[ViewVC] Diff of: group/trunk/OOPSE/ChangeLog

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 1005 by tim, Tue Feb 3 15:21:32 2004 UTC

-+
+-02-02 15:29  tim
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+        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
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+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
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+        Adding GoldenSection and Brent LineSearch Method
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+-01-30 16:47  tim
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+        * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp,
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+        MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp,
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+        NLModel0.cpp, NLModel1.cpp: using class  Minimizer1D derived from
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+        MinimizerBase instead of a functor to do line seach
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+-01-30 10:00  chrisfen
-+
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+        * forceFields/Makefile.in, libmdtools/Atom.cpp,
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+        libmdtools/Atom.hpp, libmdtools/ForceFields.hpp,
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+        libmdtools/Integrator.cpp, libmdtools/Makefile.in,
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+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
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+        libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90,
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+        libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90,
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+        libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now
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+        has a working WATER.cpp forcefield and parser.  This involved
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+        changes to WATER.cpp and ForceFields amoung other files. One
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+        important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90.
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+        This will be removed on the next commit...
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+-01-29 18:00  gezelter
-+
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+        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
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+        libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y,
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+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp,
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+        libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp,
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+        libBASS/RigidBodyStamp.hpp, libBASS/interface.c,
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+        libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c,
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+        libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h,
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+        libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl:
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+        member list fixes for rigid bodies
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+-01-29 16:44  tim
-+
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+        * libmdtools/MinimizerParameterSet.hpp: Adding
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+        MinimizerParameterSet class.
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+-01-28 17:44  tim
-+
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+        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
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+        NLModel0 and NLModel1
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+-01-28 15:40  tim
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+        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
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+        of NLModel
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+-01-27 15:34  gezelter
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+        * samples/water/: ssd.bass, water.mdl: Added point-charge models to
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+        water.mdl file, updated ssd.bass to use new SSD name
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+-01-27 15:34  gezelter
-+
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+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
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+        MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody
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+        stuff
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+-01-27 14:39  gezelter
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+        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
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+-01-27 14:39  gezelter
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+        * samples/metals/Au.bass: Longer run time to test gold in MPI
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+-01-27 14:38  gezelter
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+        * samples/argon/argon.bass: Longer run time to test argon
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+-01-27 14:38  gezelter
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+        * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS
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+        changes to do new rigidBody scheme a copy of WATER.cpp from this
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+        morning
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+-01-27 14:37  gezelter
-+
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+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
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+        BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
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+        MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp,
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+        MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp,
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+        interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h,
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+        node_list.h, parse_interface.h, parse_tree.c: More BASS changes to
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+        do new rigidBody scheme
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+-01-27 14:15  tim
-+
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+        * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp,
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+        Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp,
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+        MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of
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+        constraint for Nonlinear Optimization Model
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+-01-26 17:01  gezelter
-+
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+        * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use
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+        Euler angles for orientation instead of unit vectors required
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+        changes in MoLocator
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+-01-26 16:53  gezelter
-+
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+        * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl,
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+        beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl,
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+        water/water.mdl: Changed orientation lines from unit vectors to
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+        euler angles
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+-01-26 16:52  gezelter
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+        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
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+-01-26 16:45  gezelter
-+
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+        * libmdtools/SimSetup.cpp: Changed default orientation in BASS to
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+        use Euler angles in the following order: phi, theta, psi Removed
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+        the ability to set orientation using a unit vector
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+-01-26 16:26  gezelter
-+
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+        * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp,
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+        RigidBodyStamp.hpp: Changed default orientation in BASS to use
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+        Euler angles in the following order: phi, theta, psi Removed the
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+        ability to set orientation using a unit vector
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+-01-26 13:52  gezelter
-+
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+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
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+        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
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+-01-22 12:34  chrisfen
-+
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+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp,
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+        TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h:
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+        Corrected spelling in several directories, and stated WATER.cpp
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+-01-21 17:16  tim
-+
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+        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
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+        NLOPModel.hpp: constraint class in energy minimization
