[ViewVC] Diff of: group/trunk/OOPSE-4/ChangeLog

Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2337 by chrisfen, Wed Sep 28 18:46:04 2005 UTC vs.
Revision 2727 by chrisfen, Fri Apr 21 19:32:07 2006 UTC

-+
+-04-20 23:19  chrisfen
-+
-+
+        * samples/water/spce/spce.md,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added...
-+
-+
+-04-20 17:02  chrisfen
-+
-+
+        * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky
-+
-+
+-04-20 14:24  gezelter
-+
-+
+        * samples/metals/EAM/Au_bulk_voter.md,
-+
+        samples/metals/Sutton-Chen/Au_bulk_SC.md,
-+
+        samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp,
-+
+        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90,
-+
+        src/UseTheForce/DarkSide/eam.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90,
-+
+        src/UseTheForce/DarkSide/suttonchen.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo_interface.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo_interface.h,
-+
+        src/utils/interpolation.F90: Complete rewrite of spline code and
-+
+        everything that uses it.
-+
-+
+-04-17 17:49  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4, samples/argon/500.md,
-+
+        samples/metals/EAM/Au_bulk_voter.md,
-+
+        samples/metals/Sutton-Chen/Au_bulk_SC.md,
-+
+        samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90,
-+
+        src/UseTheForce/DarkSide/interpolation.F90,
-+
+        src/UseTheForce/DarkSide/sticky.F90,
-+
+        src/UseTheForce/DarkSide/suttonchen.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo.F90,
-+
+        src/applications/hydrodynamics/Hydro.ggo,
-+
+        src/applications/hydrodynamics/HydroCmd.c,
-+
+        src/applications/hydrodynamics/HydroCmd.h,
-+
+        src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp,
-+
+        src/utils/interpolation.F90: Many performance improvements
-+
-+
+-04-15 22:51  chrisfen
-+
-+
+        * configure, samples/argon/500.md, src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/fSwitchingFunction.h,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90,
-+
+        src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to
-+
+        switcheroo
-+
-+
+-04-15 17:58  chrisfen
-+
-+
+        * src/utils/Makefile.in: Since status.F90 is used by
-+
+        interpolation.F90, the former needs to be listed above the later in
-+
+        the Makefile.
-+
-+
+-04-14 17:59  gezelter
-+
-+
+        * src/utils/interpolation.F90: changed the interface a bit
-+
-+
+-04-14 17:49  gezelter
-+
-+
+        * src/utils/interpolation.F90: added some logical flags
-+
-+
+-04-14 17:06  chrisfen
-+
-+
+        * src/utils/interpolation.F90: Wiped the spline with derivatives
-+
+        and corrected a boundary comparision error by eliminating the
-+
+        check.  This algorithm REQUIRES known first derivatives at the
-+
+        endpoints.
-+
-+
+-04-14 16:04  gezelter
-+
-+
+        * src/utils/: Makefile.in, interpolation.F90: bug fixes for
-+
+        interpolation module
-+
-+
+-04-14 15:57  gezelter
-+
-+
+        * src/utils/interpolation.F90: Heavily modified interpolation
-+
+        module, also moved to "utils"
-+
-+
+-04-12 17:15  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation
-+
+        module.
-+
-+
+-04-11 11:33  gezelter
-+
-+
+        * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c,
-+
+        StaticPropsCmd.h: [no log message]
-+
-+
+-04-03 11:37  chuckv
-+
-+
+        * configure, ac-tools/aclocal.m4, make/Makefile.in,
-+
+        src/UseTheForce/DarkSide/simParallel.F90: Added status module to
-+
+        simParallel for error reporting.
-+
-+
+-03-31 13:09  tim
-+
-+
+        * src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now
-+
-+
+-03-30 16:08  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug
-+
+        where SCList capacity was not reset to zero on destruction.
-+
-+
+-03-30 14:37  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
-+
+        More testing of nanoparticleBuilder.
-+
-+
+-03-29 17:24  chuckv
-+
-+
+        * src/mdParser/SimplePreprocessor.hpp: Added check to make sure md
-+
+        file exists.
-+
-+
+-03-29 14:17  chuckv
-+
-+
+        * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp,
-+
+        lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed
-+
+        latticeOrt in shapedlatice and latticebuilder.
-+
-+
+-03-29 13:11  tim
-+
-+
+        * src/applications/dynamicProps/: DipoleCorrFunc.cpp,
-+
+        LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem
-+
+        in calculating correlation functions
-+
-+
+-03-29 13:09  tim
-+
-+
+        * src/applications/hydrodynamics/: ApproximationModel.cpp,
-+
+        ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo,
-+
+        HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1)
-+
+        RoughShell Model is working; (20)Adding a new option into Hydro
-+
+        which allows user to generate the beads only
-+
-+
+-03-27 11:21  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/Makefile: Makefile for
-+
+        nanoparticle builder.
-+
-+
+-03-27 11:03  chuckv
-+
-+
+        * make/Makefile.in, src/lattice/shapedLattice.cpp,
-+
+        src/lattice/shapedLattice.hpp: Added nanoparticle builder to
-+
+        makefile
-+
-+
+-03-24 15:46  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
-+
+        Debugging changes to nanoparticle builder.
-+
-+
+-03-24 12:29  tim
-+
-+
+        * src/applications/dynamicProps/: DynamicProps.cpp,
-+
+        DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile,
-+
+        RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps
-+
-+
+-03-24 11:49  tim
-+
-+
+        * src/applications/dynamicProps/: DynamicProps.cpp,
-+
+        DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile,
-+
+        RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation
-+
+        function. The command line option for DynamicProps is now changed.
-+
+        --rcorr is for position correlation and --rmsd is for mean square
-+
+        displacement.
-+
-+
+-03-23 10:03  tim
-+
-+
+        * src/applications/hydrodynamics/: AnalyticalModel.cpp,
-+
+        AnalyticalModel.hpp, ApproximationModel.cpp,
-+
+        ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads
-+
+        method
-+
-+
+-03-23 10:02  tim
-+
-+
+        * src/io/Globals.hpp: remove a unknown method
-+
-+
+-03-23 10:00  tim
-+
-+
+        * src/math/CholeskyDecomposition.hpp: The off diagnal is not set
-+
-+
+-03-23 09:59  tim
-+
-+
+        * src/mdParser/SimplePreprocessor.hpp: Throw exception if the file
-+
+        can not be opened for preprocessing
-+
-+
+-03-22 15:57  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
-+
+        shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added
-+
+        shaped lattice.
-+
-+
+-03-21 10:33  tim
-+
-+
+        * src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug
-+
+        in calculating hydrodynamics tensor when the radius of beads are
-+
+        not the same
-+
-+
+-03-20 19:26  tim
-+
-+
+        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
-+
+        applications/hydrodynamics/BeadModel.cpp,
-+
+        applications/hydrodynamics/ShapeBuilder.cpp,
-+
+        integrators/LDForceManager.cpp: Fix a bug in friction calculation
-+
+        for ellipsoid
-+
-+
+-03-20 14:12  tim
-+
-+
+        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
-+
+        applications/hydrodynamics/Ellipsoid.cpp,
-+
+        applications/hydrodynamics/Ellipsoid.hpp,
-+
+        applications/hydrodynamics/ShapeBuilder.cpp,
-+
+        integrators/LDForceManager.cpp: Verify the correctness of
-+
+        Ellipsoid's hydrodynamics properties
-+
-+
+-03-17 18:51  tim
-+
-+
+        * src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New
-+
+        version of Hydro is working now.
