--- trunk/OOPSE-1.0/ChangeLog 2004/07/26 14:36:05 1411 +++ trunk/OOPSE-1.0/ChangeLog 2004/07/26 15:14:56 1412 @@ -1,3850 +1,647 @@ -2004-07-16 11:31 gezelter - - * src/oose.cpp: New web address - -2004-07-16 11:29 gezelter - - * libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizer.cpp, - libmdtools/OOPSEMinimizer.hpp, libmdtools/SimSetup.cpp, - src/oopse.cpp: Minor changes - -2004-07-15 14:43 chrisfen - - * samples/water/: spce/water.mdl, ssde/water.mdl, tip4p/water.mdl: - Expanded the water.mdl file - -2004-07-15 14:37 chrisfen - - * forceFields/WATER.frc: Added the SPC water model - -2004-07-15 14:29 chrisfen - - * samples/water/tip4p/tp4.bass: quick change in tp4.bass - -2004-07-15 14:28 chrisfen - - * samples/water/tip4p/: TP4init.in, tp4.bass, water.mdl: Added - TIP4P water sample - -2004-07-14 17:25 chrisfen - - * samples/water/spce/: SPCEinit.in, spce.bass, water.mdl: Added - SPCE water sample - -2004-07-14 15:58 chrisfen - - * samples/water/ssde/: 256init.in, ssde.bass, water.mdl: Good ssde - simulation sample added - -2004-07-14 15:11 gezelter - - * configure, libmdtools/ConstraintIterator.hpp, - libmdtools/Integrator.hpp: Fixes for MacOS X with xlc++ and xlf - -2004-07-12 13:08 chuckv - - * ac-tools/fortran90.m4: [no log message] - -2004-07-02 16:41 gezelter - - * libmdtools/calc_shapes.F90: Added a bunch of stuff - -2004-06-29 17:52 tim - - * libmdtools/Mat3x3d.cpp: fixed a bug in Mat3x3d.cpp - -2004-06-29 16:15 gezelter - - * libmdtools/calc_shapes.F90: added SHAPE force routine - -2004-06-21 13:52 tim - - * ChangeLog, libmdtools/CallbackFunctor.hpp, - libmdtools/ConstraintAlgorithm.cpp, - libmdtools/ConstraintElement.hpp, libmdtools/Integrator.cpp, - libmdtools/Rattle.cpp, libmdtools/RigidBody.cpp, - libmdtools/RigidBody.hpp, libmdtools/Roll.cpp, libmdtools/Roll.hpp, - samples/alkane/alkanes.mdl: roll in progress - -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: Shouldn't have been in CVS - -2004-06-02 13:28 gezelter - - * samples/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: 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: 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: 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/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: 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/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/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 - third-party directory for code not written by us. Also added - Mersenne Twister random number generator code. This will eventually - replace sprng as the random number generator used by OOPSE. - -2003-12-22 16:26 chuckv - - * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, - libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: - Fixes to profile code. - -2003-12-19 15:36 mmeineke - - * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, - timing.F90, timing.f90: More profiling fixes. - -2003-12-19 15:19 chuckv - - * libmdtools/timing.f90: Another change for MPI in timing. - -2003-12-19 15:17 chuckv - - * libmdtools/timing.f90: Small update to timing in MPI - -2003-12-19 13:53 mmeineke - - * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the - profiling commands work now. Will start adding PROFILE ifdefs into - the code - -2003-12-19 12:25 mmeineke - - * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added - some profiling routines - -2003-12-19 10:12 mmeineke - - * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta - and GofRomega - - additional work on randomBilayer - -2003-12-19 10:12 mmeineke - - * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, - PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and - GofRomega - -2003-12-18 16:47 mmeineke - - * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added - some profile functionality - -2003-12-18 15:46 chuckv - - * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: - Added functions for simple profiling in fortran. - -2003-12-17 15:13 chuckv - - * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, - samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and - rho_col were scattered into the same array. Unfortunately, MPI - zeros the array between scatters so half of the sum was being lost. - Fixed by added a temp array for column scatter, then sum loop over - nlocal. - -2003-12-16 15:49 mmeineke - - * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, - PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added - gofRomega. both need to be debugged and tested. - -2003-12-12 10:42 gezelter - - * configure, ac-tools/aclocal.m4, ac-tools/configure.in, - libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for - gradients (to do minimizations) - -2003-12-12 10:33 mmeineke - - * utils/sysbuilder/randomBilayer.hpp: removed the randombilayer - header - -2003-12-10 11:52 mmeineke - - * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, - randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add - randomBilayer to the build. Also move the random bilayer builder - from bilayerSys to randomBilayer - -2003-11-25 10:44 mmeineke - - * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old - DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and - TB3 in DUFF.frc - -2003-11-21 15:09 mmeineke - - * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, - utils/sysbuilder/latticeBilayer.cpp: added a more verbose error - message in SimInfo. Added a more informative error message in - InitializeFromFile - -2003-11-21 15:07 mmeineke - - * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add - ing in the GofR,CosTheta - -2003-11-21 14:31 chrisfen - - * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed - a bug in SimInfo ordering of radii - -2003-11-11 12:20 mmeineke - - * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline - a min function. - -2003-11-10 16:50 mmeineke - - * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: - reordered the rcut/ecr/boxSize initialization - - removed the rcut/ecr shrink and grow algorithm. the simulation will - now exit when it runs into rcut or ecr. - -2003-11-07 16:46 chuckv - - * libmdtools/: Makefile.in, mpiSimulation_module.F90, - oopseMPI_module.F90: Added support for compiling fortran without - use of mpich modules. We use mpif.h instead.: - -2003-11-07 12:09 mmeineke - - * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, - NPTxyz.cpp: moved the velocity scale matrix calculation outside of - the atom loop in the NPT family of integrators. - -2003-11-06 17:01 mmeineke - - * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, - libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, - libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, - utils/sysbuilder/latticeBilayer.cpp: added the following parameters - to BASS: * useInitialExtendedSystemState * orthoBoxTolerance - * useIntiTime => useInitialTime - -2003-11-06 14:24 mmeineke - - * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, - make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, - parse_tree.h: fixed the includes in the Make.dep - -2003-11-06 14:11 mmeineke - - * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, - NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the - new-templateless branch to the main trunk. - - bug Fixes include: * fixed the switching function from ortho to - non-ortho box. !!!!! THis was responsible for all of the - sudden deaths we saw. * some formating in the string when we - write out the extended system state. * added NPT.cpp to the - makefile.in - -2003-11-06 13:20 mmeineke - - * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, - SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" - bug. The box was not switching between orthorhombic and - non-orthorhombic wrapping correctly. we added a fabs() to - the check.which should fix it. - -2003-11-05 14:16 mmeineke - - * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, - libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, - libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, - libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, - libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, - utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: - some work on trying to find the compression bug - -2003-11-03 17:07 mmeineke - - * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, - InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, - NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, SimSetup.hpp: begun work on removing templates and - most of standard template library from OOPSE. - -2003-10-31 16:06 mmeineke - - * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, - Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, - SimSetup.cpp: started work on template removal. - -2003-10-31 13:28 mmeineke - - * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: - added template stuff to the Maikefile template - - little changes to some printf format statements - -2003-10-31 13:28 mmeineke - - * libBASS/Makefile.in: added template stuff to the Maikefile - template - -2003-10-30 13:59 gezelter - - * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, - do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for - rList problems - -2003-10-30 09:11 gezelter - - * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being - queried before q0 was allocated. - -2003-10-29 15:41 mmeineke - - * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, - SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, - calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error - in bass.l - - fixed a little bug in the first time step, regarding the setting of - ecr and est in fortran - -2003-10-29 15:40 mmeineke - - * libBASS/BASSlex.l: fixed a stdlib.h include error - -2003-10-29 12:55 mmeineke - - * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, - SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way - rcut is setup, as well as additional debugging comments. - -2003-10-29 09:28 gezelter - - * configure, ac-tools/configure.in, libBASS/Makefile.in, - libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for - templates - -2003-10-28 22:16 gezelter - - * src/Makefile.in: Refixed broken makefile - -2003-10-28 22:06 gezelter - - * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility - fixes - -2003-10-28 19:19 tim - - * ChangeLog, libmdtools/AbstractClasses.hpp, - libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, - 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. - -2003-10-28 17:25 mmeineke - - * libmdtools/: ForceFields.hpp, SimInfo.hpp, - fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, - mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of - how c calls fortran. All function pointers and fortran calls are - rigidly typecast now. - -2003-10-28 15:42 gezelter - - * staticProps/Makefile.in, utils/sysbuilder/Makefile.in: - Portability fixes - -2003-10-28 15:09 gezelter - - * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, - src/Makefile.in: Compatibility fixes - -2003-10-28 12:08 mmeineke - - * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: - started work on template removal - -2003-10-28 12:04 gezelter - - * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started - trying to understand extern "C" stuff for pointers - -2003-10-28 11:20 gezelter - - * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, - ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility - -2003-10-28 11:03 gezelter - - * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, - DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, - DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, - ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, - Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, - ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, - StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, - calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, - mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with - more portable c header stuff Also, mod file fixes and portability - changes Some fortran changes will need to be reversed. - -2003-10-28 11:03 gezelter - - * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, - Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, - Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more - portable c header stuff Also, mod file fixes and portability - changes - -2003-10-28 11:02 gezelter - - * configure, ac-tools/aclocal.m4: mod file fixes and portability - stuff - -2003-10-27 18:00 gezelter - - * Makefile.in, configure, ac-tools/aclocal.m4, - ac-tools/configure.in, ac-tools/fortran90.m4, - libmdtools/Makefile.in: Stuff for MOD support in other compilers - -2003-10-27 17:08 mmeineke - - * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, - MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: - added routines for the sysbuilder to work with simSetup - - remved the QuickBass routines, and had all parsing go through - SimSetup. LatticeBilayer is in complete working order now. - -2003-10-27 17:07 mmeineke - - * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added - routines for the sysbuilder to work with simSetup - -2003-10-27 11:20 gezelter - - * configure, ac-tools/configure.in, samples/water/ssd.bass, - utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild - -2003-10-24 17:17 mmeineke - - * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, - MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, - latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put - QuickBass, MoLocator, and latticeBuilder into a Builder Library - overhauled latticeBilayer into its own program. Removed sysBuild - from the Makefile - -2003-10-24 12:36 gezelter - - * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, - latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer - builder - -2003-10-24 12:35 gezelter - - * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a - merge problem - -2003-10-23 14:57 mmeineke - - * samples/metals/Makefile.in: added eam ForceField files to the - init - - fixed an eam mpi parmeter setup bug - - added the init file to the makefile - -2003-10-23 14:57 mmeineke - - * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files - to the init - - fixed an eam mpi parmeter setup bug - -2003-10-23 14:57 mmeineke - - * forceFields/Makefile.in: added eam ForceField files to the init - -2003-10-22 16:17 mmeineke - - * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, - NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT - integrator, NPTxyz. It scales the x, y, and z direction sepeartely. - no box skew allowed. - -2003-10-21 14:33 mmeineke - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, - staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. - * useInitTime = false: sets the origin time to 0.0 regardless - of the time stamp in the .init file * default=> useInitTime = - true; - -2003-10-17 16:19 mmeineke - - * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, - Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, - staticProps.cpp, obj/placeholder: added the staticProps directory - to the build list for both configure  and configure.in - - fixed a number of bugs in the staticProps code. gofr is now - working. - -2003-10-17 16:18 mmeineke - - * ac-tools/configure.in: added the staticProps directory to the - build list for both configure  and configure.in - -2003-10-17 16:17 mmeineke - - * configure: added the staticProps directory to the build list - -2003-10-16 14:16 mmeineke - - * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, - Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to - use linked lists instead of a vector. - - Fixed the makefile to build DumpReader.cpp - - Removed a comment output in Exclude.cpp - - Modified DumpWriter and Integrator to write an eor file every time - a frame is written. This lets the .eor file represent the last - written frame of a simulation. - -2003-10-10 12:10 mmeineke - - * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, - CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, - PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, - staticProps.cpp: removed the props directory, and moved everything - over to staticProps - -2003-10-09 17:09 mmeineke - - * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in - a position where it will compile and run first runs. - -2003-10-04 13:46 chuckv - - * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, - samples/metals/Au.bass: Fixed bug in calc_eam. - -2003-10-04 13:08 chuckv - - * samples/metals/init_au.in: added Au init file for eam. - -2003-10-03 17:11 mmeineke - - * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed - entahlpy from the statwriter and thermo. - -2003-10-03 17:02 mmeineke - - * libmdtools/SimInfo.hpp: changed the formating ogf the error - statements in simError - - added a function to get the maxCutoff - -2003-10-03 17:01 mmeineke - - * libBASS/simError.c: changed the formating ogf the error - statements in simError - -2003-09-30 11:00 mmeineke - - * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed - f90Flags so they are no longer overwritten by the compiler. - -2003-09-29 17:06 mmeineke - - * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same - for conifig.in - - fixed wrappers to extern "C" - -2003-09-29 17:06 mmeineke - - * ac-tools/configure.in: added mpif90 mod check back same for - conifig.in - -2003-09-29 17:05 mmeineke - - * configure: added mpif90 mod check back - -2003-09-29 16:16 mmeineke - - * configure, ac-tools/aclocal.m4, ac-tools/configure.in, - libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, - libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, - libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, - libBASS/ZconStamp.cpp, libBASS/simError.c, - libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, - libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, - libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors - found with SUN's SUNWspro.s1s7 - -2003-09-29 12:38 mmeineke - - * libmdtools/GenericData.hpp: light change in syntax. no - signifigant change. - -2003-09-25 16:17 mmeineke - - * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some - additional remarks from icc -w3 (extra verbose output) - -2003-09-25 14:27 mmeineke - - * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, - libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, - libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, - libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, - libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with - gcc -Wall and g++ -Wall - -2003-09-25 13:54 gezelter - - * configure, ac-tools/configure.in: fixed a bug in configure - -2003-09-25 11:42 gezelter - - * Makefile.in, configure, ac-tools/aclocal.m4, - ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, - src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: - fixes for configure - -2003-09-24 14:34 mmeineke - - * libmdtools/Integrator.cpp: moved readyCheck in the integrator so - that it is called before the first Statistics are written. - -2003-09-23 15:36 gezelter - - * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a - bunch of Make.dep files to CVS - -2003-09-23 15:34 mmeineke - - * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, - SimSetup.cpp: Removed NPTfm from Integrator.hpp. - - Some small syntax cleaning in NPTfm and SimSetup - -2003-09-22 18:07 tim - - * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, - SimInfo.hpp: fix bug in calculating maxCutoff - -2003-09-22 16:23 mmeineke - - * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, - Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: - Converted NPTf to work with the NPT base class. - - Removed NPTfm and NPTim from cvs - -2003-09-19 15:00 mmeineke - - * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, - NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base - class. NPTi is up to date. NPTf is not. - -2003-09-19 11:03 mmeineke - - * utils/Makefile.in, src/Makefile.in: removed mpi++ from the - makefile - -2003-09-19 11:01 gezelter - - * samples/water/ssd.bass: goofing off to test NPTf and NPTi - -2003-09-19 11:01 gezelter - - * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found - (nearly) conserved quantities for both NPTi and NPTf - -2003-09-19 10:20 mmeineke - - * utils/Makefile.in: fixed a typo in the makefile. - -2003-09-19 09:55 gezelter - - * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, - samples/water/ssd.bass: [no log message] - -2003-09-19 09:22 tim - - * libmdtools/: NPTi.cpp, NVT.cpp: [no log message] - -2003-09-17 09:22 mmeineke - - * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now - work with constraints. - -2003-09-16 15:02 tim - - * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, - SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo - - fixed conserved quantity in NPT (Still some small bug) - - NPTi appears very stable. - -2003-09-15 11:52 tim - - * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, - libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, - libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, - libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, - libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, - utils/sysbuilder/bilayerSys.cpp: add conserved quantity to - statWriter fix bug of vector wrapping at NPTi - -2003-09-12 11:20 gezelter - - * libmdtools/: Make.dep, Makefile.in: Added integrators to - Makefile.in - -2003-09-12 11:20 gezelter - - * ChangeLog: Entered changes for configure into ChangeLog - -2003-09-09 15:35 mmeineke - - * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, - NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog - - added two new NPT integrators, they still need work. - -2003-09-09 15:34 mmeineke - - * ChangeLog: updated the ChangeLog - -2003-09-05 17:45 gezelter - - * libmdtools/Make.dep: dependency on config.h - -2003-09-05 17:36 gezelter - - * configure, ac-tools/aclocal.m4: fixed sprng problem - -2003-09-05 16:29 gezelter - - * samples/metals/Makefile.in: New Makefile for metals sample - -2003-09-05 16:27 gezelter - - * Makefile, Makefile.in, ac-tools/aclocal.m4, - ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, - forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, - libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/Makefile.in, libmdtools/Integrator.hpp, - libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, - libmdtools/Makefile, libmdtools/Makefile.in, - libmdtools/calc_eam.F90, libmdtools/config.h.in, - libmdtools/definitions_module.F90, libmdtools/fInfo.c, - libmdtools/fortranWrappers.cpp, - libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, - libmdtools/simulation_module.F90, samples/Makefile, - 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 - -2003-09-04 16:48 mmeineke - - * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, - libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, - libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: - added resetTime to the Global namespace. - - added ability to reset the integrators in the NVT and NPT family. - -2003-09-04 16:48 mmeineke - - * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global - namespace. - -2003-09-02 09:30 tim - - * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, - ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of - PolicyByMass - -2003-08-28 16:09 tim - - * ChangeLog, libmdtools/GenericData.cpp, - libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, - libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex - -2003-08-27 14:23 tim - - * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix - bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to - MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we - turn on the optimization flag, it causes a seg fault - -2003-08-27 11:25 gezelter - - * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, - calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for - stress tensor parallel bug. - -2003-08-27 11:16 tim - - * ChangeLog, libmdtools/DUFF.cpp, - libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: - fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 - molMembershipList use global index instead of local index - -2003-08-26 15:37 tim - - * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, - mpiSimulation.cpp: set default force substraction policy to - PolicyByMass - -2003-08-26 15:29 tim - - * libmdtools/Integrator.cpp: [no log message] - -2003-08-26 15:13 mmeineke - - * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to - Statwriter and Dumpwriter to handle files larger than 2 gb. - - commented out some print statements in Zconstraint - - hard coding some system init into bilayer.sys - -2003-08-26 15:12 mmeineke - - * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: - added define statemewnt to Statwriter and Dumpwriter to handle - files larger than 2 gb. - - commented out some print statements in Zconstraint - -2003-08-26 15:02 tim - - * libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed - and check the seed which is specified by user at least contains 9 - digits - -2003-08-26 13:32 mmeineke - - * libmdtools/DUFF.cpp: changed the Makefiel a litle. - - Fixed a bug in MPI_DUFF. The atom block type was not being properly - constucted in MPI. (The MPI struct had 6 doubles declared versus - the actual 11) - -2003-08-26 13:30 mmeineke - - * Makefile: changed the Makefiel a litle. - -2003-08-25 17:17 gezelter - - * utils/sysbuilder/Makefile: More FreeBSD fixes - -2003-08-25 16:51 gezelter - - * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, - libmdtools/Makefile, src/Makefile: [no log message] - -2003-08-22 15:04 mmeineke - - * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on - frequency of output dumps. - -2003-08-20 17:23 tim - - * libBASS/Globals.hpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, - if he does not specify any value for seed, oopse will take the - value of seconds of system time as seed - -2003-08-20 14:42 mmeineke - - * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, - utils/sysbuilder/bilayerSys.cpp: updated the Changelog. - - added some bug fixes for setting the random number generator seed - value. - - fixed a bug where ghostbend atom b was not being set. ( recent bug - from SimState conversion) - -2003-08-20 14:41 mmeineke - - * libBASS/Globals.hpp: updated the Changelog. - - added some bug fixes for setting the random number generator seed - value. - -2003-08-20 14:41 mmeineke - - * ChangeLog: updated the Changelog. - -2003-08-20 14:11 tim - - * libBASS/Globals.cpp, libmdtools/DUFF.cpp, - libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost - bend class - -2003-08-20 10:13 mmeineke - - * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in - make links. added -f to ln -s. - -2003-08-20 09:50 tim - - * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] - -2003-08-20 09:34 tim - - * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, - ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg - printing - -2003-08-18 15:59 chuckv - - * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, - latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, - sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. - Nanobuilder still broke. - -2003-08-15 14:24 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, - libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, - libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint - Method - -2003-08-14 11:16 tim - - * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint - with average force substraction strategy - -2003-08-13 16:20 chuckv - - * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some - profiling code -DPROFILE. - -2003-08-13 14:21 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic - potential & z-contraint method - -2003-08-12 16:44 mmeineke - - * libBASS/BASS_interface.cpp, libBASS/Globals.hpp, - libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really - annoying bug in Directional Atom, where mu was getting written to - pseudorandom memory location. - -2003-08-12 14:56 tim - - * libBASS/BASS_interface.cpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libmdtools/Atom.hpp, - libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/SimSetup.cpp: debugging globals - -2003-08-12 13:40 gezelter - - * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes - and new atypes in LJFF - -2003-08-12 13:15 gezelter - - * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older - stuff... - -2003-08-12 13:14 chuckv - - * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. - -2003-08-12 13:04 chuckv - - * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: - Missed del of files before. - -2003-08-12 13:03 chuckv - - * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log - message] - -2003-08-12 13:01 chuckv - - * utils/sysbuilder/Makefile: commit makefile - -2003-08-12 12:51 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, - libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, - libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added - harmonical potential to z-constraint method - -2003-08-11 17:31 chuckv - - * utils/Makefile: Changed makefile to only build quicklate. - -2003-08-11 17:25 chuckv - - * ac-tools/configure.in: added utils/sysbuilder to be built. - -2003-08-11 17:12 chuckv - - * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, - bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, - sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, - sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, - sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, - sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, - sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, - sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, - sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged - sysbuilder into a subdirectory. Fixed some of sysbuilder to work - with new atom allocation in libmdtools. - -2003-08-11 14:41 tim - - * libmdtools/: Integrator.cpp, Integrator.hpp: added method of - moving zconstraint molecules to specified positions - -2003-08-11 14:39 tim - - * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] - -2003-08-11 14:38 mmeineke - - * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, - libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, - libBASS/ZconStamp.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/SimInfo.hpp: Added zConstraint - into the BASS language syntax. - -2003-08-11 13:29 mmeineke - - * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of - degrees of freedom to account for zConstreints - -2003-08-08 16:22 chuckv - - * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, - libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, - samples/metals/Au.bass: EAM works...... Neighbor list also - works..... - -2003-08-08 12:48 mmeineke - - * libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated - instance of Atom::setZ and Atom::getZ in ZConstaint. - -2003-08-07 16:47 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, - DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, - GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, - SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, - SimState.hpp, Torsion.cpp: switched SimInfo to use a system - configuration from SimState rather than arrays from Atom - -2003-08-06 19:47 chuckv - - * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, - libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, - libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, - samples/metals/Au.bass: Bug fixes for eam... - -2003-08-01 11:18 tim - - * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of - Z-Constraint - -2003-07-31 14:59 tim - - * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/ZConstraint.cpp: add index range checking into - ZConstraint - -2003-07-31 10:38 tim - - * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters - to the globals - -2003-07-31 10:35 tim - - * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, - Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, - NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: - Added Z constraint. - -2003-07-30 16:17 chuckv - - * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, - libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, - libmdtools/do_Forces.F90, libmdtools/wrappers.F90, - samples/metals/Au.bass: More bug fixes for eam. - -2003-07-29 11:32 mmeineke - - * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: - working on the props code - -2003-07-29 11:32 mmeineke - - * libBASS/Globals.cpp: [no log message] - -2003-07-25 15:05 chuckv - - * samples/metals/: Au.bass, metals.mdl: Added bass models for - metals - -2003-07-25 15:00 chuckv - - * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, - notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. - -2003-07-24 16:22 chuckv - - * ac-tools/configure.in: Changed configure to look for both upper - and lower cass .mod files - -2003-07-24 14:57 chuckv - - * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for - eam and do_forces. - -2003-07-23 17:13 chuckv - - * libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, - force_globals.F90, simulation_module.F90, status_module.F90: - Finished most code for eam.... - -2003-07-22 16:49 mmeineke - - * libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan - function to the DumpReader. It should now save the start of each - frame in a vector. - -2003-07-22 15:05 mmeineke - - * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes - to read dump files - -2003-07-22 14:54 tim - - * libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, - Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, - NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log - message] - -2003-07-22 11:41 mmeineke - - * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, - SimSetup.cpp: Fixed a current time initialization bug in - InitFromFile. - -2003-07-21 16:27 mmeineke - - * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, - Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and - friends to accomadate random file access - -2003-07-21 11:23 mmeineke - - * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no - one sets it. - -2003-07-21 11:23 mmeineke - - * libmdtools/: InitializeFromFile.cpp, Integrator.cpp, - ReadWrite.hpp: fixed Initializefrom file to start the simulation - from the time specified in the init file. - -2003-07-17 16:49 gezelter - - * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, - DumpReader.cpp: Started work on a DumpReader - -2003-07-17 15:38 gezelter - - * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E - -2003-07-17 15:32 gezelter - - * forceFields/DUFF.frc, libmdtools/DUFF.cpp, - libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: - Changes for SSD/E - -2003-07-17 14:38 mmeineke - - * libmdtools/do_Forces.F90: commented out an eam line - -2003-07-17 14:32 chuckv - - * libmdtools/atype_module.F90: fixed spelling issue - -2003-07-17 14:29 chuckv - - * libmdtools/: fInfo.c, status_module.F90: added info module - -2003-07-17 14:25 chuckv - - * libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, - atype_module.F90, calc_eam.F90, do_Forces.F90, - fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, - mpiSimulation_module.F90: Added massive changes for eam.... - -2003-07-16 16:49 chuckv - - * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF - -2003-07-16 16:30 mmeineke - - * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, - calc_reaction_field.F90, do_Forces.F90, fSimulation.h, - fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, - neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, - wrappers.F90: Changed how cutoffs were handled from C. Now - notifyCutoffs in Fortran notifies those who need the information of - any changes to cutoffs. - -2003-07-16 12:35 gezelter - - * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. - quickLate is now somewhat more intelligent about periodic - boundaries and wrapping. - -2003-07-16 11:40 chuckv - - * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists - -2003-07-16 10:34 mmeineke - - * scripts/cleanSrc: added a quick wipe-and-update script for quick - rebuilds on BoB - -2003-07-15 21:11 gezelter - - * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more - fixes for box changes - -2003-07-15 17:29 mmeineke - - * libmdtools/simulation_module.F90: removed some debugging print - statements. - -2003-07-15 17:22 mmeineke - - * libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, - do_Forces.F90, simulation_module.F90: fixed a long lived bug in - do_forces. Rrf was not being used in the neighborlist correctly. - rcut was conssistently being set lowere than Rrf causing the dipole - cutoff region to be to small. Also led to the removal of the taper - region to buffer the dipole cutoff. - -2003-07-15 16:34 mmeineke - - * libmdtools/: SimInfo.cpp, simulation_module.F90: working on - fixing ssd bug - -2003-07-15 14:56 gezelter - - * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes - for the NPT ensembles - -2003-07-15 13:52 mmeineke - - * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up - simSetup - -2003-07-15 12:57 mmeineke - - * libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, - SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: - fixed some bugs, Changed entry_plug to info where appropriate - -2003-07-15 12:25 chuckv - - * utils/sysBuild.ggo: added more command line arguments - -2003-07-15 12:11 gezelter - - * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: - Fixing force field line - -2003-07-15 12:10 gezelter - - * libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, - calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, - calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure - tensor - -2003-07-15 10:50 gezelter - - * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes - -2003-07-15 10:42 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: - removed old outdated code - -2003-07-15 09:45 gezelter - - * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx - -2003-07-15 09:28 gezelter - - * libmdtools/Molecule.cpp: removing get_vx - -2003-07-14 22:28 gezelter - - * libmdtools/NPTfm.cpp: Added NPTfm - -2003-07-14 22:27 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: - Bugfix in NPTim, fixes for NPTfm - -2003-07-14 22:08 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: - Checking in changes for NPTim - -2003-07-14 18:06 gezelter - - * utils/Makefile: Broken SysBuilder - -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 - -2003-07-14 18:06 gezelter - - * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some - debugging write statements - -2003-07-14 17:38 gezelter - - * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, - NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom - -2003-07-14 16:48 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get - and set routines to Atom and DirectionalAtom - -2003-07-14 16:35 chuckv - - * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, - sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder - that takes different cmd line arguments. - -2003-07-14 16:28 mmeineke - - * libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, - ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, - SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors - were not being updated - -2003-07-14 10:04 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on - NPTim - -2003-07-14 09:55 mmeineke - - * forceFields/DUFF.frc: Switched the bond in the force field back - to constrained, to preserve energy - -2003-07-11 17:34 mmeineke - - * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, - Integrator.hpp: working on som integrator bugs - -2003-07-11 10:26 gezelter - - * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting - to worry about all the strtok() calls in our code - -2003-07-11 09:49 gezelter - - * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness - -2003-07-10 20:15 gezelter - - * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and - eor. - -2003-07-10 17:15 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, - SimInfo.cpp, Thermo.cpp: fixed some bugs - -2003-07-10 14:53 chuckv - - * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, - nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added - nanoBuilder and a general Lattice builder. - -2003-07-10 12:10 gezelter - - * libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, - Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff - -2003-07-09 17:14 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, - Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, - SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the - caclulation of HmatInverse. - -2003-07-09 10:34 mmeineke - - * libBASS/MoleculeStamp.hpp: starting some work for xlate - -2003-07-09 10:33 mmeineke - - * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff - -2003-07-09 08:56 gezelter - - * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf - -2003-07-09 08:56 gezelter - - * libBASS/Globals.cpp: Removed Qmass - -2003-07-08 21:15 gezelter - - * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf - and NPTi - -2003-07-08 20:41 gezelter - - * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf - -2003-07-08 16:10 gezelter - - * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] - -2003-07-08 16:06 gezelter - - * libmdtools/NPTi.cpp: fixed box scaling - -2003-07-08 15:56 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, - SimInfo.hpp, Thermo.cpp: NPTi - -2003-07-03 14:41 mmeineke - - * libBASS/Makefile, libmdtools/Makefile, src/Makefile, - utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy - scripts in the makefiles - -2003-07-02 16:26 mmeineke - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, - libmdtools/Makefile, libmdtools/ReadWrite.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, - utils/Makefile: fixed the bugs introduced by switching the periodic - box to a matrix - -2003-07-01 17:39 gezelter - - * libmdtools/do_Forces.F90: Fortran flexi-BOX - -2003-07-01 17:29 gezelter - - * libmdtools/simulation_module.F90: Fixes for flexi-BOX - -2003-07-01 16:33 mmeineke - - * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, - fortranWrapDefines.hpp, simulation_module.F90: working on adding - the box matrix to everything. - -2003-06-30 17:03 mmeineke - - * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - src/oopse.cpp: - Updated the ChangeLog, and Converted most of the SImInfo to use - non-Isotropic boxes. wrapVector needs to be finished. - -2003-06-25 16:12 mmeineke - - * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds - to Harmonic bonds in the DUFF frc file - - fixed constraints. - -2003-06-25 16:11 mmeineke - - * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in - the DUFF frc file - -2003-06-24 17:51 gezelter - - * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! - -2003-06-24 14:57 mmeineke - - * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, - libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into - the DUFF forcefield and BondExtensions.cpp - -2003-06-23 16:24 mmeineke - - * libmdtools/Integrator.cpp: Doing some work to debug the - constraint code. - -2003-06-20 15:50 gezelter - - * libmdtools/Integrator.hpp: NPT fix - -2003-06-20 15:29 mmeineke - - * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, - libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, - libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, - libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the - integrator and NVT seem to be working now. - -2003-06-20 11:49 gezelter - - * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions - -2003-06-19 17:02 mmeineke - - * forceFields/DUFF.frc, forceFields/LJFF.frc, - forceFields/LJ_FF.frc, forceFields/Makefile, - forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, - libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, - libmdtools/TraPPEFF.cpp: slowly converting to new integrator and - forcefield names. - -2003-06-19 14:21 mmeineke - - * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: - finished the basics of the integrator and SimSetup.cpp - -2003-06-19 14:11 mmeineke - - * libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it - up / get it to work with the new Integrator. - -2003-06-18 17:20 mmeineke - - * libmdtools/Symplectic.cpp: minor changes in an attempt to fix - output times. - -2003-06-17 16:56 mmeineke - - * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters - fro the ghost Bend in TraPPE_Ex - - some work on the integrator. ( incomplete) - -2003-06-17 16:55 mmeineke - - * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost - Bend in TraPPE_Ex - -2003-06-04 16:06 mmeineke - - * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and - constrainB to the Symplectic integrator - -2003-05-30 16:32 mmeineke - - * utils/bilayerSys.cpp: currently modifiying Symplectic to become - the basic integrator. - - bilayerSys.cpp altered for building tb3. - -2003-05-30 16:31 mmeineke - - * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, - TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently - modifiying Symplectic to become the basic integrator. - -2003-05-30 15:19 mmeineke - - * libmdtools/Integrator.hpp: added some member variables for - position, velocity, etc. - -2003-05-30 14:07 mmeineke - - * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT - is now derived from Integrator - -2003-05-20 11:44 mmeineke - - * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. - -2003-05-17 11:57 mmeineke - - * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be - working - -2003-05-16 16:37 mmeineke - - * utils/bilayerSys.cpp: still working on the bilayer code - -2003-05-16 09:28 mmeineke - - * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some - work to overhaul sysbuild. - -2003-05-13 16:23 mmeineke - - * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop - -2003-05-13 15:47 mmeineke - - * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, - beadLipid/water.mdl: Added bead lipid model to the sample directory - -2003-05-13 15:34 mmeineke - - * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into - the Trappe extended force field - -2003-05-13 12:01 mmeineke - - * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the - TraPPe_Ex forceField - -2003-05-09 14:51 mmeineke - - * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. - there were some duplicate entries - - added a two chain lipid to the lipid.mdl in sample - -2003-05-09 14:51 mmeineke - - * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. - there were some duplicate entries - -2003-05-09 11:56 mmeineke - - * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the - configure script - - added the CH branching group to the TraPPE_Ex fource field - -2003-05-09 11:55 mmeineke - - * ac-tools/configure.in: added the utils subdirectory to the - configure script - -2003-04-25 11:02 mmeineke - - * utils/bilayerSys.cpp: i quick fix to th distance in the random - bilayer builder - -2003-04-24 21:00 mmeineke - - * libmdtools/f_verlet_constrained.F90: added a new test for - constraint failure - -2003-04-17 16:54 mmeineke - - * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, - utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, - utils/bilayerSys.cpp: fixed up sysBuild to where it should now - build our systems - -2003-04-16 16:11 mmeineke - - * utils/: MoLocator.cpp, MoLocator.hpp: almost finished. - -2003-04-15 16:47 mmeineke - - * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys - and sysBuild both will build now. woot! - -2003-04-15 16:20 mmeineke - - * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, - bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp - - sysBuild still need to write the bass file. - - MoLocator.cpp is currently empty - -2003-04-15 15:40 chuckv - - * forceFields/EAM_FF.frc, forceFields/agu3.eam, - forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, - forceFields/pdu3.eam, forceFields/ptu3.eam, - libmdtools/ForceFields.hpp: Added eam force files... - -2003-04-15 11:37 chuckv - - * libmdtools/EAM_FF.cpp: More eam work. - -2003-04-14 16:22 mmeineke - - * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, - utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: - working on the system builder - -2003-04-14 16:16 chuckv - - * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed - ordering on NVT calculation in integrators. - -2003-04-14 14:51 mmeineke - - * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, - obj/placeHolder: working on a system builder - -2003-04-14 14:04 mmeineke - - * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField - - added sysBuild to the utils Makefile - -2003-04-14 14:03 mmeineke - - * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added - Ghost bends to the TraPPE_Ex forceField - -2003-04-14 13:19 chuckv - - * libmdtools/calc_eam.F90: Added first mangling of EAM. - -2003-04-11 13:46 mmeineke - - * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, - simulation_module.F90: fixed a memory bug in Fortran, where - molMembershipArray was declared nLocal instead of nGlobal. - -2003-04-11 10:16 gezelter - - * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, - SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, - fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress - for NPT - -2003-04-10 15:08 mmeineke - - * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a - globalIndex counter to Molecule - -2003-04-10 11:35 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on - ConstantStress - -2003-04-10 11:27 mmeineke - - * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. - caused a miscalculation of nLocal. - -2003-04-10 11:21 mmeineke - - * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, - do_Forces.F90: fixed a bug in symplectic, where presure was only - being calculated the first time through. - -2003-04-09 11:20 chuckv - - * samples/alkane/alkanes.mdl: added pentane to the alkane model - file - -2003-04-09 08:59 gezelter - - * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, - Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file - -2003-04-08 23:06 gezelter - - * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, - ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, - SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, - Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, - calc_reaction_field.F90, calc_sticky_pair.F90, - fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and - NVT - -2003-04-08 17:38 chuckv - - * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/simulation_module.F90, samples/water/ssd.bass: It works - (kinda)... - -2003-04-08 16:35 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, - libmdtools/SimSetup.cpp: Fixes for NPT / NVT - -2003-04-08 12:16 chuckv - - * libmdtools/: do_Forces.F90, neighborLists.F90, - simulation_module.F90: Moved expand neighborlist to init_FF. - -2003-04-08 10:20 chuckv - - * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for - NVT - -2003-04-08 09:39 gezelter - - * libmdtools/Verlet.cpp: fixes for nvt / npt - -2003-04-08 09:34 gezelter - - * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, - Thermo.cpp, Verlet.cpp: dt/2 fix in nvt - -2003-04-08 07:50 gezelter - - * libmdtools/ExtendedSystem.cpp: Fixes for affine transform - -2003-04-08 07:44 gezelter - - * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, - Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the - NVT and NPT ensembles - -2003-04-07 16:42 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp: Fixes for NPT and NVT - -2003-04-07 16:20 mmeineke - - * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial - portion of SSD. - -2003-04-07 16:16 mmeineke - - * libmdtools/: ForceFields.cpp, Symplectic.cpp: - doing some testing in sticky through Symplectic. - -2003-04-07 15:51 gezelter - - * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT - -2003-04-07 15:50 chuckv - - * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for - tau and virial. - -2003-04-07 15:06 mmeineke - - * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, - libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, - src/Makefile: bug fixes - -2003-04-07 11:56 gezelter - - * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, - StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: - Many fixes to add extended system - -2003-04-07 09:30 gezelter - - * src/Makefile: Fixed a bug caused by my experimentation - -2003-04-07 09:30 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, - Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: - Added ExtendedSystem infrastructure for NPT and NVT calculations - -2003-04-07 09:30 gezelter - - * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS - -2003-04-04 23:07 gezelter - - * src/Makefile: final mods to try a fortran compiler - -2003-04-04 22:39 gezelter - - * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, - fortranWrapDefines.hpp: Bug fixes for simulation module rewrites - -2003-04-04 21:56 gezelter - - * libmdtools/: Makefile, atype_module.F90, do_Forces.F90, - fortranWrappers.cpp, wrappers.F90: bug fixes for compilation - -2003-04-04 21:45 gezelter - - * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug - fixes to fortran wrappers - -2003-04-04 17:22 chuckv - - * libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, - calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, - do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, - simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets - smarter, fortran gets dumber... - -2003-04-04 14:57 mmeineke - - * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, - neighborLists.F90: fixed a memory read bug in neighborlist - -2003-04-04 14:47 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, - SimInfo.hpp, Thermo.cpp: Changes for Extended System - -2003-04-04 14:16 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, - SimInfo.hpp: Fixes for ExtendedSystem - -2003-04-03 20:57 gezelter - - * libmdtools/ExtendedSystem.hpp: Added extended system header - -2003-04-03 20:57 gezelter - - * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes - for extended system code - -2003-04-03 18:49 gezelter - - * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to - extendedsystem - -2003-04-03 17:19 mmeineke - - * libmdtools/Molecule.hpp: added some little fixes here and there. - -2003-04-03 17:01 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before - initialize bug. - -2003-04-03 16:12 mmeineke - - * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just - little things like deleteing unused variables and such. - -2003-04-03 15:57 mmeineke - - * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to - simError.h also some fixes to Molecule.hpp - -2003-04-03 15:57 mmeineke - - * libBASS/simError.h: a few fixes to simError.h - -2003-04-03 15:21 mmeineke - - * libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, - libBASS/simError.h, libmdtools/DumpWriter.cpp, - libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, - src/Makefile, src/oopse.cpp: fixed some small things with - simError.h - -2003-04-03 15:19 gezelter - - * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT - -2003-04-03 14:58 gezelter - - * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for - now) - -2003-04-03 08:42 gezelter - - * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: - Changed Readme, added some files - -2003-04-02 17:19 mmeineke - - * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, - Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: - dipoles mostly work, but there is a memory leak somewhere. - -2003-04-02 10:01 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting - the proper atomIdents. - -2003-04-01 11:50 chuckv - - * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, - libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, - samples/argon/argon.bass: more bug fixes.... - -2003-04-01 11:49 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed - DumpWriter to be more robust to errors. also added a little - namespace to InitFromFile to wrap it's helper functions in MPI - -2003-03-31 17:09 chuckv - - * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local - not zeroed. - -2003-03-31 16:50 chuckv - - * libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, - libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, - libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, - samples/alkane/butane.bass: Fixes in MPI force calc and in - Trappe_Ex parsing. - -2003-03-28 17:34 chuckv - - * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp - -2003-03-28 16:45 chuckv - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/InitializeFromFile.cpp: Bug fixes in read-write - routines. - -2003-03-28 14:33 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, - Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a - bug where the Excludes were not being created properly - -2003-03-28 14:30 chuckv - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes - and debugging mpi read write from file. - -2003-03-28 10:28 mmeineke - - * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range - interactions in Trappe - -2003-03-27 18:33 chuckv - - * libmdtools/: SimSetup.cpp, mpiSimulation.cpp, - mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. - -2003-03-27 17:16 mmeineke - - * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where - excludes were not being initialized - -2003-03-27 16:52 mmeineke - - * src/Makefile: [no log message] - -2003-03-27 16:52 mmeineke - - * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. - -2003-03-27 16:07 mmeineke - - * libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, - Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, - Verlet.cpp: fixed the compile time bugs, Source builds and links - -2003-03-27 15:48 mmeineke - - * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few - more bugs. - -2003-03-27 15:40 mmeineke - - * libmdtools/Molecule.cpp: added the Molecule.cpp file - -2003-03-27 15:39 mmeineke - - * libmdtools/: Makefile, Molecule.hpp: fixed the makefile - -2003-03-27 15:36 mmeineke - - * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, - ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, - SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs - -2003-03-27 15:12 mmeineke - - * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, - Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, - Verlet.cpp: I have implemeted Molecules everywhere I could remember - to. will now attempt to compile. - -2003-03-27 14:21 mmeineke - - * libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, - SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished - updating SimSetup to initialize and use the new MPI division of - labour, and Molecule class - -2003-03-27 12:55 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to - use Molecule - -2003-03-27 12:32 mmeineke - - * libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, - SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been - converted to the new Molecule model. TraPPE_Ex is currently being - updated. SimSetups routines are writtten, but not yet called. - -2003-03-27 10:07 gezelter - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, - mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom - numbering in MPI - -2003-03-27 09:30 mmeineke - - * libmdtools/mpiSimulation.cpp: little bug fixes here and there. - -2003-03-26 20:49 gezelter - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to - fileio for MPI - -2003-03-26 18:14 gezelter - - * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, - mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug - fixes many bug fixes - -2003-03-26 17:24 gezelter - - * libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on - sequence of atoms on the other processors. Node 0 now fires - potatoes at other processors to get them to send french fries back. - -2003-03-26 17:02 mmeineke - - * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for - making the molecules is in place. ForceField needs to be updated - next. - -2003-03-26 16:54 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of - the "static" bugs in Atom and Exclude - -2003-03-26 16:50 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, - SimSetup.cpp: still working on the SimSetup routine. also fixed - some things in Exclude.hpp - -2003-03-26 16:24 gezelter - - * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp - -2003-03-26 16:23 gezelter - - * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom - and Exclude list - -2003-03-26 16:04 gezelter - - * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and - delete ranges of atoms - -2003-03-26 15:45 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class - with static arrays similar to the Atom class - -2003-03-26 15:22 mmeineke - - * libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm - overhauling the molecule class to contain it's own bonds, bends, - and torsions. - - may god have mercy on my soul. - -2003-03-26 14:34 chuckv - - * libmdtools/mpiSimulation.cpp: Finished globalIndex. - -2003-03-26 13:02 gezelter - - * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, - mpiSimulation.hpp: MPI stuff for passing out molecules - -2003-03-26 11:12 chuckv - - * libmdtools/mpiSimulation.cpp: working on load balancing - -2003-03-26 10:37 chuckv - - * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - samples/argon/argon.bass: Fixes for Parallel thermalization - -2003-03-26 09:55 mmeineke - - * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in - THermo.cpp - -2003-03-25 17:54 chuckv - - * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation - of potential energy and temperature. - -2003-03-25 09:29 mmeineke - - * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, - src/MPIobj/dummy, src/obj/dummy: [no log message] - -2003-03-25 09:29 mmeineke - - * libBASS/MPIobj/dummy: added dummy files to keep the build - deirectories from being pruned. - -2003-03-24 20:07 gezelter - - * samples/Makefile: moving tests to samples - -2003-03-24 20:06 gezelter - - * samples/: alkane/Makefile, alkane/alkanes.mdl, - 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 - -2003-03-24 19:51 gezelter - - * ac-tools/configure.in: Tests are becoming samples - -2003-03-24 19:46 gezelter - - * ac-tools/Make.conf.in: Added makefiles in tests directories - -2003-03-24 16:55 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, - libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/simulation_module.F90: electrostatic changes for dipole - / RF separation - -2003-03-24 13:33 mmeineke - - * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, - do_Forces.F90: little bug fixes here and there - -2003-03-24 10:26 mmeineke - - * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug - where short range interactions were not being calculated. - - removed some debug print statements - -2003-03-21 17:11 chuckv - - * libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, - do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: - various write statements for debugging - -2003-03-21 16:26 chuckv - - * forceFields/Makefile: added links to the makefile in forceFields - -2003-03-21 15:52 gezelter - - * ac-tools/Make.conf.in, ac-tools/configure.in, - libmdtools/Makefile: Fixed F_MACH_DEP bug - -2003-03-21 15:37 gezelter - - * ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, - ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, - libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, - src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, - autoconf fixes - -2003-03-21 14:58 gezelter - - * LICENSE: Added license file - -2003-03-21 14:55 gezelter - - * forceFields/Makefile: Fixed makefile - -2003-03-21 14:49 gezelter - - * forceFields/Makefile: Makefile for forceFields - -2003-03-21 14:42 gezelter - - * README: Readme changes - -2003-03-21 12:52 mmeineke - - * src/Makefile: [no log message] - -2003-03-21 12:52 mmeineke - - * libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends - -2003-03-21 12:42 mmeineke - - * AUTHORS, ChangeLog, NEWS, Makefile, README, - ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, - ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, - ac-tools/install-sh, forceFields/DipoleTest.frc, - forceFields/LJ_FF.frc, forceFields/TraPPE.frc, - forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, - libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, - libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.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_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, - utils/sfmakedepend, ac-tools/shtool, - libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, - libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, - libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, - libmdtools/Makefile, libmdtools/Molecule.hpp, - libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, - libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, - libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, - libmdtools/Verlet.cpp, libmdtools/atype_module.F90, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - 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 - -2003-03-21 12:42 mmeineke - - * AUTHORS, ChangeLog, NEWS, Makefile, README, - ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, - ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, - ac-tools/install-sh, forceFields/DipoleTest.frc, - forceFields/LJ_FF.frc, forceFields/TraPPE.frc, - forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, - libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, - libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.