[ViewVC] Diff of: group/trunk/OOPSE-3.0/ChangeLog

Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC

-<
+-07-23 15:31  tim
->
+-10-25 12:03  tim
-<
+        * samples/lipid/5x5.bass: modify 5x5.bass
->
+        * ChangeLog, src/utils/GenericFactory.hpp,
->
+        test/utils/GenericFactoryTestCase.cpp,
->
+        test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding
->
+        GenericFactory Test Case. GenericFactory now can bed used to creat
->
+        ForcefieldFactory and IntegratorFactory etc.
-<
+-07-23 15:25  tim
->
+-10-24 23:08  tim
-<
+        * samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message]
->
+        * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
->
+        brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
->
+        brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
->
+        get reconstructed
-<
+-07-23 15:18  tim
->
+-10-24 02:55  tim
-<
+        * samples/: water/ssde/ssde.bass, argon/500.bass,
-<
+        argon/argonNVT.bass: [no log message]
->
+        * src/utils/GenericFactory.hpp: GenericFactory pass unit test
-<
+-07-23 15:12  tim
->
+-10-23 18:09  tim
-<
+        * samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in,
-<
+        ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files
->
+        * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
->
+        StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
->
+        RigidBody.cpp: Refactoring in progress
-<
+-07-23 15:10  tim
->
+-10-22 18:09  tim
-<
+        * samples/minimizer/: ssdEM.in, tip4p_two.in: add init file
->
+        * ChangeLog, src/brains/Snapshot.hpp,
->
+        src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
->
+        test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
->
+        test/brains/StuntDouble.hpp: more work in Snapshot
-<
+-07-23 15:09  tim
->
+-10-22 17:59  chrisfen
-<
+        * samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename
-<
+        NVT.bass to argonNVT.bass
->
+        * src/: UseTheForce/LJFF.cpp,
->
+        UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
->
+        god!  It runs and conserves energy!
-<
+-07-23 15:07  tim
->
+-10-22 17:54  chrisfen
-<
+        * samples/lipid/5x5.in: add 5x5.in
->
+        * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
-<
+-07-23 15:06  tim
->
+-10-22 17:53  chrisfen
-<
+        * samples/alkane/: butane.in, init_butane.eor: add butane.in
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
->
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
->
+        breakey
-<
+-07-23 14:57  gezelter
->
+-10-22 17:53  chrisfen
-<
+        * libBASS/Globals.cpp, samples/minimizer/ssdEM.bass,
-<
+        samples/minimizer/tip4p_two.bass: changed minimizer keywords
->
+        * make/Makefile.in: compiler flags
-<
+-07-23 14:34  gezelter
->
+-10-22 16:20  gezelter
-<
+        * configure, ac-tools/configure.in: fixed typo
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
->
+        brains/fSimulation.h, types/AtomType.hpp,
->
+        types/DirectionalAtomType.hpp: fixey fixey
-<
+-07-23 14:32  gezelter
->
+-10-22 15:22  gezelter
-<
+        * samples/minimizer/Makefile.in: fixed sample makefile
->
+        * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
->
+        charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
->
+        lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
->
+        fortran files and c/Fortran interfaces
-<
+-07-23 14:31  gezelter
->
+-10-22 15:21  gezelter
-<
+        * configure, ac-tools/configure.in, samples/minimizer/Makefile.in,
-<
+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass,
-<
+        samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl:
-<
+        minimizer sample changes
->
+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
->
+        DirectionalAtomType.hpp, Makefile: More on AtomType and
->
+        DirectionalAtomType
-<
+-07-23 14:15  gezelter
->
+-10-22 09:47  gezelter
-<
+        * configure, ac-tools/configure.in: removed beadLipid
->
+        * src/types/AtomType.hpp: Adding AtomType
-<
+-07-23 14:08  tim
->
+-10-21 16:31  tim
-<
+        * samples/Makefile.in: remove beadLipid
->
+        * ChangeLog, src/brains/Snapshot.hpp,
->
+        src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
->
+        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
->
+        src/math/Vector.hpp, src/math/Vector3.hpp,
->
+        test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
->
+        Snapshot and SnapshotManager in progress
-<
+-07-23 14:03  chuckv
->
+-10-21 16:30  tim
-<
+        * samples/metals/: Au_nanoparticle.eor,
-<
+        Au_nanoparticle_coreshell_12-20.bass,
-<
+        Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle
-<
+        files.
->
+        * test/brains/: BrainsTest.cpp, Makefile,
->
+        SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
->
+        SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
->
+        Snapshot and snapshotManager.
-<
+-07-23 13:51  tim
->
+-10-21 15:15  gezelter
-<
+        * samples/water/tip4p/TP4init.in: remove TP4init.in
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
->
+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
->
+        UseTheForce/WATER.cpp, UseTheForce/doForces.F90,
->
+        UseTheForce/doForces_interface.h, UseTheForce/fForceField.h,
->
+        UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h,
->
+        brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
->
+        Fixey Fixey.
-<
+-07-23 13:50  tim
->
+-10-21 11:32  tim
-<
+        * samples/water/tip4p/: Makefile.in, tp4.bass: change init file
-<
+        name for tip4p and tip3p_ice
->
+        * src/utils/GenericData.cpp, src/utils/Makefile,
->
+        test/utils/Makefile, test/utils/UtilTest: remove some junk files
-<
+-07-23 13:48  tim
->
+-10-21 11:24  tim
-<
+        * samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message]
->
+        * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
-<
+-07-23 13:48  tim
->
+-10-21 11:22  tim
-<
+        * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change
-<
+        init file name for ssd
->
+        * ChangeLog, src/brains/SimSetup.cpp,
->
+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
->
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
->
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
->
+        src/integrators/NVT.cpp, src/io/DumpReader.cpp,
->
+        src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp,
->
+        src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp,
->
+        src/utils/GenericData.cpp, src/utils/GenericData.hpp,
->
+        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
->
+        src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp,
->
+        src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp,
->
+        src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp,
->
+        src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp,
->
+        src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
->
+        GenericData
-<
+-07-23 13:46  tim
->
+-10-21 10:25  chuckv
-<
+        * samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove
-<
+        SPCEInit.in
->
+        * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
->
+        module.
-<
+-07-23 13:45  tim
->
+-10-21 10:24  chuckv
-<
+        * samples/water/dimer/: Makefile.in, two.bass, two.init: change
-<
+        names for init file
->
+        * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
->
+        fortran lj module.
-<
+-07-23 13:40  tim
->
+-10-20 17:54  tim
-<
+        * samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor:
-<
+        change init file name in lipid directory
->
+        * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
->
+        test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
->
+        test/utils/PropertyMapTestCase.cpp,
->
+        test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
->
+        GenericData and PropertyMap  pass unit test.
