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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

-+
+-06-09 11:59  tim
-+
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+        * ChangeLog, libmdtools/Roll.cpp: Roll in progress
-+
-+
+-06-09 11:16  tim
-+
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+        * libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp,
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+        Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in,
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+        Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp,
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+        Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp,
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+        Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1.
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+        adding some useful math classes(Mat3x3d, Vector3d, Quaternion,
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+        Euler3)  these classes use anonymous union and struct to support
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+        double[3], double[3][3] and double[4] 2. adding roll constraint
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+        algorithm
-+
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+-06-08 11:49  gezelter
-+
-+
+        * libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp:
-+
+        Fixed a bug in NPTf (vScale was declared in the cpp file in
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+        addition to the declaration in Integrator.hpp file)
-+
-+
+-06-07 09:26  gezelter
-+
-+
+        * libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp,
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+        libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp,
-+
+        libmdtools/ConstraintIterator.hpp,
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+        libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp,
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+        libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp,
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+        libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c,
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+        libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp,
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+        libmdtools/ZConsReader.cpp: Fixes from gcc -Wall
-+
-+
+-06-07 09:09  chrisfen
-+
-+
+        * libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a
-+
+        bit...  Got rid of some unnecessary lines of code in Thermo.cpp
-+
-+
+-06-04 16:00  gezelter
-+
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+        * libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp,
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+        StuntDouble.cpp: small bugfixes
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+-06-04 15:29  tim
-+
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+        * libmdtools/Integrator.hpp: [no log message]
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+-06-04 14:30  tim
-+
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+        * ChangeLog, libmdtools/CallbackFunctor.cpp,
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+        libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp,
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+        libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp,
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+        libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp,
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+        libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp,
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+        libmdtools/ShakeMin.hpp: constraint algorithm for minimization is
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+        working
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-+
+-06-04 11:23  gezelter
-+
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+        * forceFields/charmm27.vdw: Moved to SHAPES
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-+
+-06-04 11:23  gezelter
-+
-+
+        * forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log
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+        message]
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-+
+-06-04 09:59  gezelter
-+
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+        * libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90:
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+        More work on Fortran side of error handler
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-+
+-06-04 09:59  gezelter
-+
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+        * configure, ac-tools/aclocal.m4: fixed a typo in autoconf script
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+-06-04 09:35  gezelter
-+
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+        * libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying
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+        the error handlers
-+
-+
+-06-04 09:17  gezelter
-+
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+        * libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore
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-+
+-06-04 09:11  gezelter
-+
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+        * libBASS/: config.h.in, fError.c: forgot to add these
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-+
+-06-03 22:15  tim
-+
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+        * ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp,
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+        libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp,
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+        libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp,
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+        libmdtools/GenericData.hpp, libmdtools/Integrator.cpp,
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+        libmdtools/Integrator.hpp, libmdtools/Make.dep,
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+        libmdtools/Makefile.in, libmdtools/Molecule.cpp,
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+        libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp,
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+        libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp,
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+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
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+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
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+        libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp,
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+        libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm
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+        is working
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+-06-03 21:38  gezelter
-+
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+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
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+        libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c,
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+        libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in,
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+        libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for
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+        fortran access to SimError
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-+
+-06-03 16:51  tim
-+
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+        * libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp,
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+        ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp,
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+        ConstraintElement.cpp, ConstraintElement.hpp,
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+        ConstraintIterator.hpp, ConstraintManager.cpp,
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+        ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp,
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+        Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new
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+        implementation of constraint
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-+
+-06-03 16:06  tim
-+
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+        * libmdtools/DumpWriter.cpp: fixed a bug which only writes out the
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+        first atom of a molecule
-+
-+
+-06-03 15:02  gezelter
-+
-+
+        * libmdtools/SimSetup.cpp: Fixed groupOffset bug
-+
-+
+-06-03 15:02  gezelter
-+
-+
+        * ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for
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+        autoconf
-+
-+
+-06-02 13:28  gezelter
-+
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+        * samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't
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+        have been in CVS
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+-06-02 13:28  gezelter
-+
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+        * samples/: argon/Makefile, minimizer/argon/Makefile: Why is this
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+        in CVS?