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+-01-20 15:34  tim
-+
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+        * libmdtools/MinimizerBase.hpp: Adding energy minimization
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+-01-20 15:32  tim
-+
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+        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
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+        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
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+-01-19 16:17  gezelter
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+        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
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+        more user-friendly
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+-01-19 13:51  chrisfen
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+        * forceFields/DUFF.frc: Updated the default water to SSD/E
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+-01-19 13:36  tim
-+
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+        * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample
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+        time, status time, thermal time and reset time are not divisible by
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+        dt
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+-01-19 11:10  gezelter
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+        * third-party/Makefile.in: Added a bunch of dummy targets so make
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+        won't complain
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+-01-19 11:10  gezelter
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+        * samples/lipid/5x5.bass: Fixed old bass file
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+-01-19 11:09  gezelter
-+
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+        * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies
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+        required a change in how the MoleculeStamps are used by divideLabor
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+        in mpiSimulation.cpp
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+-01-19 11:08  gezelter
-+
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+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c,
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+        BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp,
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+        MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp,
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+        RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c,
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+        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
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+        parse_tree.c: BASS changes to add RigidBodies and LJrcut
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+-01-16 16:55  tim
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+        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
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+        eor file
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+-01-16 16:51  mmeineke
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+        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
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+        write eor files
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+-01-16 10:01  mmeineke
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+        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
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+        initialization of the AtomStruct
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+-01-15 16:57  chuckv
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+        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
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+-01-15 10:51  gezelter
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+        * ac-tools/aclocal.m4: Changes for altivec
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+-01-15 09:22  gezelter
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+        * libmdtools/DumpWriter.cpp: Documented the Spud Toss
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+-01-14 23:33  gezelter
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+        * libmdtools/do_Forces.F90: changes for charge charge interactions
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+-01-14 20:14  gezelter
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+        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
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+        notifyCutoffs.F90: More work for adding charges
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+-01-14 17:41  gezelter
-+
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+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
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+        src/Makefile.in: autoconf fixes
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+-01-14 11:28  mmeineke
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+        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug
-+
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+-01-14 10:48  gezelter
-+
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+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
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+        src/Makefile.in, third-party/Makefile.in: autoconf compatibility
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+        changes for icc8
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+-01-13 18:01  gezelter
-+
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+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp,
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+        SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90,
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+        fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90:
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+        Changes for adding direct charge-charge interactions (with
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+        switching function)
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+-01-13 17:34  gezelter
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+        * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90,
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+        oopseMPI_module.F90: Some changes for new MPI organization and
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+        direct charge-charge interactions
-+
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+-01-13 17:11  tim
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+        * Functor.hpp, libmdtools/Functor.hpp: [no log message]
-+
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+-01-13 16:22  tim
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+        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method
-+
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+-01-13 15:35  tim
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+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
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+        eor file whenever it is used instead of rewinding it
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+-01-13 15:04  tim
-+
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+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
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+        of writeFrame
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+-01-13 10:46  tim
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+        * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp:
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+        Merge the code of writeFinal and writeDump;
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+         Adding sortingIndex into DumpWriter;
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+         Fix a bug of writing last frame twice in integrator
-+
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+-01-12 17:54  tim
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+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
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+        a bug in copying string
-+
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+-01-12 15:37  tim
-+
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+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
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+        samples/water/ssd.bass: Dumpwriter only write out the atoms on
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+        master nodes
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+-01-10 04:46  tim
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+        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
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+        roll it back fix a bug of copying string to a pointer Still have
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+        Seg fault, it looks like a random MPI seg fault in totalview
-+
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+-01-09 21:15  tim
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+        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
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+-01-09 15:29  gezelter
-+
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+        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
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+-01-08 17:25  chuckv
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+        * libmdtools/DumpWriter.cpp: A work in progress...
-+
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+-01-08 13:59  gezelter
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+        * libmdtools/DumpWriter.cpp: null terminate some strings just in
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+        case
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+-01-08 13:13  mmeineke
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+        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
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+        state bug.
