--- trunk/OOPSE/ChangeLog 2004/02/10 21:33:44 1046 +++ trunk/OOPSE/ChangeLog 2004/05/10 20:28:14 1152 @@ -1,3 +1,352 @@ +2004-05-07 16:36 gezelter + + * libmdtools/: fSwitchingFunction.h, switch_module.F90: New module + for fortran group-based switching function + +2004-05-07 16:35 gezelter + + * libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, + Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, + calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, + force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, + mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, + simulation_module.F90: Many changes to get group-based cutoffs to + work + +2004-05-01 13:52 tim + + * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, + libmdtools/do_Forces.F90, libmdtools/fSimulation.h, + libmdtools/fortranWrapDefines.hpp, + libmdtools/simulation_module.F90: C++ pass groupList to fortran + +2004-04-29 11:03 tim + + * ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in + calc_charge_charge when using molecular cutoff + +2004-04-28 21:11 tim + + * libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an + unmatched c/fortran interface + +2004-04-28 18:09 tim + + * ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: + keep the previous position of cantilever in SMD + +2004-04-28 17:34 tim + + * ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug + in Molecule.cpp which initialize massRatio before creat the array. + fix two bugs in ZconsVisitor + +2004-04-28 17:06 gezelter + + * libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: + Adding molecular cutoffs + +2004-04-28 16:39 gezelter + + * libmdtools/: calc_charge_charge.F90, do_Forces.F90, + fSimulation.h, force_globals.F90, simulation_module.F90: work on + molecular cutoffs + +2004-04-28 16:39 gezelter + + * libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to + Globals + +2004-04-27 11:26 tim + + * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, + ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, + fSimulation.h, fortranWrapDefines.hpp: add center of mass of the + molecule and massRation into atom class + +2004-04-26 16:16 mmeineke + + * libBASS/Globals.cpp: modified the defaults for the system init + time and system init state. + +2004-04-26 09:29 gezelter + + * libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in + calc_charge_charge.F90 + +2004-04-23 23:31 tim + + * ChangeLog, libmdtools/AtomVisitor.cpp, + libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add + reaction field correction to charge-charge interaction + +2004-04-22 16:33 tim + + * libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, + Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the + calculation of pressure tensor + +2004-04-22 09:55 tim + + * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed + another bug in InitFromFile. MPI verion of OOPSE is working again + +2004-04-21 22:29 tim + + * libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, + InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, + SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two + bugs in MPI version of InitfromFile and one unmatch MPI command in + DumpWriter + +2004-04-21 00:32 tim + + * libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, + libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, + utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some + useless files + +2004-04-20 11:56 tim + + * libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, + SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and + velocitize at thermo + +2004-04-20 00:39 tim + + * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, + libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, + libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, + utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version + +2004-04-19 17:13 gezelter + + * libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, + Thermo.cpp: Fixed a charge bug + +2004-04-19 15:54 tim + + * libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed + a bug in CompositeVisitor which cause the double counting problem + +2004-04-19 12:44 tim + + * libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, + libmdtools/DumpReader.cpp, libmdtools/Make.dep, + libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, + libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: + Dump2XYZ is almost working except atoms in rigidbody are double + counted + +2004-04-18 22:52 tim + + * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, + libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, + libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/Integrator.cpp, libmdtools/Makefile.in, + libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, + libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, + libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, + libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, + libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, + utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new + implement of quickLate using visitor and composite pattern + +2004-04-15 17:15 tim + + * libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting + exclude list + +2004-04-15 11:18 tim + + * ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, + libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, + libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/Thermo.cpp, libmdtools/WATER.cpp, + libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix + whole bunch of bugs :-) + +2004-04-14 12:20 chrisfen + + * forceFields/WATER.frc: Added the WATER.frc force field + +2004-04-14 11:32 gezelter + + * libmdtools/Molecule.cpp: fixed for get_potential + +2004-04-14 10:37 tim + + * AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, + libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, + libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, + libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: + Change DumpWriter and InitFromFile + +2004-04-13 11:26 gezelter + + * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now + molecules can keep track of their own IntegrableObjects (and + RigidBodies). Also a bug-fix so that SimInfo can keep track of + RigidBodies (which was done incorrectly before). + +2004-04-13 11:25 gezelter + + * libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable + (will back out momentarily) + +2004-04-13 10:10 gezelter + + * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. + Those were old. + +2004-04-13 10:09 gezelter + + * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot + to add IntegrableObjects + +2004-04-12 16:02 gezelter + + * libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code + +2004-04-12 15:32 gezelter + + * samples/: alkane/butane.bass, water/ssd.bass: Slightly longer + test run + +2004-04-12 15:32 gezelter + + * libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, + DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, + DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, + ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, + Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, + MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, + NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, + SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, + SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, + WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics + (Somewhat extensive) + +2004-04-12 15:31 gezelter + + * libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, + libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, + utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: + Changes for RigidBody dynamics + +2004-03-17 09:22 tim + + * libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, + libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, + libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, + libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it + does not sound a good choice, next commit will seperate SMD and + ZConstraint + +2004-03-16 14:22 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, + libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, + libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint + now can support sequential moving. Refactorying is needed to + support SMD in ZConstraint + +2004-03-02 15:32 tim + + * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, + StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to + support large file + +2004-03-01 16:17 tim + + * utils/zsub.cpp: Fix a couple of bugs in zsub + +2004-03-01 15:01 tim + + * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, + libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, + libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, + utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, + utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a + program which can be used to replace atom type for zconstraint into + OOPSE + +2004-02-24 11:36 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log + message] + +2004-02-24 10:49 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Constraint.cpp, Constraint.hpp, ConstraintList.cpp, + ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, + NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, + OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, + SymMatrix.hpp: remove the old implement of minimizer from cvs tree + +2004-02-24 10:44 tim + + * libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, + Integrator.hpp, Makefile.in, Minimizer1D.cpp, + MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, + OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, + SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of + compose to implement Minimizer both versions are working + +2004-02-17 14:23 tim + + * ChangeLog, libmdtools/ConjugateMinimizer.cpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, + libmdtools/MinimizerParameterSet.hpp, + libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order + to remove the constraint force along bond direction + +2004-02-10 16:33 tim + + * ChangeLog, libmdtools/ConjugateMinimizer.cpp, + libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: + single version of energy minimization is working. + +2004-02-09 15:38 mmeineke + + * staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on + the massive memory overusage by OOPSE + +2004-02-09 09:48 chrisfen + + * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the + hardwired LJ_rcut + 2004-02-06 19:14 tim * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log @@ -2788,8 +3137,8 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial - revision + libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE + Tree 2003-03-21 12:42 mmeineke @@ -2846,6 +3195,6 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE - Tree + libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial + revision