-+
-+
+-03-17 18:20  tim
-+
-+
+        * src/: applications/hydrodynamics/AnalyticalModel.cpp,
-+
+        applications/hydrodynamics/AnalyticalModel.hpp,
-+
+        applications/hydrodynamics/ApproximationModel.cpp,
-+
+        applications/hydrodynamics/ApproximationModel.hpp,
-+
+        applications/hydrodynamics/BeadModel.hpp,
-+
+        applications/hydrodynamics/CompositeShape.cpp,
-+
+        applications/hydrodynamics/CompositeShape.hpp,
-+
+        applications/hydrodynamics/Ellipsoid.cpp,
-+
+        applications/hydrodynamics/Ellipsoid.hpp,
-+
+        applications/hydrodynamics/Hydro.cpp,
-+
+        applications/hydrodynamics/Hydro.ggo,
-+
+        applications/hydrodynamics/HydroCmd.c,
-+
+        applications/hydrodynamics/HydroCmd.h,
-+
+        applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        applications/hydrodynamics/HydrodynamicsModel.hpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelCreator.hpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelFactory.cpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelFactory.hpp,
-+
+        applications/hydrodynamics/Makefile,
-+
+        applications/hydrodynamics/RoughShell.cpp,
-+
+        applications/hydrodynamics/RoughShell.hpp,
-+
+        applications/hydrodynamics/Shape.hpp,
-+
+        applications/hydrodynamics/ShapeBuilder.cpp,
-+
+        applications/hydrodynamics/ShapeBuilder.hpp,
-+
+        applications/hydrodynamics/Spheric.cpp,
-+
+        applications/hydrodynamics/Spheric.hpp,
-+
+        applications/hydrodynamics/StuntDoubleShape.cpp,
-+
+        applications/hydrodynamics/StuntDoubleShape.hpp,
-+
+        integrators/LDForceManager.cpp, integrators/LDForceManager.hpp,
-+
+        io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp,
-+
+        utils/HydroProps.hpp: refactor Hydrodynamics module.
-+
-+
+-03-17 11:10  chuckv
-+
-+
+        * src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile:
-+
+        Generic Shaped Lattice for oopse. Can overload to get spherical or
-+
+        nanorod.
-+
-+
+-03-16 17:50  tim
-+
-+
+        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        integrators/LDForceManager.cpp, math/MersenneTwister.hpp:
-+
+        LagevinDynamics is working?
-+
-+
+-03-16 16:52  gezelter
-+
-+
+        * src/applications/hydrodynamics/RoughShell.hpp: fixed a const
-+
+        problem
-+
-+
+-03-15 17:08  tim
-+
-+
+        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit
-+
+        conversion for diffusion tensor is wrong
-+
-+
+-03-15 16:28  tim
-+
-+
+        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        utils/NumericConstant.hpp: change the epsilon of numeric_limit
-+
-+
+-03-15 15:58  tim
-+
-+
+        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting
-+
+        the unit in HydrodynamicsModel
-+
-+
+-03-15 12:35  tim
-+
-+
+        * src/primitives/RigidBody.cpp: using setFrc in
-+
+        RigidBody::calcForcesAndTorques will discard if there are force and
-+
+        torque applied in rigid body itself. use addFrc instead.
-+
-+
+-03-15 10:51  tim
-+
-+
+        * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp,
-+
+        RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel
-+
-+
+-03-15 10:50  tim
-+
-+
+        * make/Makefile.in, src/applications/hydrodynamics/Makefile: adding
-+
+        hydrodynamics module into build system
-+
-+
+-03-14 18:46  tim
-+
-+
+        * src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition
-+
-+
+-03-13 17:42  tim
-+
-+
+        * src/: applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        applications/hydrodynamics/HydrodynamicsModel.hpp,
-+
+        applications/hydrodynamics/StuntDoubleShape.cpp,
-+
+        applications/hydrodynamics/StuntDoubleShape.hpp,
-+
+        brains/Register.cpp, integrators/LDForceManager.cpp,
-+
+        integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp,
-+
+        integrators/LangevinDynamics.hpp, integrators/Makefile,
-+
+        io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp,
-+
+        math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in
-+
+        progress
-+
-+
+-03-07 11:43  gezelter
-+
-+
+        * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a
-+
+        double/int bug.  Surprised no one ever noticed before...
-+
-+
+-02-24 16:17  tim
-+
-+
+        * src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs
-+
+        in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out
-+
+        product of Rij
-+
-+
+-02-23 18:16  tim
-+
-+
+        * src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo,
-+
+        HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp,
-+
+        HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp,
-+
+        HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp,
-+
+        MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp,
-+
+        StuntDoubleShape.hpp: Bead Model is working
-+
-+
+-02-22 15:35  tim
-+
-+
+        * src/: applications/hydrodynamics/Hydro.cpp,
-+
+        applications/hydrodynamics/Hydro.ggo,
-+
+        applications/hydrodynamics/HydroCmd.c,
-+
+        applications/hydrodynamics/HydroCmd.h,
-+
+        applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        applications/hydrodynamics/HydrodynamicsModel.hpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelCreator.hpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelFactory.cpp,
-+
+        applications/hydrodynamics/HydrodynamicsModelFactory.hpp,
-+
+        applications/hydrodynamics/MoleculeShape.cpp,
-+
+        applications/hydrodynamics/MoleculeShape.hpp,
-+
+        math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp,
-+
+        math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics
-+
+        Module
-+
-+
+-02-16 17:05  gezelter
-+
-+
+        * src/brains/Snapshot.cpp: fixed a spelling error
-+
-+
+-02-16 16:40  gezelter
-+
-+
+        * src/: UseTheForce/doForces.F90,
-+
+        UseTheForce/DarkSide/simulation.F90, math/Makefile,
-+
+        math/linearAlgebra.F90: fixed a problem with cutoff radii being set
-+
+        larger than 1/2 the length of the shortest box dimension.  added a
-+
+        few fortran utility routines
-+
-+
+-02-15 15:46  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp,
-+
+        sphericalNanoparticle.hpp: Changed Names of class files.
-+
-+
+-02-10 10:45  kdaily
-+
-+
+        * src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log
-+
+        message]
-+
-+
+-02-10 10:12  tim
-+
-+
+        * src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in
-+
+        converting integer to double
-+
-+
+-02-08 13:21  chrisfen
-+
-+
+        * forceFields/DUFF2.frc: added DPD molecule type parameters
-+
-+
+-02-07 11:39  tim
-+
-+
+        * src/applications/dynamicProps/: DipoleCorrFunc.cpp,
-+
+        LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of
-+
+        trajectory file during analysis
-+
-+
+-02-02 12:14  tim
-+
-+
+        * src/: math/Polynomial.hpp, math/SquareMatrix3.hpp,
-+
+        types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug
-+
+        in AtomStamp where orientation is not set correctly.
-+
-+
+-02-02 11:49  gezelter
-+
-+
+        * src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that
-+
+        contain directional atoms
-+
-+
+-02-02 10:49  xsun
-+
-+
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor
-+
+        for GBlipid atom type
-+
-+
+-02-01 21:57  gezelter
-+
-+
+        * make/Makefile.in: added CXXFLAGS to the LinkOptions to allow
-+
+        compilation with icc9 (skipping the gcc-4 std c++ libraries).
-+
-+
+-02-01 16:06  chrisfen
-+
-+
+        * src/brains/SimInfo.cpp: Missing brace caused the last commit not
-+
+        to build
-+
-+
+-02-01 15:54  chrisfen
-+
-+
+        * samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to
-+
+        cutoff radius setting to a more logical procedure - still may
-+
+        change...
-+
-+
+-02-01 12:26  gezelter
-+
-+
+        * src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp:
-+
+        Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
-+
-+
+-01-30 17:25  tim
-+
-+
+        * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
-+
+        applications/dynamicProps/DynamicProps.cpp,
-+
+        applications/dynamicProps/DynamicProps.ggo,
-+
+        applications/dynamicProps/DynamicPropsCmd.c,
-+
+        applications/dynamicProps/DynamicPropsCmd.h,
-+
+        applications/dynamicProps/LegendreCorrFunc.cpp,
-+
+        applications/dynamicProps/LegendreCorrFunc.hpp,
-+
+        applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp,
-+
+        math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp:
-+
+        Adding :LegendrePolynomial
-+
-+
+-01-19 17:54  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/: Makefile,
-+
+        nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to
-+
+        nanoparticle builder
-+
-+
+-01-18 16:08  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/Makefile: Added Makefile for
-+
+        nanoparticle builder.