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+-01-08 13:05  gezelter
-+
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+        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
-+
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+-01-08 12:57  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
-+
+        exstended state bug
-+
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+-01-08 12:40  gezelter
-+
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+        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
-+
-+
+-01-08 10:44  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: added support for the ignore
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+        XS state info  flag
-+
-+
+-01-07 14:26  tim
-+
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+        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
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+        samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
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+        sending message from master node to itself in DumpWriter.cpp and
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+        InitializeFromFile.cpp
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+-01-06 14:49  chuckv
-+
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+        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
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+        performance fixes in the dipole dipole and reaction field code
-+
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+-01-06 13:54  chuckv
-+
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+        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
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+        little more sane
-+
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+-01-05 17:49  chuckv
-+
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+        * 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
-+
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+-01-05 17:18  chuckv
-+
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+        * libmdtools/do_Forces.F90: mangling forces even further
-+
-+
+-01-05 17:18  chuckv
-+
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+        * configure, ac-tools/configure.in: mpich mucking
-+
-+
+-01-05 17:12  chuckv
-+
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+        * libmdtools/do_Forces.F90: mangled do_forces...
-+
-+
+-01-05 16:00  chuckv
-+
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+        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
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+        libmdtools/do_Forces.F90: Added bitmask to do_forces property
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+        lookup
-+
-+
+-12-29 14:56  chuckv
-+
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+        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
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+        third-party directory for code not written by us. Also added
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+        Mersenne Twister random number generator code. This will eventually
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+        replace sprng as the random number generator used by OOPSE.
-+
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+-12-22 16:26  chuckv
-+
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+        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
-+
+        Fixes to profile code.
-+
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+-12-19 15:36  mmeineke
-+
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+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
-+
+        timing.F90, timing.f90: More profiling fixes.
-+
-+
+-12-19 15:19  chuckv
-+
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+        * libmdtools/timing.f90: Another change for MPI in timing.
-+
-+
+-12-19 15:17  chuckv
-+
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+        * libmdtools/timing.f90: Small update to timing in MPI
-+
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+-12-19 13:53  mmeineke
-+
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+        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
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+        profiling commands work now. Will start adding PROFILE ifdefs into
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+        the code
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+-12-19 12:25  mmeineke
-+
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+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
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+        some profiling routines
-+
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+-12-19 10:12  mmeineke
-+
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+        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
-+
+        and GofRomega
-+
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+        additional work on randomBilayer
-+
-+
+-12-19 10:12  mmeineke
-+
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+        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
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+        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
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+        GofRomega
-+
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+-12-18 16:47  mmeineke
-+
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+        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
-+
+        some profile functionality
-+
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+-12-18 15:46  chuckv
-+
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+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
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+        Added functions for simple profiling in fortran.
-+
-+
+-12-17 15:13  chuckv
-+
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+        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
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+        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
-+
+        rho_col were scattered into the same array. Unfortunately, MPI
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+        zeros the array between scatters so half of the sum was being lost.
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+        Fixed by added a temp array for column scatter, then sum loop over
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+        nlocal.
-+
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+-12-16 15:49  mmeineke
-+
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+        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
-+
+        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
-+
+        gofRomega. both need to be debugged and tested.
-+
-+
+-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)
-+
-+
+-12-12 10:33  mmeineke
-+
-+
+        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
-+
+        header
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-11-21 15:07  mmeineke
-+
-+
+        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
-+
+        ing in the GofR,CosTheta
-+
-+
+-11-21 14:31  chrisfen
-+
-+
+        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
-+
+        a bug in SimInfo ordering of radii
-+
-+
+-11-11 12:20  mmeineke
-+
-+
+        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
-+
+        a min function.
-+
-+
+-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.
-+
-+
+-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.:
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-10-31 13:28  mmeineke
-+
-+
+        * libBASS/Makefile.in: added template stuff to the Maikefile
-+
+        template
-+
-+
+-10-30 13:59  gezelter
-+
-+
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
-+
+        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
-+
+        rList problems
-+
-+
+-10-30 09:11  gezelter
-+
-+
+        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
-+
+        queried before q0 was allocated.
-+
-+
+-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
-+
-+
+-10-29 15:40  mmeineke
-+
-+
+        * libBASS/BASSlex.l: fixed a stdlib.h include error
-+
-+
+-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.
-+
-+
+-10-29 09:28  gezelter
-+
-+
+        * configure, ac-tools/configure.in, libBASS/Makefile.in,
-+
+        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
-+
+        templates
-+
-+
+-10-28 22:16  gezelter
-+
-+
+        * src/Makefile.in: Refixed broken makefile
-+
-+
+-10-28 22:06  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
-+
+        fixes
-+
-+
+-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.
-+
-+
+-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.
