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

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC

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+-01-12 15:37  tim
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+        * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass,
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+        samples/water/ssd.bass: Dumpwriter only write out the atoms on
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+        master nodes
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+-01-10 04:46  tim
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+        * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just
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+        roll it back fix a bug of copying string to a pointer Still have
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+        Seg fault, it looks like a random MPI seg fault in totalview
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+-01-09 21:15  tim
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+        * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub
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+-01-09 15:29  gezelter
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+        * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4)
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+-01-08 17:25  chuckv
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+        * libmdtools/DumpWriter.cpp: A work in progress...
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+-01-08 13:59  gezelter
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+        * libmdtools/DumpWriter.cpp: null terminate some strings just in
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+        case
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+-01-08 13:13  mmeineke
-+
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+        * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS
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+        state bug.
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+-01-08 13:05  gezelter
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+        * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter
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+-01-08 12:57  mmeineke
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+        * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT
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+        exstended state bug
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+-01-08 12:40  gezelter
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+        * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter
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+-01-08 10:44  mmeineke
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+        * libmdtools/InitializeFromFile.cpp: added support for the ignore
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+        XS state info  flag
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+-01-07 14:26  tim
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+        * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp,
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+        samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of
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+        sending message from master node to itself in DumpWriter.cpp and
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+        InitializeFromFile.cpp
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+-01-06 14:49  chuckv
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+        * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90:
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+        performance fixes in the dipole dipole and reaction field code
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+-01-06 13:54  chuckv
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+        * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a
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+        little more sane
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+-01-05 17:49  chuckv
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+        * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90,
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+        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
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+        calc_sticky_pair.F90, do_Forces.F90: Attempting to increase
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+        performance by reducing spurious function calls
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+-01-05 17:18  chuckv
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+        * libmdtools/do_Forces.F90: mangling forces even further
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+-01-05 17:18  chuckv
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+        * configure, ac-tools/configure.in: mpich mucking
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+-01-05 17:12  chuckv
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+        * libmdtools/do_Forces.F90: mangled do_forces...
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+-01-05 16:00  chuckv
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+        * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90,
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+        libmdtools/do_Forces.F90: Added bitmask to do_forces property
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+        lookup
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+-12-29 14:56  chuckv
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+        * samples/metals/Au.bass, third-party/mt19937ar.c: Added
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+        third-party directory for code not written by us. Also added
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+        Mersenne Twister random number generator code. This will eventually
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+        replace sprng as the random number generator used by OOPSE.
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+-12-22 16:26  chuckv
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+        * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp:
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+        Fixes to profile code.
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+-12-19 15:36  mmeineke
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+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp,
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+        timing.F90, timing.f90: More profiling fixes.
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+-12-19 15:19  chuckv
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+        * libmdtools/timing.f90: Another change for MPI in timing.
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+-12-19 15:17  chuckv
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+        * libmdtools/timing.f90: Small update to timing in MPI
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+-12-19 13:53  mmeineke
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+        * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the
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+        profiling commands work now. Will start adding PROFILE ifdefs into
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+        the code
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+-12-19 12:25  mmeineke
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+        * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added
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+        some profiling routines
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+-12-19 10:12  mmeineke
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+        * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta
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+        and GofRomega
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+        additional work on randomBilayer
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+-12-19 10:12  mmeineke
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+        * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp,
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+        PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and
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+        GofRomega
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+-12-18 16:47  mmeineke
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+        * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added
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+        some profile functionality
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+-12-18 15:46  chuckv
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+        * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90:
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+        Added functions for simple profiling in fortran.
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+-12-17 15:13  chuckv
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+        * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90,
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+        samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and
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+        rho_col were scattered into the same array. Unfortunately, MPI
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+        zeros the array between scatters so half of the sum was being lost.
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+        Fixed by added a temp array for column scatter, then sum loop over
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+        nlocal.
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+-12-16 15:49  mmeineke
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+        * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in,
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+        PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added
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+        gofRomega. both need to be debugged and tested.