-<
+-07-23 13:36  tim
->
+-10-20 16:52  gezelter
-<
+        * samples/argon/init_argon.eor: remove init_argon.eor
->
+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
->
+        DarkSide/sticky_interface.h: fixed a fortran name problem
-<
+-07-23 13:34  tim
->
+-10-20 16:38  tim
-<
+        * samples/: alkane/Makefile.in, alkane/butane.bass,
-<
+        alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message]
->
+        * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
->
+        GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
->
+        UtilTest, UtilTest.cpp: adding generic data test case
-<
+-07-23 13:33  tim
->
+-10-20 16:16  chuckv
-<
+        * samples/argon/Makefile.in: remove eor file
->
+        * configure, ac-tools/aclocal.m4,
->
+        src/UseTheForce/DarkSide/Makefile,
->
+        src/UseTheForce/DarkSide/mpiSimulation.F90,
->
+        src/UseTheForce/DarkSide/mpiSimulation_interface.h,
->
+        src/UseTheForce/DarkSide/simParallel.F90,
->
+        src/UseTheForce/DarkSide/simParallel_interface.h,
->
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp:
->
+        Fortran/C++ interface de-obfuscation project appears to be
->
+        complete!  Woo hoo!
-<
+-07-23 13:31  tim
->
+-10-20 15:47  chuckv
-<
+        * samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass:
-<
+        change names for argon
->
+        * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
->
+        fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
->
+        continues
-<
+-07-23 11:47  tim
->
+-10-20 15:46  chuckv
-<
+        * samples/water/ssde/SSDEinit.in: [no log message]
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
->
+        UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp,
->
+        UseTheForce/doForces_interface.h,
->
+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90,
->
+        UseTheForce/DarkSide/atype_interface.h,
->
+        UseTheForce/DarkSide/eam_interface.h,
->
+        UseTheForce/DarkSide/gb_interface.h,
->
+        UseTheForce/DarkSide/mpiSimulation_interface.h,
->
+        UseTheForce/DarkSide/shapes_interface.h,
->
+        UseTheForce/DarkSide/simulation_interface.h,
->
+        UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
->
+        de-obfuscation project (It is a very long story)
-<
+-07-23 11:45  tim
->
+-10-20 13:07  tim
-<
+        * samples/water/ssde/SSDEinit.in: add init file for ssde
->
+        * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
->
+        test/math/SquareMatrix3TestCase.cpp,
->
+        test/math/SquareMatrixTestCase.cpp,
->
+        test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
-<
+-07-23 11:43  chuckv
->
+-10-20 00:52  tim
-<
+        * libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and
-<
+        cutoffs associated with mixture.
->
+        * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
->
+        SnapshotManager in design phase
-<
+-07-23 10:35  tim
->
+-10-19 23:54  gezelter
-<
+        * libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E
-<
+        SSD_RF SSD1
->
+        * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
->
+        problem prevented linking
-<
+-07-23 09:53  tim
->
+-10-19 23:54  gezelter
-<
+        * libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E,
-<
+        SSD1 now
->
+        * src/UseTheForce/Shapes_FF.cpp: fixed include
-<
+-07-23 09:19  tim
->
+-10-19 23:26  gezelter
-<
+        * libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp
->
+        * src/utils/: Makefile, definitions.F90, definitions_module.F90,
->
+        oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
->
+        more fortran name mangling
-<
+-07-23 09:18  tim
->
+-10-19 23:23  gezelter
-<
+        * samples/lipid/5x5.bass: remove unsupport keyword
->
+        * src/profiling/timing.F90: yet more fortran renaming
-<
+-07-22 16:01  chuckv
->
+-10-19 23:19  gezelter
-<
+        * samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in:
-<
+        Changed init files to be more OOPSE like...
-<
-<
+-07-22 10:11  gezelter
-<
-<
+        * configure, ac-tools/configure.in: added sample directory
->
+        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
->
+        do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
->
+        notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
->
+        wrappers.F90: Fortran name cleanup continues
-<
+-07-22 10:06  chrisfen
->
+-10-19 23:12  gezelter
-<
+        * src/Makefile.in: fixed icc7 incompatibility in linking
->
+        * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
->
+        broken fortran stuff
-<
+-07-21 17:03  chrisfen
->
+-10-19 23:02  gezelter
-<
+        * samples/water/: Makefile.in, tip3p_ice/200.in,
-<
+        tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl:
-<
+        Added tip3p_ice to Makefile
->
+        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
->
+        atype_interface.h, atype_module.F90, atype_module_interface.h,
->
+        calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90,
->
+        calc_eam.F90, calc_gb.F90, calc_reaction_field.F90,
->
+        calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90,
->
+        eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90,
->
+        gb_interface.h, gb_module_interface.h, mpiSimulation.F90,
->
+        mpiSimulation_interface.h, mpiSimulation_module.F90,
->
+        mpisimulation_module_interface.h, reactionField.F90, shapes.F90,
->
+        shapes_interface.h, shapes_module.h, simulation.F90,
->
+        simulation_interface.h, simulation_module.F90,
->
+        simulation_module_interface.h, sticky.F90, sticky_interface.h,
->
+        sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
->
+        name sanity on the fortran side
-<
+-07-21 16:46  chuckv
->
+-10-19 19:18  tim
-<
+        * samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass,
-<
+        Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor,
-<
+        init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample
-<
+        files for bulk metals and a bass file for both voter and FBD
-<
+        formulations of EAM.
->
+        * test/math/SquareMatrix3TestCase.hpp: [no log message]
-<
+-07-21 14:53  gezelter
->
+-10-19 18:01  tim
-<
+        * samples/water/dimer/two.bass: Checked a bug where eor file wasn't
-<
+        being written at the end of the run
->
+        * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
->
+        src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
->
+        except diagonalize(), all of functions in math library pass the
->
+        test
-<
+-07-21 14:53  gezelter
->
+-10-19 17:43  chuckv
-<
+        * libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't
-<
+        being written at the end of the run
->
+        * src/UseTheForce/do_Forces.h: Added correct prototypes for
->
+        C-fortran interface functions.
-<
+-07-21 09:11  gezelter
->
+-10-19 17:37  chuckv
-<
+        * README: [no log message]
->
+        * src/UseTheForce/DarkSide/: atype_module_interface.h,
->
+        eam_module_inteface.h, gb_module_interface.h,
->
+        mpisimulation_module_interface.h, simulation_module_interface.h,
->
+        sticky_pair_module_interface.h: Added correct prototypes for
->
+        C-fortran interface functions.