-+
-+
+-10-28 15:42  gezelter
-+
-+
+        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
-+
+        Portability fixes
-+
-+
+-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
-+
-+
+-10-28 12:08  mmeineke
-+
-+
+        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
-+
+        started work on template removal
-+
-+
+-10-28 12:04  gezelter
-+
-+
+        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
-+
+        trying to understand extern "C" stuff for pointers
-+
-+
+-10-28 11:20  gezelter
-+
-+
+        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
-+
+        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-10-28 11:02  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4: mod file fixes and portability
-+
+        stuff
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-10-27 17:07  mmeineke
-+
-+
+        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
-+
+        routines for the sysbuilder to work with simSetup
-+
-+
+-10-27 11:20  gezelter
-+
-+
+        * configure, ac-tools/configure.in, samples/water/ssd.bass,
-+
+        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
-+
-+
+-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
-+
-+
+-10-24 12:36  gezelter
-+
-+
+        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
-+
+        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
-+
+        builder
-+
-+
+-10-24 12:35  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
-+
+        merge problem
-+
-+
+-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
-+
-+
+-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
-+
-+
+-10-23 14:57  mmeineke
-+
-+
+        * forceFields/Makefile.in: added eam ForceField files to the init
-+
-+
+-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.
-+
-+
+-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;
-+
-+
+-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.
-+
-+
+-10-17 16:18  mmeineke
-+
-+
+        * ac-tools/configure.in: added the staticProps directory to the
-+
+        build list for both configure  and configure.in
-+
-+
+-10-17 16:17  mmeineke
-+
-+
+        * configure: added the staticProps directory to the build list
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-10-04 13:46  chuckv
-+
-+
+        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
-+
+        samples/metals/Au.bass: Fixed bug in calc_eam.
-+
-+
+-10-04 13:08  chuckv
-+
-+
+        * samples/metals/init_au.in: added Au init file for eam.
-+
-+
+-10-03 17:11  mmeineke
-+
-+
+        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
-+
+        entahlpy from the statwriter and thermo.
-+
-+
+-10-03 17:02  mmeineke
-+
-+
+        * libmdtools/SimInfo.hpp: changed the formating ogf the error
-+
+        statements in simError
-+
-+
+        added a function to get the maxCutoff
-+
-+
+-10-03 17:01  mmeineke
-+
-+
+        * libBASS/simError.c: changed the formating ogf the error
-+
+        statements in simError
-+
-+
+-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.
-+
-+
+-09-29 17:06  mmeineke
-+
-+
+        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
-+
+        for conifig.in
-+
-+
+        fixed wrappers to extern "C"
-+
-+
+-09-29 17:06  mmeineke
-+
-+
+        * ac-tools/configure.in: added mpif90 mod check back same for
-+
+        conifig.in
-+
-+
+-09-29 17:05  mmeineke
-+
-+
+        * configure: added mpif90 mod check back
-+
-+
+-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
-+
-+
+-09-29 12:38  mmeineke
-+
-+
+        * libmdtools/GenericData.hpp: light change in syntax. no
-+
+        signifigant change.
-+
-+
+-09-25 16:17  mmeineke
-+
-+
+        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
-+
+        additional remarks from icc -w3 (extra verbose output)
-+
-+
+-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
-+
-+
+-09-25 13:54  gezelter
-+
-+
+        * configure, ac-tools/configure.in: fixed a bug in configure
-+
-+
+-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
-+
-+
+-09-24 14:34  mmeineke
-+
-+
+        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
-+
+        that it is called before the first Statistics are written.
-+
-+
+-09-23 15:36  gezelter
-+
-+
+        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
-+
+        bunch of Make.dep files to CVS
-+
-+
+-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
-+
-+
+-09-22 18:07  tim
-+
-+
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
-+
+        SimInfo.hpp: fix bug in calculating maxCutoff
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-09-19 11:03  mmeineke
-+
-+
+        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
-+
+        makefile
-+
-+
+-09-19 11:01  gezelter
-+
-+
+        * samples/water/ssd.bass: goofing off to test NPTf and NPTi
-+
-+
+-09-19 11:01  gezelter
-+
-+
+        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
-+
+        (nearly) conserved quantities for both NPTi and NPTf
-+
-+
+-09-19 10:20  mmeineke
-+
-+
+        * utils/Makefile.in: fixed a typo in the makefile.