-+
-+
+-01-17 11:16  gezelter
-+
-+
+        * AUTHORS, README: Cleaning up for 3.0.1 release
-+
-+
+-01-17 10:50  gezelter
-+
-+
+        * ChangeLog: Prepping 3.0.1 release
-+
-+
+-01-17 10:32  gezelter
-+
-+
+        * src/config.h.in: new version number
-+
-+
+-01-17 10:32  gezelter
-+
-+
+        * doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html,
-+
+        definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png,
-+
+        oopseManual.pdf: Updated Documentation
-+
-+
+-01-16 18:10  gezelter
-+
-+
+        * ChangeLog, README: Getting ready for release!
-+
-+
+-01-16 10:26  gezelter
-+
-+
+        * configure: Testing commit
-+
-+
+-01-13 16:57  chuckv
-+
-+
+        * src/: UseTheForce/SC_FF.cpp,
-+
+        applications/nanoparticleBuilder/sphericalNanoparticle.cpp,
-+
+        io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals.
-+
+        Handled by forceField now.
-+
-+
+-01-13 14:17  chuckv
-+
-+
+        * src/io/Globals.cpp: Added NPAT to Globals integrators.
-+
-+
+-01-13 11:33  gezelter
-+
-+
+        * Makefile: [no log message]
-+
-+
+-01-13 11:26  gezelter
-+
-+
+        * Makefile: testing to make sure GNU make is the make that was used
-+
+        to build OOPSE
-+
-+
+-01-13 10:48  gezelter
-+
-+
+        * configure, ac-tools/configure.in: changed compiler search order
-+
-+
+-01-12 19:09  chuckv
-+
-+
+        * forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc,
-+
+        samples/metals/Sutton-Chen/Au_bulk.in,
-+
+        samples/metals/Sutton-Chen/Au_bulk_QSC.md,
-+
+        samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen
-+
+        units
-+
-+
+-01-12 16:16  gezelter
-+
-+
+        * LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some
-+
+        version info and the copyright date
-+
-+
+-01-12 15:52  gezelter
-+
-+
+        * src/config.h.in: added some missing checks for header files
-+
+        (particularly zlib.h), used autoheader to help generate config.h.in
-+
-+
+-01-12 15:51  gezelter
-+
-+
+        * configure, ac-tools/configure.in: added some missing checks for
-+
+        header files (particularly zlib.h)
-+
-+
+-01-12 15:19  gezelter
-+
-+
+        * make/Makefile.in: fixed a dependency problem for the Executable
-+
+        builds
-+
-+
+-01-12 15:02  gezelter
-+
-+
+        * samples/gbljtest/Makefile: Missing Makefile in this sample
-+
+        directory
-+
-+
+-01-12 15:01  gezelter
-+
-+
+        * make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile:
-+
+        Old makefile.in no longer required
-+
-+
+-01-12 15:01  gezelter
-+
-+
+        * forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff
-+
+        needs to be installed
-+
-+
+-01-12 14:56  chuckv
-+
-+
+        * src/io/DumpWriter.cpp: Changed formating.
-+
-+
+-01-12 11:47  chrisfen
-+
-+
+        * samples/water/tip4p/tp4.md,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        src/UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        src/brains/SimInfo.cpp: unifying function name in electrostatics
-+
-+
+-01-12 11:04  tim
-+
-+
+        * samples/metals/: EAM/nanoparticle/Makefile,
-+
+        EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile,
-+
+        Sutton-Chen/Makefile: fix make install problem for metals samples
-+
-+
+-01-12 10:22  tim
-+
-+
+        * make/Makefile.in: remove samples/metals from install list.
-+
-+
+-01-12 09:31  tim
-+
-+
+        * src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not
-+
+        handle multiple line macro, just convert multiple line macro into
-+
+        single line macro.
-+
-+
+-01-11 23:13  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some
-+
+        changes to electrostatics for shifted-potential and shifted-force
-+
+        with mono and multipoles
-+
-+
+-01-11 18:04  gezelter
-+
-+
+        * src/config.h.in, src/UseTheForce/doForces_interface.h,
-+
+        src/UseTheForce/DarkSide/atype_interface.h,
-+
+        src/UseTheForce/DarkSide/eam_interface.h,
-+
+        src/UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        src/UseTheForce/DarkSide/fForceOptions_interface.h,
-+
+        src/UseTheForce/DarkSide/gb_interface.h,
-+
+        src/UseTheForce/DarkSide/lj_interface.h,
-+
+        src/UseTheForce/DarkSide/shapes_interface.h,
-+
+        src/UseTheForce/DarkSide/simParallel_interface.h,
-+
+        src/UseTheForce/DarkSide/simulation_interface.h,
-+
+        src/UseTheForce/DarkSide/sticky_interface.h,
-+
+        src/UseTheForce/DarkSide/suttonchen_interface.h,
-+
+        src/UseTheForce/DarkSide/switcheroo_interface.h,
-+
+        src/mdParser/MDParser.g, src/profiling/mdProfile.cpp,
-+
+        src/utils/fError.c, configure, make/Makefile.in: autoconf
-+
+        modernization and cruft removal
-+
-+
+-01-11 18:04  gezelter
-+
-+
+        * ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf
-+
+        modernization and cruft-removal
-+
-+
+-01-11 17:50  tim
-+
-+
+        * src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix
-+
+        some error messages
-+
-+
+-01-11 14:01  tim
-+
-+
+        * src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp,
-+
+        io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp,
-+
+        types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp,
-+
+        types/TorsionStamp.hpp, utils/OOPSEException.hpp,
-+
+        utils/StringUtils.hpp: instead of printing to std::cout, throwing
-+
+        an exception when error is found.
-+
-+
+-01-11 13:41  gezelter
-+
-+
+        * src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling
-+
+        error
-+
-+
+-01-10 17:55  chuckv
-+
-+
+        * forceFields/SuttonChen.frc: Changed conversion factor.
-+
-+
+-01-10 16:14  chuckv
-+
-+
+        * samples/metals/Sutton-Chen/Au_bulk_SC.md,
-+
+        src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be
-+
+        working now.
-+
-+
+-01-09 17:22  chuckv
-+
-+
+        * src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC
-+
-+
+-01-09 17:14  tim
-+
-+
+        * src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp,
-+
+        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
-+
+        StaticPropsCmd.h: fixing RhoZ
-+
-+
+-01-09 14:26  chuckv
-+
-+
+        * forceFields/SuttonChen.frc,
-+
+        samples/metals/Sutton-Chen/Au_bulk_SC.md,
-+
+        src/io/LennardJonesAtomTypesSectionParser.cpp,
-+
+        src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to
-+
+        section parsers.
-+
-+
+-01-09 14:11  tim
-+
-+
+        * src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp,
-+
+        utils/StringUtils.hpp: replace isType<int> with isInteger
-+
-+
+-01-06 16:15  tim
-+
-+
+        * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra
-+
+        forceFieldOptions from SC_FF
-+
-+
+-01-06 15:27  chuckv
-+
-+
+        * forceFields/SuttonChen.frc: Add force file.
-+
-+
+-12-31 17:42  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer
-+
+        segfaults or produces 0 potential, but rather produces Inf for the
-+
+        potential. Progress....
-+
-+
+-12-30 18:15  chuckv
-+
-+
+        * samples/metals/Sutton-Chen/Au_bulk_SC.md,
-+
+        src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp,
-+
+        src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More
-+
+        Sutton-Chen bug fixes.
-+
-+
+-12-30 16:25  tim
-+
-+
+        * src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range
-+
+        potential return from fortran is already accumulated, it should not
-+
+        be accumulated again; nGroupTypesCol is not initialized;
-+
+        GroupMaxCutoffCol is not allocated;
-+
-+
+-12-30 10:32  tim
-+
-+
+        * make/Makefile.in, src/brains/SimCreator.cpp: In order to compile
-+
+        MPI version, we need to cast const char* to void* for
-+
+        stringstream.str(); Previous Makefile use bjects of single version
-+
+        to make the MPI library;
-+
-+
+-12-29 19:18  chuckv
-+
-+
+        * make/Makefile.in, samples/metals/Makefile,
-+
+        src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90,
-+
+        src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes.
-+
+        Almost there...
-+
-+
+-12-29 15:19  chuckv
-+
-+
+        * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in
-+
+        forcefield.
