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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 385 by gezelter, Fri Mar 21 20:37:58 2003 UTC vs.
Revision 727 by tim, Wed Aug 27 16:16:01 2003 UTC

-+
+-08-26 15:37  tim
-+
-+
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
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+        mpiSimulation.cpp: set default force substraction policy to
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+        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
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+        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
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+        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
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+        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,
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+        if he does not specify any value for seed, oopse will take the
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+        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
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+        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,
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+        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
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+        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 13:32  mmeineke
-+
-+
+        * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp:
-+
+        moved frameCount's functionality into DumpReader. also split props
-+
+        into staticProps and dynamicProps. (currently only have
-+
+        staticProps)
-+
-+
+-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,
-+
+        props/frameCount.c, props/frameCount.h, props/props.cpp,
-+
+        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
-+
+        to Harmonic bonds in the DUFF frc file
-+
-+
+        fixed constraints.
-+
-+
+-06-25 16:11  mmeineke
-+
-+
+        * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in
-+
+        the DUFF frc file
-+
-+
+-06-24 17:51  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT.  Check them!
-+
-+
+-06-24 14:57  mmeineke
-+
-+
+        * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp,
-+
+        libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into
-+
+        the DUFF forcefield and BondExtensions.cpp
-+
-+
+-06-23 16:24  mmeineke
-+
-+
+        * libmdtools/Integrator.cpp: Doing some work to debug the
-+
+        constraint code.
-+
-+
+-06-20 15:50  gezelter
-+
-+
+        * libmdtools/Integrator.hpp: NPT fix
-+
-+
+-06-20 15:29  mmeineke
-+
-+
+        * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
-+
+        libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/LJFF.cpp,
-+
+        libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the
-+
+        integrator and NVT seem to be working now.
-+
-+
+-06-20 11:49  gezelter
-+
-+
+        * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions
-+
-+
+-06-19 17:02  mmeineke
-+
-+
+        * forceFields/DUFF.frc, forceFields/LJFF.frc,
-+
+        forceFields/LJ_FF.frc, forceFields/Makefile,
-+
+        forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc,
-+
+        libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp,
-+
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile,
-+
+        libmdtools/TraPPEFF.cpp: slowly converting to new integrator and
-+
+        forcefield names.
-+
-+
+-06-19 14:21  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp:
-+
+        finished the basics of the integrator and SimSetup.cpp
-+
-+
+-06-19 14:11  mmeineke
-+
-+
+        * libmdtools/SimSetup.cpp:  doing some work on SimSetup to clean it
-+
+        up / get it to work with the new Integrator.
-+
-+
+-06-18 17:20  mmeineke
-+
-+
+        * libmdtools/Symplectic.cpp: minor changes in an attempt to fix
-+
+        output times.
-+
-+
+-06-17 16:56  mmeineke
-+
-+
+        * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters
-+
+        fro the ghost Bend in TraPPE_Ex
-+
-+
+        some work on the integrator. ( incomplete)
-+
-+
+-06-17 16:55  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost
-+
+        Bend in TraPPE_Ex
-+
-+
+-06-04 16:06  mmeineke
-+
-+
+        * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and
-+
+        constrainB to the Symplectic integrator
-+
-+
+-05-30 16:32  mmeineke
-+
-+
+        * utils/bilayerSys.cpp: currently modifiying Symplectic to become
-+
+        the basic integrator.
-+
-+
+        bilayerSys.cpp altered for building tb3.
-+
-+
+-05-30 16:31  mmeineke
-+
-+
+        * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp,
-+
+        TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently
-+
+        modifiying Symplectic to become the basic integrator.
-+
-+
+-05-30 15:19  mmeineke
-+
-+
+        * libmdtools/Integrator.hpp: added some member variables for
-+
+        position, velocity, etc.
-+
-+
+-05-30 14:07  mmeineke
-+
-+
+        * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT
-+
+        is now derived from Integrator
-+
-+
+-05-20 11:44  mmeineke
-+
-+
+        * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug.
