--- trunk/OOPSE/ChangeLog 2003/10/29 00:19:10 837 +++ trunk/OOPSE/ChangeLog 2004/04/29 16:03:38 1143 @@ -1,24 +1,1157 @@ -2003-10-24 18:17 mmeineke +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 13:36 gezelter +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 13:35 gezelter +2003-10-24 12:35 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a merge problem -2003-10-23 15:57 mmeineke +2003-10-23 14:57 mmeineke * samples/metals/Makefile.in: added eam ForceField files to the init @@ -27,25 +1160,25 @@ added the init file to the makefile -2003-10-23 15:57 mmeineke +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 15:57 mmeineke +2003-10-23 14:57 mmeineke * forceFields/Makefile.in: added eam ForceField files to the init -2003-10-22 17:17 mmeineke +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 15:33 mmeineke +2003-10-21 14:33 mmeineke * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, @@ -54,7 +1187,7 @@ of the time stamp in the .init file * default=> useInitTime = true; -2003-10-17 17:19 mmeineke +2003-10-17 16:19 mmeineke * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, @@ -64,16 +1197,16 @@ fixed a number of bugs in the staticProps code. gofr is now working. -2003-10-17 17:18 mmeineke +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 17:17 mmeineke +2003-10-17 16:17 mmeineke * configure: added the staticProps directory to the build list -2003-10-16 15:16 mmeineke +2003-10-16 14:16 mmeineke * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to @@ -87,95 +1220,67 @@ a frame is written. This lets the .eor file represent the last written frame of a simulation. -2003-10-10 13:10 mmeineke +2003-10-10 12:10 mmeineke - * props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, - props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, - props/PairCorrList.hpp, props/PairCorrType.cpp, - props/PairCorrType.hpp, props/staticProps.cpp, - staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, - staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, - staticProps/GofR.cpp, staticProps/Makefile.in, - staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, - staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, - staticProps/staticProps.cpp: removed the props directory, and moved - everything over to staticProps + * 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 18:09 mmeineke +2003-10-09 17:09 mmeineke - * libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, - props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, - props/PairCorrType.cpp, props/PairCorrType.hpp, - props/staticProps.cpp: Contiuned work on staticProps. should be in + * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in a position where it will compile and run first runs. -2003-10-04 14:46 chuckv +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 14:08 chuckv +2003-10-04 13:08 chuckv * samples/metals/init_au.in: added Au init file for eam. -2003-10-03 18:11 mmeineke +2003-10-03 17:11 mmeineke * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed entahlpy from the statwriter and thermo. -2003-10-03 18:02 mmeineke +2003-10-03 17:02 mmeineke - * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, - PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, - staticProps.cpp: changed the formating ogf the error statements in - simError - - added a function to get the maxCutoff - - near completion of the staticProps code. still needs the pair loop, - and the loop to allocate and read each frame. - -2003-10-03 18:02 mmeineke - * libmdtools/SimInfo.hpp: changed the formating ogf the error statements in simError added a function to get the maxCutoff -2003-10-03 18:01 mmeineke +2003-10-03 17:01 mmeineke * libBASS/simError.c: changed the formating ogf the error statements in simError -2003-10-02 18:06 mmeineke +2003-09-30 11:00 mmeineke - * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, - PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, - staticProps.cpp: finishing up the constructs needed to get this - program up and running - -2003-09-30 12:00 mmeineke - * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed f90Flags so they are no longer overwritten by the compiler. -2003-09-29 18:06 mmeineke +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 18:06 mmeineke +2003-09-29 17:06 mmeineke * ac-tools/configure.in: added mpif90 mod check back same for conifig.in -2003-09-29 18:05 mmeineke +2003-09-29 17:05 mmeineke * configure: added mpif90 mod check back -2003-09-29 17:16 mmeineke +2003-09-29 16:16 mmeineke * configure, ac-tools/aclocal.m4, ac-tools/configure.in, libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, @@ -187,17 +1292,17 @@ libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7 -2003-09-29 13:38 mmeineke +2003-09-29 12:38 mmeineke * libmdtools/GenericData.hpp: light change in syntax. no signifigant change. -2003-09-25 17:17 mmeineke +2003-09-25 16:17 mmeineke * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some additional remarks from icc -w3 (extra verbose output) -2003-09-25 15:27 mmeineke +2003-09-25 14:27 mmeineke * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, @@ -211,40 +1316,40 @@ libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with gcc -Wall and g++ -Wall -2003-09-25 14:54 gezelter +2003-09-25 13:54 gezelter * configure, ac-tools/configure.in: fixed a bug in configure -2003-09-25 12:42 gezelter +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 15:34 mmeineke +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 16:36 gezelter +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 16:34 mmeineke +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 19:07 tim +2003-09-22 18:07 tim * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, SimInfo.hpp: fix bug in calculating maxCutoff -2003-09-22 17:23 mmeineke +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: @@ -252,45 +1357,45 @@ Removed NPTfm and NPTim from cvs -2003-09-19 16:00 mmeineke +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 12:03 mmeineke +2003-09-19 11:03 mmeineke * utils/Makefile.in, src/Makefile.in: removed mpi++ from the makefile -2003-09-19 12:01 gezelter +2003-09-19 11:01 gezelter * samples/water/ssd.bass: goofing off to test NPTf and NPTi -2003-09-19 12:01 gezelter +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 11:20 mmeineke +2003-09-19 10:20 mmeineke * utils/Makefile.in: fixed a typo in the makefile. -2003-09-19 10:55 gezelter +2003-09-19 09:55 gezelter * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, samples/water/ssd.bass: [no log message] -2003-09-19 10:22 tim +2003-09-19 09:22 tim * libmdtools/: NPTi.cpp, NVT.cpp: [no log message] -2003-09-17 10:22 mmeineke +2003-09-17 09:22 mmeineke * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now work with constraints. -2003-09-16 16:02 tim +2003-09-16 15:02 tim * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo @@ -299,7 +1404,7 @@ NPTi appears very stable. -2003-09-15 12:52 tim +2003-09-15 11:52 tim * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, @@ -310,56 +1415,39 @@ utils/sysbuilder/bilayerSys.cpp: add conserved quantity to statWriter fix bug of vector wrapping at NPTi -2003-09-12 16:51 mmeineke +2003-09-12 11:20 gezelter - * props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, - PairCorrType.hpp: added AllCorr. It eill still need some work - -2003-09-12 12:20 gezelter - * libmdtools/: Make.dep, Makefile.in: Added integrators to Makefile.in -2003-09-12 12:20 gezelter +2003-09-12 11:20 gezelter * ChangeLog: Entered changes for configure into ChangeLog -2003-09-10 17:28 mmeineke - - * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more - work on getting gofR working. - -2003-09-09 17:50 mmeineke - - * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the - beginings of the GofR pair correlation. - - added identification of identI in matchI. - -2003-09-09 16:35 mmeineke +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 16:34 mmeineke +2003-09-09 15:34 mmeineke * ChangeLog: updated the ChangeLog -2003-09-05 18:45 gezelter +2003-09-05 17:45 gezelter * libmdtools/Make.dep: dependency on config.h -2003-09-05 18:36 gezelter +2003-09-05 17:36 gezelter * configure, ac-tools/aclocal.m4: fixed sprng problem -2003-09-05 17:29 gezelter +2003-09-05 16:29 gezelter * samples/metals/Makefile.in: New Makefile for metals sample -2003-09-05 17:27 gezelter +2003-09-05 16:27 gezelter * Makefile, Makefile.in, ac-tools/aclocal.m4, ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, @@ -383,7 +1471,7 @@ utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to autoconf / configure method of configuring OOPSE -2003-09-04 17:48 mmeineke +2003-09-04 16:48 mmeineke * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, @@ -393,60 +1481,54 @@ added ability to reset the integrators in the NVT and NPT family. -2003-09-04 17:48 mmeineke +2003-09-04 16:48 mmeineke * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global namespace. -2003-09-02 10:30 tim +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 17:09 tim +2003-08-28 16:09 tim * ChangeLog, libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex -2003-08-28 12:59 mmeineke +2003-08-27 14:23 tim - * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: - added the first functional parts of the PairCorrType Abstract - classes. - -2003-08-27 15:23 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 12:25 gezelter +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 12:16 tim +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 16:37 tim +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 16:29 tim +2003-08-26 15:29 tim * libmdtools/Integrator.cpp: [no log message] -2003-08-26 16:13 mmeineke +2003-08-26 15:13 mmeineke * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. @@ -455,7 +1537,7 @@ hard coding some system init into bilayer.sys -2003-08-26 16:12 mmeineke +2003-08-26 15:12 mmeineke * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: added define statemewnt to Statwriter and Dumpwriter to handle @@ -463,13 +1545,13 @@ commented out some print statements in Zconstraint -2003-08-26 16:02 tim +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 14:32 mmeineke +2003-08-26 13:32 mmeineke * libmdtools/DUFF.cpp: changed the Makefiel a litle. @@ -477,25 +1559,25 @@ constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11) -2003-08-26 14:30 mmeineke +2003-08-26 13:30 mmeineke * Makefile: changed the Makefiel a litle. -2003-08-25 18:17 gezelter +2003-08-25 17:17 gezelter * utils/sysbuilder/Makefile: More FreeBSD fixes -2003-08-25 17:51 gezelter +2003-08-25 16:51 gezelter * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, libmdtools/Makefile, src/Makefile: [no log message] -2003-08-22 16:04 mmeineke +2003-08-22 15:04 mmeineke * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on frequency of output dumps. -2003-08-20 18:23 tim +2003-08-20 17:23 tim * libBASS/Globals.hpp, libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, @@ -503,7 +1585,7 @@ if he does not specify any value for seed, oopse will take the value of seconds of system time as seed -2003-08-20 15:42 mmeineke +2003-08-20 14:42 mmeineke * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, @@ -516,46 +1598,46 @@ fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion) -2003-08-20 15:41 mmeineke +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 15:41 mmeineke +2003-08-20 14:41 mmeineke * ChangeLog: updated the Changelog. -2003-08-20 15:11 tim +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 11:13 mmeineke +2003-08-20 10:13 mmeineke * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in make links. added -f to ln -s. -2003-08-20 10:50 tim +2003-08-20 09:50 tim * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] -2003-08-20 10:34 tim +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 16:59 chuckv +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 15:24 tim +2003-08-15 14:24 tim * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, @@ -564,24 +1646,24 @@ libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint Method -2003-08-14 12:16 tim +2003-08-14 11:16 tim * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint with average force substraction strategy -2003-08-13 17:20 chuckv +2003-08-13 16:20 chuckv * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some profiling code -DPROFILE. -2003-08-13 15:21 tim +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 17:44 mmeineke +2003-08-12 16:44 mmeineke * libBASS/BASS_interface.cpp, libBASS/Globals.hpp, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, @@ -590,42 +1672,42 @@ annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location. -2003-08-12 15:56 tim +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 14:40 gezelter +2003-08-12 13:40 gezelter * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes and new atypes in LJFF -2003-08-12 14:15 gezelter +2003-08-12 13:15 gezelter * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older stuff... -2003-08-12 14:14 chuckv +2003-08-12 13:14 chuckv * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. -2003-08-12 14:04 chuckv +2003-08-12 13:04 chuckv * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: Missed del of files before. -2003-08-12 14:03 chuckv +2003-08-12 13:03 chuckv * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log message] -2003-08-12 14:01 chuckv +2003-08-12 13:01 chuckv * utils/sysbuilder/Makefile: commit makefile -2003-08-12 13:51 tim +2003-08-12 12:51 tim * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, @@ -633,15 +1715,15 @@ libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added harmonical potential to z-constraint method -2003-08-11 18:31 chuckv +2003-08-11 17:31 chuckv * utils/Makefile: Changed makefile to only build quicklate. -2003-08-11 18:25 chuckv +2003-08-11 17:25 chuckv * ac-tools/configure.in: added utils/sysbuilder to be built. -2003-08-11 18:12 chuckv +2003-08-11 17:12 chuckv * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, @@ -655,16 +1737,16 @@ sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new atom allocation in libmdtools. -2003-08-11 15:41 tim +2003-08-11 14:41 tim * libmdtools/: Integrator.cpp, Integrator.hpp: added method of moving zconstraint molecules to specified positions -2003-08-11 15:39 tim +2003-08-11 14:39 tim * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] -2003-08-11 15:38 mmeineke +2003-08-11 14:38 mmeineke * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, @@ -675,31 +1757,24 @@ libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint into the BASS language syntax. -2003-08-11 14:29 mmeineke +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 17:22 chuckv +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 14:32 mmeineke +2003-08-08 12:48 mmeineke - * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: - moved frameCount's functionality into DumpReader. also split props - into staticProps and dynamicProps. (currently only have - staticProps) - -2003-08-08 13:48 mmeineke - * libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint. -2003-08-07 17:47 mmeineke +2003-08-07 16:47 mmeineke * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, @@ -708,31 +1783,31 @@ SimState.hpp, Torsion.cpp: switched SimInfo to use a system configuration from SimState rather than arrays from Atom -2003-08-06 20:47 chuckv +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 12:18 tim +2003-08-01 11:18 tim * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of Z-Constraint -2003-07-31 15:59 tim +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 11:38 tim +2003-07-31 10:38 tim * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters to the globals -2003-07-31 11:35 tim +2003-07-31 10:35 tim * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, @@ -740,130 +1815,129 @@ SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: Added Z constraint. -2003-07-30 17:17 chuckv +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 12:32 mmeineke +2003-07-29 11:32 mmeineke * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - props/frameCount.c, props/frameCount.h, props/props.cpp, - src/Makefile: working on the props code + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: + working on the props code -2003-07-29 12:32 mmeineke +2003-07-29 11:32 mmeineke * libBASS/Globals.cpp: [no log message] -2003-07-25 16:05 chuckv +2003-07-25 15:05 chuckv * samples/metals/: Au.bass, metals.mdl: Added bass models for metals -2003-07-25 16:00 chuckv +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 17:22 chuckv +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 15:57 chuckv +2003-07-24 14:57 chuckv * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for eam and do_forces. -2003-07-23 18:13 chuckv +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 17:49 mmeineke +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 16:05 mmeineke +2003-07-22 15:05 mmeineke * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes to read dump files -2003-07-22 15:54 tim +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 12:41 mmeineke +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 17:27 mmeineke +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 12:23 mmeineke +2003-07-21 11:23 mmeineke * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no one sets it. -2003-07-21 12:23 mmeineke +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 17:49 gezelter +2003-07-17 16:49 gezelter * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, DumpReader.cpp: Started work on a DumpReader -2003-07-17 16:38 gezelter +2003-07-17 15:38 gezelter * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E -2003-07-17 16:32 gezelter +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 15:38 mmeineke +2003-07-17 14:38 mmeineke * libmdtools/do_Forces.F90: commented out an eam line -2003-07-17 15:32 chuckv +2003-07-17 14:32 chuckv * libmdtools/atype_module.F90: fixed spelling issue -2003-07-17 15:29 chuckv +2003-07-17 14:29 chuckv * libmdtools/: fInfo.c, status_module.F90: added info module -2003-07-17 15:25 chuckv +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 17:49 chuckv +2003-07-16 16:49 chuckv * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF -2003-07-16 17:30 mmeineke +2003-07-16 16:30 mmeineke * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, @@ -874,33 +1948,33 @@ notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs. -2003-07-16 13:35 gezelter +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 12:40 chuckv +2003-07-16 11:40 chuckv * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists -2003-07-16 11:34 mmeineke +2003-07-16 10:34 mmeineke * scripts/cleanSrc: added a quick wipe-and-update script for quick rebuilds on BoB -2003-07-15 22:11 gezelter +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 18:29 mmeineke +2003-07-15 17:29 mmeineke * libmdtools/simulation_module.F90: removed some debugging print statements. -2003-07-15 18:22 mmeineke +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 @@ -909,209 +1983,209 @@ cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff. -2003-07-15 17:34 mmeineke +2003-07-15 16:34 mmeineke * libmdtools/: SimInfo.cpp, simulation_module.F90: working on fixing ssd bug -2003-07-15 15:56 gezelter +2003-07-15 14:56 gezelter * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes for the NPT ensembles -2003-07-15 14:52 mmeineke +2003-07-15 13:52 mmeineke * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up simSetup -2003-07-15 13:57 mmeineke +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 13:25 chuckv +2003-07-15 12:25 chuckv * utils/sysBuild.ggo: added more command line arguments -2003-07-15 13:11 gezelter +2003-07-15 12:11 gezelter * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: Fixing force field line -2003-07-15 13:10 gezelter +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 11:50 gezelter +2003-07-15 10:50 gezelter * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes -2003-07-15 11:42 gezelter +2003-07-15 10:42 gezelter * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: removed old outdated code -2003-07-15 10:45 gezelter +2003-07-15 09:45 gezelter * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx -2003-07-15 10:28 gezelter +2003-07-15 09:28 gezelter * libmdtools/Molecule.cpp: removing get_vx -2003-07-14 23:28 gezelter +2003-07-14 22:28 gezelter * libmdtools/NPTfm.cpp: Added NPTfm -2003-07-14 23:27 gezelter +2003-07-14 22:27 gezelter * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: Bugfix in NPTim, fixes for NPTfm -2003-07-14 23:08 gezelter +2003-07-14 22:08 gezelter * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: Checking in changes for NPTim -2003-07-14 19:06 gezelter +2003-07-14 18:06 gezelter * utils/Makefile: Broken SysBuilder -2003-07-14 19:06 gezelter +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 19:06 gezelter +2003-07-14 18:06 gezelter * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some debugging write statements -2003-07-14 18:38 gezelter +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 17:48 mmeineke +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 17:35 chuckv +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 17:28 mmeineke +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 11:04 gezelter +2003-07-14 10:04 gezelter * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on NPTim -2003-07-14 10:55 mmeineke +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 18:34 mmeineke +2003-07-11 17:34 mmeineke * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, Integrator.hpp: working on som integrator bugs -2003-07-11 11:26 gezelter +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 10:49 gezelter +2003-07-11 09:49 gezelter * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness -2003-07-10 21:15 gezelter +2003-07-10 20:15 gezelter * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and eor. -2003-07-10 18:15 mmeineke +2003-07-10 17:15 mmeineke * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, SimInfo.cpp, Thermo.cpp: fixed some bugs -2003-07-10 15:53 chuckv +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 13:10 gezelter +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 18:14 mmeineke +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 11:34 mmeineke +2003-07-09 10:34 mmeineke * libBASS/MoleculeStamp.hpp: starting some work for xlate -2003-07-09 11:33 mmeineke +2003-07-09 10:33 mmeineke * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff -2003-07-09 09:56 gezelter +2003-07-09 08:56 gezelter * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf -2003-07-09 09:56 gezelter +2003-07-09 08:56 gezelter * libBASS/Globals.cpp: Removed Qmass -2003-07-08 22:15 gezelter +2003-07-08 21:15 gezelter * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf and NPTi -2003-07-08 21:41 gezelter +2003-07-08 20:41 gezelter * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf -2003-07-08 17:10 gezelter +2003-07-08 16:10 gezelter * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] -2003-07-08 17:06 gezelter +2003-07-08 16:06 gezelter * libmdtools/NPTi.cpp: fixed box scaling -2003-07-08 16:56 gezelter +2003-07-08 15:56 gezelter * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, SimInfo.hpp, Thermo.cpp: NPTi -2003-07-03 15:41 mmeineke +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 17:26 mmeineke +2003-07-02 16:26 mmeineke * libBASS/Makefile, libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, @@ -1122,59 +2196,59 @@ utils/Makefile: fixed the bugs introduced by switching the periodic box to a matrix -2003-07-01 18:39 gezelter +2003-07-01 17:39 gezelter * libmdtools/do_Forces.F90: Fortran flexi-BOX -2003-07-01 18:29 gezelter +2003-07-01 17:29 gezelter * libmdtools/simulation_module.F90: Fixes for flexi-BOX -2003-07-01 17:33 mmeineke +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 18:03 mmeineke +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 17:12 mmeineke +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 17:11 mmeineke +2003-06-25 16:11 mmeineke * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in the DUFF frc file -2003-06-24 18:51 gezelter +2003-06-24 17:51 gezelter * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! -2003-06-24 15:57 mmeineke +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 17:24 mmeineke +2003-06-23 16:24 mmeineke * libmdtools/Integrator.cpp: Doing some work to debug the constraint code. -2003-06-20 16:50 gezelter +2003-06-20 15:50 gezelter * libmdtools/Integrator.hpp: NPT fix -2003-06-20 16:29 mmeineke +2003-06-20 15:29 mmeineke * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, @@ -1183,11 +2257,11 @@ libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the integrator and NVT seem to be working now. -2003-06-20 12:49 gezelter +2003-06-20 11:49 gezelter * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions -2003-06-19 18:02 mmeineke +2003-06-19 17:02 mmeineke * forceFields/DUFF.frc, forceFields/LJFF.frc, forceFields/LJ_FF.frc, forceFields/Makefile, @@ -1198,149 +2272,149 @@ libmdtools/TraPPEFF.cpp: slowly converting to new integrator and forcefield names. -2003-06-19 15:21 mmeineke +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 15:11 mmeineke +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 18:20 mmeineke +2003-06-18 17:20 mmeineke * libmdtools/Symplectic.cpp: minor changes in an attempt to fix output times. -2003-06-17 17:56 mmeineke +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 17:55 mmeineke +2003-06-17 16:55 mmeineke * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost Bend in TraPPE_Ex -2003-06-04 17:06 mmeineke +2003-06-04 16:06 mmeineke * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and constrainB to the Symplectic integrator -2003-05-30 17:32 mmeineke +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 17:31 mmeineke +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 16:19 mmeineke +2003-05-30 15:19 mmeineke * libmdtools/Integrator.hpp: added some member variables for position, velocity, etc. -2003-05-30 15:07 mmeineke +2003-05-30 14:07 mmeineke * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT is now derived from Integrator -2003-05-20 12:44 mmeineke +2003-05-20 11:44 mmeineke * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. -2003-05-17 12:57 mmeineke +2003-05-17 11:57 mmeineke * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be working -2003-05-16 17:37 mmeineke +2003-05-16 16:37 mmeineke * utils/bilayerSys.cpp: still working on the bilayer code -2003-05-16 10:28 mmeineke +2003-05-16 09:28 mmeineke * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some work to overhaul sysbuild. -2003-05-13 17:23 mmeineke +2003-05-13 16:23 mmeineke * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop -2003-05-13 16:47 mmeineke +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 16:34 mmeineke +2003-05-13 15:34 mmeineke * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into the Trappe extended force field -2003-05-13 13:01 mmeineke +2003-05-13 12:01 mmeineke * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the TraPPe_Ex forceField -2003-05-09 15:51 mmeineke +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 15:51 mmeineke +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 12:56 mmeineke +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 12:55 mmeineke +2003-05-09 11:55 mmeineke * ac-tools/configure.in: added the utils subdirectory to the configure script -2003-04-25 12:02 mmeineke +2003-04-25 11:02 mmeineke * utils/bilayerSys.cpp: i quick fix to th distance in the random bilayer builder -2003-04-24 22:00 mmeineke +2003-04-24 21:00 mmeineke * libmdtools/f_verlet_constrained.F90: added a new test for constraint failure -2003-04-17 17:54 mmeineke +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 17:11 mmeineke +2003-04-16 16:11 mmeineke * utils/: MoLocator.cpp, MoLocator.hpp: almost finished. -2003-04-15 17:47 mmeineke +2003-04-15 16:47 mmeineke * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys and sysBuild both will build now. woot! -2003-04-15 17:20 mmeineke +2003-04-15 16:20 mmeineke * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp @@ -1349,93 +2423,93 @@ MoLocator.cpp is currently empty -2003-04-15 16:40 chuckv +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 12:37 chuckv +2003-04-15 11:37 chuckv * libmdtools/EAM_FF.cpp: More eam work. -2003-04-14 17:22 mmeineke +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 17:16 chuckv +2003-04-14 16:16 chuckv * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed ordering on NVT calculation in integrators. -2003-04-14 15:51 mmeineke +2003-04-14 14:51 mmeineke * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, obj/placeHolder: working on a system builder -2003-04-14 15:04 mmeineke +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 15:03 mmeineke +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 14:19 chuckv +2003-04-14 13:19 chuckv * libmdtools/calc_eam.F90: Added first mangling of EAM. -2003-04-11 14:46 mmeineke +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 11:16 gezelter +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 16:08 mmeineke +2003-04-10 15:08 mmeineke * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a globalIndex counter to Molecule -2003-04-10 12:35 gezelter +2003-04-10 11:35 gezelter * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on ConstantStress -2003-04-10 12:27 mmeineke +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 12:21 mmeineke +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 12:20 chuckv +2003-04-09 11:20 chuckv * samples/alkane/alkanes.mdl: added pentane to the alkane model file -2003-04-09 09:59 gezelter +2003-04-09 08:59 gezelter * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file -2003-04-09 00:06 gezelter +2003-04-08 23:06 gezelter * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, @@ -1445,7 +2519,7 @@ fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and NVT -2003-04-08 18:38 chuckv +2003-04-08 17:38 chuckv * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, @@ -1453,90 +2527,90 @@ libmdtools/simulation_module.F90, samples/water/ssd.bass: It works (kinda)... -2003-04-08 17:35 gezelter +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 13:16 chuckv +2003-04-08 12:16 chuckv * libmdtools/: do_Forces.F90, neighborLists.F90, simulation_module.F90: Moved expand neighborlist to init_FF. -2003-04-08 11:20 chuckv +2003-04-08 10:20 chuckv * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for NVT -2003-04-08 10:39 gezelter +2003-04-08 09:39 gezelter * libmdtools/Verlet.cpp: fixes for nvt / npt -2003-04-08 10:34 gezelter +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 08:50 gezelter +2003-04-08 07:50 gezelter * libmdtools/ExtendedSystem.cpp: Fixes for affine transform -2003-04-08 08:44 gezelter +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 17:42 gezelter +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 17:20 mmeineke +2003-04-07 16:20 mmeineke * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial portion of SSD. -2003-04-07 17:16 mmeineke +2003-04-07 16:16 mmeineke * libmdtools/: ForceFields.cpp, Symplectic.cpp: doing some testing in sticky through Symplectic. -2003-04-07 16:51 gezelter +2003-04-07 15:51 gezelter * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT -2003-04-07 16:50 chuckv +2003-04-07 15:50 chuckv * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for tau and virial. -2003-04-07 16:06 mmeineke +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 12:56 gezelter +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 10:30 gezelter +2003-04-07 09:30 gezelter * src/Makefile: Fixed a bug caused by my experimentation -2003-04-07 10:30 gezelter +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 10:30 gezelter +2003-04-07 09:30 gezelter * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS @@ -1879,7 +2953,7 @@ 2003-03-25 09:29 mmeineke - * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, + * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, src/MPIobj/dummy, src/obj/dummy: [no log message] 2003-03-25 09:29 mmeineke @@ -1889,27 +2963,17 @@ 2003-03-24 20:07 gezelter - * samples/Makefile, tests/Makefile: moving tests to samples + * samples/Makefile: moving tests to samples 2003-03-24 20:06 gezelter - * samples/alkane/Makefile, samples/alkane/alkanes.mdl, - samples/alkane/butane.bass, samples/alkane/init_butane.eor, - samples/argon/Makefile, samples/argon/argon.bass, - samples/argon/init_argon.eor, samples/argon/lj.mdl, - samples/lipid/5x5.bass, samples/lipid/Makefile, - samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, - samples/lipid/water.mdl, samples/water/Makefile, - samples/water/init_ssd.eor, samples/water/ssd.bass, - samples/water/water.mdl, tests/alkane/Makefile, - tests/alkane/alkanes.mdl, tests/alkane/butane.bass, - tests/alkane/init_butane.eor, tests/argon/Makefile, - tests/argon/argon.bass, tests/argon/init_argon.eor, - tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, - tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, - tests/lipid/water.mdl, tests/water/Makefile, - tests/water/init_ssd.eor, tests/water/ssd.bass, - tests/water/water.mdl: moved tests to samples + * 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 @@ -1917,9 +2981,7 @@ 2003-03-24 19:46 gezelter - * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, - tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: - Added makefiles in tests directories + * ac-tools/Make.conf.in: Added makefiles in tests directories 2003-03-24 16:55 gezelter @@ -1936,22 +2998,6 @@ * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, do_Forces.F90: little bug fixes here and there -2003-03-24 11:04 mmeineke - - * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon - test simulation - -2003-03-24 11:02 mmeineke - - * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, - lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, - water/water.mdl: [no log message] - -2003-03-24 11:02 mmeineke - - * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added - some test bass files for experimenting with - 2003-03-24 10:26 mmeineke * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug @@ -2061,8 +3107,8 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE - Tree + libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial + revision 2003-03-21 12:42 mmeineke @@ -2119,6 +3165,6 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial - revision + libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE + Tree