--- trunk/OOPSE-2.0/ChangeLog 2004/11/03 16:08:43 1701 +++ trunk/OOPSE-2.0/ChangeLog 2005/03/11 15:00:20 2116 @@ -1,1608 +1,5267 @@ -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, - 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, - SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in - progress - -2004-10-15 20:31 tim - - * src/math/Quaternion.hpp: add quaternion class - -2004-10-15 16:11 tim - - * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, - IfstrstreamTestCase.hpp: adding test file - -2004-10-15 16:10 tim - - * src/io/basic_ifstrstream.hpp: fix a bunch of bugs - -2004-10-15 15:42 tim - - * src/io/basic_ifstrstream.hpp: change const_cast to statc_const - -2004-10-15 15:35 tim - - * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp - -2004-10-15 15:34 tim - - * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use - namespace oopse - -2004-10-15 14:38 chuckv - - * configure, ac-tools/aclocal.m4: Changed optimization flags for - XLF and XLC. - -2004-10-15 13:28 tim - - * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: - adding ifstrstream test case - -2004-10-15 13:20 tim - - * src/io/basic_ifstrstream.hpp: fix include - -2004-10-15 13:18 tim - - * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi - -2004-10-15 13:17 tim - - * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile - -2004-10-15 13:16 tim - - * test/io/: Makefile, ifstrstreamTestCase.cpp, - ifstrstreamTestCase.hpp: adding test case for ifstrstream - -2004-10-15 10:37 tim - - * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, - ifstrstreamTestCase.hpp: add ifstrstreamTestCase - -2004-10-15 10:20 tim - - * src/io/basic_ifstrstream.hpp: add checkFilename Option - -2004-10-15 10:19 tim - - * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, - SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add - SquareMatrixTestCase class - -2004-10-15 02:52 tim - - * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream - -2004-10-14 18:28 tim - - * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, - Vector.hpp: math library in progress - -2004-10-14 18:27 tim - - * src/io/FileReader.hpp: FileReader in progress - -2004-10-13 18:53 tim - - * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, - test in isOrthogonal of SquareMatrix is failed by some reasons - -2004-10-13 17:28 tim - - * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap - class - -2004-10-13 17:27 tim - - * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, - RectMatrixTestCase.hpp: adding testing unit - -2004-10-13 17:24 tim - - * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix - -2004-10-13 01:51 tim - - * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, - Vector3.hpp: refactory vector and matrix classes - -2004-10-13 01:50 tim - - * src/math/Vector3d.hpp: Remove some Makefile.in - -2004-10-12 18:57 tim - - * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and - Matrix3x3d.hpp - -2004-10-12 14:08 tim - - * doc/: cppstyle.html, style.css: adding c++ coding style - -2004-10-11 17:15 tim - - * src/: constraints/AbstractClasses.hpp, - integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: - change #include "mpi.h" to #include in AbstractClasses.hpp - -2004-10-11 16:54 tim - - * scripts/filepp: fix a bug in filepp - -2004-10-11 16:13 tim - - * make/Makefile.in: using filepp to generate dependencies instead - of compilers - -2004-10-11 16:10 tim - - * scripts/filepp: filepp can be used to generate dependencies for - c/c++ now - -2004-10-11 13:40 tim - - * make/Makefile.in: remove -module from F90Options - -2004-10-11 13:01 tim - - * make/Makefile.in: adding rules to move fortran 90 module to - target directory - -2004-10-11 10:43 gezelter - - * make/Makefile.in: fixed makefile.in - -2004-10-11 09:51 tim - - * scripts/filepp: remove "use bytes" which causes problem in sgi - machine - -2004-10-11 09:26 tim - - * forceFields/Makefile: add Makefile - -2004-10-11 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 - -2004-10-11 09:23 tim - - * samples/argon/Makefile: remove argon.dump and argon.eor from - Makefile - -2004-10-09 01:01 tim - - * samples/: alkane/Makefile.in, argon/Makefile.in, - lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: - Remove some Makefile.in - -2004-10-08 18:15 tim - - * make/Makefile.in: [no log message] - -2004-10-08 17:51 tim - - * make/Makefile.in: fix make install - -2004-10-08 17:10 tim - - * make/Makefile.in: adding make install - -2004-10-08 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 - -2004-10-06 18:03 gezelter - - * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt - stuff - -2004-10-06 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 - -2004-10-06 17:20 tim - - * make/: Doxyfile, Makefile.in: adding doxygen configuration file - -2004-10-06 17:19 tim - - * scripts/filepp: filepp can handle different fortran module case - and suffix - -2004-10-06 16:27 gezelter - - * src/restraints/Restraints.cpp: Chris doesn't know about the - OOPSE-2.0 directory structure yet - -2004-10-06 16:27 gezelter - - * ChangeLog: Yeah yeah, we'lll get around to it later - -2004-10-06 16:22 gezelter - - * configure, ac-tools/configure.in, ac-tools/fortran90.m4, - make/Makefile.in: cleaning up build process - -2004-10-06 15:01 chrisfen - - * src/restraints/Restraints.cpp: made the file reading in - restraints more intelligent - no longer gives uninformative seg - faults - -2004-10-06 14:55 gezelter - - * src/applications/simpleBuilder/Make.ftemp.old: cleaning up - -2004-10-06 14:51 gezelter - - * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, - scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit - -2004-10-06 13:53 tim - - * make/: Makefile, Makefile.in: fix make statistics - -2004-10-06 13:18 tim - - * make/: Makefile, Makefile.in: adding GNU make functions to - combine all of the static libraries to a big library - -2004-10-05 17:57 tim - - * make/: Makefile, Makefile.in: adding shared library flag - -2004-10-05 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 - -2004-10-05 14:35 tim - - * make/: Makefile, Makefile.in: building MPI version;using static - library instead of shared library - -2004-10-05 09:14 tim - - * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 - to filepp - -2004-10-04 15:56 tim - - * make/: Makefile, Makefile.in: add make cvslog - -2004-10-04 11:24 gezelter - - * make/: Makefile, Makefile.in: more work on the parallel build - -2004-10-04 11:06 gezelter - - * make/: Makefile, Makefile.in: changes to backport declare flags - -2004-10-04 10:27 gezelter - - * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, - DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging - shapes - -2004-10-01 23:40 tim - - * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree - -2004-10-01 23:22 tim - - * make/: Makefile, Makefile.in: add oopse_ as library prefix - -2004-10-01 16:59 tim - - * make/: Makefile, Makefile.in: fix a space trimming bug in filepp - -2004-10-01 16:22 gezelter - - * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A - few minor build changes - -2004-10-01 16:11 tim - - * scripts/filepp: adding fortran90 make dependency tool - -2004-09-30 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 - -2004-09-29 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 - -2004-09-29 16:54 tim - - * make/: Makefile, Makefile.in: get the relative path by shell - script - -2004-09-29 16:32 tim - - * make/Makefile: eliminate DEV_ROOT by relative path - -2004-09-29 13:37 tim - - * make/Makefile.in: add PackageLibs; fix dependency rule - -2004-09-29 12:57 gezelter - - * configure, ac-tools/configure.in: updates - -2004-09-29 12:56 gezelter - - * make/: Make.conf.in, Makefile.in: Working on make stuff - -2004-09-29 12:46 tim - - * Makefile: If makefile does not exist, print error message - -2004-09-29 12:12 tim - - * make/: Make.conf.in, Makefile: fix dependencies rule - -2004-09-29 10:58 gezelter - - * Makefile, make/Makefile: still working on build process - -2004-09-29 10:00 tim - - * make/Makefile: add print statment to rules - -2004-09-29 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 - -2004-09-28 21:55 tim - - * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c - which cause headache in bulding libutils - -2004-09-28 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 - -2004-09-28 17:15 gezelter - - * lib/dummy: Keep that lib around, please. - -2004-09-28 17:14 gezelter - - * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: - starting a configure version - -2004-09-28 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 - -2004-09-28 15:43 tim - - * 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] - -2004-09-28 15:41 tim - - * make/Makefile, scripts/sfmakedepend: fix fortran dependency - problem - -2004-09-28 11:13 tim - - * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, - src/io/Makefile: add yacc and lex rules - -2004-09-27 15:24 tim - - * make/Makefile: adding include path to F90Options - -2004-09-27 15:13 tim - - * make/Makefile: change suffix from .cc to .cpp - -2004-09-24 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 - -2004-09-23 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, 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 - -2004-09-23 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, +2005-03-11 00:43 chrisfen + + * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, + src/io/RestReader.cpp, src/restraints/Restraints.cpp, + src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in + MPI restraints + +2005-03-10 23:56 tim + + * doc/SelectionExpression.html, src/brains/SimInfo.cpp, + src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody + and cutoff group + +2005-03-10 22:06 gezelter + + * src/types/MorseBondType.hpp: fixed a doxygen problem + +2005-03-10 21:51 gezelter + + * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with + the split dipole test cases + +2005-03-10 21:51 gezelter + + * doc/SelectionExpression.html: updated some documentation + +2005-03-10 20:40 gezelter + + * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, + Makefile: LinkedList removal project starts now + +2005-03-10 20:28 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: + using map to replace link list + +2005-03-10 19:11 tim + + * samples/dipole/: splitInWater.in, splitInWater.md: adding test + case of split dipole + +2005-03-10 19:10 chrisfen + + * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, + src/io/RestWriter.cpp, + src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now + builds... + +2005-03-10 18:44 tim + + * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, + split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: + adding test case for split dipole + +2005-03-10 17:54 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side + support for split dipoles + +2005-03-10 16:27 chrisfen + + * samples/water/tip3p_ice/tp3.md, + src/restraints/ThermoIntegrationForceManager.cpp: fixes to + restraints + +2005-03-10 16:15 chrisfen + + * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, + src/UseTheForce/ForceFields.hpp, + src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints + +2005-03-10 16:14 tim + + * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, + src/io/MultipoleAtomTypesSectionParser.cpp, + src/selection/SelectionEvaluator.cpp: minor change + +2005-03-10 15:10 chrisfen + + * make/Makefile.in, samples/water/tip3p_ice/tp3.md, + src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, + src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, + src/integrators/VelocityVerletIntegrator.cpp, + src/integrators/VelocityVerletIntegrator.hpp, + src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, + src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, + src/io/RestReader.hpp, src/io/RestWriter.cpp, + src/io/RestWriter.hpp, src/io/RestraintReader.cpp, + src/io/RestraintWriter.cpp, src/restraints/Makefile, + src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, + src/restraints/ThermoIntegrationForceManager.cpp, + src/restraints/ThermoIntegrationForceManager.hpp: First commit of + the new restraints code + +2005-03-09 18:48 tim + + * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding + IndexFinder + +2005-03-09 18:46 tim + + * src/: applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: + fix compilation issue + +2005-03-09 17:58 tim + + * forceFields/DUFF2.frc, scripts/filepp, + src/UseTheForce/EAM_FF.cpp, + src/io/MultipoleAtomTypesSectionParser.cpp, + src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug + in SectionParser (lineNo is not updated) + +2005-03-09 17:30 tim + + * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, + brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, + io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, + io/SectionParserManager.cpp, selection/Makefile, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + types/AtomType.cpp, types/DirectionalAtomType.cpp, + visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp: adding IndexFinder which is used to + select the molecules; Seperate ElectrostaticAtomTypesSectionParser + into ChargeAtomTypesSectionParser and + MultipoleAtomTypesSectionParser;remove print dipole option from + Dump2XYZ; + +2005-03-09 17:28 tim + + * forceFields/DUFF2.frc: change the format of DUFF2 + +2005-03-09 15:44 gezelter + + * src/UseTheForce/DarkSide/: electrostatic.F90, + electrostatic_interface.F90, electrostatic_interface.h: new + electrostatic module + +2005-03-09 14:26 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole + and fixed quadrupole stuff + +2005-03-09 14:25 gezelter + + * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines + for outdated charge and dipole interfaces + +2005-03-08 21:08 gezelter + + * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, + mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun + charge-dipole test cases + +2005-03-08 21:07 gezelter + + * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, + OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a + strange icc8 bug (we think). + +2005-03-08 21:07 gezelter + + * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! + +2005-03-08 21:07 gezelter + + * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic + Unification Project + +2005-03-08 21:07 gezelter + + * src/io/Globals.cpp: Dunno + +2005-03-08 21:06 gezelter + + * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using + OOPSE_itoa and checking a NULL left over from the LinkedList days + +2005-03-08 21:06 gezelter + + * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, + atype_interface.F90, atype_interface.h, charge.F90, + charge_interface.F90, charge_interface.h, dipole.F90, + dipole_interface.F90, dipole_interface.h: electrostatic unification + project fixed an uninitialized variable in Lennard Jones mixing map + +2005-03-08 21:05 gezelter + + * src/UseTheForce/doForces.F90: electrostatic unification project + +2005-03-08 21:05 gezelter + + * samples/water/dimer/: two.md, water.md: making some cool test + cases + +2005-03-08 21:05 gezelter + + * forceFields/DUFF2.frc: Added a charge for Chlorine + +2005-03-07 22:39 tim + + * src/: brains/SimInfo.cpp, io/DumpReader.cpp, + math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, + primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: + Fixing a bug in BitSet.cpp + +2005-03-04 15:28 gezelter + + * src/config.h.in: Cleaning up config.h.in by adding comments + +2005-03-04 15:28 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in, + src/brains/SimCreator.cpp: SPRNG eradication project + +2005-03-03 14:40 tim + + * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the + missing atom type problem) + +2005-03-02 16:29 tim + + * src/math/RandNumGen.hpp: adding base class of Random Number + generator + +2005-03-02 16:28 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in + Velocitizer is not initialized which causes a seg fault + +2005-03-02 15:36 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, math/Makefile, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp: remove default parameter from + MersenneTwister.hpp which causes all kinds of trouble. Refactory + random number generator + +2005-03-02 07:32 tim + + * test/math/testRandNumGen.cpp: Adding unit test for random number + generator + +2005-03-01 23:17 tim + + * src/brains/Thermo.hpp: fixed a file inclusion problem + +2005-03-01 23:17 tim + + * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, + OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, + ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, + RandNumGenTestCase.hpp: fixed compilation problem + +2005-03-01 23:02 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, math/Makefile, + math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/mt19937ar.c, + math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand + +2005-03-01 23:00 tim + + * test/math/: Makefile, ParallelandNumGenTestCase.cpp, + ParallelandNumGenTestCase.hpp: Change the name of test case + +2005-03-01 21:00 tim + + * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, + OOPSERandNumGenTestCase.hpp: adding testcase for random number + generator + +2005-03-01 20:10 tim + + * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, + integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, + math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, + math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, + math/Vector3.hpp, minimizers/MinimizerCreator.