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+-12-12 10:42  gezelter
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+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
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+        libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for
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+        gradients (to do minimizations)
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+-12-12 10:33  mmeineke
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+        * utils/sysbuilder/randomBilayer.hpp:  removed the randombilayer
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+        header
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+-12-10 11:52  mmeineke
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+        * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp,
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+        randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add
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+        randomBilayer to the build. Also move the random bilayer builder
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+        from bilayerSys to randomBilayer
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+-11-25 10:44  mmeineke
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+        * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old
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+        DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and
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+        TB3 in DUFF.frc
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+-11-21 15:09  mmeineke
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+        * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp,
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+        utils/sysbuilder/latticeBilayer.cpp: added a more verbose error
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+        message in SimInfo. Added a more informative error message in
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+        InitializeFromFile
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+-11-21 15:07  mmeineke
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+        * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add
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+        ing in the GofR,CosTheta
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+-11-21 14:31  chrisfen
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+        * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed
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+        a bug in SimInfo ordering of radii
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+-11-11 12:20  mmeineke
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+        * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline
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+        a min function.
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+-11-10 16:50  mmeineke
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+        * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp:
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+        reordered the rcut/ecr/boxSize initialization
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+        removed the rcut/ecr shrink and grow algorithm. the simulation will
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+        now exit when it runs into rcut or ecr.
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+-11-07 16:46  chuckv
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+        * libmdtools/: Makefile.in, mpiSimulation_module.F90,
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+        oopseMPI_module.F90: Added support for compiling fortran without
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+        use of mpich modules. We use mpif.h instead.:
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+-11-07 12:09  mmeineke
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+        * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp,
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+        NPTxyz.cpp: moved the velocity scale matrix calculation outside of
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+        the atom loop in the NPT family of integrators.
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+-11-06 17:01  mmeineke
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+        * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep,
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+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
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+        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
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+        libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep,
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+        utils/sysbuilder/latticeBilayer.cpp: added the following parameters
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+        to BASS:    * useInitialExtendedSystemState    * orthoBoxTolerance
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+          * useIntiTime => useInitialTime
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+-11-06 14:24  mmeineke
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+        * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c,
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+        make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c,
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+        parse_tree.h: fixed the includes in the Make.dep
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+-11-06 14:11  mmeineke
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+        * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
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+        NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the
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+        new-templateless branch to the main trunk.
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+        bug Fixes include:   * fixed the switching function from ortho to
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+        non-ortho box.           !!!!! THis was responsible for all of the
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+        sudden deaths we saw.    * some formating in the string when we
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+        write out the extended system state.    * added NPT.cpp to the
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+        makefile.in
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+-11-06 13:20  mmeineke
-+
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+        * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp,
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+        SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death"
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+        bug.    The box was not switching between orthorhombic and
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+        non-orthorhombic wrapping correctly.         we added a fabs() to
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+        the check.which should fix it.
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+-11-05 14:16  mmeineke
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+        * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp,
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+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
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+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp,
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+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp,
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+        libmdtools/NVT.cpp, libmdtools/SimInfo.hpp,
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+        libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep,
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+        utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp:
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+        some work on trying to find the compression bug
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+-11-03 17:07  mmeineke
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+        * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp,
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+        InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp,
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+        NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp,
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+        SimSetup.cpp, SimSetup.hpp: begun work on removing templates and
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+        most of standard template library from OOPSE.
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+-10-31 16:06  mmeineke
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+        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
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+        Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp,
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+        SimSetup.cpp: started work on template removal.
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+-10-31 13:28  mmeineke
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+        * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp:
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+        added template stuff to the Maikefile template
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+        little changes to some printf format statements
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+-10-31 13:28  mmeineke
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+        * libBASS/Makefile.in: added template stuff to the Maikefile
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+        template
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+-10-30 13:59  gezelter
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+        * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp,
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+        do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for
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+        rList problems
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+-10-30 09:11  gezelter
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+        * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being
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+        queried before q0 was allocated.