-<
+-07-21 09:08  gezelter
->
+-10-19 16:28  tim
-<
+        * samples/argon/machines: cleaning up for export
->
+        * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
->
+        src/math/SquareMatrix.hpp, src/math/Vector.hpp,
->
+        test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp,
->
+        test/math/RectMatrixTestCase.cpp,
->
+        test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp,
->
+        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
->
+        bugs get fixed at math library
-<
+-07-21 09:04  gezelter
->
+-10-19 15:43  chuckv
-<
+        * NEWS, README: cleaning up for export
->
+        * src/UseTheForce/: DarkSide/atype_module_interface.h,
->
+        DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
->
+        DarkSide/mpisimulation_module_interface.h,
->
+        DarkSide/simulation_module_interface.h,
->
+        DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90,
->
+        DarkSide/atype_module.F90, DarkSide/calc_gb.F90,
->
+        DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90,
->
+        DarkSide/simulation_module.F90, do_Forces.F90,
->
+        fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90,
->
+        notifycutoffs_module_interface.h: Added new files for fortran
->
+        interface.
-<
+-07-21 08:45  gezelter
->
+-10-19 15:43  gezelter
-<
+        * configure, ac-tools/configure.in: removing staticProps from cvs
-<
+        tree
->
+        * src/UseTheForce/Makefile: regressing
-<
+-07-20 12:07  gezelter
->
+-10-19 15:40  gezelter
-<
+        * configure, ac-tools/aclocal.m4, utils/Makefile.in,
-<
+        utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message]
->
+        * src/: UseTheForce/DarkSide/calc_shapes.F90,
->
+        UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
->
+        working on shapes for portability
-<
+-07-20 10:17  gezelter
->
+-10-19 15:40  gezelter
-<
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-<
+        third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c,
-<
+        utils/gnugetopt.h: fixing getopt_long
->
+        * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
-<
+-07-19 16:58  gezelter
->
+-10-19 13:21  chrisfen
-<
+        * configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp,
-<
+        libmdtools/ZConsWriter.hpp, src/Makefile.in,
-<
+        third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep,
-<
+        utils/Makefile.in, utils/sysbuilder/Makefile.in,
-<
+        utils/sysbuilder/latticeBuilder.cpp: [no log message]
->
+        * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
->
+        findBegin
-<
+-07-19 16:52  tim
->
+-10-18 23:34  tim
-<
+        * utils/quickLate.c: minor fix of format string in quicklate.c
->
+        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
->
+        are fixed in Vector class
-<
+-07-19 16:30  tim
->
+-10-18 23:28  tim
-<
+        * utils/zsub: remove zsub from cvs tree
->
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
->
+        some bugs in RectMatrixTestCase
-<
+-07-19 16:25  tim
->
+-10-18 23:21  tim
-<
+        * libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some
-<
+        comment lines
->
+        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
->
+        test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
->
+        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
->
+        test/math/VectorTestCase.hpp: implement more test cases
-<
+-07-19 16:00  tim
->
+-10-18 18:13  tim
-<
+        * libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from
-<
+        OOPSEMinimizer.hpp
->
+        * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
->
+        src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
->
+        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
->
+        src/utils/StringTokenizer.hpp, test/math/Makefile,
->
+        test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
->
+        tests on math library
-<
+-07-19 13:55  gezelter
->
+-10-18 16:03  tim
-<
+        * libBASS/y.tab.h: Shouldn't have been in CVS
->
+        * test/math/: Makefile, QuaternionTestCase.cpp,
->
+        QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
->
+        SquareMatrix3TestCase.cpp, Vector3TestCase.cpp,
->
+        Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
->
+        more testing units
-<
+-07-19 13:54  gezelter
->
+-10-18 12:07  tim
-<
+        * libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for
-<
+        thermodynamic integration of rigid bodies
->
+        * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
->
+        math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
->
+        math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
->
+        utils/GenericFactory.hpp: fix some bugs in Quaternion class
-<
+-07-19 12:00  gezelter
->
+-10-18 11:30  gezelter
-<
+        * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be
-<
+        generated via lex and yacc at compile time
->
+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
->
+        Your basic run of the mill real-valued versions of Y_l^m(\theta,
->
+        \phi)
-<
+-07-19 11:47  gezelter
->
+-10-18 11:29  gezelter
-<
+        * libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h,
-<
+        libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in,
-<
+        libmdtools/MatVec3.c, src/Makefile.in: [no log message]
->
+        * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
->
+        types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
->
+        utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
->
+        Shapes into OOPSE
-<
+-07-19 11:32  gezelter
->
+-10-18 10:21  gezelter
->
->
+        * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
->
->
+-10-18 00:23  tim
->
->
+        * test/math/VectorTestCase.hpp: adding  vector test case
->
->
+-10-18 00:23  tim
-<
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
-<
+        third-party/gnugetopt.h, utils/Makefile.in,
-<
+        utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed
-<
+        SPRNG configure script
->
+        * src/utils/GenericFactory.hpp: adding generic factory and vector
->
+        test case
-<
+-07-16 16:49  gezelter
->
+-10-16 20:19  tim
-<
+        * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines
-<
+        that don't have lex and yacc
->
+        * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
->
+        SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
->
+        progress
-<
+-07-16 15:55  gezelter
->
+-10-15 20:31  tim
-<
+        * Makefile: Makefiles don't belong in cvs repository
->
+        * src/math/Quaternion.hpp: add quaternion class
-<
+-07-16 15:54  gezelter
->
+-10-15 16:11  tim
-<
+        * Makefile, forceFields/Makefile, libBASS/Makefile,
-<
+        libmdtools/Makefile, samples/Makefile, src/Makefile,
-<
+        third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile:
-<
+        Makefiles don't belong in repository
->
+        * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
->
+        IfstrstreamTestCase.hpp: adding test file
-<
+-07-16 15:49  gezelter
->
+-10-15 16:10  tim
-+
+        * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
-+
-+
+-10-15 15:42  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
-+
-+
+-10-15 15:35  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
-+
-+
+-10-15 15:34  tim
-+
-+
+        * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
-+
+        namespace oopse
-+
-+
+-10-15 14:38  chuckv
-+
-+
+        * configure, ac-tools/aclocal.m4: Changed optimization flags for
-+
+        XLF and XLC.