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, + visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 + +2005-03-01 19:11 tim + + * src/: brains/SimCreator.cpp, brains/SimInfo.hpp, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding + OOPSERandNumGen + +2005-03-01 15:44 gezelter + + * make/Makefile.in: Fixed the damned build problem with the + libraries not being removed in make clean and make distclean (at + least we think it is fixed). + +2005-03-01 15:26 gezelter + + * src/math/MersenneTwister.hpp: Making small modifications to allow + for use on MPI machines + +2005-03-01 14:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, + integrators/Velocitizer.cpp, io/DumpReader.cpp, + math/MersenneTwister.hpp: adding MersenneTwister random number + generator + +2005-03-01 03:55 tim + + * src/math/MersenneTwister.hpp: Adding a modified version of + MersenneTwister.hpp + +2005-02-28 17:24 tim + + * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, + definition.jpg: selection expression + +2005-02-25 21:22 tim + + * src/: UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, + types/AtomType.hpp: adding soft potential to LJ Module + +2005-02-25 16:38 tim + + * doc/SelectionExpression.html: adding documentation for selection + expression + +2005-02-24 20:55 tim + + * src/: applications/simpleBuilder/simpleBuilder.cpp, + integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, + io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: + adding basic_teebuf which can operate on multiple stream + simutaneously. + +2005-02-22 18:56 tim + + * src/: UseTheForce/DarkSide/reactionField.F90, + primitives/RigidBody.cpp: reactionfield get fixed + +2005-02-21 16:57 tim + + * src/: applications/staticProps/GofRAngle.cpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix + a bug in GofRAngle + +2005-02-21 15:28 tim + + * src/primitives/Molecule.cpp: Fix for compilation on the Sun + +2005-02-21 15:22 tim + + * src/utils/next_combination.hpp: fix for compilation on the Sun + +2005-02-21 15:21 tim + + * src/utils/GenericData.hpp: fix problem in sun + +2005-02-18 23:07 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/RCorrFunc.cpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + io/ElectrostaticAtomTypesSectionParser.cpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/Makefile: adding LipidTransVisitor, GofXyz is working now + +2005-02-18 15:58 gezelter + + * src/brains/Register.cpp: Corrected filename collision for EAM on + Mac OS X + +2005-02-18 15:58 gezelter + + * src/applications/oopse/oopse.cpp: Updated copyright information + +2005-02-18 15:58 gezelter + + * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, + Makefile: corrected filename collision for EAM on operating systems + which are not case sensitive (aka Mac OS X) + +2005-02-17 20:15 tim + + * src/applications/staticProps/GofXyz.cpp: more bug get fixed + +2005-02-17 19:50 tim + + * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug + in GofXyz + +2005-02-17 19:09 tim + + * src/applications/staticProps/RadialDistrFunc.hpp: make + processHistogram non-abstrct function + +2005-02-17 18:41 tim + + * src/applications/staticProps/GofXyz.cpp: [no log message] + +2005-02-17 18:30 tim + + * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, + GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: + finish GofXyz + +2005-02-17 16:21 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, + GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial + distribution function + +2005-02-17 15:23 tim + + * src/utils/BitSet.hpp: forget the const correctness for BitSet + +2005-02-17 15:18 tim + + * src/: brains/BlockSnapshotManager.cpp, + selection/DistanceFinder.cpp: The change of interface of BitSet + cause a bug in SelectionEvaluation + +2005-02-16 21:13 tim + + * src/utils/residentMem.c: return residentMem in byte + +2005-02-16 21:00 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix + a bug in writing out the value of cosang + +2005-02-16 20:43 tim + + * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to + estimate avaliable memory + +2005-02-16 20:30 tim + + * src/: applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp: change the default bin number + +2005-02-16 19:36 tim + + * src/: applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output + files;fix the problem of counting in staticProps + +2005-02-15 19:39 tim + + * src/brains/BlockSnapshotManager.cpp: fix a bug in + BlockSnapshotManager + +2005-02-15 19:36 tim + + * src/: applications/dynamicProps/TimeCorrFunc.cpp, + applications/staticProps/RadialDistrFunc.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + selection/SelectionEvaluator.cpp: BlockSnapshotManager is using + reference counting now + +2005-02-15 17:49 tim + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + replace std::make_pair by VariablesType::value_type to make Sun + Compiler happy + +2005-02-15 17:35 tim + + * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to + TokenMap, using TokenMapType::value_type instead of std::make_pair + to make Sun compiler happy + +2005-02-15 17:24 tim + + * src/applications/staticProps/: GofRAngle.cpp, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps + +2005-02-15 17:11 tim + + * src/: applications/staticProps/GofR.cpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding + #ifdef __RWSTD to make sun compiler happy (2) fix pair density + calculation problem when two selections intersect with each other + +2005-02-15 15:24 gezelter + + * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy + xlc++ + +2005-02-15 15:17 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/residentMem.c: [no log message] + +2005-02-15 06:17 gezelter + + * src/utils/residentMem.c: bug fix for null termination + +2005-02-15 06:11 gezelter + + * configure, ac-tools/configure.in, src/utils/residentMem.c: + bugfixing residentMem + +2005-02-15 05:59 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/residentMem.c: bugfixes for residentMem on LINUX + +2005-02-15 05:08 gezelter + + * src/utils/Makefile.in: added residentMem + +2005-02-15 05:05 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in, + src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, + src/utils/residentMem.h: modifications to estimate memory in use by + other processes autoconf fixes ps syntax checking config.h file + cleaning + +2005-02-14 23:26 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in: ps niceness + +2005-02-14 23:16 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps + strangeness + +2005-02-14 19:42 tim + + * src/brains/BlockSnapshotManager.cpp: fix a bug in + BlockSnapshotManager.hpp + +2005-02-14 18:51 tim + + * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, + StaticPropsCmd.c: default length for staticProps is 1/2 smallest + length of first frame + +2005-02-14 18:12 tim + + * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in + VelocityVerletIntegrator : last frame is written twice + +2005-02-14 17:57 tim + + * src/: applications/dynamicProps/TimeCorrFunc.cpp, + brains/SimInfo.cpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp: begin bug fix + +2005-02-14 17:35 tim + + * src/applications/dynamicProps/: CorrelationFunction.cpp, + CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, + CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, + DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, + ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, + RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, + VCorrFunc.hpp: refactory CorrelationFunction + +2005-02-14 15:18 gezelter + + * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix + and start of switch for type of correlation function + +2005-02-13 21:18 tim + + * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in + calculating bytes per stuntdouble + +2005-02-13 21:03 tim + + * src/applications/dynamicProps/CorrelationFunction.cpp: more fix + +2005-02-13 20:57 tim + + * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a + bug in CorrelationFunction + +2005-02-13 20:36 tim + + * src/: applications/staticProps/GofR.cpp, + applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a + bug in SimInfo::getCutoff() + +2005-02-13 20:08 tim + + * make/Makefile.in: adding staticProps and dynamicProps into + Makefile.in + +2005-02-13 20:05 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, + brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length + defaults to the cutoff radius + +2005-02-13 19:14 tim + + * src/utils/Algorithm.hpp: adding Algorithm.hpp + +2005-02-13 19:10 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/dynamicProps/DynamicProps.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + integrators/Integrator.cpp, integrators/Integrator.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, + io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, + visitors/OtherVisitor.cpp: dynamicProps get built + +2005-02-13 15:56 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in + progress + +2005-02-13 08:04 tim + + * src/: applications/dynamicProps/CorrelationFunction.hpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more + work in dynamicProps + +2005-02-13 07:25 tim + + * src/applications/dynamicProps/DynamicProps.cpp: adding + dynamicProps + +2005-02-13 07:14 tim + + * src/applications/dynamicProps/: DynamicPropsCmd.c, + DynamicPropsCmd.h: adding command line option to DynamicProps + +2005-02-13 07:13 tim + + * src/applications/dynamicProps/: DynamicProps.ggo, Makefile: + adding command line option for DynamicProps + +2005-02-13 06:57 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/staticProps/RadialDistrFunc.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding + dynamicProps + +2005-02-12 20:09 tim + + * src/selection/SelectionManager.cpp: adding SelectionManager.cpp + +2005-02-11 22:41 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one + more constructor to Snapshot to create customized DataStorage + +2005-02-11 22:39 tim + + * src/selection/: DistanceFinder.hpp, Makefile, + SelectionManager.hpp: adding beginSelected, nextSelected method to + SelectionManager + +2005-02-11 22:36 tim + + * src/config.h.in, configure: adding support for physmem + +2005-02-11 22:35 tim + + * ac-tools/configure.in: adding supprot for physmem + +2005-02-11 22:35 tim + + * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding + physmem + +2005-02-10 22:37 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, + GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, + GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: more work in StaticProps + +2005-02-10 18:14 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, + GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, + GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, + Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: change the filenames + +2005-02-10 14:15 tim + + * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, + GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, + RadialDistrFunc.hpp: adding GofRAngle + +2005-02-09 18:21 tim + + * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some + useless files + +2005-02-09 18:12 tim + + * src/applications/staticProps/: GofR.cpp, Makefile, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress + +2005-02-09 17:08 tim + + * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, + GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR + +2005-02-07 22:39 tim + + * src/primitives/Molecule.hpp: add getRigidBodyAt function into + Molecule class + +2005-02-07 22:38 tim + + * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info + +2005-02-07 22:36 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp: support select internal index selection, for + example, select DMPC.3 + +2005-02-07 21:11 tim + + * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update + help info for Dump2XYZ + +2005-02-07 20:39 chrisfen + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + selection librarys added + +2005-02-07 20:31 tim + + * src/selection/Makefile, make/Makefile.in: adding Makefile + +2005-02-07 20:20 chrisfen + + * src/utils/wildcards.hpp: issue commented out in wildcards + +2005-02-07 20:06 tim + + * src/selection/SelectionEvaluator.cpp: forget to reset the pc + which cause reevaluate return NULL + +2005-02-07 19:14 tim + + * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: fix a bug in determing the global index for + rigidbodies + +2005-02-07 19:13 tim + + * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change + in Bitset + +2005-02-07 19:13 tim + + * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, + TokenMap.cpp: selection library is working + +2005-02-04 22:46 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor + +2005-02-04 22:45 tim + + * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor + and XYZVisitor now use selection library + +2005-02-04 22:44 tim + + * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: + adding SelectionManager into SimInfo + +2005-02-04 22:43 tim + + * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, + Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of + selection library + +2005-02-04 22:42 tim + + * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change + in BitSet + +2005-02-04 22:41 tim + + * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing + implementation + +2005-02-04 22:39 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, + SelectionManager.hpp, Token.hpp: half of the selection