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+-10-29 15:41  mmeineke
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+        * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp,
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+        SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90,
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+        calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error
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+        in bass.l
-+
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+        fixed a little bug in the first time step, regarding the setting of
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+        ecr and est in fortran
-+
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+-10-29 15:40  mmeineke
-+
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+        * libBASS/BASSlex.l: fixed a stdlib.h include error
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+-10-29 12:55  mmeineke
-+
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+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
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+        SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way
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+        rcut is setup, as well as additional debugging comments.
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+-10-29 09:28  gezelter
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+        * configure, ac-tools/configure.in, libBASS/Makefile.in,
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+        libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for
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+        templates
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+-10-28 22:16  gezelter
-+
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+        * src/Makefile.in: Refixed broken makefile
-+
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+-10-28 22:06  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility
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+        fixes
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+-10-28 19:19  tim
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+        * ChangeLog, libmdtools/AbstractClasses.hpp,
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+        libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp,
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+        libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp,
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+        libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
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+        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
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+        libmdtools/ReadWrite.hpp, samples/argon/argon.bass,
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+        samples/water/ssd.bass: add chi and eta to the comment line of dump
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+        file.
-+
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+-10-28 17:25  mmeineke
-+
-+
+        * libmdtools/: ForceFields.hpp, SimInfo.hpp,
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+        fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp,
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+        mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of
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+        how c calls fortran. All function pointers and fortran calls are
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+        rigidly typecast now.
-+
-+
+-10-28 15:42  gezelter
-+
-+
+        * staticProps/Makefile.in, utils/sysbuilder/Makefile.in:
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+        Portability fixes
-+
-+
+-10-28 15:09  gezelter
-+
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+        * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90,
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+        libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90,
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+        src/Makefile.in: Compatibility fixes
-+
-+
+-10-28 12:08  mmeineke
-+
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+        * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in:
-+
+        started work on template removal
-+
-+
+-10-28 12:04  gezelter
-+
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+        * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started
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+        trying to understand extern "C" stuff for pointers
-+
-+
+-10-28 11:20  gezelter
-+
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+        * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp,
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+        ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility
-+
-+
+-10-28 11:03  gezelter
-+
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+        * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp,
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+        DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp,
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+        DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp,
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+        ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp,
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+        Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp,
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+        ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp,
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+        StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp,
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+        calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp,
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+        mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with
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+        more portable c header stuff Also, mod file fixes and portability
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+        changes Some fortran changes will need to be reversed.
-+
-+
+-10-28 11:03  gezelter
-+
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+        * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp,
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+        Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp,
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+        Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more
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+        portable c header stuff Also, mod file fixes and portability
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+        changes
-+
-+
+-10-28 11:02  gezelter
-+
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+        * configure, ac-tools/aclocal.m4: mod file fixes and portability
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+        stuff
-+
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+-10-27 18:00  gezelter
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+        * Makefile.in, configure, ac-tools/aclocal.m4,
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+        ac-tools/configure.in, ac-tools/fortran90.m4,
-+
+        libmdtools/Makefile.in: Stuff for MOD support in other compilers
-+
-+
+-10-27 17:08  mmeineke
-+
-+
+        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
-+
+        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp:
-+
+        added routines for the sysbuilder to work with simSetup
-+
-+
+        remved the QuickBass routines, and had all parsing go through
-+
+        SimSetup.  LatticeBilayer is in complete working order now.