-+
-+
+-10-15 13:28  tim
-+
-+
+        * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
-+
+        adding ifstrstream test case
-+
-+
+-10-15 13:20  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: fix include
-+
-+
+-10-15 13:18  tim
-+
-+
+        * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
-+
-+
+-10-15 13:17  tim
-+
-+
+        * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
-+
-+
+-10-15 13:16  tim
-+
-+
+        * test/io/: Makefile, ifstrstreamTestCase.cpp,
-+
+        ifstrstreamTestCase.hpp: adding test case for ifstrstream
-+
-+
+-10-15 10:37  tim
-+
-+
+        * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
-+
+        ifstrstreamTestCase.hpp: add ifstrstreamTestCase
-+
-+
+-10-15 10:20  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: add checkFilename Option
-+
-+
+-10-15 10:19  tim
-+
-+
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
-+
+        SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
-+
+        SquareMatrixTestCase class
-+
-+
+-10-15 02:52  tim
-+
-+
+        * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
-+
-+
+-10-14 18:28  tim
-+
-+
+        * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
-+
+        Vector.hpp: math library in progress
-+
-+
+-10-14 18:27  tim
-+
-+
+        * src/io/FileReader.hpp: FileReader in progress
-+
-+
+-10-13 18:53  tim
-+
-+
+        * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
-+
+        test in isOrthogonal of SquareMatrix is failed by some reasons
-+
-+
+-10-13 17:28  tim
-+
-+
+        * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
-+
+        class
-+
-+
+-10-13 17:27  tim
-+
-+
+        * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
-+
+        RectMatrixTestCase.hpp: adding testing unit
-+
-+
+-10-13 17:24  tim
-+
-+
+        * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
-+
-+
+-10-13 01:51  tim
-+
-+
+        * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
-+
+        Vector3.hpp: refactory vector and matrix classes
-+
-+
+-10-13 01:50  tim
-+
-+
+        * src/math/Vector3d.hpp: Remove some Makefile.in
-+
-+
+-10-12 18:57  tim
-+
-+
+        * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
-+
+        Matrix3x3d.hpp
-+
-+
+-10-12 14:08  tim
-+
-+
+        * doc/: cppstyle.html, style.css: adding c++ coding style
-+
-+
+-10-11 17:15  tim
-+
-+
+        * src/: constraints/AbstractClasses.hpp,
-+
+        integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
-+
+        change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
-+
-+
+-10-11 16:54  tim
-+
-+
+        * scripts/filepp: fix a bug in filepp
-+
-+
+-10-11 16:13  tim
-+
-+
+        * make/Makefile.in: using filepp to generate dependencies instead
-+
+        of compilers
-+
-+
+-10-11 16:10  tim
-+
-+
+        * scripts/filepp: filepp can be used to generate dependencies for
-+
+        c/c++ now
-+
-+
+-10-11 13:40  tim
-+
-+
+        * make/Makefile.in: remove -module from F90Options
-+
-+
+-10-11 13:01  tim
-+
-+
+        * make/Makefile.in: adding rules to move fortran 90 module to
-+
+        target directory
-+
-+
+-10-11 10:43  gezelter
-+
-+
+        * make/Makefile.in: fixed makefile.in
-+
-+
+-10-11 09:51  tim
-+
-+
+        * scripts/filepp: remove "use bytes" which causes problem in sgi
-+
+        machine
-+
-+
+-10-11 09:26  tim
-+
-+
+        * forceFields/Makefile: add Makefile
-+
-+
+-10-11 09:23  tim
-+
-+
+        * samples/: water/dimer/Makefile, water/spce/Makefile,
-+
+        water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
-+
+        water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
-+
+        directory
-+
-+
+-10-11 09:23  tim
-+
-+
+        * samples/argon/Makefile: remove argon.dump and argon.eor from
-+
+        Makefile
-+
-+
+-10-09 01:01  tim
-+
-+
+        * samples/: alkane/Makefile.in, argon/Makefile.in,
-+
+        lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
-+
+        Remove some Makefile.in
-+
-+
+-10-08 18:15  tim
-+
-+
+        * make/Makefile.in: [no log message]
-+
-+
+-10-08 17:51  tim
-+
-+
+        * make/Makefile.in: fix make install
-+
-+
+-10-08 17:10  tim
-+
-+
+        * make/Makefile.in: adding make install
-+
-+
+-10-08 17:04  tim
-+
+        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
-<
+        metals/Makefile: Makefiles don't belong in repository
->
+        metals/Makefile, minimizer/Makefile, water/Makefile.in,
->
+        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
->
+        water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in,
->
+        water/ssde/Makefile, water/ssde/Makefile.in,
->
+        water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in,
->
+        water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
->
+        zcons/Makefile.in: add Makefile to sample directory
-<
+-07-16 15:20  chrisfen
->
+-10-06 18:03  gezelter
-<
+        * Makefile, configure, ac-tools/configure.in, forceFields/Makefile,
-<
+        libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile,
-<
+        samples/argon/Makefile, samples/lipid/Makefile,
-<
+        samples/metals/Makefile, src/Makefile, utils/Makefile,
-<
+        utils/sysbuilder/Makefile: Updated configure for new samples
->
+        * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
->
+        stuff
-<
+-07-16 14:57  chrisfen
->
+-10-06 18:03  gezelter
-<
+        * samples/water/tip4p/Makefile.in: tip4p makefile.in added
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
->
+        make/Doxyfile, src/applications/getopt.c,
->
+        src/applications/getopt1.c, src/applications/gnugetopt.h: more
->
+        build fixes
-<
+-07-16 14:57  chrisfen
->
+-10-06 17:20  tim
-<
+        * samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde
-<
+        makefile.in added
->
+        * make/: Doxyfile, Makefile.in: adding doxygen configuration file
-<
+-07-16 14:57  chrisfen
->
+-10-06 17:19  tim
-<
+        * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass,
-<
+        water.mdl: ssd files sorted added
->
+        * scripts/filepp: filepp can handle different fortran module case
->
+        and suffix
-<
+-07-16 14:57  chrisfen
->
+-10-06 16:27  gezelter
-<
+        * samples/water/spce/Makefile.in: spce makefile.in added
->
+        * src/restraints/Restraints.cpp: Chris doesn't know about the
->
+        OOPSE-2.0 directory structure yet
-<
+-07-16 14:56  chrisfen
->
+-10-06 16:27  gezelter
-<
+        * samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl:
-<
+        dimer files added
->
+        * ChangeLog: Yeah yeah, we'lll get around to it later
-<
+-07-16 14:56  chrisfen
->
+-10-06 16:22  gezelter
-<
+        * samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor,
-<
+        spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor,
-<
+        tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass,
-<