-+
-+
+-09-19 09:55  gezelter
-+
-+
+        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
-+
+        samples/water/ssd.bass: [no log message]
-+
-+
+-09-19 09:22  tim
-+
-+
+        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
-+
-+
+-09-17 09:22  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
-+
+        work with constraints.
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * libmdtools/: Make.dep, Makefile.in: Added integrators to
-+
+        Makefile.in
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * ChangeLog: Entered changes for configure into ChangeLog
-+
-+
+-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.
-+
-+
+-09-09 15:34  mmeineke
-+
-+
+        * ChangeLog: updated the ChangeLog
-+
-+
+-09-05 17:45  gezelter
-+
-+
+        * libmdtools/Make.dep: dependency on config.h
-+
-+
+-09-05 17:36  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4: fixed sprng problem
-+
-+
+-09-05 16:29  gezelter
-+
-+
+        * samples/metals/Makefile.in: New Makefile for metals sample
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-09-04 16:48  mmeineke
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
-+
+        namespace.
-+
-+
+-09-02 09:30  tim
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
-+
+        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
-+
+        PolicyByMass
-+
-+
+-08-28 16:09  tim
-+
-+
+        * ChangeLog, libmdtools/GenericData.cpp,
-+
+        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-08-26 15:37  tim
-+
-+
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
-+
+        mpiSimulation.cpp: set default force substraction policy to
-+
+        PolicyByMass
-+
-+
+-08-26 15:29  tim
-+
-+
+        * libmdtools/Integrator.cpp: [no log message]
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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)
-+
-+
+-08-26 13:30  mmeineke
-+
-+
+        * Makefile: changed the Makefiel a litle.
-+
-+
+-08-25 17:17  gezelter
-+
-+
+        * utils/sysbuilder/Makefile: More FreeBSD fixes
-+
-+
+-08-25 16:51  gezelter
-+
-+
+        * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
-+
+        libmdtools/Makefile, src/Makefile: [no log message]
-+
-+
+-08-22 15:04  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
-+
+        frequency of output dumps.
-+
-+
+-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
-+
-+
+-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)
-+
-+
+-08-20 14:41  mmeineke
-+
-+
+        * libBASS/Globals.hpp: updated the Changelog.
-+
-+
+        added some bug fixes for setting the random number generator seed
-+
+        value.
-+
-+
+-08-20 14:41  mmeineke
-+
-+
+        * ChangeLog: updated the Changelog.
-+
-+
+-08-20 14:11  tim
-+
-+
+        * libBASS/Globals.cpp, libmdtools/DUFF.cpp,
-+
+        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
-+
+        bend class
-+
-+
+-08-20 10:13  mmeineke
-+
-+
+        * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
-+
+        make links. added -f to ln -s.
-+
-+
+-08-20 09:50  tim
-+
-+
+        * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]
-+
-+
+-08-20 09:34  tim
-+
-+
+        * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
-+
+        ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
-+
+        printing
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-08-14 11:16  tim
-+
-+
+        * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
-+
+        with average force substraction strategy
-+
-+
+-08-13 16:20  chuckv
-+
-+
+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
-+
+        profiling code -DPROFILE.
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-08-12 13:40  gezelter
-+
-+
+        * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
-+
+        and new atypes in LJFF
-+
-+
+-08-12 13:15  gezelter
-+
-+
+        * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
-+
+        stuff...
-+
-+
+-08-12 13:14  chuckv
-+
-+
+        * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.
-+
-+
+-08-12 13:04  chuckv
-+
-+
+        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
-+
+        Missed del of files before.
-+
-+
+-08-12 13:03  chuckv
-+
-+
+        * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
-+
+        message]
-+
-+
+-08-12 13:01  chuckv
-+
-+
+        * utils/sysbuilder/Makefile: commit makefile
-+
-+
+-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
-+
-+
+-08-11 17:31  chuckv
-+
-+
+        * utils/Makefile: Changed makefile to only build quicklate.
-+
-+
+-08-11 17:25  chuckv
-+
-+
+        * ac-tools/configure.in: added utils/sysbuilder to be built.
-+
-+
+-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.
-+
-+
+-08-11 14:41  tim
-+
-+
+        * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
-+
+        moving zconstraint molecules to specified positions
-+
-+
+-08-11 14:39  tim
-+
-+
+        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]
-+
-+
+-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.
