/_files/style.css, 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, @@ -1201,7 +1673,8 @@ 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, + src/visitors/ZconsVisitor.hpp, make/Makefile, + make/_files/style.css, 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,