utility is + working need to debug within keyword and atomproperty keyword + +2005-02-04 05:42 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library + get built + +2005-02-04 05:42 tim + + * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet + +2005-02-04 05:26 tim + + * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: + remove some useless files + +2005-02-04 04:57 tim + + * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, + selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: + adding wildcard class; NameFinder is finished + +2005-02-03 23:14 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, + SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in + selection library + +2005-02-03 14:04 tim + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + selection in progress + +2005-02-02 23:13 tim + + * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, + Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in + progress, except SelectionEvaluator, other files are compiled + +2005-02-02 23:12 tim + + * src/utils/: Makefile.in, any.hpp: adding boost::any + +2005-02-02 12:51 tim + + * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp + +2005-02-01 22:49 tim + + * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, + selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, + selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, + selection/Token.hpp: Selection in progress + +2005-02-01 06:55 tim + + * src/: selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.hpp, selection/Token.hpp, + utils/BitSet.cpp, utils/BitSet.hpp: adding selection library + +2005-01-26 15:26 tim + + * src/integrators/: Integrator.cpp, Integrator.hpp, + VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget + to add eorWriter + +2005-01-26 15:15 tim + + * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: + (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the + wrong column of electroframe + +2005-01-25 21:59 tim + + * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in + SimInfo, use number of cutoff stamp as counter to loop over + rigidbody stamp + +2005-01-25 17:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, + io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, + io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, + io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.cpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, + primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, + primitives/GhostTorsion.hpp, primitives/Makefile, + primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete + section parser's error message (2) add GhostTorsion (3) accumulate + inertial tensor from the directional atoms before calculate + rigidbody's inertial tensor + +2005-01-17 22:17 tim + + * forceFields/DUFF2.frc: forget to set dipole for lipid head group + +2005-01-17 16:58 tim + + * src/integrators/NVT.cpp: fix a bug in loading initial extended + system parameters + +2005-01-17 16:05 tim + + * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT + +2005-01-14 22:02 tim + + * src/UseTheForce/WATER.cpp: remove WATER.cpp + +2005-01-14 21:37 tim + + * forceFields/Makefile: sync Makefile + +2005-01-14 21:13 gezelter + + * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, + src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, + src/applications/dump2Xyz/Makefile, + src/applications/oopse/Makefile, + src/applications/simpleBuilder/Makefile, src/brains/Makefile, + src/constraints/Makefile, src/integrators/Makefile, + src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, + src/primitives/Makefile, src/profiling/Makefile, + src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, + src/visitors/Makefile: moved Package variable into subdirectory + makefiles to speed up the building process + +2005-01-14 20:48 gezelter + + * src/applications/oopse/oopse.cpp: Fixed publication details in + banner + +2005-01-14 20:48 gezelter + + * src/UseTheForce/DarkSide/: simParallel_interface.F90, + simParallel_interface.h: added dummy subroutine to avoid empty + unit, synchronized this dummy routine between C and fortran + +2005-01-14 20:31 gezelter + + * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, + notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, + DarkSide/Makefile, DarkSide/atype.F90, + DarkSide/atype_interface.F90, DarkSide/charge.F90, + DarkSide/charge_interface.F90, DarkSide/dipole.F90, + DarkSide/dipole_interface.F90, DarkSide/eam.F90, + DarkSide/eam_interface.F90, DarkSide/gb.F90, + DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, + DarkSide/shapes.F90, DarkSide/shapes_interface.F90, + DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, + DarkSide/simulation.F90, DarkSide/simulation_interface.F90, + DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating + modules and C/Fortran interface subroutines + +2005-01-14 20:15 gezelter + + * configure, ac-tools/aclocal.m4: more fixes for gnugetopt + +2005-01-14 20:09 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt + +2005-01-14 16:49 tim + + * src/: io/EAMAtomTypesSectionParser.cpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp: using c library to do conversion instead of + using iostream due to a bug in libstdc++(GCC 3.2) + +2005-01-14 02:40 tim + + * src/brains/SimSetup.cpp: no message + +2005-01-14 01:56 tim + + * src/primitives/Molecule.hpp: fix a bug in global index + +2005-01-14 01:04 tim + + * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include + Integrator.hpp in Minimizer + +2005-01-13 22:14 gezelter + + * src/utils/Makefile: compile getopt and getopt1 if we need to + +2005-01-13 21:56 gezelter + + * make/Makefile.in: template flags + +2005-01-13 21:48 gezelter + + * src/applications/oopse/Makefile: formatting + +2005-01-13 21:48 gezelter + + * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir + target + +2005-01-13 19:40 tim + + * src/: UseTheForce/fSwitchingFunction.h, + UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, + math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, + primitives/RigidBody.cpp, types/AtomTypeProperties.h, + types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform + +2005-01-13 18:26 tim + + * make/Makefile.in: change the order of linking (object file comes + first and then follow by user built library) + +2005-01-12 23:24 tim + + * src/io/DumpWriter.cpp: remove useless debug info + +2005-01-12 23:21 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix + +2005-01-12 23:17 tim + + * make/: Makefile.in, Makefile.in: missing tab + +2005-01-12 23:15 tim + + * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor + get fixed + +2005-01-12 22:40 gezelter + + * make/Makefile.in, src/UseTheForce/DUFF.cpp, + src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, + src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, + src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, + src/UseTheForce/ForceFieldCreator.hpp, + src/UseTheForce/ForceFieldFactory.cpp, + src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, + src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, + src/UseTheForce/fSwitchingFunction.h, + src/UseTheForce/mpiComponentPlan.h, + src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, + src/UseTheForce/notifyCutoffs.F90, + src/UseTheForce/notifyCutoffs_interface.h, + src/UseTheForce/DarkSide/LJ.F90, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/atype_interface.h, + src/UseTheForce/DarkSide/charge.F90, + src/UseTheForce/DarkSide/charge_interface.h, + src/UseTheForce/DarkSide/dipole.F90, + src/UseTheForce/DarkSide/dipole_interface.h, + src/UseTheForce/DarkSide/eam.F90, + src/UseTheForce/DarkSide/eam_interface.h, + src/UseTheForce/DarkSide/force_globals.F90, + src/UseTheForce/DarkSide/gb.F90, + src/UseTheForce/DarkSide/gb_interface.h, + src/UseTheForce/DarkSide/lj_interface.h, + src/UseTheForce/DarkSide/neighborLists.F90, + src/UseTheForce/DarkSide/reactionField.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.h, + src/UseTheForce/DarkSide/simParallel.F90, + src/UseTheForce/DarkSide/simParallel_interface.h, + src/UseTheForce/DarkSide/simulation.F90, + src/UseTheForce/DarkSide/simulation_interface.h, + src/UseTheForce/DarkSide/sticky.F90, + src/UseTheForce/DarkSide/sticky_interface.h, + src/UseTheForce/DarkSide/switcheroo.F90, + src/applications/Makedepend, src/applications/quickLate.c, + src/applications/dump2Xyz/Dump2XYZ.cpp, + src/applications/oopse/oopse.cpp, + src/applications/simpleBuilder/BaseLattice.cpp, + src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/Lattice.cpp, + src/applications/simpleBuilder/Lattice.hpp, + src/applications/simpleBuilder/LatticeCreator.cpp, + src/applications/simpleBuilder/LatticeCreator.hpp, + src/applications/simpleBuilder/LatticeFactory.cpp, + src/applications/simpleBuilder/LatticeFactory.hpp, + src/applications/simpleBuilder/MoLocator.cpp, + src/applications/simpleBuilder/MoLocator.hpp, + src/applications/simpleBuilder/simpleBuilder.cpp, + src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, + src/brains/Exclude.cpp, src/brains/Exclude.hpp, + src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, + src/brains/Makefile, src/brains/Migrator.hpp, + src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, + src/brains/Register.cpp, src/brains/Register.hpp, + src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, + src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, + src/brains/SimModel.hpp, src/brains/SimSetup.hpp, + src/brains/SimSnapshotManager.cpp, + src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, + src/brains/SimState.hpp, src/brains/SkipList.cpp, + src/brains/SkipList.hpp, src/brains/Snapshot.cpp, + src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, + src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, + src/brains/Thermo.hpp, src/brains/fSimulation.h, + src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, + src/constraints/AbstractClasses.hpp, + src/constraints/ConstraintElem.hpp, + src/constraints/ConstraintPair.hpp, src/constraints/Makefile, + src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, + src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, + src/constraints/ZconsStruct.hpp, + src/constraints/ZconstraintForceManager.cpp, + src/constraints/ZconstraintForceManager.hpp, + src/integrators/AbstractClasses.hpp, + src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, + src/integrators/DLM.hpp, src/integrators/Integrator.cpp, + src/integrators/Integrator.hpp, + src/integrators/IntegratorCreator.hpp, + src/integrators/IntegratorFactory.cpp, + src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, + src/integrators/NPT.cpp, src/integrators/NPT.hpp, + src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, + src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, + src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, + src/integrators/NVE.cpp, src/integrators/NVE.hpp, + src/integrators/NVT.cpp, src/integrators/NVT.hpp, + src/integrators/RotationAlgorithm.hpp, + src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, + src/integrators/VelocityVerletIntegrator.cpp, + src/integrators/VelocityVerletIntegrator.hpp, + src/io/AtomTypesSectionParser.cpp, + src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, + src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, + src/io/BendTypesSectionParser.cpp, + src/io/BendTypesSectionParser.hpp, + src/io/BondTypesSectionParser.cpp, + src/io/BondTypesSectionParser.hpp, + src/io/DirectionalAtomTypesSectionParser.cpp, + src/io/DirectionalAtomTypesSectionParser.hpp, + src/io/DumpReader.cpp, src/io/DumpReader.hpp, + src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, + src/io/EAMAtomTypesSectionParser.cpp, + src/io/EAMAtomTypesSectionParser.hpp, + src/io/ElectrostaticAtomTypesSectionParser.cpp, + src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, + src/io/Globals.hpp, src/io/InitializeFromFile.cpp, + src/io/LennardJonesAtomTypesSectionParser.cpp, + src/io/LennardJonesAtomTypesSectionParser.hpp, + src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, + src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, + src/io/Makefile, src/io/SectionParser.cpp, + src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, + src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, + src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, + src/io/StickyAtomTypesSectionParser.hpp, + src/io/TorsionTypesSectionParser.cpp, + src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, + src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, + src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.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/math/ChebyshevPolynomials.cpp, + src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, + src/math/MatVec3.h, src/math/Polynomial.hpp, + src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, + src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, + src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, + src/math/Vector.hpp, src/math/Vector3.hpp, + src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, + src/minimizers/CGFamilyMinimizer.cpp, + src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, + src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, + src/minimizers/MinimizerCreator.hpp, + src/minimizers/MinimizerFactory.cpp, + src/minimizers/MinimizerFactory.hpp, + src/minimizers/MinimizerParameterSet.cpp, + src/minimizers/MinimizerParameterSet.hpp, + src/minimizers/OOPSEMinimizer.cpp, + src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, + src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, + src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, + src/primitives/Atom.cpp, src/primitives/Atom.hpp, + src/primitives/Bend.cpp, src/primitives/Bend.hpp, + src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, + src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, + src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/primitives/GhostBend.hpp, 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/Torsion.hpp, src/primitives/TorsionExtensions.cpp, + src/primitives/UreyBradleyBend.cpp, + src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, + src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, + src/types/AtomStamp.hpp, src/types/AtomType.cpp, + src/types/AtomType.hpp, src/types/AtomTypeProperties.h, + src/types/BendStamp.cpp, src/types/BendStamp.hpp, + src/types/BendType.hpp, src/types/BondStamp.cpp, + src/types/BondStamp.hpp, src/types/BondType.hpp, + src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, + src/types/Component.cpp, src/types/Component.hpp, + src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, + src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, + src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, + src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, + src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, + src/types/Makefile, src/types/MoleculeStamp.cpp, + src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, + src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, + src/types/PolynomialBondType.hpp, + src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, + src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, + src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, + src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, + src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, + src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, + src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, + src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, + src/utils/LocalIndexManager.hpp, src/utils/Makefile, + src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, + src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, + src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, + src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, + src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, + src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, + src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, + src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, + src/utils/Utility.cpp, src/utils/Utility.hpp, + src/utils/definitions.F90, src/utils/fError.c, + src/utils/next_combination.hpp, src/utils/oopseMPI.F90, + src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, + src/utils/vector_class.F90, src/visitors/AtomData.hpp, + src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, + src/visitors/BaseVisitor.