+        two.eor, two.init, two.xyz, water.mdl: Cleaned up this file
-<
+        considerably
->
+        * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
->
+        make/Makefile.in: cleaning up build process
-<
+-07-16 13:57  gezelter
->
+-10-06 15:01  chrisfen
-<
+        * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
-<
+        configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
-<
+        ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
-<
+        ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
-<
+        forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
-<
+        forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
-<
+        forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
->
+        * src/restraints/Restraints.cpp: made the file reading in
->
+        restraints more intelligent - no longer gives uninformative seg
->
+        faults
->
->
+-10-06 14:55  gezelter
->
->
+        * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
->
->
+-10-06 14:51  gezelter
->
->
+        * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
->
+        scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
->
->
+-10-06 13:53  tim
->
->
+        * make/: Makefile, Makefile.in: fix make statistics
->
->
+-10-06 13:18  tim
->
->
+        * make/: Makefile, Makefile.in: adding GNU make functions to
->
+        combine all of the static libraries to a big library
->
->
+-10-05 17:57  tim
->
->
+        * make/: Makefile, Makefile.in:  adding shared library flag
->
->
+-10-05 14:37  tim
->
->
+        * src/: Makefile, UseTheForce/Makefile,
->
+        UseTheForce/mpiSimulation_module.F90,
->
+        UseTheForce/DarkSide/Makefile,
->
+        UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
->
+        mpiSimulation_module to DarkSide
->
->
+-10-05 14:35  tim
->
->
+        * make/: Makefile, Makefile.in: building MPI version;using static
->
+        library instead of shared library
->
->
+-10-05 09:14  tim
->
->
+        * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
->
+        to filepp
->
->
+-10-04 15:56  tim
->
->
+        * make/: Makefile, Makefile.in: add make cvslog
->
->
+-10-04 11:24  gezelter
->
->
+        * make/: Makefile, Makefile.in: more work on the parallel build
->
->
+-10-04 11:06  gezelter
->
->
+        * make/: Makefile, Makefile.in: changes to backport declare flags
->
->
+-10-04 10:27  gezelter
->
->
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
->
+        DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
->
+        shapes
->
->
+-10-01 23:40  tim
->
->
+        * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
->
->
+-10-01 23:22  tim
->
->
+        * make/: Makefile, Makefile.in: add oopse_ as library prefix
->
->
+-10-01 16:59  tim
->
->
+        * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
->
->
+-10-01 16:22  gezelter
->
->
+        * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
->
+        few minor build changes
->
->
+-10-01 16:11  tim
->
->
+        * scripts/filepp: adding fortran90 make dependency tool
->
->
+-09-30 10:41  tim
->
->
+        * make/: Makefile, Makefile.in: make clean is smart enough to only
->
+        remove object files belong to current package.  turn off silent
->
+        mode
->
->
+-09-29 16:55  tim
->
->
+        * src/: Makefile, UseTheForce/Makefile,
->
+        UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
->
+        applications/oopse/Makefile, applications/simpleBuilder/Makefile,
->
+        brains/Makedepend, brains/Makefile, constraints/Makefile,
->
+        integrators/Makefile, io/Makefile, math/Makefile,
->
+        minimizers/Makefile, primitives/Makefile, profiling/Makefile,
->
+        restraints/Makefile, types/Makefile, utils/Makefile,
->
+        visitors/Makefile: define DEV_ROOT as relative path
->
->
+-09-29 16:54  tim
->
->
+        * make/: Makefile, Makefile.in: get the relative path by shell
->
+        script
->
->
+-09-29 16:32  tim
->
->
+        * make/Makefile: eliminate DEV_ROOT by relative path
->
->
+-09-29 13:37  tim
->
->
+        * make/Makefile.in: add PackageLibs;  fix dependency rule
->
->
+-09-29 12:57  gezelter
->
->
+        * configure, ac-tools/configure.in: updates
->
->
+-09-29 12:56  gezelter
->
->
+        * make/: Make.conf.in, Makefile.in: Working on make stuff
->
->
+-09-29 12:46  tim
->
->
+        * Makefile: If makefile does not exist, print error message
->
->
+-09-29 12:12  tim
->
->
+        * make/: Make.conf.in, Makefile: fix dependencies rule
->
->
+-09-29 10:58  gezelter
->
->
+        * Makefile, make/Makefile: still working on build process
->
->
+-09-29 10:00  tim
->
->
+        * make/Makefile: add print statment to rules
->
->
+-09-29 09:59  tim
->
->
+        * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
->
+        applications/dump2Xyz/Makefile, applications/oopse/Makefile,
->
+        applications/simpleBuilder/Makefile, brains/Makefile,
->
+        constraints/Makefile, integrators/Makefile, io/Makefile,
->
+        math/Makefile, minimizers/Makefile, primitives/Makefile,
->
+        profiling/Makefile, restraints/Makefile, types/Makefile,
->
+        utils/Makefile, visitors/Makefile: change Makefile to relative path
->
->
+-09-28 21:55  tim
->
->
+        * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
->
+        which cause headache in bulding libutils
->
->
+-09-28 18:24  tim
->
->
+        * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
->
+        Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
->
+        Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
->
+        LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp,
->
+        MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp,
->
+        nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo,
->
+        simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp,
->
+        dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c,
->
+        dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile,
->
+        oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp,
->
+        simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp,
->
+        simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp,
->
+        simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp,
->
+        simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old,
->
+        simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp,
->
+        simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp,
->
+        simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo,
->
+        simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h:
->
+        change directory structure of application. Every executable file is
->
+        replaced in seperate directory
->
->
+-09-28 17:15  gezelter
->
->
+        * lib/dummy: Keep that lib around, please.