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_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, - utils/sfmakedepend, ac-tools/shtool, - libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, - libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, - libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, - libmdtools/Makefile, libmdtools/Molecule.hpp, - libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, - libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, - libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, - libmdtools/Verlet.cpp, libmdtools/atype_module.F90, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - 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 +2004-07-23 15:31 tim + + * samples/lipid/5x5.bass: modify 5x5.bass + +2004-07-23 15:25 tim + + * samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message] + +2004-07-23 15:18 tim + + * samples/: water/ssde/ssde.bass, argon/500.bass, + argon/argonNVT.bass: [no log message] + +2004-07-23 15:12 tim + + * samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in, + ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files + +2004-07-23 15:10 tim + + * samples/minimizer/: ssdEM.in, tip4p_two.in: add init file + +2004-07-23 15:09 tim + + * samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename + NVT.bass to argonNVT.bass + +2004-07-23 15:07 tim + + * samples/lipid/5x5.in: add 5x5.in + +2004-07-23 15:06 tim + + * samples/alkane/: butane.in, init_butane.eor: add butane.in + +2004-07-23 14:57 gezelter + + * libBASS/Globals.cpp, samples/minimizer/ssdEM.bass, + samples/minimizer/tip4p_two.bass: changed minimizer keywords + +2004-07-23 14:34 gezelter + + * configure, ac-tools/configure.in: fixed typo + +2004-07-23 14:32 gezelter + + * samples/minimizer/Makefile.in: fixed sample makefile + +2004-07-23 14:31 gezelter + + * configure, ac-tools/configure.in, samples/minimizer/Makefile.in, + samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass, + samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl: + minimizer sample changes + +2004-07-23 14:15 gezelter + + * configure, ac-tools/configure.in: removed beadLipid + +2004-07-23 14:08 tim + + * samples/Makefile.in: remove beadLipid + +2004-07-23 14:03 chuckv + + * samples/metals/: Au_nanoparticle.eor, + Au_nanoparticle_coreshell_12-20.bass, + Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle + files. + +2004-07-23 13:51 tim + + * samples/water/tip4p/TP4init.in: remove TP4init.in + +2004-07-23 13:50 tim + + * samples/water/tip4p/: Makefile.in, tp4.bass: change init file + name for tip4p and tip3p_ice + +2004-07-23 13:48 tim + + * samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message] + +2004-07-23 13:48 tim + + * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change + init file name for ssd + +2004-07-23 13:46 tim + + * samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove + SPCEInit.in + +2004-07-23 13:45 tim + + * samples/water/dimer/: Makefile.in, two.bass, two.init: change + names for init file + +2004-07-23 13:40 tim + + * samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor: + change init file name in lipid directory + +2004-07-23 13:36 tim + + * samples/argon/init_argon.eor: remove init_argon.eor + +2004-07-23 13:34 tim + + * samples/: alkane/Makefile.in, alkane/butane.bass, + alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message] + +2004-07-23 13:33 tim + + * samples/argon/Makefile.in: remove eor file + +2004-07-23 13:31 tim + + * samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass: + change names for argon + +2004-07-23 11:47 tim + + * samples/water/ssde/SSDEinit.in: [no log message] + +2004-07-23 11:45 tim + + * samples/water/ssde/SSDEinit.in: add init file for ssde + +2004-07-23 11:43 chuckv + + * libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and + cutoffs associated with mixture. + +2004-07-23 10:35 tim + + * libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E + SSD_RF SSD1 + +2004-07-23 09:53 tim + + * libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E, + SSD1 now + +2004-07-23 09:19 tim + + * libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp + +2004-07-23 09:18 tim + + * samples/lipid/5x5.bass: remove unsupport keyword + +2004-07-22 16:01 chuckv + + * samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in: + Changed init files to be more OOPSE like... + +2004-07-22 10:11 gezelter + + * configure, ac-tools/configure.in: added sample directory + +2004-07-22 10:06 chrisfen + + * src/Makefile.in: fixed icc7 incompatibility in linking + +2004-07-21 17:03 chrisfen + + * samples/water/: Makefile.in, tip3p_ice/200.in, + tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl: + Added tip3p_ice to Makefile + +2004-07-21 16:46 chuckv + + * samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass, + Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor, + init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample + files for bulk metals and a bass file for both voter and FBD + formulations of EAM. + +2004-07-21 14:53 gezelter + + * samples/water/dimer/two.bass: Checked a bug where eor file wasn't + being written at the end of the run + +2004-07-21 14:53 gezelter + + * libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't + being written at the end of the run + +2004-07-21 09:11 gezelter + + * README: [no log message] + +2004-07-21 09:08 gezelter + + * samples/argon/machines: cleaning up for export + +2004-07-21 09:04 gezelter + + * NEWS, README: cleaning up for export + +2004-07-21 08:45 gezelter + + * configure, ac-tools/configure.in: removing staticProps from cvs + tree + +2004-07-20 12:07 gezelter + + * configure, ac-tools/aclocal.m4, utils/Makefile.in, + utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message] + +2004-07-20 10:17 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c, + utils/gnugetopt.h: fixing getopt_long + +2004-07-19 16:58 gezelter + + * configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp, + libmdtools/ZConsWriter.hpp, src/Makefile.in, + third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep, + utils/Makefile.in, utils/sysbuilder/Makefile.in, + utils/sysbuilder/latticeBuilder.cpp: [no log message] + +2004-07-19 16:52 tim + + * utils/quickLate.c: minor fix of format string in quicklate.c + +2004-07-19 16:30 tim + + * utils/zsub: remove zsub from cvs tree + +2004-07-19 16:25 tim + + * libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some + comment lines + +2004-07-19 16:00 tim + + * libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from + OOPSEMinimizer.hpp + +2004-07-19 13:55 gezelter + + * libBASS/y.tab.h: Shouldn't have been in CVS + +2004-07-19 13:54 gezelter + + * libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for + thermodynamic integration of rigid bodies + +2004-07-19 12:00 gezelter + + * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be + generated via lex and yacc at compile time + +2004-07-19 11:47 gezelter + + * libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h, + libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in, + libmdtools/MatVec3.c, src/Makefile.in: [no log message] + +2004-07-19 11:32 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + third-party/gnugetopt.h, utils/Makefile.in, + utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed + SPRNG configure script + +2004-07-16 16:49 gezelter + + * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines + that don't have lex and yacc + +2004-07-16 15:55 gezelter + + * Makefile: Makefiles don't belong in cvs repository + +2004-07-16 15:54 gezelter + + * Makefile, forceFields/Makefile, libBASS/Makefile, + libmdtools/Makefile, samples/Makefile, src/Makefile, + third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile: + Makefiles don't belong in repository + +2004-07-16 15:49 gezelter + + * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, + metals/Makefile: Makefiles don't belong in repository + +2004-07-16 15:20 chrisfen + + * Makefile, configure, ac-tools/configure.in, forceFields/Makefile, + libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile, + samples/argon/Makefile, samples/lipid/Makefile, + samples/metals/Makefile, src/Makefile, utils/Makefile, + utils/sysbuilder/Makefile: Updated configure for new samples + +2004-07-16 14:57 chrisfen + + * samples/water/tip4p/Makefile.in: tip4p makefile.in added + +2004-07-16 14:57 chrisfen + + * samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde + makefile.in added + +2004-07-16 14:57 chrisfen + + * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass, + water.mdl: ssd files sorted added + +2004-07-16 14:57 chrisfen + + * samples/water/spce/Makefile.in: spce makefile.in added + +2004-07-16 14:56 chrisfen + + * samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl: + dimer files added + +2004-07-16 14:56 chrisfen + + * samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor, + spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor, + tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass, + two.eor, two.init, two.xyz, water.mdl: Cleaned up this file + considerably + +2004-07-16 13:57 gezelter + + * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, + configure, 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, + forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, + forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, + forceFields/Au.VC.funcfl, forceFields/Au.u3.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/LJFF.frc, forceFields/Makefile, + forceFields/Makefile.in, forceFields/Ni.VC.funcfl, + forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, + forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, + forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, + forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, + forceFields/WATER.frc, libBASS/AtomStamp.cpp, + libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, + libBASS/BASS_interface.h, libBASS/BASS_parse.c, + libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, + libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, + libBASS/Component.cpp, libBASS/Component.hpp, + libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, + libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, + libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, + libBASS/LinkedCommand.hpp, libBASS/Make.dep, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, + libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, + libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, + libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, + libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, + libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, + 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_me.h, + libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, + libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, + libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, + libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, + libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, + libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, + libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, + libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, + libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, + libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, + libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, + libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, + libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, + libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, + libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, + libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, + libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, + libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, + libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, + libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/SimState.cpp, libmdtools/SimState.hpp, + libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, + libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, + libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, + libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, + libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, + libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, + libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, + libmdtools/Utility.cpp, libmdtools/Utility.hpp, + libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, + libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, + libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, + libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, + libmdtools/atype_module.F90, 