-+
-+
+-12-29 15:07  chuckv
-+
-+
+        * samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile,
-+
+        metals.md: added files for sutton-chen
-+
-+
+-12-29 11:37  chuckv
-+
-+
+        * samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile,
-+
+        metals.md: More cvs changing.
-+
-+
+-12-29 11:34  chuckv
-+
-+
+        * samples/metals/Au_nanoparticle.in: More moving...
-+
-+
+-12-29 11:33  chuckv
-+
-+
+        * samples/metals/EAM/nanoparticle/:
-+
+        Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md,
-+
+        Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More
-+
+        changes to directory structure.
-+
-+
+-12-29 11:21  chuckv
-+
-+
+        * samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md,
-+
+        Au_bulk_voter.md, Makefile, metals.md: More Directory changes...
-+
-+
+-12-29 11:17  chuckv
-+
-+
+        * samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in,
-+
+        Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md,
-+
+        Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of
-+
+        directory structure
-+
-+
+-12-29 11:03  chuckv
-+
-+
+        * src/: UseTheForce/DarkSide/fForceOptions_interface.F90,
-+
+        brains/SimCreator.cpp: Fixed issue with symbol naming and added
-+
+        call to set force options in SimCreator.
-+
-+
+-12-28 16:44  chuckv
-+
-+
+        * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More
-+
+        changes to forcefield options.
-+
-+
+-12-28 16:42  chuckv
-+
-+
+        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options
-+
+        passed to fortran.
-+
-+
+-12-23 18:04  chuckv
-+
-+
+        * src/: UseTheForce/DarkSide/fForceOptions_interface.h,
-+
+        io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option
-+
+        changes.
-+
-+
+-12-16 16:52  tim
-+
-+
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-+
+        src/config.h.in, src/UseTheForce/DarkSide/gb.F90,
-+
+        src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp,
-+
+        src/openbabel/chains.cpp, src/openbabel/chiral.cpp,
-+
+        src/openbabel/data.cpp, src/openbabel/fingerprint.cpp,
-+
+        src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp,
-+
+        src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp,
-+
+        src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp,
-+
+        src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp,
-+
+        src/openbabel/obbond.cpp, src/openbabel/oberror.cpp,
-+
+        src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp,
-+
+        src/openbabel/obutil.cpp, src/openbabel/patty.cpp,
-+
+        src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp,
-+
+        src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp,
-+
+        src/openbabel/ring.cpp, src/openbabel/rotor.cpp,
-+
+        src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp,
-+
+        src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed
-+
+        __FUNCTION__ to __func__ to match C99 standard, and then added an
-+
+        autoconf test to check for __func__ usability.  Changed some
-+
+        default compile flags for the Sun architecture
-+
-+
+-12-16 14:01  gezelter
-+
-+
+        * ac-tools/AC_CXX_HAVE_STL.m4: added the STL check
-+
-+
+-12-16 13:55  tim
-+
-+
+        * src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor
-+
+        change to build oopse under solaris
-+
-+
+-12-16 13:26  tim
-+
-+
+        * src/: brains/SimCreator.cpp, io/Globals.cpp,
-+
+        types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library
-+
+        came with SUN compiler does not have a conforming std::use_facet,
-+
+        define a macro to handle it. Adding exception handling to
-+
+        SimCreator.
-+
-+
+-12-16 10:53  gezelter
-+
-+
+        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
-+
+        GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom
-+
+        which was living inside the GB particle.  No alien-like ripping out
-+
+        of the stomach was required.
-+
-+
+-12-15 21:57  tim
-+
-+
+        * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
-+
+        MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
-+
+        MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp:
-+
+        replace grammar for numerical parsing
-+
-+
+-12-15 16:43  gezelter
-+
-+
+        * src/UseTheForce/doForces.F90: fixed a cutoff bug
-+
-+
+-12-15 09:48  gezelter
-+
-+
+        * src/antlr/: CharScanner.hpp, config.hpp: Removing compiler
-+
+        dependencies and replacing them with real autoconf checks
-+
-+
+-12-15 09:47  gezelter
-+
-+
+        * configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4,
-+
+        ac-tools/configure.in, src/config.h.in: Adding checks for various
-+
+        features used by ANTLR
-+
-+
+-12-14 13:02  tim
-+
-+
+        * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp,
-+
+        MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp,
-+
+        MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a
-+
+        nasty negative integer parsing problem by refining the grammar
-+
-+
+-12-12 14:32  gezelter
-+
-+
+        * src/: UseTheForce/doForces_interface.F90,
-+
+        UseTheForce/doForces_interface.h,
-+
+        UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        brains/MoleculeCreator.cpp, brains/SimInfo.cpp,
-+
+        math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made
-+
+        some minor changes to allow compilation with the portland group
-+
+        compilers
-+
-+
+-12-10 11:54  tim
-+
-+
+        * src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation
-+
+        problem for icc7
-+
-+
+-12-09 16:18  gezelter
-+
-+
+        * src/utils/CaseConversion.hpp: added missing include
-+
-+
+-12-09 12:11  gezelter
-+
-+
+        * configure, ac-tools/aclocal.m4: added some checks for pathscale
-+
+        compiler
-+
-+
+-12-08 17:05  gezelter
-+
-+
+        * src/io/ForceFieldOptions.cpp: added copyright
-+
-+
+-12-08 17:04  gezelter
-+
-+
+        * src/UseTheForce/doForces.F90: added info printout
-+
-+
+-12-08 17:04  gezelter
-+
-+
+        * configure, ac-tools/configure.in: added pathscale
-+
-+
+-12-08 10:38  chuckv
-+
-+
+        * src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp,
-+
+        UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp,
-+
+        UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp,
-+
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
-+
+        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
-+
+        io/ChargeAtomTypesSectionParser.hpp,
-+
+        io/DirectionalAtomTypesSectionParser.cpp,
-+
+        io/DirectionalAtomTypesSectionParser.hpp,
-+
+        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
-+
+        io/GayBerneAtomTypesSectionParser.cpp,
-+
+        io/GayBerneAtomTypesSectionParser.hpp,
-+
+        io/MultipoleAtomTypesSectionParser.cpp,
-+
+        io/MultipoleAtomTypesSectionParser.hpp,
-+
+        io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
-+
+        io/ShapeAtomTypesSectionParser.cpp,
-+
+        io/ShapeAtomTypesSectionParser.hpp,
-+
+        io/StickyAtomTypesSectionParser.cpp,
-+
+        io/StickyAtomTypesSectionParser.hpp,
-+
+        io/StickyPowerAtomTypesSectionParser.cpp,
-+
+        io/StickyPowerAtomTypesSectionParser.hpp,
-+
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp:
-+
+        Wow thats alot o' files. Now passing forceFieldOptions to all of
-+
+        the parsers.
-+
-+
+-12-07 18:10  chuckv
-+
-+
+        * src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp,
-+
+        SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things....
-+
+        Started adding support for ForceOptions to section parsers.
-+
-+
+-12-07 18:01  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/gb_interface.h: [no log message]
-+
-+
+-12-07 18:00  chuckv
-+
-+
+        * src/io/: LennardJonesAtomTypesSectionParser.cpp,
-+
+        LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to
-+
+        section parser
-+
-+
+-12-07 14:58  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90,
-+
+        lj_interface.h, suttonchen.F90, suttonchen_interface.F90,
-+
+        suttonchen_interface.h: Removed geometric distance mixing from
-+
+        individual modules and now use force options to detemine what the
-+
+        deal is.
-+
-+
+-12-07 14:46  chuckv
-+
-+
+        * src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90:
-+
+        Further fixes for compiler issues.
-+
-+
+-12-07 14:44  chuckv
-+
-+
+        * src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue.
-+
-+
+-12-07 14:38  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90,
-+
+        fForceOptions_interface.F90, fForceOptions_interface.h: Added
-+
+        support for fortran force options.
-+
-+
+-12-06 16:01  tim
-+
-+
+        * src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion
-+
-+
+-12-06 14:26  chuckv
-+
-+
+        * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC.
-+
-+
+-12-06 12:53  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
-+
+        GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned
-+
+        crystal
-+
-+
+-12-06 12:52  chuckv
-+
-+
+        * src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for
-+
+        dumpwriter.