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: merging new_design branch into + OOPSE-2.0 + +2005-01-12 18:13 tim + + * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, + utils/TypeContainer.hpp: forget to include + +2005-01-12 17:25 tim + + * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, + newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force + fields + +2005-01-12 17:14 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, + UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.h, + UseTheForce/DarkSide/charge.F90, + UseTheForce/DarkSide/charge_interface.h, + UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/dipole_interface.h, + UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, + brains/Snapshot.cpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, + brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, + constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, + constraints/Rattle.cpp, constraints/Rattle.hpp, + constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, + io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, + io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, + io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/Polynomial.hpp, math/Quaternion.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, + math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, + math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, + minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, + minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, + minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + restraints/Restraints.cpp, restraints/Restraints.hpp, + types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, + types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, + types/FixedBondType.hpp, types/HarmonicBendType.hpp, + types/HarmonicBondType.hpp, types/MakeStamps.cpp, + types/MakeStamps.hpp, types/MoleculeStamp.cpp, + types/MoleculeStamp.hpp, types/MorseBondType.hpp, + types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, + types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp, + types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, + types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, + types/ShapeAtomType.hpp, types/TorsionStamp.cpp, + types/TorsionStamp.hpp, types/TorsionType.hpp, + types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, + types/ZconStamp.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/NumericConstant.hpp, + utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, + utils/PropertyMap.hpp, utils/StringTokenizer.cpp, + utils/StringTokenizer.hpp, utils/StringUtils.cpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, + utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, + utils/simError.c, utils/simError.h, utils/status.F90, + utils/vector_class.F90, visitors/AtomData.hpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, + visitors/BaseVisitor.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 license + +2005-01-12 17:14 tim + + * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on + branch new_design. + +2005-01-11 21:03 tim + + * src/: constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp: change const static double + data member to const double + +2005-01-11 20:50 tim + + * src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: + +2005-01-11 20:39 tim + + * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: + change data type from logical to integer in AtomTypeProperties.h + +2005-01-11 16:36 tim + + * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding + new format of EAM force field + +2005-01-11 16:24 tim + + * src/UseTheForce/DUFF.cpp: change default name of DUFF force field + to DUFF2.frc + +2005-01-11 16:23 tim + + * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to + DUFF2.frc + +2005-01-11 16:09 tim + + * make/Makefile.in: adding constraints and minimizers into + Makefile.in + +2005-01-11 16:03 tim + + * src/io/: ChargeAtomTypesSectionParser.cpp, + ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, + DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless + files + +2005-01-11 15:59 tim + + * src/io/ZConsWriter.cpp: [no log message] + +2005-01-11 15:53 tim + + * src/UseTheForce/EAM.cpp: minor fix + +2005-01-11 15:52 tim + + * src/constraints/Rattle.hpp: file Rattle.hpp was initially added + on branch new_design. + +2005-01-11 15:52 tim + + * src/constraints/Rattle.cpp: file Rattle.cpp was initially added + on branch new_design. + +2005-01-11 15:52 tim + + * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm + +2005-01-11 15:47 tim + + * make/Makefile.in: forget a '$' sign + +2005-01-11 15:46 tim + + * make/Makefile.in: missing tab in rules + +2005-01-10 22:04 tim + + * src/: UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, + brains/Register.cpp, brains/Register.hpp, + integrators/IntegratorCreator.cpp, + integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, + minimizers/Makefile, minimizers/MinimizerCreator.cpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp: create a register module to + register force fields, integrators and minimizers + +2005-01-10 22:04 tim + + * src/brains/Register.cpp: file Register.cpp was initially added on + branch new_design. + +2005-01-10 22:04 tim + + * src/brains/Register.hpp: file Register.hpp was initially added on + branch new_design. + +2005-01-10 20:52 tim + + * src/: UseTheForce/ForceFieldFactory.cpp, + applications/oopse/oopse.cpp, brains/ForceManager.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + integrators/IntegratorFactory.cpp, + integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint + method is working now + +2005-01-10 18:05 tim + + * src/: constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, + io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in + zconstraint + +2005-01-10 18:05 tim + + * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was + initially added on branch new_design. + +2005-01-07 21:50 tim + + * src/constraints/ZconstraintForceManager.cpp: file + ZconstraintForceManager.cpp was initially added on branch + new_design. + +2005-01-07 21:50 tim + + * src/constraints/ZconstraintForceManager.hpp: file + ZconstraintForceManager.hpp was initially added on branch + new_design. + +2005-01-07 21:50 tim + + * src/: applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, + constraints/ConstraintElem.hpp, constraints/Makefile, + constraints/ZConstraint.cpp, constraints/ZconsData.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, + utils/NumericConstant.hpp: ZConstraintForceManager in progress + +2005-01-07 21:50 tim + + * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was + initially added on branch new_design. + +2005-01-06 22:31 tim + + * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + constraints/ConstraintPair.hpp, integrators/Integrator.cpp, + integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, + io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: + constraint is almost working + +2005-01-06 00:36 tim + + * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is + working + +2005-01-06 00:16 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/oopse/oopse.cpp, + applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, + minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder + in progress + +2005-01-05 17:35 tim + + * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp + was initially added on branch new_design. + +2005-01-05 17:35 tim + + * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially + added on branch new_design. + +2005-01-05 17:35 tim + + * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, + Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, + MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, + OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, + SDMinimizer.hpp: minimizer in progress + +2005-01-05 17:35 tim + + * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp + was initially added on branch new_design. + +2005-01-05 17:35 tim + + * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp + was initially added on branch new_design. + +2005-01-05 17:35 tim + + * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp + was initially added on branch new_design. + +2005-01-05 17:35 tim + + * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially + added on branch new_design. + +2005-01-04 22:18 tim + + * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, + brains/Thermo.cpp, constraints/ConstraintPair.hpp, + constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, + integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, + primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in + progress + +2005-01-04 22:18 tim + + * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was + initially added on branch new_design. + +2005-01-04 22:18 tim + + * src/minimizers/MinimizerParameterSet.cpp: file + MinimizerParameterSet.cpp was initially added on branch new_design. + +2005-01-04 22:18 tim + + * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was + initially added on branch new_design. + +2005-01-04 22:18 tim + + * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp + was initially added on branch new_design. + +2005-01-04 22:18 tim + + * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, + Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, + OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, + SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress + +2005-01-04 22:18 tim + + * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on + branch new_design. + +2004-12-20 20:50 chuckv + + * make/Makefile.in: Fixed Makefile test bug under OSX and possibly + other BSD's, replaced test -f *.mod with ls function since BSD test + apparently doesn't support wildcards. + +2004-12-20 20:36 tim + + * make/Makefile.in: fix a test command incompatiable problem + +2004-12-20 19:49 tim + + * src/integrators/NPTi.cpp: NPT is working now + +2004-12-16 19:20 tim + + * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the + invalid stamp id + +2004-12-16 19:00 tim + + * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, + newEAM.u6.frc: adding new EAM force field files + +2004-12-16 18:55 tim + + * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays + in EAM parameter file is incorrect + +2004-12-16 17:27 tim + + * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, + brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, + utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM + +2004-12-15 22:34 tim + + * src/: applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream + +2004-12-15 21:07 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: + add EAM Force Field + +2004-12-15 19:40 tim + + * src/applications/oopse/oopse.cpp: add more force fields + +2004-12-15 16:44 tim + + * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget + to call All_reduce in MPI version) + +2004-12-15 16:13 tim + + * src/: brains/SimCreator.cpp, brains/SimInfo.cpp, + io/DumpReader.cpp: MPI in NVE is working + +2004-12-14 21:57 tim + + * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. + Master nodes does not brocast the total number of frames + +2004-12-14 19:08 tim + + * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, + integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, + minimizers/CGFamilyMinimizer.cpp, + minimizers/MinimizerParameterSet.hpp, + minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, + minimizers/SDMinimizer.cpp: more fix in MPI version + +2004-12-13 22:30 tim + + * src/: UseTheForce/DarkSide/simParallel.F90, + applications/oopse/oopse.cpp, brains/SimCreator.cpp, + brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, + integrators/DLM.cpp, integrators/Integrator.cpp, + integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, + io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, + io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, + math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, + primitives/RigidBody.cpp, primitives/StuntDouble.cpp, + primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, + utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, + utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version + is built + +2004-12-10 18:41 tim + + * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp + +2004-12-10 16:14 tim + + * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, + primitives/StuntDouble.hpp: forget to zero out the torque. Sticky + and Dipole is working now + +2004-12-09 23:15 tim + + * src/: UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: + fix an index problem in eFrame matrix + +2004-12-09 23:09 tim + + * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when + initializing the new Charge AtomType + +2004-12-09 21:15 tim + + * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, + types/DirectionalAtomType.cpp: sticky module get compiled + +2004-12-09 20:43 gezelter + + * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, + reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for + GB + +2004-12-09 20:42 gezelter + + * src/UseTheForce/doForces.F90: u_l -> eFrame + +2004-12-09 20:27 gezelter + + * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky + module now has the option for multiple sticky types + +2004-12-09 20:27 gezelter + + * src/UseTheForce/doForces.F90: sticky + +2004-12-09 16:22 tim + + * src/integrators/: NPT.cpp, NVT.cpp: fix an interface + inconsistency in lab2Bidy + +2004-12-09 15:45 tim + + * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug + in calculating torque in rigid body + +2004-12-08 20:37 tim + + * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, + brains/SnapShot.cpp, brains/Snapshot.hpp, + integrators/Integrator.