-+
-+
+-10-27 17:07  mmeineke
-+
-+
+        * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added
-+
+        routines for the sysbuilder to work with simSetup
-+
-+
+-10-27 11:20  gezelter
-+
-+
+        * configure, ac-tools/configure.in, samples/water/ssd.bass,
-+
+        utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild
-+
-+
+-10-24 17:17  mmeineke
-+
-+
+        * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp,
-+
+        MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp,
-+
+        latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put
-+
+        QuickBass, MoLocator, and latticeBuilder into a Builder Library
-+
+        overhauled latticeBilayer into its own program. Removed sysBuild
-+
+        from the Makefile
-+
-+
+-10-24 12:36  gezelter
-+
-+
+        * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp,
-+
+        latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer
-+
+        builder
-+
-+
+-10-24 12:35  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a
-+
+        merge problem
-+
-+
+-10-23 14:57  mmeineke
-+
-+
+        * samples/metals/Makefile.in: added eam ForceField files to the
-+
+        init
-+
-+
+        fixed an eam mpi parmeter setup bug
-+
-+
+        added the init file to the makefile
-+
-+
+-10-23 14:57  mmeineke
-+
-+
+        * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files
-+
+        to the init
-+
-+
+        fixed an eam mpi parmeter setup bug
-+
-+
+-10-23 14:57  mmeineke
-+
-+
+        * forceFields/Makefile.in: added eam ForceField files to the init
-+
-+
+-10-22 16:17  mmeineke
-+
-+
+        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in,
-+
+        NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT
-+
+        integrator, NPTxyz. It scales the x, y, and z direction sepeartely.
-+
+        no box skew allowed.
-+
-+
+-10-21 14:33  mmeineke
-+
-+
+        * libBASS/Globals.cpp, libBASS/Globals.hpp,
-+
+        libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp,
-+
+        staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax.
-+
+            * useInitTime = false: sets the origin time to 0.0 regardless
-+
+        of the time stamp in the .init file     * default=> useInitTime =
-+
+        true;
-+
-+
+-10-17 16:19  mmeineke
-+
-+
+        * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp,
-+
+        Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
-+
+        staticProps.cpp, obj/placeholder: added the staticProps directory
-+
+        to the build list for both configure  and configure.in
-+
-+
+        fixed a number of bugs in the staticProps code. gofr is now
-+
+        working.
-+
-+
+-10-17 16:18  mmeineke
-+
-+
+        * ac-tools/configure.in: added the staticProps directory to the
-+
+        build list for both configure  and configure.in
-+
-+
+-10-17 16:17  mmeineke
-+
-+
+        * configure: added the staticProps directory to the build list
-+
-+
+-10-16 14:16  mmeineke
-+
-+
+        * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp,
-+
+        Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to
-+
+        use linked lists instead of a vector.
-+
-+
+        Fixed the makefile to build DumpReader.cpp
-+
-+
+        Removed a comment output in Exclude.cpp
-+
-+
+        Modified DumpWriter and Integrator to write an eor file every time
-+
+        a frame is written.  This lets the .eor file represent the last
-+
+        written frame of a simulation.
-+
-+
+-10-10 12:10  mmeineke
-+
-+
+        * props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp,
-+
+        props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp,
-+
+        props/PairCorrList.hpp, props/PairCorrType.cpp,
-+
+        props/PairCorrType.hpp, props/staticProps.cpp,
-+
+        staticProps/AllCorr.cpp, staticProps/AllCorr.hpp,
-+
+        staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp,
-+
+        staticProps/GofR.cpp, staticProps/Makefile.in,
-+
+        staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp,
-+
+        staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp,
-+
+        staticProps/staticProps.cpp: removed the props directory, and moved
-+
+        everything over to staticProps
-+
-+
+-10-09 17:09  mmeineke
-+
-+
+        * libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp,
-+
+        props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp,
-+
+        props/PairCorrType.cpp, props/PairCorrType.hpp,
-+
+        props/staticProps.cpp: Contiuned work on staticProps. should be in
-+
+        a position where it will compile and run first runs.
-+
-+
+-10-04 13:46  chuckv
-+
-+
+        * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90,
-+
+        samples/metals/Au.bass: Fixed bug in calc_eam.
-+
-+
+-10-04 13:08  chuckv
-+
-+
+        * samples/metals/init_au.in: added Au init file for eam.
-+
-+
+-10-03 17:11  mmeineke
-+
-+
+        * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed
-+
+        entahlpy from the statwriter and thermo.
-+
-+
+-10-03 17:02  mmeineke
-+
-+
+        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
-+
+        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
-+
+        staticProps.cpp: changed the formating ogf the error statements in
-+
+        simError
-+
-+
+        added a function to get the maxCutoff
-+
-+
+        near completion of the staticProps code. still needs the pair loop,
-+
+        and the loop to allocate and read each frame.