-+
-+
+-05-17 11:57  mmeineke
-+
-+
+        * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be
-+
+        working
-+
-+
+-05-16 16:37  mmeineke
-+
-+
+        * utils/bilayerSys.cpp: still working on the bilayer code
-+
-+
+-05-16 09:28  mmeineke
-+
-+
+        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some
-+
+        work to overhaul sysbuild.
-+
-+
+-05-13 16:23  mmeineke
-+
-+
+        * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop
-+
-+
+-05-13 15:47  mmeineke
-+
-+
+        * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl,
-+
+        beadLipid/water.mdl: Added bead lipid model to the sample directory
-+
-+
+-05-13 15:34  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into
-+
+        the Trappe extended force field
-+
-+
+-05-13 12:01  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the
-+
+        TraPPe_Ex forceField
-+
-+
+-05-09 14:51  mmeineke
-+
-+
+        * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field.
-+
+        there were some duplicate entries
-+
-+
+        added a two chain lipid to the lipid.mdl in sample
-+
-+
+-05-09 14:51  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field.
-+
+        there were some duplicate entries
-+
-+
+-05-09 11:56  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the
-+
+        configure script
-+
-+
+        added the CH branching group to the TraPPE_Ex fource field
-+
-+
+-05-09 11:55  mmeineke
-+
-+
+        * ac-tools/configure.in: added the utils subdirectory to the
-+
+        configure script
-+
-+
+-04-25 11:02  mmeineke
-+
-+
+        * utils/bilayerSys.cpp: i quick fix to th distance in the random
-+
+        bilayer builder
-+
-+
+-04-24 21:00  mmeineke
-+
-+
+        * libmdtools/f_verlet_constrained.F90: added a new test for
-+
+        constraint failure
-+
-+
+-04-17 16:54  mmeineke
-+
-+
+        * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp,
-+
+        utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp,
-+
+        utils/bilayerSys.cpp: fixed up sysBuild to where it should now
-+
+        build our systems
-+
-+
+-04-16 16:11  mmeineke
-+
-+
+        * utils/: MoLocator.cpp, MoLocator.hpp: almost finished.
-+
-+
+-04-15 16:47  mmeineke
-+
-+
+        * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys
-+
+        and sysBuild both will build now. woot!
-+
-+
+-04-15 16:20  mmeineke
-+
-+
+        * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
-+
+        bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp
-+
-+
+        sysBuild still need to write the bass file.
-+
-+
+        MoLocator.cpp is currently empty
-+
-+
+-04-15 15:40  chuckv
-+
-+
+        * forceFields/EAM_FF.frc, forceFields/agu3.eam,
-+
+        forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam,
-+
+        forceFields/pdu3.eam, forceFields/ptu3.eam,
-+
+        libmdtools/ForceFields.hpp: Added eam force files...
-+
-+
+-04-15 11:37  chuckv
-+
-+
+        * libmdtools/EAM_FF.cpp: More eam work.
-+
-+
+-04-14 16:22  mmeineke
-+
-+
+        * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp,
-+
+        utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp:
-+
+        working on the system builder
-+
-+
+-04-14 16:16  chuckv
-+
-+
+        * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed
-+
+        ordering on NVT calculation in integrators.
-+
-+
+-04-14 14:51  mmeineke
-+
-+
+        * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder,
-+
+        obj/placeHolder:  working on a system builder
-+
-+
+-04-14 14:04  mmeineke
-+
-+
+        * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField
-+
-+
+        added sysBuild to the utils Makefile
-+
-+
+-04-14 14:03  mmeineke
-+
-+
+        * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added
-+
+        Ghost bends to the TraPPE_Ex forceField
-+
-+
+-04-14 13:19  chuckv
-+
-+
+        * libmdtools/calc_eam.F90: Added first mangling of EAM.
-+
-+
+-04-11 13:46  mmeineke
-+
-+
+        * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90,
-+
+        simulation_module.F90: fixed a memory bug in Fortran, where
-+
+        molMembershipArray was declared nLocal instead of nGlobal.