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: + fix a parsing bug in ElectroStaticAtomTypesSectionParser + +2004-12-08 17:03 tim + + * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane + in NVT is working + +2004-12-07 23:08 tim + + * src/: UseTheForce/Makefile, brains/SimInfo.hpp, + integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, + io/DumpWriter.cpp: NPT in progress + +2004-12-07 14:43 tim + + * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log + message] + +2004-12-07 05:12 tim + + * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in + UseInitXSstate + +2004-12-07 05:00 tim + + * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message + +2004-12-07 04:47 tim + + * src/types/DirectionalAtomType.cpp: [no log message] + +2004-12-07 02:18 tim + + * forceFields/newDUFF.frc: merge WATER force field into DUFF + +2004-12-07 01:33 tim + + * forceFields/newDUFF.frc: change the force constant of bonds + +2004-12-06 23:29 tim + + * src/: UseTheForce/DarkSide/charge.F90, + UseTheForce/DarkSide/charge_interface.h, + UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: + fix atom type ident in Charge and Dipole Module + +2004-12-06 22:56 tim + + * src/primitives/Torsion.cpp: butane is working now + +2004-12-06 20:15 tim + + * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, + primitives/Bond.hpp, primitives/Torsion.cpp: short range + interaction for butane is correct.Still something wrong with long + range one + +2004-12-06 04:49 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/BendTypesSectionParser.cpp, math/Polynomial.hpp, + primitives/Atom.hpp, utils/NumericConstant.hpp, + utils/TypeContainer.hpp: fix a bug in Exclude List + +2004-12-05 22:21 tim + + * forceFields/newDUFF.frc: minor fix in DUFF + +2004-12-05 22:02 tim + + * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, + utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: + fix a bug in filling MolMembership + +2004-12-05 17:12 tim + + * forceFields/newDUFF.frc: minor fix in force field file + +2004-12-05 17:09 tim + + * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp + +2004-12-04 20:09 tim + + * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, + math/Vector3.hpp: NVE is working now, get the same result as + OOPSE-1.0 + +2004-12-04 19:29 tim + + * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy + +2004-12-04 19:24 gezelter + + * src/primitives/: Bend.cpp, Torsion.cpp: What? + +2004-12-04 19:24 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion + +2004-12-04 05:24 tim + + * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, + integrators/Integrator.hpp, + integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, + utils/TypeContainer.hpp: NVE conserved energy, however, potential + is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf + and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, + dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step + 4 EAM Step 5 Shape Step 6 Constraint & Restraint + +2004-12-04 00:01 tim + + * src/: UseTheForce/DarkSide/LJ.F90, + applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, + energy of NVE is not conserved + +2004-12-03 22:36 tim + + * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, + primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running + +2004-12-03 21:30 tim + + * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, + integrators/NVE.cpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/StuntDouble.hpp, + primitives/Torsion.hpp: more missing function get implemented + +2004-12-03 20:30 tim + + * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, + SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo + +2004-12-03 17:59 tim + + * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, + io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, + io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, + utils/TypeContainer.hpp: begin to fix bugs + +2004-12-03 00:26 tim + + * src/utils/Trim.cpp: file Trim.cpp was initially added on branch + new_design. + +2004-12-03 00:26 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, + integrators/IntegratorCreator.cpp, + integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, utils/Makefile, + utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a + bug in countTokens in StringTokenizer + +2004-12-03 00:06 tim + + * forceFields/newDUFF.frc: minor fix + +2004-12-02 23:15 tim + + * forceFields/newDUFF.frc: new ForceField format + +2004-12-02 22:15 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, + applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, + integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, + integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Makefile: refine factory pattern to make it initialized + correctly + +2004-12-02 22:15 tim + + * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp + was initially added on branch new_design. + +2004-12-02 22:15 tim + + * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp + was initially added on branch new_design. + +2004-12-02 22:15 tim + + * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp + was initially added on branch new_design. + +2004-12-02 22:15 tim + + * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp + was initially added on branch new_design. + +2004-12-02 16:53 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, + types/DirectionalAtomType.cpp, types/Makefile: oopse get built + +2004-12-02 16:04 tim + + * src/: applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, + brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapshotManager.hpp, brains/Stats.cpp, + constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, + io/basic_ifstrstream.hpp, primitives/Bend.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, + utils/PropertyMap.hpp, utils/TypeContainer.hpp, + visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still + have two linking problem + +2004-12-02 05:17 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, + minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, + restraints/Restraints.cpp, visitors/AtomVisitor.cpp, + visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, + visitors/ZconsVisitor.cpp: change endl to std::endl + +2004-12-02 05:14 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, + io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, + minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp: minor fix + +2004-12-02 05:09 tim + + * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: + remove StreamTokenizer + +2004-12-02 05:06 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, + io/ZConsWriter.cpp, math/randomSPRNG.cpp, + restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using + namespace std in .cpp file + +2004-12-02 05:04 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, + brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, io/ZConsWriter.hpp, + minimizers/MinimizerParameterSet.hpp, + minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, + minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, + restraints/Restraints.cpp, restraints/Restraints.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + utils/GenericData.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding + qulified name prefix std + +2004-12-02 04:55 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, + io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, + minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp: replace string by std::string + +2004-12-02 03:12 tim + + * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, + src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/Lattice.hpp, + src/applications/simpleBuilder/LatticeCreator.hpp, + src/applications/simpleBuilder/LatticeFactory.hpp, + src/applications/simpleBuilder/MoLocator.hpp, + src/brains/SimInfo.cpp, src/brains/SkipList.hpp, + src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, + src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, + src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, + src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, + src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, + src/utils/Makefile, src/utils/StringUtils.cpp, + src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, + src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, + src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, + test/brains/RigidBody.cpp: replace misuse of using namespace std in + header files + +2004-12-02 02:23 tim + + * src/: primitives/Atom.hpp, primitives/RigidBody.hpp, + primitives/StuntDouble.hpp, utils/TypeContainer.hpp, + utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: + begin to fix linking problem + +2004-12-02 02:08 tim + + * src/: applications/oopse/oopse.cpp, brains/Stats.cpp, + brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, + integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, + integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, + integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, + math/SquareMatrix3.hpp, primitives/Atom.hpp, + primitives/RigidBody.hpp, primitives/StuntDouble.hpp, + utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, + still has some linking problem + +2004-12-02 00:26 tim + + * src/: integrators/NVT.cpp, integrators/NVT.hpp, + utils/OOPSEConstant.hpp: NVT get built + +2004-12-02 00:09 tim + + * src/integrators/DLM.cpp: file DLM.cpp was initially added on + branch new_design. + +2004-12-02 00:09 tim + + * src/integrators/DLM.hpp: file DLM.hpp was initially added on + branch new_design. + +2004-12-02 00:09 tim + + * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, + brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, + brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, + integrators/Integrator.hpp, integrators/Makefile, + integrators/NVE.cpp, integrators/NVE.hpp, + integrators/RotationAlgorithm.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE + get built + +2004-12-02 00:09 tim + + * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp + was initially added on branch new_design. + +2004-12-01 22:45 tim + + * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, + io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, + io/StatWriter.hpp: rename DumpWrite to DumpWriter + +2004-12-01 22:45 tim + + * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on + branch new_design. + +2004-12-01 20:05 tim + + * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, + io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, + utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, + visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, + visitors/ZconsVisitor.hpp: visitors get built + +2004-12-01 19:32 chrisfen + + * samples/water/tip3p_ice/tp3.md: fixed a sample + +2004-12-01 19:10 tim + + * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/types/AtomType.hpp, src/utils/Utility.hpp, + src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, + src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: + spell check + +2004-12-01 18:42 tim + + * src/: UseTheForce/DarkSide/atype.F90, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, + primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator + and constraint, other directories get built + +2004-12-01 17:38 tim + + * src/: brains/DataStorage.cpp, brains/DataStorage.hpp, + brains/ForceManager.cpp, brains/MoleculeCreator.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/RigidBody.cpp, + primitives/RigidBody.hpp, primitives/StuntDouble.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: + refactory AtomType + +2004-12-01 03:11 tim + + * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change + +2004-12-01 02:30 tim + + * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change + NumericConstant + +2004-12-01 02:24 tim + + * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, + primitives/RigidBody.cpp: minor fix + +2004-11-30 23:14 tim + + * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, + io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, + io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io + get built, next is integrator + +2004-11-30 22:43 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceField.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/BASS_interface.cpp, primitives/StuntDouble.hpp, + utils/StringUtils.hpp: brains get built + +2004-11-30 20:50 tim + + * src/: brains/ForceManager.cpp, brains/Makefile, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + utils/StringUtils.hpp: brains get built, io is next + +2004-11-30 19:58 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/ForceManager.cpp, brains/ForceManager.hpp, + brains/MoleculeCreator.cpp, brains/SimCreator.hpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, + brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, + math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo + +2004-11-30 19:58 tim + + * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially + added on branch new_design. + +2004-11-30 17:54 tim + + * src/: primitives/Bend.hpp, primitives/Bond.hpp, + primitives/StuntDouble.hpp, primitives/Torsion.hpp, + utils/LocalIndexManager.hpp: more get fixed + +2004-11-30 05:03 tim + + * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was + initially added on branch new_design. + +2004-11-30 05:03 tim + + * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename + LocalndexManager.hpp to LocalIndexManager.hpp + +2004-11-30 04:43 tim + + * src/: io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp: Section Parsers get compiled + +2004-11-30 04:14 tim + + * src/: io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor + fixed + +2004-11-30 03:49 tim + + * src/: io/TorsionTypesSectionParser.cpp, + io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, + types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, + types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, + types/QuarticTorsionType.hpp: minor fixed + +2004-11-30 03:32 tim + + * src/: io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp: #inlcude statement can not be + embedded + +2004-11-29 21:42 tim + + * test/math/: Makefile, PolynomialTestCase.cpp, + PolynomialTestCase.hpp: add PolynomialTestCase + +2004-11-29 21:42 tim + + * src/math/Polynomial.hpp: Polynomial passes unit test + +2004-11-29 20:03 tim + + * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename + QuarticTorsion.hpp to QuarticTorsionType.hpp + +2004-11-29 20:03 tim + + * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was + initially added on branch new_design. + +2004-11-29 19:56 tim + + * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was + initially added on branch new_design. + +2004-11-29 19:56 tim + + * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add + CubicTorsionType and QuarticTorsionType + +2004-11-29 19:56 tim + + * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was + initially added on branch new_design. + +2004-11-29 18:00 tim + + * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get + fixed + +2004-11-29 17:59 tim + + * src/utils/Trim.hpp: file Trim.hpp was initially added on branch + new_design. + +2004-11-29 17:59 tim + + * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim + Algorithm for std::string + +2004-11-29 15:52 tim + + * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove + some useless files + +2004-11-29 15:50 tim + + * src/io/: BondTypesSectionParser.cpp, + ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, + ElectrostaticAtomTypesSectionParser.cpp, + HarmonicBondTypesSectionParser.cpp, + HarmonicBondTypesSectionParser.hpp, + LennardJonesAtomTypesSectionParser.cpp, Makefile, + SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, + StickyAtomTypesSectionParser.hpp: more files get fixed + +2004-11-29 15:27 tim + + * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, + DirectionalAtomTypesSectionParser.cpp, + EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, + Makefile, SectionParser.cpp, SectionParser.hpp, + SectionParserManager.cpp, SectionParserManager.hpp: part of io get + built + +2004-11-29 14:49 tim + + * src/types/UreyBradleyBendType.hpp: types get built + +2004-11-29 14:40 tim + + * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: + types get built + +2004-11-26 02:13 tim + + * src/: UseTheForce/ForceField.hpp, + io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, + types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some + files + +2004-11-25 20:18 tim + + * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was + initially added on branch new_design. + +2004-11-25 20:18 tim + + * src/: io/AtomTypesSectionParser.cpp, + io/BondTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.cpp, + types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some + files + +2004-11-25 20:18 tim + + * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was + initially added on branch new_design. + +2004-11-24 22:12 tim + + * src/: io/AtomTypesSectionParser.cpp, + io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DipoleAtomTypesSectionParser.cpp, + io/DipoleAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, + io/EAMAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, + io/HarmonicBondTypesSectionParser.