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-+
+-06-02 13:27  gezelter
-+
-+
+        * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep,
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+        Makefile.in, WATER.cpp: formatting error messages, dependency fixes
-+
-+
+-06-02 13:27  gezelter
-+
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+        * libBASS/simError.h: starting fortran-usable version of simError
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+-06-02 09:56  chrisfen
-+
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+        * samples/: argon/Makefile, minimizer/argon/Makefile: Probably
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+        shouldn't be in CVS
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-+
+-06-02 09:56  chrisfen
-+
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+        * libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp,
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+        Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes,
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+        removed writeRaw
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-+
+-06-02 09:56  chrisfen
-+
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+        * libBASS/simError.c: Formatting Changes
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-+
+-06-02 09:21  gezelter
-+
-+
+        * libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp:
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+        severity levels in simError
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-+
+-06-01 16:45  gezelter
-+
-+
+        * libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90,
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+        do_Forces.F90, mpiSimulation.cpp, neighborLists.F90,
-+
+        simulation_module.F90: Bug fix (fixes of skipList and neighbor list
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+        under MPI)
-+
-+
+-06-01 16:44  gezelter
-+
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+        * libBASS/MoleculeStamp.cpp: Bug fix (memory leak)
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+-06-01 13:43  gezelter
-+
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+        * samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing
-+
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+-06-01 13:42  gezelter
-+
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+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
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+        SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp,
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+        mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90:
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+        Cutoff Groups for MPI
-+
-+
+-06-01 13:07  chrisfen
-+
-+
+        * libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in
-+
+        useLiquidThermInt routine in ForceFields.cpp
-+
-+
+-06-01 12:15  chrisfen
-+
-+
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
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+        SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate
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+        solid and liquid thermodynamic integration routines
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-+
+-06-01 10:57  tim
-+
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+        * libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in
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+        progress
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+-06-01 09:27  chrisfen
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt
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+        keyword and changed useThermInt to useSolidThermInt
-+
-+
+-06-01 09:21  chrisfen
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate
-+
+        solid and liquid thermodynamic integration routines
-+
-+
+-05-28 10:21  gezelter
-+
-+
+        * libmdtools/do_Forces.F90: bugfix starting
-+
-+
+-05-27 15:06  chrisfen
-+
-+
+        * libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in
-+
+        Integrator.cpp where it called writeRaw() when useThermInt =
-+
+        false...
-+
-+
+-05-27 14:51  tim
-+
-+
+        * ChangeLog, libmdtools/do_Forces.F90,
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+        libmdtools/simulation_module.F90: Bug fix for SkipList
-+
-+
+-05-27 14:26  gezelter
-+
-+
+        * libmdtools/SimSetup.cpp: bugfix in simsetup?
-+
-+
+-05-27 13:59  gezelter
-+
-+
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp,
-+
+        InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp,
-+
+        ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp,
-+
+        mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp,
-+
+        mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90:
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+        Cutoff group changes under MPI
-+
-+
+-05-27 11:20  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for
-+
+        xlc++
-+
-+
+-05-27 10:31  tim
-+
-+
+        * libmdtools/SimInfo.cpp: groupList new bases on global index of
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+        atoms
-+
-+
+-05-27 10:21  gezelter
-+
-+
+        * src/: oopse.cpp, oose.cpp: Modified the nifty banner
-+
-+
+-05-27 10:21  gezelter
-+
-+
+        * libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90:
-+
+        Fixed off-by-one error in groupStartRow and groupStartCol
-+
-+
+-05-26 19:48  tim
-+
-+
+        * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90,
-+
+        libmdtools/calc_charge_charge.F90,
-+
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
-+
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
-+
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
-+
+        libmdtools/force_globals.F90, libmdtools/mdProfile.cpp,
-+
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp,
-+
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
-+
+        libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp,
-+
+        libmdtools/simulation_module.F90: in the progress of fixing MPI
-+
+        version of cutoff group
-+
-+
+-05-26 11:41  gezelter
-+
-+
+        * libmdtools/do_Forces.F90: Compacted all of the 8 copies of the
-+
+        force loop into one.