-+
-+
+-04-11 10:16  gezelter
-+
-+
+        * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp,
-+
+        SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90,
-+
+        fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress
-+
+        for NPT
-+
-+
+-04-10 15:08  mmeineke
-+
-+
+        * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp:  added a
-+
+        globalIndex counter to Molecule
-+
-+
+-04-10 11:35  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on
-+
+        ConstantStress
-+
-+
+-04-10 11:27  mmeineke
-+
-+
+        * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup.
-+
+        caused a miscalculation of nLocal.
-+
-+
+-04-10 11:21  mmeineke
-+
-+
+        * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90,
-+
+        do_Forces.F90: fixed a bug in symplectic, where presure was only
-+
+        being calculated the first time through.
-+
-+
+-04-09 11:20  chuckv
-+
-+
+        * samples/alkane/alkanes.mdl: added pentane to the alkane model
-+
+        file
-+
-+
+-04-09 08:59  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp,
-+
+        Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file
-+
-+
+-04-08 23:06  gezelter
-+
-+
+        * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp,
-+
+        ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp,
-+
+        SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp,
-+
+        Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90,
-+
+        calc_reaction_field.F90, calc_sticky_pair.F90,
-+
+        fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and
-+
+        NVT
-+
-+
+-04-08 17:38  chuckv
-+
-+
+        * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp,
-+
+        libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90,
-+
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
-+
+        libmdtools/simulation_module.F90, samples/water/ssd.bass: It works
-+
+        (kinda)...
-+
-+
+-04-08 16:35  gezelter
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp,
-+
+        libmdtools/SimSetup.cpp: Fixes for NPT / NVT
-+
-+
+-04-08 12:16  chuckv
-+
-+
+        * libmdtools/: do_Forces.F90, neighborLists.F90,
-+
+        simulation_module.F90: Moved expand neighborlist to init_FF.
-+
-+
+-04-08 10:20  chuckv
-+
-+
+        * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for
-+
+        NVT
-+
-+
+-04-08 09:39  gezelter
-+
-+
+        * libmdtools/Verlet.cpp: fixes for nvt / npt
-+
-+
+-04-08 09:34  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp,
-+
+        Thermo.cpp, Verlet.cpp: dt/2 fix in nvt
-+
-+
+-04-08 07:50  gezelter
-+
-+
+        * libmdtools/ExtendedSystem.cpp: Fixes for affine transform
-+
-+
+-04-08 07:44  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
-+
+        Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the
-+
+        NVT and NPT ensembles
-+
-+
+-04-07 16:42  gezelter
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimSetup.cpp: Fixes for NPT and NVT
-+
-+
+-04-07 16:20  mmeineke
-+
-+
+        * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial
-+
+        portion of SSD.
-+
-+
+-04-07 16:16  mmeineke
-+
-+
+        * libmdtools/: ForceFields.cpp, Symplectic.cpp:
-+
+        doing some testing in sticky through Symplectic.
-+
-+
+-04-07 15:51  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT
-+
-+
+-04-07 15:50  chuckv
-+
-+
+        * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for
-+
+        tau and virial.
-+
-+
+-04-07 15:06  mmeineke
-+
-+
+        * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp,
-+
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90,
-+
+        src/Makefile: bug fixes
-+
-+
+-04-07 11:56  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp,
-+
+        StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp:
-+
+        Many fixes to add extended system
-+
-+
+-04-07 09:30  gezelter
-+
-+
+        * src/Makefile: Fixed a bug caused by my experimentation
-+
-+
+-04-07 09:30  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp,
-+
+        Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp:
-+
+        Added ExtendedSystem infrastructure for NPT and NVT calculations
-+
-+
+-04-07 09:30  gezelter
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS
-+
-+
+-04-04 23:07  gezelter
-+
-+
+        * src/Makefile: final mods to try a fortran compiler
-+
-+
+-04-04 22:39  gezelter
-+
-+
+        * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp,
-+
+        fortranWrapDefines.hpp: Bug fixes for simulation module rewrites
-+
-+
+-04-04 21:56  gezelter
-+
-+
+        * libmdtools/: Makefile, atype_module.F90, do_Forces.F90,
-+
+        fortranWrappers.cpp, wrappers.F90: bug fixes for compilation
-+
-+
+-04-04 21:45  gezelter
-+
-+
+        * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug
-+
+        fixes to fortran wrappers
-+
-+
+-04-04 17:22  chuckv
-+
-+
+        * libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90,
-+
+        calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90,
-+
+        do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp,
-+
+        simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets
-+
+        smarter, fortran gets dumber...