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, + io/SectionParser.hpp, io/SectionParserManager.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built + +2004-11-24 21:33 tim + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, + ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, + LJFF.cpp, Makefile: UseTheForce get built + +2004-11-24 20:55 tim + + * src/: math/RectMatrix.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, + primitives/Makefile, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp, primitives/Torsion.cpp, + primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp: types and primitives get built + +2004-11-24 19:49 tim + + * test/utils/: Makefile, NextCombinationTestCase.cpp, + StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint + StringTokenizerTestCase + +2004-11-24 19:49 tim + + * src/utils/: GenericData.hpp, StringTokenizer.cpp, + StringTokenizer.hpp: StringTokenizer passes unit test + +2004-11-24 18:20 tim + + * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, + src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: + change Makefile + +2004-11-24 18:06 chrisfen + + * src/io/RestraintReader.cpp: improved restraints - mpi should work + fine + +2004-11-24 18:06 chrisfen + + * src/integrators/Integrator.cpp: improved restraints + +2004-11-24 18:05 chrisfen + + * samples/water/tip3p_ice/tp3.md: oops... + +2004-11-24 17:42 tim + + * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, + brains/DataStorage.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, integrators/Integrator.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + primitives/DirectionalAtom.cpp: add SetForceManager method to + integrator + +2004-11-23 23:12 tim + + * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, + integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, + integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, + integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, + integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, + integrators/NVT.hpp, integrators/Velocitizer.cpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/UreyBradleyBendType.hpp: refactory NPT integrator + +2004-11-23 22:50 chrisfen + + * samples/water/tip3p_ice/tp3.md: Back to normal... Oh... + Restraints should work in parallel now + +2004-11-23 22:48 chrisfen + + * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + integrators/Integrator.cpp, integrators/Integrator.hpp, + io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, + io/RestraintReader.cpp, io/RestraintWriter.cpp, + restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements + to restraints + +2004-11-23 22:47 chrisfen + + * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll + return to the original on next commit + +2004-11-23 17:53 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + io/ChargeAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, + io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, types/DirectionalAtomType.cpp, + utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser + +2004-11-23 17:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.hpp: file + ElectrostaticAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-23 17:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.cpp: file + ElectrostaticAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-23 06:03 tim + + * src/: io/EAMAtomTypesSectionParser.cpp, + io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, + types/AtomType.hpp, types/DirectionalAtomType.cpp, + types/DirectionalAtomType.hpp: add EAM AtomType Section Parser + +2004-11-23 06:03 tim + + * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp + was initially added on branch new_design. + +2004-11-23 06:03 tim + + * src/io/EAMAtomTypesSectionParser.hpp: file + EAMAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 06:03 tim + + * src/io/EAMAtomTypesSectionParser.cpp: file + EAMAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/TorsionTypesSectionParser.hpp: file + TorsionTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/BendTypesSectionParser.hpp: file + BendTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/BondTypesSectionParser.hpp: file + BondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/BondTypesSectionParser.cpp: file + BondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/TorsionTypesSectionParser.cpp: file + TorsionTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-23 04:35 tim + + * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, + BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, + TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add + BondTypesSectionParser, BendTypesSectionParser and + TorsionTypeSectionParser + +2004-11-23 04:35 tim + + * src/io/BendTypesSectionParser.cpp: file + BendTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:04 tim + + * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in + DUFF and EAM + +2004-11-22 23:02 tim + + * src/io/: DirectionalAtomTypesParser.hpp, + DirectionalAtomTypesSectionParser.hpp: adding section parsers + +2004-11-22 23:02 tim + + * src/io/DirectionalAtomTypesSectionParser.hpp: file + DirectionalAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/DipoleAtomTypesSectionParser.hpp: file + DipoleAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/AtomTypesSectionParser.hpp: file + AtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/HarmonicBondTypesSectionParser.hpp: file + HarmonicBondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/StickyAtomTypesSectionParser.cpp: file + StickyAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.hpp: file + LennardJonesAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-22 20:55 tim + + * src/io/HarmonicBondTypesSectionParser.cpp: file + HarmonicBondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/DirectionalAtomTypesSectionParser.cpp: file + DirectionalAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/SectionParserManager.cpp: file SectionParserManager.cpp + was initially added on branch new_design. + +2004-11-22 20:55 tim + + * src/io/AtomTypesSectionParser.cpp: file + AtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/ChargeAtomTypesSectionParser.cpp: file + ChargeAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/DipoleAtomTypesSectionParser.cpp: file + DipoleAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.cpp: file + LennardJonesAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-22 20:55 tim + + * src/io/ChargeAtomTypesSectionParser.hpp: file + ChargeAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/StickyAtomTypesSectionParser.hpp: file + StickyAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/SectionParser.hpp: file SectionParser.hpp was initially + added on branch new_design. + +2004-11-22 20:55 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, + brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, + brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, + integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, + io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DipoleAtomTypesSectionParser.cpp, + io/DipoleAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, + types/AtomType.hpp, types/DirectionalAtomType.hpp, + utils/GenericData.hpp: adding section parsers + +2004-11-22 20:55 tim + + * src/io/DirectionalAtomTypesParser.hpp: file + DirectionalAtomTypesParser.hpp was initially added on branch + new_design. + +2004-11-22 20:55 tim + + * src/io/SectionParserManager.hpp: file SectionParserManager.hpp + was initially added on branch new_design. + +2004-11-22 20:55 tim + + * src/io/SectionParser.cpp: file SectionParser.cpp was initially + added on branch new_design. + +2004-11-19 22:12 tim + + * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially + added on branch new_design. + +2004-11-19 22:12 tim + + * src/: brains/SimState.cpp, brains/SimState.hpp, + io/InitializeFromFile.cpp, types/FixBondType.hpp, + types/FixedBondType.hpp: remove more useless files + +2004-11-19 21:47 tim + + * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, + integrators/Integrator.cpp, applications/Makedepend: remove more + useless files + +2004-11-19 21:38 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, + integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, + integrators/NVT.hpp: refactory integrator + +2004-11-19 21:38 tim + + * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on + branch new_design. + +2004-11-19 21:38 tim + + * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on + branch new_design. + +2004-11-19 21:38 tim + + * src/integrators/NPT.hpp: file NPT.hpp was initially added on + branch new_design. + +2004-11-19 21:38 tim + + * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added + on branch new_design. + +2004-11-19 21:38 tim + + * src/integrators/NVT.hpp: file NVT.hpp was initially added on + branch new_design. + +2004-11-19 20:37 tim + + * forceFields/newDUFF.frc: new DUFF forcefield + +2004-11-19 20:23 tim + + * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on + branch new_design. + +2004-11-19 20:23 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, + UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, + utils/TypeContainer.hpp: add EAM + +2004-11-19 20:23 tim + + * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on + branch new_design. + +2004-11-19 18:02 tim + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except + error checking + +2004-11-19 17:56 tim + + * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp + was initially added on branch new_design. + +2004-11-19 17:56 tim + + * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp + was initially added on branch new_design. + +2004-11-19 17:56 tim + + * src/types/FixBondType.hpp: file FixBondType.hpp was initially + added on branch new_design. + +2004-11-19 17:56 tim + + * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, + UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, + utils/StringTokenizer.cpp: DUFF is almost done except error + checking + +2004-11-19 00:11 tim + + * src/UseTheForce/DUFF.cpp: adding DUFF parser + +2004-11-18 23:26 tim + + * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was + initially added on branch new_design. + +2004-11-18 23:26 tim + + * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding + DUFF parser + +2004-11-18 21:42 tim + + * forceFields/newDUFF.frc: adding new format DUFF force field + +2004-11-18 15:57 chrisfen + + * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that + slowed down the force loop + +2004-11-18 05:42 tim + + * src/utils/NumericConstant.cpp: file NumericConstant.cpp was + initially added on branch new_design. + +2004-11-18 05:42 tim + + * src/utils/NumericConstant.hpp: file NumericConstant.hpp was + initially added on branch new_design. + +2004-11-18 05:42 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, + primitives/Bend.cpp, utils/NumericConstant.cpp, + utils/NumericConstant.hpp: Adding NumericConstant class + +2004-11-18 04:16 tim + + * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, + UseTheForce/ForceFields.hpp: remove more junk files + +2004-11-18 04:12 tim + + * src/: brains/ForceFields.cpp, brains/SimSetup.cpp, + brains/SimSetup.hpp, constraints/AbstractClasses.hpp, + integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, + primitives/AbstractClasses.hpp, primitives/Bond.cpp, + primitives/BondExtensions.cpp, primitives/SRI.hpp, + primitives/TorsionExtensions.cpp: remove some junk files + +2004-11-18 04:07 tim + + * src/primitives/BendExtensions.cpp: remove some junk files + +2004-11-18 04:04 tim + + * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, + QuadraticBondType.hpp: refine QudraticBond + +2004-11-18 03:57 tim + + * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp + +2004-11-18 03:57 tim + + * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was + initially added on branch new_design. + +2004-11-17 21:47 tim + + * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp + was initially added on branch new_design. + +2004-11-17 21:47 tim + + * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially + added on branch new_design. + +2004-11-17 21:47 tim + + * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially + added on branch new_design. + +2004-11-17 21:47 tim + + * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was + initially added on branch new_design. + +2004-11-17 21:47 tim + + * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was + initially added on branch new_design. + +2004-11-17 21:47 tim + + * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was + initially added on branch new_design. + +2004-11-17 21:47 tim + + * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially + added on branch new_design. + +2004-11-17 21:47 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/GhostBend.cpp, + primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp, types/BondType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: + UreyBradleyBend and GhostBend + +2004-11-17 18:58 tim + + * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp + was initially added on branch new_design. + +2004-11-17 18:58 tim + + * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp + was initially added on branch new_design. + +2004-11-17 18:58 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, + primitives/Bond.hpp, types/CharmmTorsionType.hpp, + types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types + stuff and Chebyshev Polynomial + +2004-11-17 18:58 tim + + * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 06:37 tim + + * src/types/PolynomialTorsionType.hpp: file + PolynomialTorsionType.hpp was initially added on branch new_design. + +2004-11-17 06:37 tim + + * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was + initially added on branch new_design. + +2004-11-17 06:37 tim + + * src/: math/Polynomial.