-+
-+
+-08-11 13:29  mmeineke
-+
-+
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
-+
+        degrees of freedom to account for zConstreints
-+
-+
+-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.....
-+
-+
+-08-08 12:48  mmeineke
-+
-+
+        * libmdtools/: Makefile, ZConstraint.cpp:  fixed a deprcated
-+
+        instance of Atom::setZ and Atom::getZ in ZConstaint.
-+
-+
+-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
-+
-+
+-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...
-+
-+
+-08-01 11:18  tim
-+
-+
+        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of
-+
+        Z-Constraint
-+
-+
+-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
-+
-+
+-07-31 10:38  tim
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters
-+
+        to the globals
-+
-+
+-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.
-+
-+
+-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.
-+
-+
+-07-29 11:32  mmeineke
-+
-+
+        * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile:
-+
+        working on the props code
-+
-+
+-07-29 11:32  mmeineke
-+
-+
+        * libBASS/Globals.cpp: [no log message]
-+
-+
+-07-25 15:05  chuckv
-+
-+
+        * samples/metals/: Au.bass, metals.mdl: Added bass models for
-+
+        metals
-+
-+
+-07-25 15:00  chuckv
-+
-+
+        * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90,
-+
+        notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam.
-+
-+
+-07-24 16:22  chuckv
-+
-+
+        * ac-tools/configure.in: Changed configure to look for both upper
-+
+        and lower cass .mod files
-+
-+
+-07-24 14:57  chuckv
-+
-+
+        * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for
-+
+        eam and do_forces.
-+
-+
+-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....
-+
-+
+-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.
-+
-+
+-07-22 15:05  mmeineke
-+
-+
+        * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes
-+
+        to read dump files
-+
-+
+-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]
-+
-+
+-07-22 11:41  mmeineke
-+
-+
+        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp,
-+
+        SimSetup.cpp: Fixed a current time initialization bug in
-+
+        InitFromFile.
-+
-+
+-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
-+
-+
+-07-21 11:23  mmeineke
-+
-+
+        * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no
-+
+        one sets it.
-+
-+
+-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.
-+
-+
+-07-17 16:49  gezelter
-+
-+
+        * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp,
-+
+        DumpReader.cpp: Started work on a DumpReader
-+
-+
+-07-17 15:38  gezelter
-+
-+
+        * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E
-+
-+
+-07-17 15:32  gezelter
-+
-+
+        * forceFields/DUFF.frc, libmdtools/DUFF.cpp,
-+
+        libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp:
-+
+        Changes for SSD/E
-+
-+
+-07-17 14:38  mmeineke
-+
-+
+        * libmdtools/do_Forces.F90: commented out an eam line
-+
-+
+-07-17 14:32  chuckv
-+
-+
+        * libmdtools/atype_module.F90: fixed spelling issue
-+
-+
+-07-17 14:29  chuckv
-+
-+
+        * libmdtools/: fInfo.c, status_module.F90: added info module
-+
-+
+-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....
-+
-+
+-07-16 16:49  chuckv
-+
-+
+        * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF
-+
-+
+-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.
-+
-+
+-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.
-+
-+
+-07-16 11:40  chuckv
-+
-+
+        * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists
-+
-+
+-07-16 10:34  mmeineke
-+
-+
+        * scripts/cleanSrc: added a quick wipe-and-update script for quick
-+
+        rebuilds on BoB
-+
-+
+-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
-+
-+
+-07-15 17:29  mmeineke
-+
-+
+        * libmdtools/simulation_module.F90: removed some debugging print
-+
+        statements.
-+
-+
+-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.