-+
-+
+-04-04 14:57  mmeineke
-+
-+
+        * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90,
-+
+        neighborLists.F90: fixed a memory read bug in neighborlist
-+
-+
+-04-04 14:47  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
-+
+        SimInfo.hpp, Thermo.cpp: Changes for Extended System
-+
-+
+-04-04 14:16  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp,
-+
+        SimInfo.hpp: Fixes for ExtendedSystem
-+
-+
+-04-03 20:57  gezelter
-+
-+
+        * libmdtools/ExtendedSystem.hpp: Added extended system header
-+
-+
+-04-03 20:57  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes
-+
+        for extended system code
-+
-+
+-04-03 18:49  gezelter
-+
-+
+        * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to
-+
+        extendedsystem
-+
-+
+-04-03 17:19  mmeineke
-+
-+
+        * libmdtools/Molecule.hpp: added some little fixes here and there.
-+
-+
+-04-03 17:01  mmeineke
-+
-+
+        * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before
-+
+        initialize bug.
-+
-+
+-04-03 16:12  mmeineke
-+
-+
+        * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just
-+
+        little things like deleteing unused variables and such.
-+
-+
+-04-03 15:57  mmeineke
-+
-+
+        * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to
-+
+        simError.h also some fixes to Molecule.hpp
-+
-+
+-04-03 15:57  mmeineke
-+
-+
+        * libBASS/simError.h: a few fixes to simError.h
-+
-+
+-04-03 15:21  mmeineke
-+
-+
+        * libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c,
-+
+        libBASS/simError.h, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp,
-+
+        libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp,
-+
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp,
-+
+        src/Makefile, src/oopse.cpp: fixed some small things with
-+
+        simError.h
-+
-+
+-04-03 15:19  gezelter
-+
-+
+        * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT
-+
-+
+-04-03 14:58  gezelter
-+
-+
+        * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for
-+
+        now)
-+
-+
+-04-03 08:42  gezelter
-+
-+
+        * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c:
-+
+        Changed Readme, added some files
-+
-+
+-04-02 17:19  mmeineke
-+
-+
+        * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp,
-+
+        Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90:
-+
+        dipoles mostly work, but there is a memory leak somewhere.
-+
-+
+-04-02 10:01  mmeineke
-+
-+
+        * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting
-+
+        the proper atomIdents.
-+
-+
+-04-01 11:50  chuckv
-+
-+
+        * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90,
-+
+        libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90,
-+
+        samples/argon/argon.bass: more bug fixes....
-+
-+
+-04-01 11:49  mmeineke
-+
-+
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed
-+
+        DumpWriter to be more robust to errors. also added a little
-+
+        namespace to InitFromFile to wrap it's helper functions in MPI
-+
-+
+-03-31 17:09  chuckv
-+
-+
+        * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local
-+
+        not zeroed.
-+
-+
+-03-31 16:50  chuckv
-+
-+
+        * libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp,
-+
+        libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp,
-+
+        libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
-+
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90,
-+
+        samples/alkane/butane.bass: Fixes in MPI force calc and in
-+
+        Trappe_Ex parsing.
-+
-+
+-03-28 17:34  chuckv
-+
-+
+        * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp
-+
-+
+-03-28 16:45  chuckv
-+
-+
+        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/InitializeFromFile.cpp: Bug fixes in read-write
-+
+        routines.
-+
-+
+-03-28 14:33  mmeineke
-+
-+
+        * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp,
-+
+        Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a
-+
+        bug where the Excludes were not being created properly
-+
-+
+-03-28 14:30  chuckv
-+
-+
+        * libBASS/Makefile, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes
-+
+        and debugging mpi read write from file.