->
->
+-09-28 17:14  gezelter
->
->
+        * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
->
+        starting a configure version
->
->
+-09-28 16:08  tim
->
->
+        * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
->
+        UseTheForce/DarkSide/Makefile,
->
+        UseTheForce/DarkSide/notifyCutoffs.F90,
->
+        UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend,
->
+        brains/Makefile, brains/simulation_module.F90: move fortran files
->
+        around to solve dependency problem
->
->
+-09-28 15:43  tim
->
->
+        * Makefile, src/UseTheForce/ForceFields.hpp,
->
+        src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
->
+        src/applications/Makedepend, src/applications/Makefile,
->
+        src/brains/Makedepend, src/brains/simulation_module.F90,
->
+        src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp,
->
+        src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
->
+        src/utils/Makefile: [no log message]
->
->
+-09-28 15:41  tim
->
->
+        * make/Makefile, scripts/sfmakedepend: fix fortran dependency
->
+        problem
->
->
+-09-28 11:13  tim
->
->
+        * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
->
+        src/io/Makefile: add yacc and lex rules
->
->
+-09-27 15:24  tim
->
->
+        * make/Makefile: adding include path to F90Options
->
->
+-09-27 15:13  tim
->
->
+        * make/Makefile: change suffix from .cc to .cpp
->
->
+-09-24 11:27  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
->
+        UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp,
->
+        UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp,
->
+        UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp,
->
+        UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90,
->
+        UseTheForce/DarkSide/calc_LJ_FF.F90,
->
+        UseTheForce/DarkSide/notifyCutoffs.F90,
->
+        UseTheForce/DarkSide/switch_module.F90,
->
+        applications/BaseLattice.cpp, applications/Dump2XYZ.cpp,
->
+        applications/Dump2XYZCmd.c, applications/Lattice.cpp,
->
+        applications/Lattice.hpp, applications/LatticeCreator.cpp,
->
+        applications/LatticeCreator.hpp, applications/LatticeFactory.cpp,
->
+        applications/MoLocator.cpp, applications/MoLocator.hpp,
->
+        applications/cmdline.c, applications/nanoBuilder.cpp,
->
+        applications/oopse.cpp, applications/simpleBuilder.cpp,
->
+        applications/simpleBuilderCmd.c, brains/Exclude.cpp,
->
+        brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp,
->
+        brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
->
+        brains/mpiSimulation.cpp, brains/mpiSimulation.hpp,
->
+        constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp,
->
+        integrators/AbstractClasses.hpp, integrators/Integrator.cpp,
->
+        integrators/Integrator.hpp, integrators/NPT.cpp,
->
+        integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp,
->
+        integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c,
->
+        io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp,
->
+        io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp,
->
+        io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp,
->
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
->
+        io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c,
->
+        io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h,
->
+        io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c,
->
+        math/MatVec3.h, math/randomSPRNG.cpp,
->
+        minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp,
->
+        minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp,
->
+        minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp,
->
+        primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp,
->
+        primitives/BendExtensions.cpp, primitives/Bond.cpp,
->
+        primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
->
+        primitives/GhostBend.cpp, primitives/Molecule.cpp,
->
+        primitives/Molecule.hpp, primitives/RigidBody.cpp,
->
+        primitives/RigidBody.hpp, primitives/SRI.hpp,
->
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
->
+        primitives/Torsion.cpp, primitives/TorsionExtensions.cpp,
->
+        profiling/mdProfile.cpp, restraints/Restraints.cpp,
->
+        restraints/Restraints.hpp, types/AtomStamp.cpp,
->
+        types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp,
->
+        types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp,
->
+        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
->
+        types/MakeStamps.cpp, types/MakeStamps.hpp,
->
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
->
+        types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp,
->
+        types/TorsionStamp.cpp, types/TorsionStamp.hpp,
->
+        types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp,
->
+        utils/StreamTokenizer.cpp, utils/StringUtils.c,
->
+        utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c,
->
+        utils/simError.c, visitors/AtomVisitor.cpp,
->
+        visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
->
+        visitors/ZconsVisitor.hpp: change the #include in source files
->
->
+-09-23 23:16  gezelter
->
->
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
->
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
->
+        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
->
+        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
->
+        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
->
+        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
->
+        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
->
+        src/UseTheForce/fForceField.h,
->
+        src/UseTheForce/fSwitchingFunction.h,
->
+        src/UseTheForce/fortranWrapDefines.hpp,
->
+        src/UseTheForce/fortranWrappers.cpp,
->
+        src/UseTheForce/fortranWrappers.hpp,
->
+        src/UseTheForce/mpiComponentPlan.h,
->
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
->
+        src/UseTheForce/mpiSimulation_module.F90,
->
+        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
->
+        src/UseTheForce/DarkSide/atype_module.F90,
->
+        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
->
+        src/UseTheForce/DarkSide/calc_charge_charge.F90,
->
+        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
->
+        src/UseTheForce/DarkSide/calc_eam.F90,
->
+        src/UseTheForce/DarkSide/calc_gb.F90,
->
+        src/UseTheForce/DarkSide/calc_reaction_field.F90,
->
+        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
->
+        src/UseTheForce/DarkSide/force_globals.F90,
->
+        src/UseTheForce/DarkSide/neighborLists.F90,
->
+        src/UseTheForce/DarkSide/notifyCutoffs.F90,
->
+        src/UseTheForce/DarkSide/switch_module.F90,
->
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
->
+        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
->
+        src/io/DumpWriter.cpp, src/io/Globals.cpp,
->
+        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
->
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
->
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
->
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
->
+        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
->
+        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
->
+        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
->
+        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
->
+        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
->
+        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
->
+        src/types/BondStamp.hpp, src/types/Component.cpp,
->
+        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
->
+        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
->
+        src/types/MakeStamps.hpp, src/types/Makefile,
->
+        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
->
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
->
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
->
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
->
+        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
->
+        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
->
+        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
->
+        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
->
+        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
->
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
->
+        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
->
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
->
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
->
+        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
->
+        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
->
+        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
->
+        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
->
+        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
->
+        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
->
+        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
->
+        src/minimizers/OOPSEMinimizer.cpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
->
+        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
->
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
->
+        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
->
+        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
->
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/primitives/Makefile, src/primitives/Molecule.cpp,
->
+        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
->
+        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
->
+        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
->
+        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
->
+        src/restraints/Makefile, src/restraints/Restraints.cpp,
->
+        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
->
+        src/utils/GenericData.hpp, src/utils/Makefile,
->
+        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
->
+        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
->
+        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
->
+        src/utils/Utility.hpp, src/utils/definitions_module.F90,
->
+        src/utils/fError.c, src/utils/oopseMPI_module.F90,
->
+        src/utils/simError.c, src/utils/simError.h,
->
+        src/utils/status_module.F90, src/utils/vector_class.F90,
->
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
->
+        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
->
+        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
->
+        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,
->
+        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,
->
+        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
->
+        samples/zcons/Makefile.in, samples/zcons/water.md,
->
+        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
->
+        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
->
+        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