-+
-+
+-12-06 11:49  tim
-+
-+
+        * samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md,
-+
+        argon/ar864.md, argon/argonNVT.md, argon/lj.md,
-+
+        dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md,
-+
+        dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md,
-+
+        gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md,
-+
+        gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md,
-+
+        lipid/5x5.md, lipid/lipid.md, lipid/water.md,
-+
+        metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md,
-+
+        metals/Au_bulk_voter.md, metals/Au_nanoparticle.md,
-+
+        metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md,
-+
+        minimizer/water.md, shape/linear.md,
-+
+        thermoIntegration/liquid/ssde.md,
-+
+        thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md,
-+
+        thermoIntegration/solid/water.md, water/dimer/cl.md,
-+
+        water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md,
-+
+        water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md,
-+
+        water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md,
-+
+        water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md,
-+
+        water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md,
-+
+        water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md,
-+
+        water/tip3p_ice/tp3.md, water/tip3p_ice/water.md,
-+
+        water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md,
-+
+        zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated
-+
+        keywords from samples
-+
-+
+-12-05 18:37  tim
-+
-+
+        * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp,
-+
+        Globals.cpp, Makefile: Fix parsing error in OptionSectionParser
-+
-+
+-12-05 17:23  gezelter
-+
-+
+        * src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp,
-+
+        UseTheForce/Makefile, brains/Register.cpp,
-+
+        io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding
-+
+        handler for CLAY force field
-+
-+
+-12-05 16:45  chuckv
-+
-+
+        * src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug
-+
+        in openbabel.
-+
-+
+-12-05 14:10  tim
-+
-+
+        * src/types/MoleculeStamp.cpp: reformat error message
-+
-+
+-12-05 14:07  gezelter
-+
-+
+        * forceFields/CLAYFF.frc: Adding .frc file for CLAYFF
-+
-+
+-12-05 13:23  tim
-+
-+
+        * src/: types/AtomStamp.cpp, types/AtomStamp.hpp,
-+
+        types/BendStamp.hpp, types/MoleculeStamp.cpp,
-+
+        types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp:
-+
+        adding more checking for topology
-+
-+
+-12-02 17:37  gezelter
-+
-+
+        * src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon
-+
+        removal
-+
-+
+-12-02 17:37  gezelter
-+
-+
+        * src/config.h.in: We've made big changes.  This isn't 2.0 anymore.
-+
-+
+-12-02 17:37  gezelter
-+
-+
+        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
-+
+        GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md,
-+
+        traditional.md: removing deprecated nAtoms and nComponents lines
-+
-+
+-12-02 15:34  tim
-+
-+
+        * src/selection/SelectionToken.cpp: adding SelectionToken.cpp
-+
-+
+-12-02 15:18  tim
-+
-+
+        * src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding
-+
+        FragmentStamp
-+
-+
+-12-02 15:11  gezelter
-+
-+
+        * src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no
-+
+        longer thrown with consts (fixes compilation bug on the Mac).
-+
-+
+-12-02 15:10  gezelter
-+
-+
+        * src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious
-+
+        printing out of timestep
-+
-+
+-12-02 15:10  gezelter
-+
-+
+        * src/brains/ForceManager.cpp: Got rid of spurious printing out of
-+
+        junk
-+
-+
+-12-02 15:10  gezelter
-+
-+
+        * make/Makefile.in: Change build process for libOOPSE.a so that the
-+
+        libraries aren't unpacked.  libOOPSE.a is now made directly from
-+
+        the object files
-+
-+
+-12-02 15:09  gezelter
-+
-+
+        * configure, ac-tools/configure.in: added check for egrep (grep -E)
-+
+        needed for new build of libOOPSE.a
-+
-+
+-12-02 13:43  tim
-+
-+
+        * src/types/DataHolder.hpp: adding DataHolder
-+
-+
+-12-02 12:01  gezelter
-+
-+
+        * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md,
-+
+        GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test
-+
+        case for the cutoff policies
-+
-+
+-12-02 10:38  tim
-+
-+
+        * make/Makefile.in: update Makefile
-+
-+
+-12-02 10:38  tim
-+
-+
+        * src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp,
-+
+        antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp,
-+
+        antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp,
-+
+        antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp,
-+
+        antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp,
-+
+        antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp,
-+
+        antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp,
-+
+        antlr/CharScanner.cpp, antlr/CharScanner.hpp,
-+
+        antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp,
-+
+        antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp,
-+
+        antlr/CommonASTWithHiddenTokens.cpp,
-+
+        antlr/CommonASTWithHiddenTokens.hpp,
-+
+        antlr/CommonHiddenStreamToken.cpp,
-+
+        antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp,
-+
+        antlr/CommonToken.hpp, antlr/IOException.hpp,
-+
+        antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp,
-+
+        antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp,
-+
+        antlr/Makefile, antlr/MismatchedCharException.cpp,
-+
+        antlr/MismatchedCharException.hpp,
-+
+        antlr/MismatchedTokenException.cpp,
-+
+        antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp,
-+
+        antlr/NoViableAltException.hpp,
-+
+        antlr/NoViableAltForCharException.cpp,
-+
+        antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp,
-+
+        antlr/Parser.hpp, antlr/ParserSharedInputState.hpp,
-+
+        antlr/RecognitionException.cpp, antlr/RecognitionException.hpp,
-+
+        antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp,
-+
+        antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp,
-+
+        antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp,
-+
+        antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp,
-+
+        antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp,
-+
+        antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp,
-+
+        antlr/TokenStreamHiddenTokenFilter.cpp,
-+
+        antlr/TokenStreamHiddenTokenFilter.hpp,
-+
+        antlr/TokenStreamIOException.hpp,
-+
+        antlr/TokenStreamRecognitionException.hpp,
-+
+        antlr/TokenStreamRetryException.hpp,
-+
+        antlr/TokenStreamRewriteEngine.cpp,
-+
+        antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp,
-+
+        antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp,
-+
+        antlr/TreeParser.cpp, antlr/TreeParser.hpp,
-+
+        antlr/TreeParserSharedInputState.hpp, antlr/config.hpp,
-+
+        applications/oopse/oopse.cpp, brains/ForceManager.cpp,
-+
+        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
-+
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        constraints/ZconstraintForceManager.cpp,
-+
+        integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp,
-+
+        io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h,
-+
+        io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp,
-+
+        io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile,
-+
+        io/ZConsReader.cpp, io/interface.c, io/make_nodes.c,
-+
+        io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h,
-+
+        io/parse_interface.h, io/parse_me.h, io/parse_tree.c,
-+
+        io/parse_tree.h, mdParser/FilenameObserver.cpp,
-+
+        mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp,
-+
+        mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g,
-+
+        mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp,
-+
+        mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g,
-+
+        mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp,
-+
+        mdParser/Makefile, mdParser/SimplePreprocessor.hpp,
-+
+        openbabel/obconversion.cpp, openbabel/oopseformat.cpp,
-+
+        openbabel/xyzformat.cpp, primitives/RigidBody.cpp,
-+
+        selection/DistanceFinder.cpp, selection/DistanceFinder.hpp,
-+
+        selection/IndexFinder.cpp, selection/IndexFinder.hpp,
-+
+        selection/Makefile, selection/NameFinder.cpp,
-+
+        selection/NameFinder.hpp, selection/SelectionCompiler.hpp,
-+
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
-+
+        selection/SelectionManager.hpp, selection/SelectionToken.hpp,
-+
+        selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp,
-+
+        types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp,
-+
+        types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp,
-+
+        types/Component.cpp, types/Component.hpp,
-+
+        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
-+
+        types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile,
-+
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
-+
+        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
-+
+        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
-+
+        types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp,
-+
+        types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp,
-+
+        utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp,
-+
+        utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp,
-+
+        utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the
-+
+        Link --> List Return of the Oject-Oriented replace yacc/lex parser
-+
+        with antlr parser
-+
-+
+-11-30 16:00  chuckv
-+
-+
+        * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to
-+
+        calculate rho(Z) to calculate density profiles for water slabs.
-+
-+
+-11-29 17:54  chuckv
-+
-+
+        * configure, ac-tools/configure.in: added checks for some functions
-+
+        to configure script
-+
-+
+-11-22 20:05  chuckv
-+
-+
+        * src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp,
-+
+        obbond.cpp: Changed file names that conflict w/ oopse file name
-+
+        object files.