-+
-+
+-03-28 10:28  mmeineke
-+
-+
+        * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range
-+
+        interactions in Trappe
-+
-+
+-03-27 18:33  chuckv
-+
-+
+        * libmdtools/: SimSetup.cpp, mpiSimulation.cpp,
-+
+        mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue.
-+
-+
+-03-27 17:16  mmeineke
-+
-+
+        * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where
-+
+        excludes were not being initialized
-+
-+
+-03-27 16:52  mmeineke
-+
-+
+        * src/Makefile: [no log message]
-+
-+
+-03-27 16:52  mmeineke
-+
-+
+        * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug.
-+
-+
+-03-27 16:07  mmeineke
-+
-+
+        * libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp,
-+
+        Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp,
-+
+        Verlet.cpp: fixed the compile time bugs, Source builds and links
-+
-+
+-03-27 15:48  mmeineke
-+
-+
+        * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few
-+
+        more bugs.
-+
-+
+-03-27 15:40  mmeineke
-+
-+
+        * libmdtools/Molecule.cpp: added the Molecule.cpp file
-+
-+
+-03-27 15:39  mmeineke
-+
-+
+        * libmdtools/: Makefile, Molecule.hpp:  fixed the makefile
-+
-+
+-03-27 15:36  mmeineke
-+
-+
+        * libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
-+
+        ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp,
-+
+        SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs
-+
-+
+-03-27 15:12  mmeineke
-+
-+
+        * libmdtools/: AbstractClasses.hpp, ForceFields.cpp,
-+
+        Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp,
-+
+        Verlet.cpp: I have implemeted Molecules everywhere I could remember
-+
+        to.  will now attempt to compile.
-+
-+
+-03-27 14:21  mmeineke
-+
-+
+        * libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp,
-+
+        SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished
-+
+        updating SimSetup to initialize and use the new MPI division of
-+
+        labour, and Molecule class
-+
-+
+-03-27 12:55  mmeineke
-+
-+
+        * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to
-+
+        use Molecule
-+
-+
+-03-27 12:32  mmeineke
-+
-+
+        * libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp,
-+
+        SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been
-+
+        converted to the new Molecule model. TraPPE_Ex is currently being
-+
+        updated.  SimSetups routines are writtten, but not yet called.
-+
-+
+-03-27 10:07  gezelter
-+
-+
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp,
-+
+        mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom
-+
+        numbering in MPI
-+
-+
+-03-27 09:30  mmeineke
-+
-+
+        * libmdtools/mpiSimulation.cpp: little bug fixes here and there.
-+
-+
+-03-26 20:49  gezelter
-+
-+
+        * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to
-+
+        fileio for MPI
-+
-+
+-03-26 18:14  gezelter
-+
-+
+        * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp,
-+
+        mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug
-+
+        fixes   many bug fixes
-+
-+
+-03-26 17:24  gezelter
-+
-+
+        * libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on
-+
+        sequence of atoms on the other processors.  Node 0 now fires
-+
+        potatoes at other processors to get them to send french fries back.
-+
-+
+-03-26 17:02  mmeineke
-+
-+
+        * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for
-+
+        making the molecules is in place. ForceField needs to be updated
-+
+        next.
-+
-+
+-03-26 16:54  mmeineke
-+
-+
+        * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of
-+
+        the "static" bugs in  Atom and Exclude
-+
-+
+-03-26 16:50  mmeineke
-+
-+
+        * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp,
-+
+        SimSetup.cpp: still working on the SimSetup routine. also fixed
-+
+        some things in Exclude.hpp
-+
-+
+-03-26 16:24  gezelter
-+
-+
+        * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp
-+
-+
+-03-26 16:23  gezelter
-+
-+
+        * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom
-+
+        and Exclude list
-+
-+
+-03-26 16:04  gezelter
-+
-+
+        * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and
-+
+        delete ranges of atoms
-+
-+
+-03-26 15:45  mmeineke
-+
-+
+        * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class
-+
+        with static arrays similar to the Atom class
-+
-+
+-03-26 15:22  mmeineke
-+
-+
+        * libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm
-+
+        overhauling the molecule class to contain it's own bonds, bends,
-+
+        and torsions.