-+
-+
+-10-03 17:02  mmeineke
-+
-+
+        * libmdtools/SimInfo.hpp: changed the formating ogf the error
-+
+        statements in simError
-+
-+
+        added a function to get the maxCutoff
-+
-+
+-10-03 17:01  mmeineke
-+
-+
+        * libBASS/simError.c: changed the formating ogf the error
-+
+        statements in simError
-+
-+
+-10-02 17:06  mmeineke
-+
-+
+        * props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp,
-+
+        PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp,
-+
+        staticProps.cpp: finishing up the constructs needed to get this
-+
+        program up and running
-+
-+
+-09-30 11:00  mmeineke
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed
-+
+        f90Flags so they are no longer overwritten by the compiler.
-+
-+
+-09-29 17:06  mmeineke
-+
-+
+        * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same
-+
+        for conifig.in
-+
-+
+        fixed wrappers to extern "C"
-+
-+
+-09-29 17:06  mmeineke
-+
-+
+        * ac-tools/configure.in: added mpif90 mod check back same for
-+
+        conifig.in
-+
-+
+-09-29 17:05  mmeineke
-+
-+
+        * configure: added mpif90 mod check back
-+
-+
+-09-29 16:16  mmeineke
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        libBASS/BendStamp.cpp, libBASS/BondStamp.cpp,
-+
+        libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp,
-+
+        libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp,
-+
+        libBASS/ZconStamp.cpp, libBASS/simError.c,
-+
+        libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90,
-+
+        libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors
-+
+        found with SUN's SUNWspro.s1s7
-+
-+
+-09-29 12:38  mmeineke
-+
-+
+        * libmdtools/GenericData.hpp: light change in syntax. no
-+
+        signifigant change.
-+
-+
+-09-25 16:17  mmeineke
-+
-+
+        * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some
-+
+        additional remarks from icc -w3 (extra verbose output)
-+
-+
+-09-25 14:27  mmeineke
-+
-+
+        * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp,
-+
+        libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp,
-+
+        libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp,
-+
+        libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp,
-+
+        libmdtools/Integrator.cpp, libmdtools/LJFF.cpp,
-+
+        libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp,
-+
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp,
-+
+        libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp,
-+
+        libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with
-+
+        gcc -Wall and g++ -Wall
-+
-+
+-09-25 13:54  gezelter
-+
-+
+        * configure, ac-tools/configure.in: fixed a bug in configure
-+
-+
+-09-25 11:42  gezelter
-+
-+
+        * Makefile.in, configure, ac-tools/aclocal.m4,
-+
+        ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in,
-+
+        src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in:
-+
+        fixes for configure
-+
-+
+-09-24 14:34  mmeineke
-+
-+
+        * libmdtools/Integrator.cpp: moved readyCheck in the integrator so
-+
+        that it is called before the first Statistics are written.
-+
-+
+-09-23 15:36  gezelter
-+
-+
+        * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a
-+
+        bunch of Make.dep files to CVS
-+
-+
+-09-23 15:34  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp,
-+
+        SimSetup.cpp: Removed NPTfm from Integrator.hpp.
-+
-+
+        Some small syntax cleaning in NPTfm and SimSetup
-+
-+
+-09-22 18:07  tim
-+
-+
+        * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp,
-+
+        SimInfo.hpp: fix bug in calculating maxCutoff
-+
-+
+-09-22 16:23  mmeineke
-+
-+
+        * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep,
-+
+        Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp:
-+
+        Converted NPTf to work with the NPT base class.
-+
-+
+        Removed NPTfm and NPTim from cvs
-+
-+
+-09-19 15:00  mmeineke
-+
-+
+        * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp,
-+
+        NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base
-+
+        class. NPTi is up to date. NPTf is not.