-+
-+
+-05-24 17:24  gezelter
-+
-+
+        * libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes
-+
-+
+-05-24 16:23  chrisfen
-+
-+
+        * libmdtools/Restraints.cpp: Removed unnecessary variables and
-+
+        changed error messages in Restraints.cpp
-+
-+
+-05-24 16:03  gezelter
-+
-+
+        * libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90,
-+
+        calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
-+
+        calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes
-+
+        for stress / pressure tensor by cutoff group
-+
-+
+-05-22 15:55  chrisfen
-+
-+
+        * libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp...
-+
+        Too many arguements in a function call.
-+
-+
+-05-22 13:17  chrisfen
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword
-+
+        useThermInt.
-+
-+
+-05-22 13:16  chrisfen
-+
-+
+        * libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
-+
+        ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp,
-+
+        Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp,
-+
+        SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp,
-+
+        StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration
-+
+        code.
-+
-+
+-05-21 10:58  gezelter
-+
-+
+        * libmdtools/: do_Forces.F90, simulation_module.F90: Major changes
-+
+        to skipThisPair for efficiency
-+
-+
+-05-21 09:22  gezelter
-+
-+
+        * configure, ac-tools/configure.in, forceFields/LJ.vdw,
-+
+        forceFields/amber99.vdw, forceFields/charmm27.vdw,
-+
+        forceFields/gaff.vdw, forceFields/oplsaal.vdw,
-+
+        samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes
-+
+        for SHAPES potential
-+
-+
+-05-20 15:27  chrisfen
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit
-+
+        included the bass keywords
-+
-+
+-05-20 15:24  chrisfen
-+
-+
+        * libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp,
-+
+        Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp,
-+
+        Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several
-+
+        additions... Restraints.cpp and .hpp were included for restraining
-+
+        particles in thermodynamic integration.  By including these,
-+
+        changes were made in Integrator, SimInfo, ForceFeilds, SimSetup,
-+
+        StatWriter, and possibly some other files.  Two bass keywords were
-+
+        also added for performing thermodynamic integration: a lambda value
-+
+        one and a k power one.
-+
-+
+-05-13 16:08  gezelter
-+
-+
+        * libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list
-+
-+
+-05-12 17:01  tim
-+
-+
+        * samples/: argon/Makefile, argon/argonEM.bass,
-+
+        argon/init_argon.eor, minimizer/argon/Makefile,
-+
+        minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor,
-+
+        minimizer/water/Makefile, minimizer/water/Makefile.in,
-+
+        minimizer/water/WATER.frc, minimizer/water/init_ssd.eor,
-+
+        minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass,
-+
+        minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add
-+
+        minimizer sample
-+
-+
+-05-12 16:54  gezelter
-+
-+
+        * libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X
-+
+        compilation
-+
-+
+-05-12 15:54  gezelter
-+
-+
+        * libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes
-+
+        for compilation under Mac OS X with IBM's xl compilers
-+
-+
+-05-12 15:14  gezelter
-+
-+
+        * src/: oopse.cpp, oose.cpp: Added a nifty neato banner
-+
-+
+-05-12 15:14  gezelter
-+
-+
+        * libmdtools/LJFF.cpp: Removed an extraneous write
-+
-+
+-05-12 15:13  gezelter
-+
-+
+        * libBASS/simError.h: Starting to change the error model
-+
-+
+-05-12 14:45  gezelter
-+
-+
+        * utils/Dump2XYZ.cpp: const char* fix
-+
-+
+-05-12 14:44  gezelter
-+
-+
+        * libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
-+
+        src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous
-+
+        write statements
-+
-+
+-05-12 11:38  tim
-+
-+
+        * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp,
-+
+        ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
-+
+        SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and
-+
+        massratio from simState, creat cutoff group forevery atom which
-+
+        does not belong to cutoff group defined at mdl file
-+
-+
+-05-12 10:58  gezelter
-+
-+
+        * libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in
-+
+        CutoffGroup
-+
-+
+-05-12 10:35  gezelter
-+
-+