->
+        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
->
+        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
->
+        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
->
+        src/applications/LatticeCreator.cpp,
->
+        src/applications/LatticeCreator.hpp,
->
+        src/applications/LatticeFactory.cpp,
->
+        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
->
+        src/applications/Makefile, src/applications/MoLocator.cpp,
->
+        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
->
+        src/applications/cmdline.c, src/applications/cmdline.h,
->
+        src/applications/getopt.c, src/applications/getopt1.c,
->
+        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
->
+        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
->
+        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
->
+        src/applications/simpleBuilder.ggo,
->
+        src/applications/simpleBuilderCmd.c,
->
+        src/integrators/AbstractClasses.hpp,
->
+        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
->
+        src/integrators/Integrator.hpp, src/integrators/Makefile,
->
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
->
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
->
+        src/integrators/NVT.cpp, src/profiling/Makefile,
->
+        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
->
+        src/profiling/timing.F90, samples/metals/Au_bulk.in,
->
+        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
->
+        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
->
+        samples/water/dimer/two.in, samples/water/dimer/two.md,
->
+        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
->
+        samples/water/spce/spce.in, samples/water/spce/spce.md,
->
+        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
->
+        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
->
+        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
->
+        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
->
+        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
->
+        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
->
+        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
->
+        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
->
+        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
->
+        samples/alkane/butane.in, samples/alkane/butane.md,
->
+        samples/argon/500.in, samples/argon/500.md,
->
+        samples/argon/Makefile.in, samples/argon/ar864.in,
->
+        samples/argon/ar864.md, samples/argon/argonNVT.in,
->
+        samples/argon/argonNVT.md, samples/argon/lj.md,
->
+        samples/lipid/5x5.in, samples/lipid/5x5.md,
->
+        samples/lipid/Makefile.in, samples/lipid/lipid.md,
->
+        samples/lipid/water.md, samples/minimizer/Makefile.in,
->
+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
->
+        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
->
+        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
->
+        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
->
+        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
+        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
+        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
+        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
+        forceFields/EAM.VC.frc, forceFields/EAM.frc,
+        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
-<
+        forceFields/LJFF.frc, forceFields/Makefile,
-<
+        forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
-<
+        forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
-<
+        forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
-<
+        forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
-<
+        forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
-<
+        forceFields/WATER.frc, libBASS/AtomStamp.cpp,
-<
+        libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
-<
+        libBASS/BASS_interface.h, libBASS/BASS_parse.c,
-<
+        libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
-<
+        libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
-<
+        libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
-<
+        libBASS/Component.cpp, libBASS/Component.hpp,
-<
+        libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp,
-<
+        libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
-<
+        libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
-<
+        libBASS/LinkedCommand.hpp, libBASS/Make.dep,
-<
+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
-<
+        libBASS/Makefile.in, libBASS/MoleculeStamp.cpp,
-<
+        libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp,
-<
+        libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp,
-<
+        libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp,
-<
+        libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c,
-<
+        libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h,
-<
+        libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h,
-<
+        libBASS/parse_interface.h, libBASS/parse_me.h,
-<
+        libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
-<
+        libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy,
-<
+        libBASS/obj/dummy, libmdtools/AbstractClasses.hpp,
-<
+        libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp,
-<
+        libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp,
-<
+        libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp,
-<
+        libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
-<
+        libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
-<
+        libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp,
-<
+        libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp,
-<
+        libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp,
-<
+        libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp,
-<
+        libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp,
-<
+        libmdtools/Euler3.cpp, libmdtools/Euler3.hpp,
-<
+        libmdtools/Exclude.cpp, libmdtools/Exclude.hpp,
-<
+        libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp,
-<
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
-<
+        libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp,
-<
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-<
+        libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile,
-<
+        libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h,
-<
+        libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp,
-<
+        libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
-<
+        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
-<
+        libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp,
-<
+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
-<
+        libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp,
-<
+        libmdtools/Restraints.cpp, libmdtools/Restraints.hpp,
-<
+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
-<
+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
-<
+        libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp,
-<
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-<
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
-<
+        libmdtools/SimState.cpp, libmdtools/SimState.hpp,
-<
+        libmdtools/SkipList.cpp, libmdtools/SkipList.hpp,
-<
+        libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp,
-<
+        libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c,
-<
+        libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp,
-<
+        libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp,
-<
+        libmdtools/Thermo.hpp, libmdtools/Torsion.cpp,
-<
+        libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp,
-<
+        libmdtools/Utility.cpp, libmdtools/Utility.hpp,
-<
+        libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp,
-<
+        libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp,
-<
+        libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp,
-<
+        libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp,
-<
+        libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90,
-<
+        libmdtools/calc_charge_charge.F90,
-<
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
-<
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
-<
+        libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in,
-<
+        libmdtools/definitions_module.F90, libmdtools/do_Forces.F90,
-<
+        libmdtools/fForceField.h, libmdtools/fSimulation.h,
-<
+        libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp,
-<
+        libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
-<
+        libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
-<
+        libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp,
-<
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
-<
+        libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
-<
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
-<
+        libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90,
-<
+        libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp,
-<
+        libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-<
+        libmdtools/status_module.F90, libmdtools/switch_module.F90,
-<
+        libmdtools/timing.F90, libmdtools/vector_class.F90,
-<
+        libmdtools/wrappers.F90, libmdtools/MPIobj/dummy,
-<
+        libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in,
-<
+        samples/alkane/Makefile, samples/alkane/Makefile.in,
-<
+        samples/alkane/alkanes.mdl, samples/alkane/butane.bass,
-<
+        samples/alkane/butane.eor, samples/alkane/init_butane.eor,
-<
+        samples/argon/500.bass, samples/argon/500.eor,
-<
+        samples/argon/500.in, samples/argon/Makefile,
-<
+        samples/argon/Makefile.in, samples/argon/NVT.bass,
-<
+        samples/argon/ar864.bass, samples/argon/ar864.eor,
-<
+        samples/argon/ar864.in, samples/argon/argon.bass,
-<
+        samples/argon/argon.eor, samples/argon/argonEM.bass,
-<
+        samples/argon/init_argon.eor, samples/argon/lj.mdl,
-<
+        samples/argon/machines, samples/lipid/5x5.bass,
-<
+        samples/lipid/5x5.eor, samples/lipid/Makefile,
-<
+        samples/lipid/Makefile.in, samples/lipid/init_5x5.eor,
-<
+        samples/lipid/lipid.mdl, samples/lipid/water.mdl,
-<
+        samples/metals/Au.bass, samples/metals/Au.eor,
-<
+        samples/metals/Makefile, samples/metals/Makefile.in,
-<
+        samples/metals/init_au.in, samples/metals/metals.mdl,
-<
+        samples/water/200.in, samples/water/Makefile,
-<
+        samples/water/Makefile.in, samples/water/init_ssd.eor,
-<
+        samples/water/spce.bass, samples/water/spce.eor,
-<
+        samples/water/ssd.bass, samples/water/ssd.eor,
-<
+        samples/water/tim.bass, samples/water/tim.eor,
-<
+        samples/water/tim.init, samples/water/tim.xyz,
-<
+        samples/water/tip3p.bass, samples/water/tip3p.eor,
-<
+        samples/water/tip3p.init, samples/water/two.bass,