-+
-+
+-07-15 16:34  mmeineke
-+
-+
+        * libmdtools/: SimInfo.cpp, simulation_module.F90: working on
-+
+        fixing ssd bug
-+
-+
+-07-15 14:56  gezelter
-+
-+
+        * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes
-+
+        for the NPT ensembles
-+
-+
+-07-15 13:52  mmeineke
-+
-+
+        * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up
-+
+        simSetup
-+
-+
+-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
-+
-+
+-07-15 12:25  chuckv
-+
-+
+        * utils/sysBuild.ggo: added more command line arguments
-+
-+
+-07-15 12:11  gezelter
-+
-+
+        * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass:
-+
+        Fixing force field line
-+
-+
+-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
-+
-+
+-07-15 10:50  gezelter
-+
-+
+        * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes
-+
-+
+-07-15 10:42  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp:
-+
+        removed old outdated code
-+
-+
+-07-15 09:45  gezelter
-+
-+
+        * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx
-+
-+
+-07-15 09:28  gezelter
-+
-+
+        * libmdtools/Molecule.cpp: removing get_vx
-+
-+
+-07-14 22:28  gezelter
-+
-+
+        * libmdtools/NPTfm.cpp: Added NPTfm
-+
-+
+-07-14 22:27  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
-+
+        Bugfix in NPTim, fixes for NPTfm
-+
-+
+-07-14 22:08  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp:
-+
+        Checking in changes for NPTim
-+
-+
+-07-14 18:06  gezelter
-+
-+
+        * utils/Makefile: Broken SysBuilder
-+
-+
+-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
-+
-+
+-07-14 18:06  gezelter
-+
-+
+        * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some
-+
+        debugging write statements
-+
-+
+-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
-+
-+
+-07-14 16:48  mmeineke
-+
-+
+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get
-+
+        and set routines to Atom and DirectionalAtom
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-07-14 10:04  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on
-+
+        NPTim
-+
-+
+-07-14 09:55  mmeineke
-+
-+
+        * forceFields/DUFF.frc: Switched the bond in the force field back
-+
+        to constrained, to preserve energy
-+
-+
+-07-11 17:34  mmeineke
-+
-+
+        * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp,
-+
+        Integrator.hpp: working on som integrator bugs
-+
-+
+-07-11 10:26  gezelter
-+
-+
+        * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting
-+
+        to worry about all the strtok() calls in our code
-+
-+
+-07-11 09:49  gezelter
-+
-+
+        * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness
-+
-+
+-07-10 20:15  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and
-+
+        eor.
-+
-+
+-07-10 17:15  mmeineke
-+
-+
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp,
-+
+        SimInfo.cpp, Thermo.cpp: fixed some bugs
-+
-+
+-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.
-+
-+
+-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
-+
-+
+-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.
-+
-+
+-07-09 10:34  mmeineke
-+
-+
+        * libBASS/MoleculeStamp.hpp: starting some work for xlate
-+
-+
+-07-09 10:33  mmeineke
-+
-+
+        * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff
-+
-+
+-07-09 08:56  gezelter
-+
-+
+        * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf
-+
-+
+-07-09 08:56  gezelter
-+
-+
+        * libBASS/Globals.cpp: Removed Qmass
-+
-+
+-07-08 21:15  gezelter
-+
-+
+        * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf
-+
+        and NPTi
-+
-+
+-07-08 20:41  gezelter
-+
-+
+        * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf
-+
-+
+-07-08 16:10  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message]
-+
-+
+-07-08 16:06  gezelter
-+
-+
+        * libmdtools/NPTi.cpp: fixed box scaling
-+
-+
+-07-08 15:56  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp,
-+
+        SimInfo.hpp, Thermo.cpp: NPTi
-+
-+
+-07-03 14:41  mmeineke
-+
-+
+        * libBASS/Makefile, libmdtools/Makefile, src/Makefile,
-+
+        utils/Makefile, utils/bilayerSys.cpp:  cleaned up the dependecy
-+
+        scripts in the makefiles
-+
-+
+-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
-+
-+
+-07-01 17:39  gezelter
-+
-+
+        * libmdtools/do_Forces.F90: Fortran flexi-BOX
-+
-+
+-07-01 17:29  gezelter
-+
-+
+        * libmdtools/simulation_module.F90: Fixes for flexi-BOX
-+
-+
+-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.
-+
-+
+-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.
-+
+-06-25 16:12  mmeineke
+        * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds
+-03-25 09:29  mmeineke
-<
+        * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
-<
+        src/MPIobj/dummy, src/obj/dummy: [no log message]
->
+        * libBASS/obj/dummy, libmdtools/obj/dummy, src/MPIobj/dummy,
->
+        src/obj/dummy: [no log message]
+-03-25 09:29  mmeineke
+        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
+-03-21 12:42  mmeineke
+        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

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+Removed lines
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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs. Revision 1005 by tim, Tue Feb 3 15:21:32 2004 UTC

Diff Legend

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 1005 by tim, Tue Feb 3 15:21:32 2004 UTC