+        * samples/water/water.mdl: Added the cutoff Groups to the default
-+
+        water.mdl file
-+
-+
+-05-12 10:02  tim
-+
-+
+        * ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp:
-+
+        fixed a bug in CutoffGroup::getCOM()
-+
-+
+-05-12 09:29  gezelter
-+
-+
+        * libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90,
-+
+        samples/water/ssd.bass: bug fixes for cutoffGroups
-+
-+
+-05-11 17:28  tim
-+
-+
+        * utils/Vector3.hpp: adding generic Vector3 class
-+
-+
+-05-11 16:44  tim
-+
-+
+        * libmdtools/Integrator.hpp: adding instantiation of
-+
+        Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
-+
-+
+-05-11 16:31  gezelter
-+
-+
+        * libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90,
-+
+        calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90,
-+
+        calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90:
-+
+        Fortran-side changes for group-based cutoffs
-+
-+
+-05-11 16:20  tim
-+
-+
+        * libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp
-+
-+
+-05-11 16:14  tim
-+
-+
+        * libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp,
-+
+        SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix
-+
+        anoter one in CutoffGroup which causes seg fault
-+
-+
+-05-11 15:33  tim
-+
-+
+        * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp,
-+
+        libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup
-+
+        into OOPSE
-+
-+
+-05-11 15:07  gezelter
-+
-+
+        * libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup
-+
-+
+-05-11 11:00  gezelter
-+
-+
+        * libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
-+
+        fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to
-+
+        use the simplified cutoff stuff in the BASS library
-+
-+
+-05-10 23:21  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y,
-+
+        CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp,
-+
+        Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in,
-+
+        MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c,
-+
+        make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h,
-+
+        parse_tree.c: BASS changes for adding CutoffGroups to molecules.
-+
+        Also restructured the plethora of cutoff radii into one
-+
+        cutoffRadius and one switchingRadius.  Also removed the
-+
+        useMolecularCutoffs keyword
-+
-+
+-05-10 15:28  tim
-+
-+
+        * ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize
-+
+        DumpWriter
-+
-+
+-05-07 16:36  gezelter
-+
-+
+        * libmdtools/: fSwitchingFunction.h, switch_module.F90: New module
-+
+        for fortran group-based switching function
-+
-+
+-05-07 16:35  gezelter
-+
-+
+        * libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp,
-+
+        Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp,
-+
+        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
-+
+        calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90,
-+
+        force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h,
-+
+        mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90,
-+
+        simulation_module.F90: Many changes to get group-based cutoffs to
-+
+        work
-+
-+
+-05-01 13:52  tim
-+
-+
+        * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90,
-+
+        libmdtools/do_Forces.F90, libmdtools/fSimulation.h,
-+
+        libmdtools/fortranWrapDefines.hpp,
-+
+        libmdtools/simulation_module.F90: C++ pass groupList to fortran
-+
-+
+-04-29 11:03  tim
-+
-+
+        * ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in
-+
+        calc_charge_charge when using molecular cutoff
-+
-+
+-04-28 21:11  tim
-+
-+
+        * libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an
-+
+        unmatched c/fortran interface
-+
-+
+-04-28 18:09  tim
-+
-+
+        * ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp:
-+
+        keep the previous position of cantilever in SMD
-+
-+
+-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
-+
-+
+-04-28 17:06  gezelter
-+
-+
+        * libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
-+
+        Adding molecular cutoffs
-+
-+
+-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
-+
-+
+-04-28 16:39  gezelter
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to
-+
+        Globals
-+
-+
+-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
-+
-+
+-04-26 16:16  mmeineke
-+
-+
+        * libBASS/Globals.cpp: modified the defaults for the system init
-+
+        time and system init state.