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, + types/BondType.hpp, types/CharmmTorsionType.cpp, + types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp, + utils/StringTokenizer.hpp: add PolynomialBondType, + PolynomialBendType, PolynomialTorsionType, HarmonicBendType and + CharmmTorsionType. Need to refine the design and add document for + them + +2004-11-17 06:37 tim + + * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 06:37 tim + + * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was + initially added on branch new_design. + +2004-11-17 06:37 tim + + * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was + initially added on branch new_design. + +2004-11-17 01:11 tim + + * src/types/: BendType.hpp, PolynomialBondType.hpp, + TorsionType.hpp: add PolynomialBondType + +2004-11-17 01:11 tim + + * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was + initially added on branch new_design. + +2004-11-16 23:20 tim + + * src/math/Polynomial.hpp: file Polynomial.hpp was initially added + on branch new_design. + +2004-11-16 23:20 tim + + * src/math/Polynomial.hpp: Adding Polynomial class + +2004-11-16 22:04 gezelter + + * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially + added on branch new_design. + +2004-11-16 22:04 gezelter + + * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was + initially added on branch new_design. + +2004-11-16 22:04 gezelter + + * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, + MorseBondType.hpp, TorsionType.hpp: added some new stuff + +2004-11-16 20:36 tim + + * src/: primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, + types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and + TorsionType + +2004-11-16 02:07 tim + + * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on + branch new_design. + +2004-11-16 02:07 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, + utils/StringTokenizer.cpp: adding DUFF class; adding checking + statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer + +2004-11-15 23:00 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, + UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, + types/AtomType.hpp: adding ForceFieldFactory and LJFF classes + +2004-11-15 23:00 tim + + * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp + was initially added on branch new_design. + +2004-11-15 23:00 tim + + * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp + was initially added on branch new_design. + +2004-11-15 23:00 tim + + * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on + branch new_design. + +2004-11-15 18:02 tim + + * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was + initially added on branch new_design. + +2004-11-15 18:02 tim + + * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on + branch new_design. + +2004-11-15 18:02 tim + + * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on + branch new_design. + +2004-11-15 18:02 tim + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, + integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, + io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, + DumpWriter.Next Step is LJFF and integrators + +2004-11-13 05:08 tim + + * src/: brains/ForceManager.cpp, brains/ForceManager.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, + refactory, refactory + +2004-11-12 22:43 tim + + * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, + StringTokenizer.cpp: bug fix in hasMoreTokens + +2004-11-12 22:28 tim + + * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was + initially added on branch new_design. + +2004-11-12 22:28 tim + + * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding + StringUtils, a c-style strtok like class, need unit test + +2004-11-12 17:40 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test + +2004-11-12 07:05 tim + + * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + primitives/CutoffGroup.hpp, primitives/Molecule.cpp: + MoleculeCreator forget to create CutoffGroups for free atoms + +2004-11-12 06:19 tim + + * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: + OOPSE = Object-Obfuscated Parallel Simulation Engine + +2004-11-11 21:48 chrisfen + + * samples/water/tip3p_ice/tp3.md: working sample + +2004-11-11 21:47 chrisfen + + * src/restraints/Restraints.cpp: working towards parallel + restraints + +2004-11-11 21:47 chrisfen + + * src/integrators/Integrator.cpp: Commented out some write + statements + +2004-11-11 21:46 chrisfen + + * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some + write statements + +2004-11-11 21:46 chrisfen + + * samples/water/tip3p_ice/tp3.md: Fun with ice + +2004-11-11 16:41 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, + brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, + io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove + useless mpiSimulation + +2004-11-11 16:41 tim + + * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on + branch new_design. + +2004-11-10 22:50 tim + + * src/: brains/ForceManager.cpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, + integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo + +2004-11-10 22:01 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, + visitors/AtomVisitor.cpp: another painful day (1) SimCreator, + SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom + File will be removed) (3) ForceField (at least LJ) and BondType, + BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & + Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint + +2004-11-10 14:52 tim + + * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a + configurable StatWriter + +2004-11-10 14:52 tim + + * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on + branch new_design. + +2004-11-10 02:58 tim + + * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation + in progress + +2004-11-09 23:11 tim + + * src/brains/ForceManager.cpp: file ForceManager.cpp was initially + added on branch new_design. + +2004-11-09 23:11 tim + + * src/integrators/VelocityVerletIntegrator.cpp: file + VelocityVerletIntegrator.cpp was initially added on branch + new_design. + +2004-11-09 23:11 tim + + * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, + brains/mpiSimulation.hpp, integrators/Integrator.hpp, + integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp: adding ForceManager + +2004-11-09 23:11 tim + + * src/brains/ForceManager.hpp: file ForceManager.hpp was initially + added on branch new_design. + +2004-11-09 23:11 tim + + * src/integrators/NVE.cpp: file NVE.cpp was initially added on + branch new_design. + +2004-11-09 01:08 tim + + * src/integrators/VelocityVerletIntegrator.hpp: file + VelocityVerletIntegrator.hpp was initially added on branch + new_design. + +2004-11-09 01:08 tim + + * src/integrators/NVE.hpp: file NVE.hpp was initially added on + branch new_design. + +2004-11-09 01:08 tim + + * src/: brains/Exclude.hpp, brains/Stats.hpp, + integrators/Integrator.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + utils/TypeContainer.hpp: More to break + +2004-11-06 05:21 tim + + * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially + added on branch new_design. + +2004-11-06 05:21 tim + + * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, + utils/TypeContainer.hpp, utils/next_combination.hpp: adding + ForceField and TypeContainer classes + +2004-11-05 23:38 tim + + * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was + initially added on branch new_design. + +2004-11-05 23:38 tim + + * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was + initially added on branch new_design. + +2004-11-05 23:38 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.hpp, + utils/LocalndexManager.hpp: Fix Exclude class etc. + +2004-11-05 21:45 chrisfen + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the + linear visitor + +2004-11-05 21:04 chrisfen + + * src/UseTheForce/DarkSide/shapes.F90: current status of the + debugging process + +2004-11-05 21:04 chrisfen + + * make/Makefile.in: included visitors and minimizer + +2004-11-05 21:03 chrisfen + + * ChangeLog: new changes + +2004-11-05 02:56 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + primitives/Molecule.hpp: Pain...... + +2004-11-04 20:55 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 20:51 gezelter + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new + classes in progress + +2004-11-04 19:48 tim + + * src/brains/Stats.cpp: file Stats.cpp was initially added on + branch new_design. + +2004-11-04 19:48 tim + + * src/brains/Stats.hpp: file Stats.hpp was initially added on + branch new_design. + +2004-11-04 19:48 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, + SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats + class + +2004-11-04 16:22 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 16:20 gezelter + + * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't + remember what I did + +2004-11-04 16:20 gezelter + + * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky + +2004-11-04 16:20 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 16:20 gezelter + + * samples/water/ssd/ssd.md: testing force fields + +2004-11-04 16:19 gezelter + + * samples/shape/linear.in: testing shapes + +2004-11-03 19:56 tim + + * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator + class(similar as SimSetup) + +2004-11-03 19:56 tim + + * src/brains/SimCreator.hpp: file SimCreator.hpp was initially + added on branch new_design. + +2004-11-03 19:56 tim + + * src/brains/SimCreator.cpp: file SimCreator.cpp was initially + added on branch new_design. + +2004-11-03 18:00 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 16:08 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 22:41 tim + + * src/: brains/Migrator.hpp, brains/SimModel.cpp, + utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. + Need unit test + +2004-11-02 22:41 tim + + * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was + initially added on branch new_design. + +2004-11-02 22:41 tim + + * src/brains/Migrator.hpp: file Migrator.hpp was initially added on + branch new_design. + +2004-11-02 16:59 tim + + * src/brains/SimModel.cpp: file SimModel.cpp was initially added on + branch new_design. + +2004-11-02 16:59 tim + + * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: SimModel in progress + +2004-11-02 15:28 chrisfen + + * src/: UseTheForce/DarkSide/shapes.F90, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes + looks like it's working + +2004-11-02 15:27 tim + + * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some + functions for dealing with memory issue + +2004-11-02 15:27 tim + + * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially + added on branch new_design. + +2004-11-02 15:23 tim + + * src/: brains/SimModel.hpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding + SimModel(something similar as SimInfo) + +2004-11-01 22:52 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 21:40 tim + + * src/primitives/Torsion.hpp: file Torsion.hpp was initially added + on branch new_design. + +2004-11-01 21:40 tim + + * src/primitives/Bend.hpp: file Bend.hpp was initially added on + branch new_design. + +2004-11-01 21:40 tim + + * src/primitives/Bond.hpp: file Bond.hpp was initially added on + branch new_design. + +2004-11-01 21:40 tim + + * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial + version of Bond, Bend and Torsion. + +2004-11-01 21:37 tim + + * src/types/BendType.hpp: file BendType.hpp was initially added on + branch new_design. + +2004-11-01 21:37 tim + + * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding + BondType, BendType, TorsionType + +2004-11-01 21:37 tim + + * src/types/TorsionType.hpp: file TorsionType.hpp was initially + added on branch new_design. + +2004-11-01 21:37 tim + + * src/types/BondType.hpp: file BondType.hpp was initially added on + branch new_design. + +2004-11-01 20:15 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 19:57 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 22:37 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule + class + +2004-10-29 22:28 chrisfen + + * src/: UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, + types/ShapeAtomType.cpp: still debugging + +2004-10-29 22:28 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: + shapes rcut calculator added + +2004-10-29 22:27 chrisfen + + * samples/shape/linear.md: shorter run + +2004-10-29 20:54 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. + +2004-10-29 16:22 tim + + * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove + some deprecated files + +2004-10-29 16:20 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 22:34 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 22:26 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 21:42 tim + + * src/utils/next_combination.hpp: Minor change in next_combination + +2004-10-28 21:28 tim + + * src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/ReplaceWildCardTestCase.cpp: Done with combination + +2004-10-28 21:11 tim + + * src/utils/next_combination.hpp: change documentation of + next_combination.hpp + +2004-10-28 20:41 tim + + * ChangeLog, src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working + +2004-10-28 20:01 tim + + * src/utils/next_combination.hpp: adding replace wildcard function + +2004-10-28 19:33 tim + + * src/utils/next_combination.hpp: Minor change + +2004-10-28 19:06 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 17:22 chrisfen + + * src/UseTheForce/WATER.cpp: fix of setDipoles + +2004-10-28 17:20 gezelter + + * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the + shapeFile + +2004-10-28 17:20 gezelter + + * samples/shape/linear.md: forgot the orientation line + +2004-10-28 16:56 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 16:55 gezelter + + * samples/lipid/5x5.md: uncommented .in line + +2004-10-28 15:42 tim + + * test/utils/: Makefile, NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp, next_combination.hpp: next_combination + in progress + +2004-10-28 15:15 tim + + * test/utils/: NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp: adding next_combination test case + +2004-10-28 15:02 tim + + * test/utils/next_combination.hpp: STL Compatible combination + sequence generator + +2004-10-28 06:23 tim + + * test/utils/: GenerateCombination.hpp, + ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp + +2004-10-28 06:16 tim + + * test/utils/GenerateCombination.hpp: a STL next_permutaion like + next_combination function. + +2004-10-28 03:27 tim + + * test/utils/ReplaceWildCard.hpp: no message + +2004-10-28 03:14 tim + + * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: + ReplaceWildCard(recursive version) is working, need refactoring. An + iterative version is on the way + +2004-10-28 02:28 tim + + * test/utils/: Makefile, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress + +2004-10-28 02:08 tim + + * test/utils/: ReplaceWildCardTestCase.cpp, + ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard + +2004-10-27 23:17 tim + + * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need + test + +2004-10-27 06:25 tim + + * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild + char matching is on the way + +2004-10-27 06:07 tim + + * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 + +2004-10-27 03:00 gezelter + + * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix + +2004-10-27 02:20 gezelter + + * src/UseTheForce/ForceFields.hpp: subclass foo + +2004-10-27 02:16 gezelter + + * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> + string conversion + +2004-10-27 00:01 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, + brains/SimSetup.hpp: char* -> string + +2004-10-26 22:25 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 22:25 gezelter + + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + define name collision + +2004-10-26 22:24 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 22:24 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 22:19 