--- trunk/OOPSE/ChangeLog 2004/01/05 21:00:05 894 +++ trunk/OOPSE/ChangeLog 2004/06/21 18:52:21 1284 @@ -1,3 +1,1397 @@ +2004-06-11 14:46 gezelter + + * libmdtools/notifyCutoffs.F90: nicer error message formatting + +2004-06-11 14:24 gezelter + + * libmdtools/: Make.dep, Makefile.in: Fixed dependency bug (we + hope) + +2004-06-11 12:16 tim + + * ChangeLog, libBASS/MoleculeStamp.cpp, + libmdtools/ConstraintAlgorithm.cpp, + libmdtools/ConstraintAlgorithm.hpp, + libmdtools/ConstraintElement.cpp, libmdtools/DumpReader.cpp, + libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, + libmdtools/Mat3x3d.cpp, libmdtools/Mat3x3d.hpp, libmdtools/NPT.cpp, + libmdtools/NVT.cpp, libmdtools/Rattle.hpp, libmdtools/Roll.cpp, + libmdtools/Roll.hpp: roll in progress + +2004-06-11 11:46 gezelter + + * samples/metals/Au.bass: Sample now does variant + +2004-06-11 11:46 gezelter + + * libmdtools/EAM_FF.cpp: General fixes for formatting + +2004-06-11 11:45 gezelter + + * forceFields/: Ag.VC.funcfl, Al.VC.funcfl, Au.VC.funcfl, + Cu.VC.funcfl, Ni.VC.funcfl, Pd.VC.funcfl, Pt.VC.funcfl: Converted + D's to E's in the funcfl files so that C can read them. + +2004-06-11 11:35 gezelter + + * forceFields/: Ag.VC.funcfl, Ag.Voter.eam, Ag.u3.eam, + Ag.u3.funcfl, Ag.u6.eam, Ag.u6.funcfl, Al.VC.funcfl, Al.Voter.eam, + Au.VC.funcfl, Au.Voter.eam, Au.u3.eam, Au.u3.funcfl, Au.u6.eam, + Au.u6.funcfl, Cu.VC.funcfl, Cu.Voter.eam, Cu.u3.eam, Cu.u3.funcfl, + Cu.u6.eam, Cu.u6.funcfl, EAM.VC.frc, EAM.Voter.frc, EAM.frc, + EAM.u3.frc, EAM.u6.frc, Ni.VC.funcfl, Ni.Voter.eam, Ni.u3.eam, + Ni.u3.funcfl, Ni.u6.eam, Ni.u6.funcfl, Pd.VC.funcfl, Pd.Voter.eam, + Pd.u3.eam, Pd.u3.funcfl, Pd.u6.eam, Pd.u6.funcfl, Pt.VC.funcfl, + Pt.u3.eam, Pt.u3.funcfl, Pt.u6.eam, Pt.u6.funcfl: changing file + extensions to be more in line with what's actually in the file + +2004-06-11 10:31 gezelter + + * forceFields/: Ag.Voter.eam, Ag.u3.eam, Ag.u6.eam, Al.Voter.eam, + Au.Voter.eam, Au.u3.eam, Au.u6.eam, Cu.Voter.eam, Cu.u3.eam, + Cu.u6.eam, EAM.frc, EAM.u6.frc, Ni.Voter.eam, Ni.u3.eam, Ni.u6.eam, + Pd.Voter.eam, Pd.u3.eam, Pd.u6.eam, Pt.u3.eam, Pt.u6.eam, + ag.u3.eam, au.u3.eam, cu.u3.eam, ni.u3.eam, pd.u3.eam, pt.u3.eam: + Added a bunch of files for EAM variants + +2004-06-11 09:14 gezelter + + * samples/metals/Au.bass: Modified EAM to use forceFieldVariant, + show sample in Au.bass + +2004-06-11 09:14 gezelter + + * libmdtools/: EAM_FF.cpp, ForceFields.hpp, SimSetup.cpp, + SimSetup.hpp: Modified EAM to use forceFieldVariant + +2004-06-11 09:13 gezelter + + * libBASS/: Globals.cpp, Globals.hpp: Added forceFieldVariant + global + +2004-06-10 17:15 gezelter + + * forceFields/: EAM.Voter.frc, EAM.frc, EAM.u3.frc, EAM_FF.frc, + ag.u3.eam, agu3.eam, au.u3.eam, auu3.eam, backup.DUFF.frc, + cu.u3.eam, cuu3.eam, ni.u3.eam, niu3.eam, pd.u3.eam, pdu3.eam, + pt.u3.eam, ptu3.eam: reorg of EAM force fields to have variants + +2004-06-10 12:09 chrisfen + + * libmdtools/ForceFields.cpp: Fixed a thermodynamic integration + issue. Force and torque scaling loops over atoms, not stuntdoubles + +2004-06-10 10:00 gezelter + + * libBASS/: MakeStamps.cpp, MoleculeStamp.cpp: Removed debugging + printf statements + +2004-06-10 09:59 gezelter + + * libBASS/: MakeStamps.cpp, MoleculeStamp.cpp, make_nodes.c: Fixed + indexing bug in stamps + +2004-06-09 11:59 tim + + * ChangeLog, libmdtools/Roll.cpp: Roll in progress + +2004-06-09 11:16 tim + + * libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, + Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, + Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, + Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, + Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. + adding some useful math classes(Mat3x3d, Vector3d, Quaternion, + Euler3) these classes use anonymous union and struct to support + double[3], double[3][3] and double[4] 2. adding roll constraint + algorithm + +2004-06-08 11:49 gezelter + + * libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: + Fixed a bug in NPTf (vScale was declared in the cpp file in + addition to the declaration in Integrator.hpp file) + +2004-06-07 09:26 gezelter + + * libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, + libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, + libmdtools/ConstraintIterator.hpp, + libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, + libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, + libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, + libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, + libmdtools/ZConsReader.cpp: Fixes from gcc -Wall + +2004-06-07 09:09 chrisfen + + * libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a + bit... Got rid of some unnecessary lines of code in Thermo.cpp + +2004-06-04 16:00 gezelter + + * libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, + StuntDouble.cpp: small bugfixes + +2004-06-04 15:29 tim + + * libmdtools/Integrator.hpp: [no log message] + +2004-06-04 14:30 tim + + * ChangeLog, libmdtools/CallbackFunctor.cpp, + libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, + libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, + libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, + libmdtools/ShakeMin.hpp: constraint algorithm for minimization is + working + +2004-06-04 11:23 gezelter + + * forceFields/charmm27.vdw: Moved to SHAPES + +2004-06-04 11:23 gezelter + + * forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log + message] + +2004-06-04 09:59 gezelter + + * libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: + More work on Fortran side of error handler + +2004-06-04 09:59 gezelter + + * configure, ac-tools/aclocal.m4: fixed a typo in autoconf script + +2004-06-04 09:35 gezelter + + * libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying + the error handlers + +2004-06-04 09:17 gezelter + + * libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore + +2004-06-04 09:11 gezelter + + * libBASS/: config.h.in, fError.c: forgot to add these + +2004-06-03 22:15 tim + + * ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, + libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, + libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, + libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, + libmdtools/Makefile.in, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, + libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm + is working + +2004-06-03 21:38 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, + libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, + libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for + fortran access to SimError + +2004-06-03 16:51 tim + + * libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, + ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, + ConstraintElement.cpp, ConstraintElement.hpp, + ConstraintIterator.hpp, ConstraintManager.cpp, + ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, + Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new + implementation of constraint + +2004-06-03 16:06 tim + + * libmdtools/DumpWriter.cpp: fixed a bug which only writes out the + first atom of a molecule + +2004-06-03 15:02 gezelter + + * libmdtools/SimSetup.cpp: Fixed groupOffset bug + +2004-06-03 15:02 gezelter + + * ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for + autoconf + +2004-06-02 13:28 gezelter + + * samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't + have been in CVS + +2004-06-02 13:28 gezelter + + * samples/: argon/Makefile, minimizer/argon/Makefile: Why is this + in CVS? + +2004-06-02 13:27 gezelter + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, + Makefile.in, WATER.cpp: formatting error messages, dependency fixes + +2004-06-02 13:27 gezelter + + * libBASS/simError.h: starting fortran-usable version of simError + +2004-06-02 09:56 chrisfen + + * samples/: argon/Makefile, minimizer/argon/Makefile: Probably + shouldn't be in CVS + +2004-06-02 09:56 chrisfen + + * libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, + Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, + removed writeRaw + +2004-06-02 09:56 chrisfen + + * libBASS/simError.c: Formatting Changes + +2004-06-02 09:21 gezelter + + * libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: + severity levels in simError + +2004-06-01 16:45 gezelter + + * libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, + do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, + simulation_module.F90: Bug fix (fixes of skipList and neighbor list + under MPI) + +2004-06-01 16:44 gezelter + + * libBASS/MoleculeStamp.cpp: Bug fix (memory leak) + +2004-06-01 13:43 gezelter + + * samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing + +2004-06-01 13:42 gezelter + + * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, + SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, + mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: + Cutoff Groups for MPI + +2004-06-01 13:07 chrisfen + + * libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in + useLiquidThermInt routine in ForceFields.cpp + +2004-06-01 12:15 chrisfen + + * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, + SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate + solid and liquid thermodynamic integration routines + +2004-06-01 10:57 tim + + * libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in + progress + +2004-06-01 09:27 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt + keyword and changed useThermInt to useSolidThermInt + +2004-06-01 09:21 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate + solid and liquid thermodynamic integration routines + +2004-05-28 10:21 gezelter + + * libmdtools/do_Forces.F90: bugfix starting + +2004-05-27 15:06 chrisfen + + * libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in + Integrator.cpp where it called writeRaw() when useThermInt = + false... + +2004-05-27 14:51 tim + + * ChangeLog, libmdtools/do_Forces.F90, + libmdtools/simulation_module.F90: Bug fix for SkipList + +2004-05-27 14:26 gezelter + + * libmdtools/SimSetup.cpp: bugfix in simsetup? + +2004-05-27 13:59 gezelter + + * libmdtools/: DumpReader.cpp, DumpWriter.cpp, + InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, + ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, + mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, + mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: + Cutoff group changes under MPI + +2004-05-27 11:20 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for + xlc++ + +2004-05-27 10:31 tim + + * libmdtools/SimInfo.cpp: groupList new bases on global index of + atoms + +2004-05-27 10:21 gezelter + + * src/: oopse.cpp, oose.cpp: Modified the nifty banner + +2004-05-27 10:21 gezelter + + * libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: + Fixed off-by-one error in groupStartRow and groupStartCol + +2004-05-26 19:48 tim + + * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, + libmdtools/calc_charge_charge.F90, + libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, + libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, + libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, + libmdtools/simulation_module.F90: in the progress of fixing MPI + version of cutoff group + +2004-05-26 11:41 gezelter + + * libmdtools/do_Forces.F90: Compacted all of the 8 copies of the + force loop into one. + +2004-05-24 17:24 gezelter + + * libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes + +2004-05-24 16:23 chrisfen + + * libmdtools/Restraints.cpp: Removed unnecessary variables and + changed error messages in Restraints.cpp + +2004-05-24 16:03 gezelter + + * libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, + calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, + calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes + for stress / pressure tensor by cutoff group + +2004-05-22 15:55 chrisfen + + * libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... + Too many arguements in a function call. + +2004-05-22 13:17 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword + useThermInt. + +2004-05-22 13:16 chrisfen + + * libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, + ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, + Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, + SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, + StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration + code. + +2004-05-21 10:58 gezelter + + * libmdtools/: do_Forces.F90, simulation_module.F90: Major changes + to skipThisPair for efficiency + +2004-05-21 09:22 gezelter + + * configure, ac-tools/configure.in, forceFields/LJ.vdw, + forceFields/amber99.vdw, forceFields/charmm27.vdw, + forceFields/gaff.vdw, forceFields/oplsaal.vdw, + samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes + for SHAPES potential + +2004-05-20 15:27 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit + included the bass keywords + +2004-05-20 15:24 chrisfen + + * libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, + Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, + Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several + additions... Restraints.cpp and .hpp were included for restraining + particles in thermodynamic integration. By including these, + changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, + StatWriter, and possibly some other files. Two bass keywords were + also added for performing thermodynamic integration: a lambda value + one and a k power one. + +2004-05-13 16:08 gezelter + + * libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list + +2004-05-12 17:01 tim + + * samples/: argon/Makefile, argon/argonEM.bass, + argon/init_argon.eor, minimizer/argon/Makefile, + minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, + minimizer/water/Makefile, minimizer/water/Makefile.in, + minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, + minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, + minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add + minimizer sample + +2004-05-12 16:54 gezelter + + * libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X + compilation + +2004-05-12 15:54 gezelter + + * libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes + for compilation under Mac OS X with IBM's xl compilers + +2004-05-12 15:14 gezelter + + * src/: oopse.cpp, oose.cpp: Added a nifty neato banner + +2004-05-12 15:14 gezelter + + * libmdtools/LJFF.cpp: Removed an extraneous write + +2004-05-12 15:13 gezelter + + * libBASS/simError.h: Starting to change the error model + +2004-05-12 14:45 gezelter + + * utils/Dump2XYZ.cpp: const char* fix + +2004-05-12 14:44 gezelter + + * libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, + src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous + write statements + +2004-05-12 11:38 tim + + * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, + ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, + SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and + massratio from simState, creat cutoff group forevery atom which + does not belong to cutoff group defined at mdl file + +2004-05-12 10:58 gezelter + + * libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in + CutoffGroup + +2004-05-12 10:35 gezelter + + * samples/water/water.mdl: Added the cutoff Groups to the default + water.mdl file + +2004-05-12 10:02 tim + + * ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: + fixed a bug in CutoffGroup::getCOM() + +2004-05-12 09:29 gezelter + + * libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, + samples/water/ssd.bass: bug fixes for cutoffGroups + +2004-05-11 17:28 tim + + * utils/Vector3.hpp: adding generic Vector3 class + +2004-05-11 16:44 tim + + * libmdtools/Integrator.hpp: adding instantiation of + Integrator in order to make OOPSE compiled by icc8 + +2004-05-11 16:31 gezelter + + * libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, + calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, + calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: + Fortran-side changes for group-based cutoffs + +2004-05-11 16:20 tim + + * libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp + +2004-05-11 16:14 tim + + * libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, + SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix + anoter one in CutoffGroup which causes seg fault + +2004-05-11 15:33 tim + + * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup + into OOPSE + +2004-05-11 15:07 gezelter + + * libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup + +2004-05-11 11:00 gezelter + + * libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, + fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to + use the simplified cutoff stuff in the BASS library + +2004-05-10 23:21 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, + CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, + Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, + MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, + make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, + parse_tree.c: BASS changes for adding CutoffGroups to molecules. + Also restructured the plethora of cutoff radii into one + cutoffRadius and one switchingRadius. Also removed the + useMolecularCutoffs keyword + +2004-05-10 15:28 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize + DumpWriter + +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 + message] + +2004-02-06 16:37 tim + + * ChangeLog, libBASS/Globals.cpp, + libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of + energy minimization for argon is working, need to add constraint + +2004-02-06 14:05 tim + + * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add + one more file into Makefile.in + +2004-02-06 13:58 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, + libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, + libmdtools/Integrator.hpp, libmdtools/Makefile.in, + libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, + libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, + libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add + some lines into global.cpp to make it work with energy minimization + +2004-02-04 17:26 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) + Single version of conjugate gradient with golden search linesearch + pass a couple of functions test. Brent's algorithm is still broken + +2004-02-03 17:54 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, + SteepestDescent.hpp: NLModel0, NLModel1 pass uit test + +2004-02-03 15:47 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, + ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, + NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, + SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, + SteepestDescent.hpp: [no log message] + +2004-02-03 15:43 tim + + * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, + Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory + constraint class + +2004-02-03 12:10 tim + + * libmdtools/Functor.hpp: Functor.hpp pass unit test + +2004-02-03 10:21 tim + + * ChangeLog, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp: begin unit test of minimizer + +2004-02-02 15:29 tim + + * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: + Adding GoldenSection and Brent LineSearch Method + +2004-01-30 16:47 tim + + * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from + MinimizerBase instead of a functor to do line seach + +2004-01-30 10:00 chrisfen + + * forceFields/Makefile.in, libmdtools/Atom.cpp, + libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, + libmdtools/Integrator.cpp, libmdtools/Makefile.in, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, + libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, + libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now + has a working WATER.cpp forcefield and parser. This involved + changes to WATER.cpp and ForceFields amoung other files. One + important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. + This will be removed on the next commit... + +2004-01-29 18:00 gezelter + + * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, + libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, + libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, + libBASS/RigidBodyStamp.hpp, libBASS/interface.c, + libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, + libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, + libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: + member list fixes for rigid bodies + +2004-01-29 16:44 tim + + * libmdtools/MinimizerParameterSet.hpp: Adding + MinimizerParameterSet class. + +2004-01-28 17:44 tim + + * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of + NLModel0 and NLModel1 + +2004-01-28 15:40 tim + + * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision + of NLModel + +2004-01-27 15:34 gezelter + + * samples/water/: ssd.bass, water.mdl: Added point-charge models to + water.mdl file, updated ssd.bass to use new SSD name + +2004-01-27 15:34 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody + stuff + +2004-01-27 14:39 gezelter + + * samples/water/ssd.bass: Longer run time to test SSD water in MPI + +2004-01-27 14:39 gezelter + + * samples/metals/Au.bass: Longer run time to test gold in MPI + +2004-01-27 14:38 gezelter + + * samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer + run time to test argon + +2004-01-27 14:38 gezelter + + * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS + changes to do new rigidBody scheme a copy of WATER.cpp from this + morning + +2004-01-27 14:37 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, + MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, + MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, + interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, + node_list.h, parse_interface.h, parse_tree.c: More BASS changes to + do new rigidBody scheme + +2004-01-27 14:15 tim + + * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, + Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, + MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of + constraint for Nonlinear Optimization Model + +2004-01-26 17:01 gezelter + + * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use + Euler angles for orientation instead of unit vectors required + changes in MoLocator + +2004-01-26 16:53 gezelter + + * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, + beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, + water/water.mdl: Changed orientation lines from unit vectors to + euler angles + +2004-01-26 16:52 gezelter + + * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians + +2004-01-26 16:45 gezelter + + * libmdtools/SimSetup.cpp: Changed default orientation in BASS to + use Euler angles in the following order: phi, theta, psi Removed + the ability to set orientation using a unit vector + +2004-01-26 16:26 gezelter + + * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, + RigidBodyStamp.hpp: Changed default orientation in BASS to use + Euler angles in the following order: phi, theta, psi Removed the + ability to set orientation using a unit vector + +2004-01-26 13:52 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies + +2004-01-22 12:34 chrisfen + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, + TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: + Corrected spelling in several directories, and stated WATER.cpp + +2004-01-21 17:16 tim + + * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, + NLOPModel.hpp: constraint class in energy minimization + +2004-01-20 15:34 tim + + * libmdtools/MinimizerBase.hpp: Adding energy minimization + +2004-01-20 15:32 tim + + * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, + NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer + +2004-01-19 16:17 gezelter + + * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages + more user-friendly + +2004-01-19 13:51 chrisfen + + * forceFields/DUFF.frc: Updated the default water to SSD/E + +2004-01-19 13:36 tim + + * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample + time, status time, thermal time and reset time are not divisible by + dt + +2004-01-19 11:10 gezelter + + * third-party/Makefile.in: Added a bunch of dummy targets so make + won't complain + +2004-01-19 11:10 gezelter + + * samples/lipid/5x5.bass: Fixed old bass file + +2004-01-19 11:09 gezelter + + * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies + required a change in how the MoleculeStamps are used by divideLabor + in mpiSimulation.cpp + +2004-01-19 11:08 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, + MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, + RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, + make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, + parse_tree.c: BASS changes to add RigidBodies and LJrcut + +2004-01-16 16:55 tim + + * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating + eor file + +2004-01-16 16:51 mmeineke + + * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could + write eor files + +2004-01-16 10:01 mmeineke + + * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi + initialization of the AtomStruct + +2004-01-15 16:57 chuckv + + * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps + +2004-01-15 10:51 gezelter + + * ac-tools/aclocal.m4: Changes for altivec + +2004-01-15 09:22 gezelter + + * libmdtools/DumpWriter.cpp: Documented the Spud Toss + +2004-01-14 23:33 gezelter + + * libmdtools/do_Forces.F90: changes for charge charge interactions + +2004-01-14 20:14 gezelter + + * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, + notifyCutoffs.F90: More work for adding charges + +2004-01-14 17:41 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in: autoconf fixes + +2004-01-14 11:28 mmeineke + + * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug + +2004-01-14 10:48 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in, third-party/Makefile.in: autoconf compatibility + changes for icc8 + +2004-01-13 18:01 gezelter + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, + SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, + fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: + Changes for adding direct charge-charge interactions (with + switching function) + +2004-01-13 17:34 gezelter + + * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, + oopseMPI_module.F90: Some changes for new MPI organization and + direct charge-charge interactions + +2004-01-13 17:11 tim + + * Functor.hpp, libmdtools/Functor.hpp: [no log message] + +2004-01-13 16:22 tim + + * Functor.hpp, samples/water/ssd.bass: Energy Minimization method + +2004-01-13 15:35 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the + eor file whenever it is used instead of rewinding it + +2004-01-13 15:04 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface + of writeFrame + +2004-01-13 10:46 tim + + * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: + Merge the code of writeFinal and writeDump; + Adding sortingIndex into DumpWriter; + Fix a bug of writing last frame twice in integrator + +2004-01-12 17:54 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix + a bug in copying string + +2004-01-12 15:37 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, + samples/minimizer/argon/argon.bass, samples/water/ssd.bass: + Dumpwriter only write out the atoms on master nodes + +2004-01-10 04:46 tim + + * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just + roll it back fix a bug of copying string to a pointer Still have + Seg fault, it looks like a random MPI seg fault in totalview + +2004-01-09 21:15 tim + + * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub + +2004-01-09 15:29 gezelter + + * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) + +2004-01-08 17:25 chuckv + + * libmdtools/DumpWriter.cpp: A work in progress... + +2004-01-08 13:59 gezelter + + * libmdtools/DumpWriter.cpp: null terminate