-+
-+
+-11-21 17:59  gezelter
-+
-+
+        * src/utils/residentMem.c: compilation bug
-+
-+
+-11-21 17:59  gezelter
-+
-+
+        * src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp
-+
-+
+-11-21 17:59  gezelter
-+
-+
+        * src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes
-+
-+
+-11-21 17:59  gezelter
-+
-+
+        * src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation
-+
+        issue
-+
-+
+-11-21 17:58  gezelter
-+
-+
+        * src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90,
-+
+        doForces_interface.F90, doForces_interface.h, fForceOptions.h,
-+
+        notifyCutoffs.F90, notifyCutoffs_interface.F90,
-+
+        notifyCutoffs_interface.h, DarkSide/LJ.F90,
-+
+        DarkSide/electrostatic.F90, DarkSide/gb.F90,
-+
+        DarkSide/suttonchen.F90: Cutoff mixing fixes have been made.
-+
-+
+-11-21 11:22  tim
-+
-+
+        * src/io/ParamConstraint.cpp: Adding  ParamConstraint.cpp
-+
-+
+-11-21 09:59  tim
-+
-+
+        * forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt,
-+
+        atomtyp.txt, bondtyp.txt, element.txt, extable.txt,
-+
+        isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt,
-+
+        resdata.txt, torlib.txt, types.txt: adding openbabel data files
-+
-+
+-11-18 15:17  tim
-+
-+
+        * src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp:
-+
+        adding support for soft linking
-+
-+
+-11-18 15:17  tim
-+
-+
+        * make/Makefile.in: Adding support for soft linking
-+
-+
+-11-18 12:50  gezelter
-+
-+
+        * make/Makefile.in: Adding linking stuff
-+
-+
+-11-18 11:38  tim
-+
-+
+        * make/Makefile.in, src/applications/atom2mdin/Makefile,
-+
+        src/applications/atom2mdin/atom2mdin.cpp,
-+
+        src/applications/mdinConverter/Makefile,
-+
+        src/applications/mdinConverter/mdinConverter.cpp,
-+
+        src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp:
-+
+        rename mdinConverter to atom2mdin
-+
-+
+-11-17 15:44  gezelter
-+
-+
+        * src/openbabel/obconversion.cpp: fixed a bug
-+
-+
+-11-17 15:39  gezelter
-+
-+
+        * configure: Adding some config checks for OpenBabel codes we are
-+
+        using
-+
-+
+-11-17 15:39  gezelter
-+
-+
+        * ac-tools/configure.in: Adding some checks for OpenBabel code
-+
-+
+-11-17 15:39  gezelter
-+
-+
+        * src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel
-+
-+
+-11-17 15:38  gezelter
-+
-+
+        * src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp,
-+
+        bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp,
-+
+        fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp,
-+
+        obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp,
-+
+        patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp,
-+
+        residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp:
-+
+        Unifying config.h stuff and making sure the OpenBabel codes can
-+
+        find our default (and environment variable) Force Field
-+
+        directories.
-+
-+
+-11-17 13:35  tim
-+
-+
+        * src/io/ForceFieldOptions.hpp: adding ForceFieldOptions
-+
-+
+-11-16 18:10  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
-+
+        brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp,
-+
+        brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp,
-+
+        integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
-+
+        io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp,
-+
+        io/OptionSectionParser.hpp, io/ParamConstraint.hpp,
-+
+        io/SectionParser.hpp, io/SectionParserManager.cpp,
-+
+        io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp,
-+
+        math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp,
-+
+        primitives/Bend.hpp, primitives/GhostBend.cpp,
-+
+        primitives/GhostBend.hpp, primitives/GhostTorsion.cpp,
-+
+        primitives/GhostTorsion.hpp, primitives/Torsion.cpp,
-+
+        primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
-+
+        primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp,
-+
+        types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp,
-+
+        types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser
-+
+        get compiled
-+
-+
+-11-16 16:37  chuckv
-+
-+
+        * src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp,
-+
+        io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp,
-+
+        UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField
-+
+        optional parameters....
-+
-+
+-11-16 16:24  tim
-+
-+
+        * src/applications/mdinConverter/: Makefile, mdinConverter.cpp:
-+
+        adding mdinConverter
-+
-+
+-11-16 16:22  tim
-+
-+
+        * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp,
-+
+        fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp,
-+
+        gromos96format.cpp, gromos96format.hpp, oopseformat.cpp,
-+
+        oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp,
-+
+        povrayformat.hpp, smilesformat.cpp, smilesformat.hpp,
-+
+        tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp:
-+
+        adding more readers/writers
-+
-+
+-11-16 16:20  tim
-+
-+
+        * make/Makefile.in: adding openbabel
-+
-+
+-11-16 16:20  tim
-+
-+
+        * src/brains/: Register.cpp, Register.hpp: register openbabel
-+
+        readers/writers
-+
-+
+-11-16 14:57  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: included shifted
-+
+        potential self term
-+
-+
+-11-16 14:57  chrisfen
-+
-+
+        * samples/water/spce/spce.md: just some parameters
-+
-+
+-11-16 14:42  tim
-+
-+
+        * src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp,
-+
+        babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp,
-+
+        bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp,
-+
+        chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp,
-+
+        data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp,
-+
+        fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp,
-+
+        isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp,
-+
+        matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp,
-+
+        obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp,
-+
+        oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp,
-+
+        obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp,
-+
+        patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp,
-+
+        phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp,
-+
+        ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp,
-+
+        snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp,
-+
+        tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp,
-+
+        types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp,
-+
+        zipstreamimpl.hpp: adding openbabel
-+
-+
+-11-15 14:42  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary
-+
+        commented code
-+
-+
+-11-15 14:04  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the
-+
+        charge-charge interactions a bit...
-+
-+
+-11-15 14:03  chrisfen
-+
-+
+        * samples/water/spce/: spce.md, water.md: just playing
-+
-+
+-11-15 11:38  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the
-+
+        shifted_potential case
-+
-+
+-11-15 11:37  chrisfen
-+
-+
+        * samples/: argon/500.md, water/spce/spce.md, water/spce/water.md:
-+
+        just playing around - we need to refresh all the samples sometime
-+
+        soon...
-+
-+
+-11-15 11:18  chuckv
-+
-+
+        * src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made
-+
+        preforce calc public in suttonchen.
-+
-+
+-11-15 11:05  chuckv
-+
-+
+        * src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to
-+
+        SimInfo
-+
-+
+-11-15 11:01  chuckv
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h,
-+
+        DarkSide/simulation.F90: Added Sutton-Chen to force loop...
-+
-+
+-11-15 10:34  chuckv
-+
-+
+        * forceFields/Makefile: Added sutton-chen to makefile.
-+
-+
+-11-14 17:20  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: suttonchen.F90,
-+
+        suttonchen_interface.h: Build Fixes for sutton-chen.
-+
-+
+-11-14 17:03  chuckv
-+
-+
+        * src/io/Makefile: Missed makefile for sutton-chen.
-+
-+
+-11-14 17:03  chuckv
-+
-+
+        * src/UseTheForce/: Makefile, DarkSide/Makefile,
-+
+        DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff
-+
-+
+-11-14 16:29  chuckv
-+
-+
+        * src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp,
-+
+        io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp,
-+
+        UseTheForce/DarkSide/suttonchen.F90,
-+
+        UseTheForce/DarkSide/suttonchen_interface.F90,
-+
+        UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp,
-+
+        brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp,
-+
+        types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to
-+
+        fix do_forces to use Sutton-Chen.