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/config.h.in, + libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, + libmdtools/fForceField.h, libmdtools/fSimulation.h, + libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, + libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, + libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, + libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, + libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, + libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, + libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, + libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, + libmdtools/status_module.F90, libmdtools/switch_module.F90, + libmdtools/timing.F90, libmdtools/vector_class.F90, + libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, + libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, + samples/alkane/Makefile, samples/alkane/Makefile.in, + samples/alkane/alkanes.mdl, samples/alkane/butane.bass, + samples/alkane/butane.eor, samples/alkane/init_butane.eor, + samples/argon/500.bass, samples/argon/500.eor, + samples/argon/500.in, samples/argon/Makefile, + samples/argon/Makefile.in, samples/argon/NVT.bass, + samples/argon/ar864.bass, samples/argon/ar864.eor, + samples/argon/ar864.in, samples/argon/argon.bass, + samples/argon/argon.eor, samples/argon/argonEM.bass, + samples/argon/init_argon.eor, samples/argon/lj.mdl, + samples/argon/machines, samples/lipid/5x5.bass, + samples/lipid/5x5.eor, samples/lipid/Makefile, + samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, + samples/lipid/lipid.mdl, samples/lipid/water.mdl, + samples/metals/Au.bass, samples/metals/Au.eor, + samples/metals/Makefile, samples/metals/Makefile.in, + samples/metals/init_au.in, samples/metals/metals.mdl, + samples/water/200.in, samples/water/Makefile, + samples/water/Makefile.in, samples/water/init_ssd.eor, + samples/water/spce.bass, samples/water/spce.eor, + samples/water/ssd.bass, samples/water/ssd.eor, + samples/water/tim.bass, samples/water/tim.eor, + samples/water/tim.init, samples/water/tim.xyz, + samples/water/tip3p.bass, samples/water/tip3p.eor, + samples/water/tip3p.init, samples/water/two.bass, + samples/water/two.eor, samples/water/two.init, + samples/water/two.xyz, samples/water/water.mdl, + samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, + samples/water/spce/water.mdl, samples/water/ssde/256init.in, + samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, + samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, + samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, + scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, + src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, + third-party/Makefile, third-party/Makefile.in, + third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, + utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, + utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, + utils/MPIobj/placeHolder, utils/obj/placeHolder, + utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, + utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, + utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, + utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, + utils/sysbuilder/latticeBuilder.cpp, + utils/sysbuilder/latticeBuilder.hpp, + utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, + utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, + utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, + utils/sysbuilder/MPIobj/placeHolder, + utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0 + source tree + +2004-07-16 13:57 gezelter + + * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, + configure, 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, + forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, + forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, + forceFields/Au.VC.funcfl, forceFields/Au.u3.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/LJFF.frc, forceFields/Makefile, + forceFields/Makefile.in, forceFields/Ni.VC.funcfl, + forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, + forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, + forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, + forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, + forceFields/WATER.frc, libBASS/AtomStamp.cpp, + libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, + libBASS/BASS_interface.h, libBASS/BASS_parse.c, + libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, + libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, + libBASS/Component.cpp, libBASS/Component.hpp, + libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, + libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, + libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, + libBASS/LinkedCommand.hpp, libBASS/Make.dep, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, + libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, + libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, + libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, + libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, + libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, + 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_me.h, + libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, + libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, + libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, + libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, + libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, + libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, + libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, + libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, + libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, + libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, + libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, + libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, + libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, + libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, + libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, + libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, + libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, + libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, + libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, + libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/SimState.cpp, libmdtools/SimState.hpp, + libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, + libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, + libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, + libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, + libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, + libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, + libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, + libmdtools/Utility.cpp, libmdtools/Utility.hpp, + libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, + libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, + libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, + libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, + libmdtools/atype_module.F90, 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/config.h.in, + libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, + libmdtools/fForceField.h, libmdtools/fSimulation.h, + libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, + libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, + libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, + libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, + libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, + libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, + libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, + libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, + libmdtools/status_module.F90, libmdtools/switch_module.F90, + libmdtools/timing.F90, libmdtools/vector_class.F90, + libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, + libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, + samples/alkane/Makefile, samples/alkane/Makefile.in, + samples/alkane/alkanes.mdl, samples/alkane/butane.bass, + samples/alkane/butane.eor, samples/alkane/init_butane.eor, + samples/argon/500.bass, samples/argon/500.eor, + samples/argon/500.in, samples/argon/Makefile, + samples/argon/Makefile.in, samples/argon/NVT.bass, + samples/argon/ar864.bass, samples/argon/ar864.eor, + samples/argon/ar864.in, samples/argon/argon.bass, + samples/argon/argon.eor, samples/argon/argonEM.bass, + samples/argon/init_argon.eor, samples/argon/lj.mdl, + samples/argon/machines, samples/lipid/5x5.bass, + samples/lipid/5x5.eor, samples/lipid/Makefile, + samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, + samples/lipid/lipid.mdl, samples/lipid/water.mdl, + samples/metals/Au.bass, samples/metals/Au.eor, + samples/metals/Makefile, samples/metals/Makefile.in, + samples/metals/init_au.in, samples/metals/metals.mdl, + samples/water/200.in, samples/water/Makefile, + samples/water/Makefile.in, samples/water/init_ssd.eor, + samples/water/spce.bass, samples/water/spce.eor, + samples/water/ssd.bass, samples/water/ssd.eor, + samples/water/tim.bass, samples/water/tim.eor, + samples/water/tim.init, samples/water/tim.xyz, + samples/water/tip3p.bass, samples/water/tip3p.eor, + samples/water/tip3p.init, samples/water/two.bass, + samples/water/two.eor, samples/water/two.init, + samples/water/two.xyz, samples/water/water.mdl, + samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, + samples/water/spce/water.mdl, samples/water/ssde/256init.in, + samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, + samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, + samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, + scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, + src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, + third-party/Makefile, third-party/Makefile.in, + third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, + utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, + utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, + utils/MPIobj/placeHolder, utils/obj/placeHolder, + utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, + utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, + utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, + utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, + utils/sysbuilder/latticeBuilder.cpp, + utils/sysbuilder/latticeBuilder.hpp, + utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, + utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, + utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, + utils/sysbuilder/MPIobj/placeHolder, + utils/sysbuilder/obj/placeHolder: Initial revision