-+
-+
+-04-26 09:29  gezelter
-+
-+
+        * libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in
-+
+        calc_charge_charge.F90
-+
-+
+-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
-+
-+
+-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
-+
-+
+-04-22 09:55  tim
-+
-+
+        * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed
-+
+        another bug in InitFromFile. MPI verion of OOPSE is working again
-+
-+
+-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
-+
-+
+-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
-+
-+
+-04-20 11:56  tim
-+
-+
+        * libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp,
-+
+        SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel  and
-+
+        velocitize at thermo
-+
-+
+-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
-+
-+
+-04-19 17:13  gezelter
-+
-+
+        * libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp,
-+
+        Thermo.cpp: Fixed a charge bug
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-04-15 17:15  tim
-+
-+
+        * libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting
-+
+        exclude list
-+
-+
+-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 :-)
-+
-+
+-04-14 12:20  chrisfen
-+
-+
+        * forceFields/WATER.frc: Added the WATER.frc force field
-+
-+
+-04-14 11:32  gezelter
-+
-+
+        * libmdtools/Molecule.cpp: fixed for get_potential
-+
-+
+-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
-+
-+
+-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).
-+
-+
+-04-13 11:25  gezelter
-+
-+
+        * libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable
-+
+        (will back out momentarily)
-+
-+
+-04-13 10:10  gezelter
-+
-+
+        * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops.
-+
+        Those were old.
-+
-+
+-04-13 10:09  gezelter
-+
-+
+        * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot
-+
+        to add IntegrableObjects
-+
-+
+-04-12 16:02  gezelter
-+
-+
+        * libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code
-+
-+
+-04-12 15:32  gezelter
-+
-+
+        * samples/: alkane/butane.bass, water/ssd.bass: Slightly longer
-+
+        test run
-+
-+
+-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)
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-03-02 15:32  tim
-+
-+
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp,
-+
+        StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to
-+
+        support large file
-+
-+
+-03-01 16:17  tim
-+
-+
+        * utils/zsub.cpp: Fix a couple of bugs in zsub
-+
-+
+-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
-+
-+
+-02-24 11:36  tim
-+
-+
+        * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log
-+
+        message]
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-02-10 16:33  tim
-+
-+
+        * ChangeLog, libmdtools/ConjugateMinimizer.cpp,
-+
+        libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp:
-+
+        single version of energy minimization is working.
-+
-+
+-02-09 15:38  mmeineke
-+
-+
+        * staticProps/: AllCorr.cpp, staticProps.cpp:  started a bug fix on
-+
+        the massive memory overusage by OOPSE
-+
-+
+-02-09 09:48  chrisfen
-+
-+
+        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the
-+
+        hardwired LJ_rcut
-+
-+
+-02-06 19:14  tim
-+
-+
+        * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log
-+
+        message]
-+
-+
+-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
-+
-+
+-02-06 14:05  tim
-+
-+
+        * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add
-+
+        one more file into Makefile.in
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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]
-+
-+
+-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
-+
-+
+-02-03 12:10  tim
-+
-+
+        * libmdtools/Functor.hpp: Functor.hpp pass unit test
-+
-+
+-02-03 10:21  tim
-+
-+
+        * ChangeLog, libmdtools/Minimizer1D.cpp,
-+
+        libmdtools/Minimizer1D.hpp: begin unit test of minimizer
-+
-+
+-02-02 15:29  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp,
-+
+        Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp:
-+
+        Adding GoldenSection and Brent LineSearch Method
-+
-+
+-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
-+
-+
+-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...
-+
-+
+-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
-+
-+
+-01-29 16:44  tim
-+
-+
+        * libmdtools/MinimizerParameterSet.hpp: Adding
-+
+        MinimizerParameterSet class.