-+
-+
+-11-11 12:21  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/: fSwitchingFunctionType.h,
-+
+        switcheroo_interface.F90, switcheroo_interface.h: Forgot to add
-+
+        some files
-+
-+
+-11-11 10:22  chrisfen
-+
-+
+        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp,
-+
+        io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial
-+
+        switching function option
-+
-+
+-11-11 10:21  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a
-+
+th order polynomial switching function
-+
-+
+-11-11 10:21  chrisfen
-+
-+
+        * samples/water/ssd/ssd.md: playing with switching functions again
-+
-+
+-11-11 10:21  chrisfen
-+
-+
+        * samples/argon/500.md: playing with switching functions
-+
-+
+-11-08 19:11  chuckv
-+
-+
+        * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force
-+
+        files for Sutton-Chen and Quantum Sutton-Chen
-+
-+
+-11-08 08:32  chrisfen
-+
-+
+        * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp,
-+
+        DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and
-+
+        ability to output forces and torques
-+
-+
+-11-08 08:32  chrisfen
-+
-+
+        * src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for
-+
+        output of forces and torques
-+
-+
+-11-08 08:31  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90:
-+
+        Working on shifted_force...
-+
-+
+-11-08 08:31  chrisfen
-+
-+
+        * samples/water/: spce/spce.md, ssde/ssde.md: Just testing...
-+
-+
+-11-03 18:22  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly
-+
+        commented section
-+
-+
+-11-03 18:12  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/fElectrostaticScreeningMethod.h,
-+
+        UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp,
-+
+        io/Globals.cpp, io/Globals.hpp: improvements in shifted-force
-+
-+
+-11-03 18:11  chrisfen
-+
-+
+        * samples/water/spce/spce.md: mmm...  damped shifted force...
-+
-+
+-11-03 18:06  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/suttonchen.F90: More work on SC.
-+
-+
+-11-02 18:50  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen.
-+
-+
+-11-02 16:01  chrisfen
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
-+
+        removed some test code
-+
-+
+-11-02 15:45  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the
-+
+        screening method header
-+
-+
+-11-02 15:36  chrisfen
-+
-+
+        * src/brains/SimInfo.cpp: again, changing how we deal with
-+
+        summation and screening methods
-+
-+
+-11-02 15:36  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        UseTheForce/DarkSide/fElectrostaticSummationMethod.h,
-+
+        io/Globals.cpp, io/Globals.hpp: changing how we deal with summation
-+
+        and screening methods
-+
-+
+-11-02 15:35  chrisfen
-+
-+
+        * src/UseTheForce/doForces.F90: debug stuff for rf removed
-+
-+
+-11-01 18:32  chuckv
-+
-+
+        * src/: UseTheForce/DarkSide/atype.F90,
-+
+        UseTheForce/DarkSide/atype_interface.F90,
-+
+        UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp,
-+
+        types/AtomTypeProperties.h: Added suppport to atypes for MEAM and
-+
+        sutton-chen
-+
-+
+-11-01 14:24  chrisfen
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
-+
+        removed some testing code...
-+
-+
+-11-01 14:14  chrisfen
-+
-+
+        * src/: brains/Register.cpp, brains/SimInfo.cpp,
-+
+        brains/fSimulation.h, integrators/IntegratorFactory.hpp,
-+
+        io/Globals.cpp: fixed a capitalization problem with NPT integrator
-+
+        initialization
-+
-+
+-11-01 14:13  chrisfen
-+
-+
+        * src/applications/oopse/oopse.cpp: nothing
-+
-+
+-11-01 14:09  chrisfen
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
-+
+        DarkSide/simulation.F90: still fixing up wolf...
-+
-+
+-11-01 13:29  chuckv
-+
-+
+        * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In
-+
+        process of adding sutton-chen forcefield.
-+
-+
+-10-26 18:32  chrisfen
-+
-+
+        * src/brains/SimInfo.cpp: changed the default switching radius to
-+
+% of rcut
-+
-+
+-10-26 18:31  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks
-+
+        to be working now - for charges and dipoles alike
-+
-+
+-10-26 18:31  chrisfen
-+
-+
+        * src/UseTheForce/doForces.F90: reaction field looks to be working
-+
+        now
-+
-+
+-10-26 18:30  chrisfen
-+
-+
+        * samples/water/ssdrf/water.md: added a test molecule
-+
-+
+-10-26 18:30  chrisfen
-+
-+
+        * forceFields/DUFF2.frc: added a test atom type
-+
-+
+-10-24 09:06  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole
-+
+        reaction field - don't know if it works...
-+
-+
+-10-23 16:08  chrisfen
-+
-+
+        * src/: UseTheForce/doForces.F90,
-+
+        UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp:
-+
+        streamlined reaction field for dipoles (now a good bit faster) and
-+
+        added reaction field for charges - still need to do charge-dipole
-+
+        RF
-+
-+
+-10-23 16:07  chrisfen
-+
-+
+        * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction
-+
+        field
-+
-+
+-10-23 16:06  chrisfen
-+
-+
+        * samples/water/spce/spce.md: reaction field now works for charges
-+
-+
+-10-20 15:27  tim
-+
-+
+        * src/primitives/Torsion.cpp: Fix the other branch of force
-+
+        calculation in Torision.cpp
-+
-+
+-10-19 14:24  chrisfen
-+
-+
+        * src/: UseTheForce/doForces.F90,
-+
+        UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp,
-+
+        brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals
-+
+        toUpper problems - these changes should fix those...
-+
-+
+-10-19 14:23  chrisfen
-+
-+
+        * samples/water/ssdrf/ssdrf.md: nothing
-+
-+
+-10-19 12:03  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in
-+
+        GayBerne
-+
-+
+-10-19 11:49  tim
-+
-+
+        * src/: UseTheForce/DarkSide/fInteractionMap.h,
-+
+        brains/ForceManager.cpp: fix an index mismathcing between c and
-+
+        fortran
-+
-+
+-10-18 18:03  gezelter
-+
-+
+        * samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added
-+
+        samples for the cutoff methods that Yang Zheng has been working on
-+
-+
+-10-18 16:13  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques
-+
+        and a rotation matrix bug
-+
-+
+-10-18 16:13  gezelter
-+
-+
+        * samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md,
-+
+        gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
-+
+        added a few GB test cases
-+
-+
+-10-18 16:13  gezelter
-+
-+
+        * forceFields/DUFF2.frc: Fixing GB parameters
-+
-+
+-10-18 13:36  kdaily
-+
-+
+        * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne
-+
+        type
-+
-+
+-10-18 10:01  chrisfen
-+
-+
+        * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
-+
+        UseTheForce/DarkSide/Makefile,
-+
+        UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.F90,
-+
+        UseTheForce/DarkSide/electrostatic_interface.h,
-+
+        UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged
-+
+        reaction field with electrostatics.F90
-+
-+
+-10-17 18:13  tim
-+
-+
+        * src/: brains/ForceManager.cpp, brains/Stats.cpp,
-+
+        brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp,
-+
+        io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp,
-+
+        io/StatWriter.hpp: Customized StatWriter is working
-+
-+
+-10-17 17:42  kdaily
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver
-+
+        paper
-+
-+
+-10-17 16:47  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: bugtracking gb
-+
-+
+-10-17 14:24  tim
-+
-+
+        * src/io/ParamConstraint.hpp: Another bug fix
-+
-+
+-10-17 14:22  tim
-+
-+
+        * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace
-+
+        issues in Globals
-+
-+
+-10-17 14:12  gezelter
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90,
-+
+        UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90,
-+
+        UseTheForce/DarkSide/gb_interface.F90,
-+
+        UseTheForce/DarkSide/gb_interface.h,
-+
+        io/GayBerneAtomTypesSectionParser.cpp,
-+
+        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
-+
+        changing GB architecture
-+
-+
+-10-17 14:12  gezelter
-+
-+
+        * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in,
-+
+        gbRotRoundZ.in: Adding samples for gb tests
-+
-+
+-10-16 22:06  tim
-+
-+
+        * src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy
-+
+        a  string to event's err_msg, there are still tons of memory
-+
+        leaking problem in Globals
-+
-+
+-10-16 19:51  tim
-+
-+
+        * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change
-+
+        error message in Globals
-+
-+
+-10-14 16:43  tim
-+
-+
+        * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for
-+
+        parameters are working now
-+
-+
+-10-14 11:43  gezelter
-+
-+
+        * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests
-+
-+
+-10-14 11:05  gezelter
-+
-+
+        * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md,
-+
+        gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
-+
+        Adding some Gay Berne tests
-+
-+
+-10-14 11:05  gezelter
-+
-+
+        * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some
-+
+        cutoff tests
-+
-+
+-10-14 10:44  kdaily
-+
-+
+        * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp,
-+
+        src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90,
-+
+        src/UseTheForce/DarkSide/gb_interface.F90,
-+
+        src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne
-+
+        LJ
-+
-+
+-10-14 09:48  tim
-+
-+
+        * src/io/ParamConstraint.hpp: Adding Parameter Constraint class
-+
-+
+-10-14 09:18  chrisfen
-+
-+
+        * samples/thermoIntegration/liquid/ssde.md,
-+
+        samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp,
-+
+        src/restraints/Restraints.cpp: added default restraint spring
-+
+        constants into Globals
-+
-+
+-10-13 17:26  tim
-+
-+
+        * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp,
-+
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp,
-+
+        constraints/ZconstraintForceManager.cpp,
-+
+        integrators/Integrator.cpp, integrators/NPT.cpp,
-+
+        integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp,
-+
+        io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp,
-+
+        minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp,
-+
+        restraints/ThermoIntegrationForceManager.cpp,
-+
+        visitors/ZconsVisitor.cpp: rewrite Globals
-+
-+
+-10-12 16:57  chuckv
-+
-+
+        * src/brains/ForceManager.cpp: Fix to forceManager to pass
-+
+        potential array to fortran.