some strings just in + case + +2004-01-08 13:13 mmeineke + + * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS + state bug. + +2004-01-08 13:05 gezelter + + * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter + +2004-01-08 12:57 mmeineke + + * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT + exstended state bug + +2004-01-08 12:40 gezelter + + * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter + +2004-01-08 10:44 mmeineke + + * libmdtools/InitializeFromFile.cpp: added support for the ignore + XS state info flag + +2004-01-07 14:26 tim + + * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, + samples/argon/argon.bass, samples/minimizer/argon/argon.bass, + samples/water/ssd.bass: Fixed a bug of sending message from master + node to itself in DumpWriter.cpp and InitializeFromFile.cpp + +2004-01-06 14:49 chuckv + + * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: + performance fixes in the dipole dipole and reaction field code + +2004-01-06 13:54 chuckv + + * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a + little more sane + +2004-01-05 17:49 chuckv + + * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, + calc_sticky_pair.F90, do_Forces.F90: Attempting to increase + performance by reducing spurious function calls + +2004-01-05 17:18 chuckv + + * libmdtools/do_Forces.F90: mangling forces even further + +2004-01-05 17:18 chuckv + + * configure, ac-tools/configure.in: mpich mucking + +2004-01-05 17:12 chuckv + + * libmdtools/do_Forces.F90: mangled do_forces... + +2004-01-05 16:00 chuckv + + * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, + libmdtools/do_Forces.F90: Added bitmask to do_forces property + lookup + 2003-12-29 14:56 chuckv * samples/metals/Au.bass, third-party/mt19937ar.c: Added @@ -267,8 +1661,8 @@ libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, libmdtools/ReadWrite.hpp, samples/argon/argon.bass, - samples/water/ssd.bass: add chi and eta to the comment line of dump - file. + samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi + and eta to the comment line of dump file. 2003-10-28 17:25 mmeineke @@ -689,12 +2083,15 @@ samples/Makefile.in, samples/alkane/Makefile, samples/alkane/Makefile.in, samples/argon/Makefile, samples/argon/Makefile.in, samples/argon/argon.bass, - samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, - samples/lipid/Makefile, samples/lipid/Makefile.in, - samples/water/Makefile, samples/water/Makefile.in, src/Makefile, - src/Makefile.in, utils/Makefile, utils/Makefile.in, - utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to - autoconf / configure method of configuring OOPSE + samples/minimizer/argon/Makefile, + samples/minimizer/argon/Makefile.in, + samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, + samples/beadLipid/Makefile.in, samples/lipid/Makefile, + samples/lipid/Makefile.in, samples/water/Makefile, + samples/water/Makefile.in, src/Makefile, src/Makefile.in, + utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, + utils/sysbuilder/Makefile.in: Changes to autoconf / configure + method of configuring OOPSE 2003-09-04 16:48 mmeineke @@ -1283,8 +2680,9 @@ 2003-07-14 18:06 gezelter * samples/: alkane/init_butane.eor, argon/argon.bass, - argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes - for samples + argon/init_argon.eor, minimizer/argon/argon.bass, + minimizer/argon/init_argon.eor, lipid/init_5x5.eor, + water/init_ssd.eor: Fixes for samples 2003-07-14 18:06 gezelter @@ -1957,7 +3355,8 @@ * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, - samples/argon/argon.bass: more bug fixes.... + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more + bug fixes.... 2003-04-01 11:49 mmeineke @@ -2164,7 +3563,8 @@ 2003-03-26 10:37 chuckv * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - samples/argon/argon.bass: Fixes for Parallel thermalization + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes + for Parallel thermalization 2003-03-26 09:55 mmeineke @@ -2178,7 +3578,7 @@ 2003-03-25 09:29 mmeineke - * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, + * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, src/MPIobj/dummy, src/obj/dummy: [no log message] 2003-03-25 09:29 mmeineke @@ -2196,9 +3596,10 @@ alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, - lipid/lipid.mdl, lipid/water.mdl, water/Makefile, - water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to - samples + lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, + minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, + minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, + water/ssd.bass, water/water.mdl: moved tests to samples 2003-03-24 19:51 gezelter