-+
-+
+-01-28 17:44  tim
-+
-+
+        * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of
-+
+        NLModel0 and NLModel1
-+
-+
+-01-28 15:40  tim
-+
-+
+        * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision
-+
+        of NLModel
-+
-+
+-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
-+
-+
+-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
-+
-+
+-01-27 14:39  gezelter
-+
-+
+        * samples/water/ssd.bass: Longer run time to test SSD water in MPI
-+
-+
+-01-27 14:39  gezelter
-+
-+
+        * samples/metals/Au.bass: Longer run time to test gold in MPI
-+
-+
+-01-27 14:38  gezelter
-+
-+
+        * samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer
-+
+        run time to test argon
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-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
-+
-+
+-01-26 16:52  gezelter
-+
-+
+        * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians
-+
-+
+-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
-+
-+
+-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
-+
-+
+-01-26 13:52  gezelter
-+
-+
+        * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp,
-+
+        MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies
-+
-+
+-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
-+
-+
+-01-21 17:16  tim
-+
-+
+        * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp,
-+
+        NLOPModel.hpp: constraint class in energy minimization
-+
-+
+-01-20 15:34  tim
-+
-+
+        * libmdtools/MinimizerBase.hpp: Adding energy minimization
-+
-+
+-01-20 15:32  tim
-+
-+
+        * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp,
-+
+        NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer
-+
-+
+-01-19 16:17  gezelter
-+
-+
+        * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages
-+
+        more user-friendly
-+
-+
+-01-19 13:51  chrisfen
-+
-+
+        * forceFields/DUFF.frc: Updated the default water to SSD/E
-+
-+
+-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
-+
-+
+-01-19 11:10  gezelter
-+
-+
+        * third-party/Makefile.in: Added a bunch of dummy targets so make
-+
+        won't complain
-+
-+
+-01-19 11:10  gezelter
-+
-+
+        * samples/lipid/5x5.bass: Fixed old bass file
-+
-+
+-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
-+
-+
+-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
-+
-+
+-01-16 16:55  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating
-+
+        eor file
-+
-+
+-01-16 16:51  mmeineke
-+
-+
+        * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could
-+
+        write eor files
-+
-+
+-01-16 10:01  mmeineke
-+
-+
+        * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi
-+
+        initialization of the AtomStruct
-+
-+
+-01-15 16:57  chuckv
-+
-+
+        * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps
-+
-+
+-01-15 10:51  gezelter
-+
-+
+        * ac-tools/aclocal.m4: Changes for altivec
-+
-+
+-01-15 09:22  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: Documented the Spud Toss
-+
-+
+-01-14 23:33  gezelter
-+
-+
+        * libmdtools/do_Forces.F90: changes for charge charge interactions
-+
-+
+-01-14 20:14  gezelter
-+
-+
+        * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90,
-+
+        notifyCutoffs.F90: More work for adding charges
-+
-+
+-01-14 17:41  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        src/Makefile.in: autoconf fixes
-+
-+
+-01-14 11:28  mmeineke
-+
-+
+        * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug
-+
-+
+-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
-+
-+
+-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)
-+
-+
+-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
-+
-+
+-01-13 17:11  tim
-+
-+
+        * Functor.hpp, libmdtools/Functor.hpp: [no log message]
-+
-+
+-01-13 16:22  tim
-+
-+
+        * Functor.hpp, samples/water/ssd.bass: Energy Minimization method
-+
-+
+-01-13 15:35  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the
-+
+        eor file whenever it is used instead of rewinding it
-+
-+
+-01-13 15:04  tim
-+
-+
+        * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface
-+
+        of writeFrame
-+
-+
+-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
-+
-+
+-01-12 17:54  tim
-+
-+
+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix
-+
+        a bug in copying string
-+
-+
+-01-12 15:37  tim
-+
-+
+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
-+
+        samples/minimizer/argon/argon.bass, samples/water/ssd.bass:
-+
+        Dumpwriter only write out the atoms on master nodes
-+
-+
+-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
-+
-+
+-01-09 21:15  tim
-+
-+
+        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
-+
-+
+-01-09 15:29  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
-+
-+
+-01-08 17:25  chuckv
-+
-+
+        * libmdtools/DumpWriter.cpp: A work in progress...
-+
-+
+-01-08 13:59  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: null terminate some strings just in
-+
+        case
-+
-+
+-01-08 13:13  mmeineke
-+
-+
+        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
-+
+        state bug.