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 18:03 chrisfen + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: + Changes to help advance shapes + +2004-10-26 18:02 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to + Shapes force field reader + +2004-10-26 17:28 tim + + * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and + SnapshotTestCase in progress + +2004-10-25 22:46 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 17:03 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. + +2004-10-25 04:08 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 07:55 tim + + * src/utils/GenericFactory.hpp: GenericFactory pass unit test + +2004-10-23 23:09 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 23:09 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 22:59 chrisfen + + * src/: UseTheForce/LJFF.cpp, + UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear + god! It runs and conserves energy! + +2004-10-22 22:54 chrisfen + + * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY + +2004-10-22 22:53 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 22:53 chrisfen + + * make/Makefile.in: compiler flags + +2004-10-22 21:20 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 20:22 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 20:21 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.hpp, Makefile: More on AtomType and + DirectionalAtomType + +2004-10-22 14:47 gezelter + + * src/types/AtomType.hpp: Adding AtomType + +2004-10-21 21:31 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 21:30 tim + + * test/brains/: BrainsTest.cpp, Makefile, + SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, + SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for + Snapshot and snapshotManager. + +2004-10-21 20:15 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 16:32 tim + + * src/utils/GenericData.cpp, src/utils/Makefile, + test/utils/Makefile, test/utils/UtilTest: remove some junk files + +2004-10-21 16:24 tim + + * test/utils/GenericData.hpp: remove backup of GenericData.hpp + +2004-10-21 16:22 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 15:25 chuckv + + * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj + module. + +2004-10-21 15:24 chuckv + + * src/UseTheForce/DarkSide/lj_interface.h: Added interface for + fortran lj module. + +2004-10-20 22:54 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 21:52 gezelter + + * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, + DarkSide/sticky_interface.h: fixed a fortran name problem + +2004-10-20 21:38 tim + + * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, + GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, + UtilTest, UtilTest.cpp: adding generic data test case + +2004-10-20 21:16 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 20:47 chuckv + + * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, + fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project + continues + +2004-10-20 20:46 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 18:07 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 05:52 tim + + * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and + SnapshotManager in design phase + +2004-10-20 04:54 gezelter + + * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace + problem prevented linking + +2004-10-20 04:54 gezelter + + * src/UseTheForce/Shapes_FF.cpp: fixed include + +2004-10-20 04:26 gezelter + + * src/utils/: Makefile, definitions.F90, definitions_module.F90, + oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: + more fortran name mangling + +2004-10-20 04:23 gezelter + + * src/profiling/timing.F90: yet more fortran renaming + +2004-10-20 04:19 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 + +2004-10-20 04:12 gezelter + + * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some + broken fortran stuff + +2004-10-20 04:02 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 + +2004-10-20 00:18 tim + + * test/math/SquareMatrix3TestCase.hpp: [no log message] + +2004-10-19 23:01 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 22:43 chuckv + + * src/UseTheForce/do_Forces.h: Added correct prototypes for + C-fortran interface functions. + +2004-10-19 22:37 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 21:28 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 20:43 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 20:43 gezelter + + * src/UseTheForce/Makefile: regressing + +2004-10-19 20:40 gezelter + + * src/: UseTheForce/DarkSide/calc_shapes.F90, + UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: + working on shapes for portability + +2004-10-19 20:40 gezelter + + * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes + +2004-10-19 18:21 chrisfen + + * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around + findBegin + +2004-10-19 04:34 tim + + * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs + are fixed in Vector class + +2004-10-19 04:28 tim + + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix + some bugs in RectMatrixTestCase + +2004-10-19 04:21 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 23:13 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 21:03 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 17:07 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 16:30 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 16:29 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 15:21 gezelter + + * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType + +2004-10-18 05:23 tim + + * test/math/VectorTestCase.hpp: adding vector test case + +2004-10-18 05:23 tim + + * src/utils/GenericFactory.hpp: adding generic factory and vector + test case + +2004-10-17 01:19 tim + + * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, + SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in + progress + +2004-10-16 01:31 tim + + * src/math/Quaternion.hpp: add quaternion class + +2004-10-15 21:11 tim + + * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, + IfstrstreamTestCase.hpp: adding test file + +2004-10-15 21:10 tim + + * src/io/basic_ifstrstream.hpp: fix a bunch of bugs + +2004-10-15 20:42 tim + + * src/io/basic_ifstrstream.hpp: change const_cast to statc_const + +2004-10-15 20:35 tim + + * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp + +2004-10-15 20:34 tim + + * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use + namespace oopse + +2004-10-15 19:38 chuckv + + * configure, ac-tools/aclocal.m4: Changed optimization flags for + XLF and XLC. + +2004-10-15 18:28 tim + + * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: + adding ifstrstream test case + +2004-10-15 18:20 tim + + * src/io/basic_ifstrstream.hpp: fix include + +2004-10-15 18:18 tim + + * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi + +2004-10-15 18:17 tim + + * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile + +2004-10-15 18:16 tim + + * test/io/: Makefile, ifstrstreamTestCase.cpp, + ifstrstreamTestCase.hpp: adding test case for ifstrstream + +2004-10-15 15:37 tim + + * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, + ifstrstreamTestCase.hpp: add ifstrstreamTestCase + +2004-10-15 15:20 tim + + * src/io/basic_ifstrstream.hpp: add checkFilename Option + +2004-10-15 15:19 tim + + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, + SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add + SquareMatrixTestCase class + +2004-10-15 07:52 tim + + * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream + +2004-10-14 23:28 tim + + * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, + Vector.hpp: math library in progress + +2004-10-14 23:27 tim + + * src/io/FileReader.hpp: FileReader in progress + +2004-10-13 23:53 tim + + * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, + test in isOrthogonal of SquareMatrix is failed by some reasons + +2004-10-13 22:28 tim + + * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap + class + +2004-10-13 22:27 tim + + * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, + RectMatrixTestCase.hpp: adding testing unit + +2004-10-13 22:24 tim + + * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix + +2004-10-13 06:51 tim + + * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, + Vector3.hpp: refactory vector and matrix classes + +2004-10-13 06:50 tim + + * src/math/Vector3d.hpp: Remove some Makefile.in + +2004-10-12 23:57 tim + + * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and + Matrix3x3d.hpp + +2004-10-12 19:08 tim + + * doc/: cppstyle.html, style.css: adding c++ coding style + +2004-10-11 22:15 tim + + * src/: constraints/AbstractClasses.hpp, + integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: + change #include "mpi.h" to #include in AbstractClasses.hpp + +2004-10-11 21:54 tim + + * scripts/filepp: fix a bug in filepp + +2004-10-11 21:13 tim + + * make/Makefile.in: using filepp to generate dependencies instead + of compilers + +2004-10-11 21:10 tim + + * scripts/filepp: filepp can be used to generate dependencies for + c/c++ now + +2004-10-11 18:40 tim + + * make/Makefile.in: remove -module from F90Options + +2004-10-11 18:01 tim + + * make/Makefile.in: adding rules to move fortran 90 module to + target directory + +2004-10-11 15:43 gezelter + + * make/Makefile.in: fixed makefile.in + +2004-10-11 14:51 tim + + * scripts/filepp: remove "use bytes" which causes problem in sgi + machine + +2004-10-11 14:26 tim + + * forceFields/Makefile: add Makefile + +2004-10-11 14:23 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 + +2004-10-09 06:01 tim + + * samples/: alkane/Makefile.in, lipid/Makefile.in, + metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in + +2004-10-08 23:15 tim + + * make/Makefile.in: [no log message] + +2004-10-08 22:51 tim + + * make/Makefile.in: fix make install + +2004-10-08 22:10 tim + + * make/Makefile.in: adding make install + +2004-10-08 22:04 tim + + * samples/: alkane/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 + +2004-10-06 23:03 gezelter + + * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt + stuff + +2004-10-06 23:03 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 + +2004-10-06 22:20 tim + + * make/: Doxyfile, Makefile.in: adding doxygen configuration file + +2004-10-06 22:19 tim + + * scripts/filepp: filepp can handle different fortran module case + and suffix + +2004-10-06 21:27 gezelter + + * src/restraints/Restraints.cpp: Chris doesn't know about the + OOPSE-2.0 directory structure yet + +2004-10-06 21:27 gezelter + + * ChangeLog: Yeah yeah, we'lll get around to it later + +2004-10-06 21:22 gezelter + + * configure, ac-tools/configure.in, ac-tools/fortran90.m4, + make/Makefile.in: cleaning up build process + +2004-10-06 20:01 chrisfen + + * src/restraints/Restraints.cpp: made the file reading in + restraints more intelligent - no longer gives uninformative seg + faults + +2004-10-06 19:55 gezelter + + * src/applications/simpleBuilder/Make.ftemp.old: cleaning up + +2004-10-06 19:51 gezelter + + * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, + scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit + +2004-10-06 18:53 tim + + * make/: Makefile, Makefile.in: fix make statistics + +2004-10-06 18:18 tim + + * make/: Makefile, Makefile.in: adding GNU make functions to + combine all of the static libraries to a big library + +2004-10-05 22:57 tim + + * make/: Makefile, Makefile.in: adding shared library flag + +2004-10-05 19:37 tim + + * src/: Makefile, UseTheForce/Makefile, + UseTheForce/mpiSimulation_module.F90, + UseTheForce/DarkSide/Makefile, + UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move + mpiSimulation_module to DarkSide + +2004-10-05 19:35 tim + + * make/: Makefile, Makefile.in: building MPI version;using static + library instead of shared library + +2004-10-05 14:14 tim + + * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 + to filepp + +2004-10-04 20:56 tim + + * make/: Makefile, Makefile.in: add make cvslog + +2004-10-04 16:24 gezelter + + * make/: Makefile, Makefile.in: more work on the parallel build + +2004-10-04 16:06 gezelter + + * make/: Makefile, Makefile.in: changes to backport declare flags + +2004-10-04 15:27 gezelter + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, + DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging + shapes + +2004-10-02 04:40 tim + + * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree + +2004-10-02 04:22 tim + + * make/: Makefile, Makefile.in: add oopse_ as library prefix + +2004-10-01 21:59 tim + + * make/: Makefile, Makefile.in: fix a space trimming bug in filepp + +2004-10-01 21:22 gezelter + + * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A + few minor build changes + +2004-10-01 21:11 tim + + * scripts/filepp: adding fortran90 make dependency tool + +2004-09-30 15:41 tim + + * make/: Makefile, Makefile.in: make clean is smart enough to only + remove object files belong to current package. turn off silent + mode + +2004-09-29 21:55 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 + +2004-09-29 21:54 tim + + * make/: Makefile, Makefile.in: get the relative path by shell + script + +2004-09-29 21:32 tim + + * make/Makefile: eliminate DEV_ROOT by relative path + +2004-09-29 18:37 tim + + * make/Makefile.in: add PackageLibs; fix dependency rule + +2004-09-29 17:57 gezelter + + * configure, ac-tools/configure.in: updates + +2004-09-29 17:56 gezelter + + * make/: Make.conf.in, Makefile.in, _files/style.css: Working on + make stuff + +2004-09-29 17:46 tim + + * Makefile: If makefile does not exist, print error message + +2004-09-29 17:12 tim + + * make/: Make.conf.in, Makefile: fix dependencies rule + +2004-09-29 15:58 gezelter + + * Makefile, make/Makefile: still working on build process + +2004-09-29 15:00 tim + + * make/Makefile: add print statment to rules + +2004-09-29 14:59 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 + +2004-09-29 02:55 tim + + * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c + which cause headache in bulding libutils + +2004-09-28 23:24 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 + +2004-09-28 22:15 gezelter + + * lib/dummy: Keep that lib around, please. + +2004-09-28 22:14 gezelter + + * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: + starting a configure version + +2004-09-28 21:08 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 + +2004-09-28 20:43 tim + + * 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] + +2004-09-28 20:41 tim + + * make/Makefile, scripts/sfmakedepend: fix fortran dependency + problem + +2004-09-28 16:13 tim + + * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, + src/io/Makefile: add yacc and lex rules + +2004-09-27 20:24 tim + + * make/Makefile: adding include path to F90Options + +2004-09-27 20:13 tim + + * make/Makefile: change suffix from .cc to .cpp + +2004-09-24 16:27 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 + +2004-09-24 04:16 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, + 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, + 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/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, 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 + +2004-09-24 04:16 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, + 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, + 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/lipid/5x5.in, samples/lipid/5x5.md, samples/lipid/Makefile.in, samples/lipid/lipid.md, samples/lipid/water.md, samples/minimizer/Makefile.in,