-+
-+
+-09-19 11:03  mmeineke
-+
-+
+        * utils/Makefile.in, src/Makefile.in: removed mpi++ from the
-+
+        makefile
-+
-+
+-09-19 11:01  gezelter
-+
-+
+        * samples/water/ssd.bass: goofing off to test NPTf and NPTi
-+
-+
+-09-19 11:01  gezelter
-+
-+
+        * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found
-+
+        (nearly) conserved quantities for both NPTi and NPTf
-+
-+
+-09-19 10:20  mmeineke
-+
-+
+        * utils/Makefile.in: fixed a typo in the makefile.
-+
-+
+-09-19 09:55  gezelter
-+
-+
+        * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp,
-+
+        samples/water/ssd.bass: [no log message]
-+
-+
+-09-19 09:22  tim
-+
-+
+        * libmdtools/: NPTi.cpp, NVT.cpp: [no log message]
-+
-+
+-09-17 09:22  mmeineke
-+
-+
+        * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now
-+
+        work with constraints.
-+
-+
+-09-16 15:02  tim
-+
-+
+        * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp,
-+
+        SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo
-+
-+
+        fixed conserved quantity in NPT (Still some small bug)
-+
-+
+        NPTi appears very stable.
-+
-+
+-09-15 11:52  tim
-+
-+
+        * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp,
-+
+        libmdtools/Integrator.hpp, libmdtools/NPTf.cpp,
-+
+        libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp,
-+
+        libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-+
+        libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp,
-+
+        libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp,
-+
+        utils/sysbuilder/bilayerSys.cpp: add conserved quantity to
-+
+        statWriter fix bug of vector wrapping at NPTi
-+
-+
+-09-12 15:51  mmeineke
-+
-+
+        * props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp,
-+
+        PairCorrType.hpp: added AllCorr. It eill still need some work
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * libmdtools/: Make.dep, Makefile.in: Added integrators to
-+
+        Makefile.in
-+
-+
+-09-12 11:20  gezelter
-+
-+
+        * ChangeLog: Entered changes for configure into ChangeLog
-+
-+
+-09-10 16:28  mmeineke
-+
-+
+        * 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,
-+
+        libmdtools/calc_eam.F90, libmdtools/config.h.in,
-+
+        libmdtools/definitions_module.F90, libmdtools/fInfo.c,
-+
+        libmdtools/fortranWrappers.cpp,
-+
+        libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90,
-+
+        libmdtools/simulation_module.F90, samples/Makefile,
-+
+        samples/Makefile.in, samples/alkane/Makefile,
-+
+        samples/alkane/Makefile.in, samples/argon/Makefile,
-+
+        samples/argon/Makefile.in, samples/argon/argon.bass,
-+
+        samples/beadLipid/Makefile, samples/beadLipid/Makefile.in,
-+
+        samples/lipid/Makefile, samples/lipid/Makefile.in,
-+
+        samples/water/Makefile, samples/water/Makefile.in, src/Makefile,
-+
+        src/Makefile.in, utils/Makefile, utils/Makefile.in,
-+
+        utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to
-+
+        autoconf / configure method of configuring OOPSE
-+
-+
+-09-04 16:48  mmeineke
-+
-+
+        * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-+
+        libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp,
-+
+        libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp,
-+
+        libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile:
-+
+        added resetTime to the Global namespace.
-+
-+
+        added ability to reset the integrators in the NVT and NPT family.
-+
-+
+-09-04 16:48  mmeineke
-+
-+
+        * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global
-+
+        namespace.
-+
-+
+-09-02 09:30  tim
-+
-+
+        * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp,
-+
+        ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of
-+
+        PolicyByMass
-+
-+
+-08-28 16:09  tim
-+
-+
+        * ChangeLog, libmdtools/GenericData.cpp,
-+
+        libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp,
-+
+        libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex
-+
-+
+-08-28 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
+-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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+Removed lines
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Comparing trunk/OOPSE/ChangeLog (file contents): Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs. Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC

Diff Legend

Comparing trunk/OOPSE/ChangeLog (file contents):
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 927 by tim, Mon Jan 12 22:54:42 2004 UTC