-+
-+
+-01-08 13:05  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
-+
-+
+-01-08 12:57  mmeineke
-+
-+
+        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
-+
+        exstended state bug
-+
-+
+-01-08 12:40  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
-+
-+
+-01-08 10:44  mmeineke
-+
-+
+        * libmdtools/InitializeFromFile.cpp: added support for the ignore
-+
+        XS state info  flag
-+
-+
+-01-07 14:26  tim
-+
-+
+        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
-+
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass,
-+
+        samples/water/ssd.bass: Fixed a bug of sending message from master
-+
+        node to itself in DumpWriter.cpp and InitializeFromFile.cpp
-+
-+
+-01-06 14:49  chuckv
-+
-+
+        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
-+
+        performance fixes in the dipole dipole and reaction field code
-+
-+
+-01-06 13:54  chuckv
-+
-+
+        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
-+
+        little more sane
-+
-+
+-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
-+
-+
+-01-05 17:18  chuckv
-+
-+
+        * libmdtools/do_Forces.F90: mangling forces even further
-+
-+
+-01-05 17:18  chuckv
-+
-+
+        * configure, ac-tools/configure.in: mpich mucking
-+
-+
+-01-05 17:12  chuckv
-+
-+
+        * libmdtools/do_Forces.F90: mangled do_forces...
-+
-+
+-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
-+
+-12-29 14:56  chuckv
+        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
+        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
+        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
+        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
-<
+        samples/water/ssd.bass: add chi and eta to the comment line of dump
-<
+        file.
->
+        samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi
->
+        and eta to the comment line of dump file.
+-10-28 17:25  mmeineke
+        samples/Makefile.in, samples/alkane/Makefile,
+        samples/alkane/Makefile.in, samples/argon/Makefile,
+        samples/argon/Makefile.in, samples/argon/argon.bass,
-<
+        samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
-<
+        samples/lipid/Makefile, samples/lipid/Makefile.in,
-<
+        samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
-<
+        src/Makefile.in, utils/Makefile, utils/Makefile.in,
-<
+        utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
-<
+        autoconf / configure method of configuring OOPSE
->
+        samples/minimizer/argon/Makefile,
->
+        samples/minimizer/argon/Makefile.in,
->
+        samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile,
->
+        samples/beadLipid/Makefile.in, samples/lipid/Makefile,
->
+        samples/lipid/Makefile.in, samples/water/Makefile,
->
+        samples/water/Makefile.in, src/Makefile, src/Makefile.in,
->
+        utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile,
->
+        utils/sysbuilder/Makefile.in: Changes to autoconf / configure
->
+        method of configuring OOPSE
+-09-04 16:48  mmeineke
+-07-14 18:06  gezelter
+        * samples/: alkane/init_butane.eor, argon/argon.bass,
-<
+        argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes
-<
+        for samples
->
+        argon/init_argon.eor, minimizer/argon/argon.bass,
->
+        minimizer/argon/init_argon.eor, lipid/init_5x5.eor,
->
+        water/init_ssd.eor: Fixes for samples
+-07-14 18:06  gezelter
+        * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
+        libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
-<
+        samples/argon/argon.bass: more bug fixes....
->
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more
->
+        bug fixes....
+-04-01 11:49  mmeineke
+-03-26 10:37  chuckv
+        * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
-<
+        samples/argon/argon.bass: Fixes for Parallel thermalization
->
+        samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes
->
+        for Parallel thermalization
+-03-26 09:55  mmeineke
+-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]
+-03-25 09:29  mmeineke
+        alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
+        argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
+        lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
-<
+        lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
-<
+        water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
-<
+        samples
->
+        lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile,
->
+        minimizer/argon/argon.bass, minimizer/argon/init_argon.eor,
->
+        minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor,
->
+        water/ssd.bass, water/water.mdl: moved tests to samples
+-03-24 19:51  gezelter
+        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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+Changed lines
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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs. Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

Diff Legend

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 894 by chuckv, Mon Jan 5 21:00:05 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC