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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC

-+
+-09-10 16:28  mmeineke
-+
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+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more
-+
+        work on getting gofR working.
-+
-+
+-09-09 16:50  mmeineke
-+
-+
+        * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the
-+
+        beginings of the GofR pair correlation.
-+
-+
+        added identification of identI in matchI.
-+
-+
+-09-09 15:35  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp,
-+
+        NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog
-+
-+
+        added two new NPT integrators, they still need work.
-+
-+
+-09-09 15:34  mmeineke
-+
-+
+        * ChangeLog: updated the ChangeLog
-+
-+
+-09-05 17:45  gezelter
-+
-+
+        * libmdtools/Make.dep: dependency on config.h
-+
-+
+-09-05 17:36  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4: fixed sprng problem
-+
-+
+-09-05 16:29  gezelter
-+
-+
+        * samples/metals/Makefile.in: New Makefile for metals sample
-+
-+
+-09-05 16:27  gezelter
-+
-+
+        * Makefile, Makefile.in, ac-tools/aclocal.m4,
-+
+        ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile,
-+
+        forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
-+
+        libBASS/Makefile.in, libmdtools/Integrator.hpp,
-+
+        libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep,
-+
+        libmdtools/Makefile, libmdtools/Makefile.in,
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+        libmdtools/calc_eam.F90, libmdtools/config.h.in,
-+
+        libmdtools/definitions_module.F90, libmdtools/fInfo.c,
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+        libmdtools/fortranWrappers.cpp,
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+        libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90,
-+
+        libmdtools/simulation_module.F90, samples/Makefile,
-+
+        samples/Makefile.in, samples/alkane/Makefile,
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+        samples/alkane/Makefile.in, samples/argon/Makefile,
-+
+        samples/argon/Makefile.in, samples/argon/argon.bass,
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+        samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
-+
+        samples/lipid/Makefile, samples/lipid/Makefile.in,
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+        samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
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+        src/Makefile.in, utils/Makefile, utils/Makefile.in,
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+        utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
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+        autoconf / configure method of configuring OOPSE
-+
-+
+-09-04 16:48  mmeineke
-+
-+
+        * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
-+
+        libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile:
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+        added resetTime to the Global namespace.
-+
-+
+        added ability to reset the integrators in the NVT and NPT family.
-+
-+
+-09-04 16:48  mmeineke
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
-+
+        namespace.
-+
-+
+-09-02 09:30  tim
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
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+        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
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+        PolicyByMass
-+
-+
+-08-28 16:09  tim
-+
-+
+        * ChangeLog, libmdtools/GenericData.cpp,
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+        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
-+
-+
+-08-28 11:59  mmeineke
-+
-+
+        * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp:
-+
+        added the first functional parts of the PairCorrType Abstract
-+
+        classes.
-+
-+
+-08-27 14:23  tim
-+
-+
+        * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix
-+
+        bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to
-+
+        MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we
-+
+        turn on the optimization flag, it causes a seg fault
-+
-+
+-08-27 11:25  gezelter
-+
-+
+        * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90,
-+
+        calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for
-+
+        stress tensor parallel bug.
-+
-+
+-08-27 11:16  tim
-+
-+
+        * ChangeLog, libmdtools/DUFF.cpp,
-+
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90:
-+
+        fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90
-+
+        molMembershipList use global index instead of local index
-+
-+
+-08-26 15:37  tim
-+
-+
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90,
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+        mpiSimulation.cpp: set default force substraction policy to
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+        PolicyByMass
-+
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+-08-26 15:29  tim
-+
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+        * 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
-+
+        and check the seed which is specified by user at least contains 9
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+        digits
-+
-+
+-08-26 13:32  mmeineke
-+
-+
+        * libmdtools/DUFF.cpp: changed the Makefiel a litle.
-+
-+
+        Fixed a bug in MPI_DUFF. The atom block type was not being properly
-+
+        constucted in MPI. (The MPI struct had 6 doubles declared versus
-+
+        the actual 11)
-+
-+
+-08-26 13:30  mmeineke
-+
-+
+        * Makefile: changed the Makefiel a litle.
-+
-+
+-08-25 17:17  gezelter
-+
-+
+        * utils/sysbuilder/Makefile: More FreeBSD fixes
-+
-+
+-08-25 16:51  gezelter
-+
-+
+        * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp,
-+
+        libmdtools/Makefile, src/Makefile: [no log message]
-+
-+
+-08-22 15:04  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on
-+
+        frequency of output dumps.
-+
-+
+-08-20 17:23  tim
-+
-+
+        * libBASS/Globals.hpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
-+
+        libmdtools/mpiSimulation.cpp: user can setup seed in bass file now,
-+
+        if he does not specify any value for seed, oopse will take the
-+
+        value of seconds of system time as seed
-+
-+
+-08-20 14:42  mmeineke
-+
-+
+        * libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
-+
+        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/SimState.cpp,
-+
+        utils/sysbuilder/bilayerSys.cpp: updated the Changelog.
-+
-+
+        added some bug fixes for setting the random number generator seed
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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,
-+
+        libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost
-+
+        bend class
-+
-+
+-08-20 10:13  mmeineke
-+
-+
+        * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in
-+
+        make links. added -f to ln -s.
-+
-+
+-08-20 09:50  tim
-+
-+
+        * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message]
-+
-+
+-08-20 09:34  tim
-+
-+
+        * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp,
-+
+        ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg
-+
+        printing
-+
-+
+-08-18 15:59  chuckv
-+
-+
+        * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
-+
+        latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp,
-+
+        sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works.
-+
+        Nanobuilder still broke.
-+
-+
+-08-15 14:24  tim
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/GenericData.hpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp,
-+
+        libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint
-+
+        Method
-+
-+
+-08-14 11:16  tim
-+
-+
+        * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint
-+
+        with average force substraction strategy
-+
-+
+-08-13 16:20  chuckv
-+
-+
+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some
-+
+        profiling code -DPROFILE.
-+
-+
+-08-13 14:21  tim
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic
-+
+        potential & z-contraint method
-+
-+
+-08-12 16:44  mmeineke
-+
-+
+        * libBASS/BASS_interface.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
-+
+        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really
-+
+        annoying bug in Directional Atom, where mu was getting written to
-+
+        pseudorandom memory location.
-+
-+
+-08-12 14:56  tim
-+
-+
+        * libBASS/BASS_interface.cpp, libBASS/Globals.cpp,
-+
+        libBASS/Globals.hpp, libmdtools/Atom.hpp,
-+
+        libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp,
-+
+        libmdtools/SimSetup.cpp: debugging globals
-+
-+
+-08-12 13:40  gezelter
-+
-+
+        * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes
-+
+        and new atypes in LJFF
-+
-+
+-08-12 13:15  gezelter
-+
-+
+        * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older
-+
+        stuff...
-+
-+
+-08-12 13:14  chuckv
-+
-+
+        * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt.
-+
-+
+-08-12 13:04  chuckv
-+
-+
+        * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp:
-+
+        Missed del of files before.
-+
-+
+-08-12 13:03  chuckv
-+
-+
+        * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log
-+
+        message]
-+
-+
+-08-12 13:01  chuckv
-+
-+
+        * utils/sysbuilder/Makefile: commit makefile
-+
-+
+-08-12 12:51  tim
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added
-+
+        harmonical potential to z-constraint method
-+
-+
+-08-11 17:31  chuckv
-+
-+
+        * utils/Makefile: Changed makefile to only build quicklate.
-+
-+
+-08-11 17:25  chuckv
-+
-+
+        * ac-tools/configure.in: added utils/sysbuilder to be built.
-+
-+
+-08-11 17:12  chuckv
-+
-+
+        * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp,
-+
+        bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp,
-+
+        sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp,
-+
+        sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp,
-+
+        sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c,
-+
+        sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp,
-+
+        sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp,
-+
+        sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp,
-+
+        sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged
-+
+        sysbuilder into a subdirectory. Fixed some of sysbuilder to work
-+
+        with new atom allocation in libmdtools.
-+
-+
+-08-11 14:41  tim
-+
-+
+        * libmdtools/: Integrator.cpp, Integrator.hpp: added method of
-+
+        moving zconstraint molecules to specified positions
-+
-+
+-08-11 14:39  tim
-+
-+
+        * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message]
-+
-+
+-08-11 14:38  mmeineke
-+
-+
+        * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h,
-+
+        libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp,
-+
+        libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp,
-+
+        libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c,
-+
+        libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h,
-+
+        libBASS/node_list.h, libBASS/parse_interface.h,
-+
+        libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint
-+
+        into the BASS language syntax.
-+
-+
+-08-11 13:29  mmeineke
-+
-+
+        * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of
-+
+        degrees of freedom to account for zConstreints
-+
-+
+-08-08 16:22  chuckv
-+
-+
+        * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90,
-+
+        libmdtools/do_Forces.F90, libmdtools/neighborLists.F90,
-+
+        samples/metals/Au.bass: EAM works...... Neighbor list also
-+
+        works.....
-+
-+
+-08-08 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
+-03-24 20:07  gezelter
-<
+        * samples/Makefile: moving tests to samples
->
+        * samples/Makefile, tests/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
->
+        * samples/alkane/Makefile, samples/alkane/alkanes.mdl,
->
+        samples/alkane/butane.bass, samples/alkane/init_butane.eor,
->
+        samples/argon/Makefile, samples/argon/argon.bass,
->
+        samples/argon/init_argon.eor, samples/argon/lj.mdl,
->
+        samples/lipid/5x5.bass, samples/lipid/Makefile,
->
+        samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl,
->
+        samples/lipid/water.mdl, samples/water/Makefile,
->
+        samples/water/init_ssd.eor, samples/water/ssd.bass,
->
+        samples/water/water.mdl, tests/alkane/Makefile,
->
+        tests/alkane/alkanes.mdl, tests/alkane/butane.bass,
->
+        tests/alkane/init_butane.eor, tests/argon/Makefile,
->
+        tests/argon/argon.bass, tests/argon/init_argon.eor,
->
+        tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile,
->
+        tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl,
->
+        tests/lipid/water.mdl, tests/water/Makefile,
->
+        tests/water/init_ssd.eor, tests/water/ssd.bass,
->
+        tests/water/water.mdl: moved tests to samples
+-03-24 19:51  gezelter
+-03-24 19:46  gezelter
-<
+        * ac-tools/Make.conf.in: Added makefiles in tests directories
->
+        * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile,
->
+        tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile:
->
+        Added makefiles in tests directories
+-03-24 16:55  gezelter
+        * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp,
+        do_Forces.F90: little bug fixes here and there
-+
+-03-24 11:04  mmeineke
-+
-+
+        * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon
-+
+        test simulation
-+
-+
+-03-24 11:02  mmeineke
-+
-+
+        * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl,
-+
+        lipid/water.mdl, water/init_ssd.eor, water/ssd.bass,
-+
+        water/water.mdl: [no log message]
-+
-+
+-03-24 11:02  mmeineke
-+
-+
+        * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added
-+
+        some test bass files for experimenting with
-+
+-03-24 10:26  mmeineke
+        * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug
+        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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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs. Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC

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Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 760 by gezelter, Fri Sep 12 16:20:05 2003 UTC