-+
-+
+        may god have mercy on my soul.
-+
-+
+-03-26 14:34  chuckv
-+
-+
+        * libmdtools/mpiSimulation.cpp: Finished globalIndex.
-+
-+
+-03-26 13:02  gezelter
-+
-+
+        * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp,
-+
+        mpiSimulation.hpp: MPI stuff for passing out molecules
-+
-+
+-03-26 11:12  chuckv
-+
-+
+        * libmdtools/mpiSimulation.cpp: working on load balancing
-+
-+
+-03-26 10:37  chuckv
-+
-+
+        * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp,
-+
+        samples/argon/argon.bass: Fixes for Parallel thermalization
-+
-+
+-03-26 09:55  mmeineke
-+
-+
+        * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in
-+
+        THermo.cpp
-+
-+
+-03-25 17:54  chuckv
-+
-+
+        * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation
-+
+        of potential energy and temperature.
-+
-+
+-03-25 09:29  mmeineke
-+
-+
+        * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy,
-+
+        src/MPIobj/dummy, src/obj/dummy: [no log message]
-+
-+
+-03-25 09:29  mmeineke
-+
-+
+        * libBASS/MPIobj/dummy: added dummy files to keep the build
-+
+        deirectories from being pruned.
-+
-+
+-03-24 20:07  gezelter
-+
-+
+        * samples/Makefile: moving tests to samples
-+
-+
+-03-24 20:06  gezelter
-+
-+
+        * samples/: alkane/Makefile, alkane/alkanes.mdl,
-+
+        alkane/butane.bass, alkane/init_butane.eor, argon/Makefile,
-+
+        argon/argon.bass, argon/init_argon.eor, argon/lj.mdl,
-+
+        lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor,
-+
+        lipid/lipid.mdl, lipid/water.mdl, water/Makefile,
-+
+        water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to
-+
+        samples
-+
-+
+-03-24 19:51  gezelter
-+
-+
+        * ac-tools/configure.in: Tests are becoming samples
-+
-+
+-03-24 19:46  gezelter
-+
-+
+        * ac-tools/Make.conf.in: Added makefiles in tests directories
-+
-+
+-03-24 16:55  gezelter
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90,
-+
+        libmdtools/calc_reaction_field.F90,
-+
+        libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90,
-+
+        libmdtools/simulation_module.F90: electrostatic changes for dipole
-+
+        / RF separation
-+
-+
+-03-24 13:33  mmeineke
-+
-+
+        * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
-+
+        do_Forces.F90: little bug fixes here and there
-+
-+
+-03-24 10:26  mmeineke
-+
-+
+        * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
-+
+        where short range interactions were not being calculated.
-+
-+
+        removed some debug print statements
-+
-+
+-03-21 17:11  chuckv
-+
-+
+        * libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90,
-+
+        do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90:
-+
+        various write statements for debugging
-+
-+
+-03-21 16:26  chuckv
-+
-+
+        * forceFields/Makefile: added links to the makefile in forceFields
-+
-+
+-03-21 15:52  gezelter
-+
-+
+        * ac-tools/Make.conf.in, ac-tools/configure.in,
-+
+        libmdtools/Makefile: Fixed F_MACH_DEP bug
-+
-+
+-03-21 15:37  gezelter
-+
-+
+        * ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in,
-+
+        ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile,
-+
+        libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend,
-+
+        src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org,
-+
+        autoconf fixes
-+
+-03-21 14:58  gezelter
+        * LICENSE: Added license file

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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 385 by gezelter, Fri Mar 21 20:37:58 2003 UTC vs. Revision 727 by tim, Wed Aug 27 16:16:01 2003 UTC

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Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 385 by gezelter, Fri Mar 21 20:37:58 2003 UTC vs.
Revision 727 by tim, Wed Aug 27 16:16:01 2003 UTC