-+
-+
+-10-12 16:00  gezelter
-+
-+
+        * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't
-+
+        remember what we did
-+
-+
+-10-12 16:00  gezelter
-+
-+
+        * src/UseTheForce/: doForces.F90, doForces_interface.F90,
-+
+        DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h,
-+
+        DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90,
-+
+        DarkSide/sticky.F90: simplifying long range potential array
-+
-+
+-10-12 16:00  gezelter
-+
-+
+        * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new
-+
+        cutoff methods
-+
-+
+-10-12 16:00  gezelter
-+
-+
+        * forceFields/DUFF2.frc: Messing with 2-point water models
-+
-+
+-10-12 15:22  chuckv
-+
-+
+        * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran
-+
+        interface now expects an array for pot.
-+
-+
+-10-12 15:18  chuckv
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/gb.F90,
-+
+        DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for
-+
+        calculation of potential.
-+
-+
+-10-12 14:55  chuckv
-+
-+
+        * src/UseTheForce/doForces.F90: More changes to MPI potential
-+
+        calculations.
-+
-+
+-10-12 13:59  chuckv
-+
-+
+        * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90,
-+
+        DarkSide/eam.F90, DarkSide/electrostatic.F90,
-+
+        DarkSide/fInteractionMap.h, DarkSide/force_globals.F90,
-+
+        DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky
-+
+        Breaky: Add Support for seperating potential contributions.
-+
-+
+-10-11 17:00  chuckv
-+
-+
+        * src/UseTheForce/doForces.F90: Free some variables that weren't
-+
+        freed before.
-+
-+
+-10-11 16:59  chuckv
-+
-+
+        * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
-+
+        GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod
-+
+        builder --twinned.
-+
-+
+-10-11 16:57  chuckv
-+
-+
+        * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
-+
+        nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c,
-+
+        nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp,
-+
+        sphericalNanoparticle.hpp: Added code for nanoparticle builder to
-+
+        cvs.
-+
-+
+-10-10 16:34  chuckv
-+
-+
+        * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable
-+
+        in MPI.
-+
-+
+-10-10 16:20  chuckv
-+
-+
+        * src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column
-+
+        indexing of groupToGtype. We now have two seperate maps
-+
+        groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer
-+
+        that is set to groupToGtypeRow in the single processor version.
-+
-+
+-10-06 13:44  chrisfen
-+
-+
+        * samples/water/: dimer/water.md, spce/water.md, ssd/water.md,
-+
+        ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md,
-+
+        tip3p_ice/water.md, tip4p/water.md: fixing up the samples
-+
-+
+-10-05 16:12  tim
-+
-+
+        * src/primitives/RigidBody.cpp: There is still something wrong with
-+
+        inertia tensor projection
-+
-+
+-10-05 14:35  tim
-+
-+
+        * src/primitives/RigidBody.cpp: erase output of inertia tensor.
-+
+        There is still something wrong with current implementation.
-+
-+
+-10-05 14:34  tim
-+
-+
+        * src/brains/MoleculeCreator.cpp: fix a bug in creating
-+
+        cutoffGroup. When cutoffGroup is turned off, there is a mismatch
-+
+        between group and center of mass array
-+
-+
+-10-05 14:12  tim
-+
-+
+        * src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup.
-+
+        When cutoffGroup is turned off, there is a mismatch between group
-+
+        and center of mass array
-+
-+
+-10-04 14:34  chrisfen
-+
-+
+        * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying
-+
+        mass ratio bug that results in simulation failure with massless
-+
+        particles
-+
-+
+-10-04 14:33  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on
-+
+        wolf
-+
-+
+-10-04 14:32  chrisfen
-+
-+
+        * samples/water/dimer/two.md, samples/water/dimer/water.md,
-+
+        samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md,
-+
+        samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some
-+
+        random changes when testing
-+
-+
+-10-03 10:54  tim
-+
-+
+        * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in
-+
+        projecting the inertia tensor of directional atom in rigibody into
-+
+        rigidbody's body frame (previous commit is wrong)
-+
-+
+-10-03 09:31  tim
-+
-+
+        * src/primitives/RigidBody.cpp: fix a bug in projecting the inertia
-+
+        tensor of directional atom in rigibody into rigidbody's body frame
-+
-+
+-09-28 13:47  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf
-+
-+
+-09-28 13:46  chrisfen
-+
-+
+        * samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md,
-+
+        dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md,
-+
+        ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md,
-+
+        tip4p/tp4.md: fixed some samples
-+
-+
+-09-28 13:46  chrisfen
-+
-+
+        * ChangeLog: updated
-+
+-09-28 11:55  tim
+        * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid
+-05-22 16:36  chuckv
-<
+        * samples/metals/nanorod/Au_nanoparticle_FCC.md,
-<
+        src/applications/nanoRodBuilder/Geometry.cpp,
-<
+        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
-<
+        src/applications/nanoRodBuilder/GeometryFactory.cpp,
-<
+        src/applications/nanoRodBuilder/GeometryFactory.hpp,
-<
+        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
-<
+        src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
->
+        * src/: applications/nanoRodBuilder/Geometry.cpp,
->
+        applications/nanoRodBuilder/GeometryBuilder.cpp,
->
+        applications/nanoRodBuilder/GeometryFactory.cpp,
->
+        applications/nanoRodBuilder/GeometryFactory.hpp,
->
+        applications/nanoRodBuilder/nanorodBuilder.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
+        tensor.
+-05-22 16:05  tim
+        * src/utils/vector_class.F90: Added code to delete vector.
-–
+-04-11 17:03  chuckv
-–
-–
+        * samples/metals/nanorod/: Au_nanoparticle.md,
-–
+        Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why
-–
+        aren't these here?
-–
+-04-11 16:58  tim
+        * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
+-09-29 12:56  gezelter
-<
+        * make/: Make.conf.in, Makefile.in: Working on make stuff
->
+        * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
->
+        make stuff
+-09-29 12:46  tim
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
+        src/visitors/RigidBodyVisitor.cpp,
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-<
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
->
+        src/visitors/ZconsVisitor.hpp, make/Makefile,
->
+        make/_files/style.css, samples/Makefile.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,
+        src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp,
+        src/visitors/RigidBodyVisitor.cpp,
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
-<
+        src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in,
->
+        src/visitors/ZconsVisitor.hpp, make/Makefile,
->
+        make/_files/style.css, samples/Makefile.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.in,
+        samples/metals/Au-Core-Ag-Shell_Nanoparticle.md,
+        samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md,

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/OOPSE-4/ChangeLog (file contents): Revision 2337 by chrisfen, Wed Sep 28 18:46:04 2005 UTC vs. Revision 2727 by chrisfen, Fri Apr 21 19:32:07 2006 UTC

Diff Legend

Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2337 by chrisfen, Wed Sep 28 18:46:04 2005 UTC vs.
Revision 2727 by chrisfen, Fri Apr 21 19:32:07 2006 UTC