-<
+        samples/water/two.eor, samples/water/two.init,
-<
+        samples/water/two.xyz, samples/water/water.mdl,
-<
+        samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass,
-<
+        samples/water/spce/water.mdl, samples/water/ssde/256init.in,
-<
+        samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl,
-<
+        samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass,
-<
+        samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl,
-<
+        scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in,
-<
+        src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy,
-<
+        third-party/Makefile, third-party/Makefile.in,
-<
+        third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo,
-<
+        utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep,
-<
+        utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub,
-<
+        utils/MPIobj/placeHolder, utils/obj/placeHolder,
-<
+        utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile,
-<
+        utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp,
-<
+        utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c,
-<
+        utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp,
-<
+        utils/sysbuilder/latticeBuilder.cpp,
-<
+        utils/sysbuilder/latticeBuilder.hpp,
-<
+        utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp,
-<
+        utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp,
-<
+        utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp,
-<
+        utils/sysbuilder/MPIobj/placeHolder,
-<
+        utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0
-<
+        source tree
->
+        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
->
+        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
->
+        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
->
+        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
->
+        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
->
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
->
+        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
->
+        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
->
+        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
->
+        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
->
+        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
->
+        forceFields/Pt.VC.funcfl: Initial revision
-<
+-07-16 13:57  gezelter
->
+-09-23 23:16  gezelter
-<
+        * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README,
-<
+        configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4,
-<
+        ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in,
-<
+        ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool,
-<
+        forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl,
-<
+        forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl,
-<
+        forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl,
->
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
->
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
->
+        src/constraints/Makefile, src/constraints/ZConstraint.cpp,
->
+        src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp,
->
+        src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp,
->
+        src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile,
->
+        src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90,
->
+        src/UseTheForce/fForceField.h,
->
+        src/UseTheForce/fSwitchingFunction.h,
->
+        src/UseTheForce/fortranWrapDefines.hpp,
->
+        src/UseTheForce/fortranWrappers.cpp,
->
+        src/UseTheForce/fortranWrappers.hpp,
->
+        src/UseTheForce/mpiComponentPlan.h,
->
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
->
+        src/UseTheForce/mpiSimulation_module.F90,
->
+        src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile,
->
+        src/UseTheForce/DarkSide/atype_module.F90,
->
+        src/UseTheForce/DarkSide/calc_LJ_FF.F90,
->
+        src/UseTheForce/DarkSide/calc_charge_charge.F90,
->
+        src/UseTheForce/DarkSide/calc_dipole_dipole.F90,
->
+        src/UseTheForce/DarkSide/calc_eam.F90,
->
+        src/UseTheForce/DarkSide/calc_gb.F90,
->
+        src/UseTheForce/DarkSide/calc_reaction_field.F90,
->
+        src/UseTheForce/DarkSide/calc_sticky_pair.F90,
->
+        src/UseTheForce/DarkSide/force_globals.F90,
->
+        src/UseTheForce/DarkSide/neighborLists.F90,
->
+        src/UseTheForce/DarkSide/notifyCutoffs.F90,
->
+        src/UseTheForce/DarkSide/switch_module.F90,
->
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
->
+        src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp,
->
+        src/io/DumpWriter.cpp, src/io/Globals.cpp,
->
+        src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp,
->
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
->
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp,
->
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
->
+        src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c,
->
+        src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h,
->
+        src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h,
->
+        src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp,
->
+        src/types/AtomStamp.hpp, src/types/BendStamp.cpp,
->
+        src/types/BendStamp.hpp, src/types/BondStamp.cpp,
->
+        src/types/BondStamp.hpp, src/types/Component.cpp,
->
+        src/types/Component.hpp, src/types/CutoffGroupStamp.cpp,
->
+        src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp,
->
+        src/types/MakeStamps.hpp, src/types/Makefile,
->
+        src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp,
->
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
->
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
->
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
->
+        src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp,
->
+        src/brains/Exclude.hpp, src/brains/ForceFields.cpp,
->
+        src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp,
->
+        src/brains/SimInfo.hpp, src/brains/SimSetup.cpp,
->
+        src/brains/SimSetup.hpp, src/brains/SimState.cpp,
->
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
->
+        src/brains/SkipList.hpp, src/brains/Thermo.cpp,
->
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
->
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
->
+        src/brains/simulation_module.F90, src/io/BASS_interface.cpp,
->
+        src/io/Globals.hpp, src/io/LinkedAssign.cpp,
->
+        src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp,
->
+        src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h,
->
+        src/math/mt19937ar.c, src/math/randomSPRNG.cpp,
->
+        src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp,
->
+        src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp,
->
+        src/minimizers/OOPSEMinimizer.cpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
->
+        src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp,
->
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
->
+        src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp,
->
+        src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp,
->
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/primitives/Makefile, src/primitives/Molecule.cpp,
->
+        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
->
+        src/primitives/RigidBody.hpp, src/primitives/SRI.hpp,
->
+        src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp,
->
+        src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp,
->
+        src/restraints/Makefile, src/restraints/Restraints.cpp,
->
+        src/restraints/Restraints.hpp, src/utils/GenericData.cpp,
->
+        src/utils/GenericData.hpp, src/utils/Makefile,
->
+        src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp,
->
+        src/utils/StringUtils.c, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.h, src/utils/StringUtils.hpp,
->
+        src/utils/TypeInfo.hpp, src/utils/Utility.cpp,
->
+        src/utils/Utility.hpp, src/utils/definitions_module.F90,
->
+        src/utils/fError.c, src/utils/oopseMPI_module.F90,
->
+        src/utils/simError.c, src/utils/simError.h,
->
+        src/utils/status_module.F90, src/utils/vector_class.F90,
->
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
->
+        src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp,
->
+        src/visitors/CompositeVisitor.hpp, src/visitors/Makefile,
->
+        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,
->
+        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,
->
+        samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in,
->
+        samples/zcons/Makefile.in, samples/zcons/water.md,
->
+        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
->
+        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
->
+        src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp,
->
+        src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo,
->
+        src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h,
->
+        src/applications/Lattice.cpp, src/applications/Lattice.hpp,
->
+        src/applications/LatticeCreator.cpp,
->
+        src/applications/LatticeCreator.hpp,
->
+        src/applications/LatticeFactory.cpp,
->
+        src/applications/LatticeFactory.hpp, src/applications/Makedepend,
->
+        src/applications/Makefile, src/applications/MoLocator.cpp,
->
+        src/applications/MoLocator.hpp, src/applications/Vector3d.hpp,
->
+        src/applications/cmdline.c, src/applications/cmdline.h,
->
+        src/applications/getopt.c, src/applications/getopt1.c,
->
+        src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp,
->
+        src/applications/nanoBuilder.hpp, src/applications/oopse.cpp,
->
+        src/applications/quickLate.c, src/applications/simpleBuilder.cpp,
->
+        src/applications/simpleBuilder.ggo,
->
+        src/applications/simpleBuilderCmd.c,
->
+        src/integrators/AbstractClasses.hpp,
->
+        src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp,
->
+        src/integrators/Integrator.hpp, src/integrators/Makefile,
->
+        src/integrators/NPT.cpp, src/integrators/NPTf.cpp,
->
+        src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp,
->
+        src/integrators/NVT.cpp, src/profiling/Makefile,
->
+        src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp,
->
+        src/profiling/timing.F90, samples/metals/Au_bulk.in,
->
+        samples/metals/Au_nanoparticle.in, samples/metals/metals.md,
->
+        samples/water/Makefile.in, samples/water/dimer/Makefile.in,
->
+        samples/water/dimer/two.in, samples/water/dimer/two.md,
->
+        samples/water/dimer/water.md, samples/water/spce/Makefile.in,
->
+        samples/water/spce/spce.in, samples/water/spce/spce.md,
->
+        samples/water/spce/water.md, samples/water/ssde/Makefile.in,
->
+        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
->
+        samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in,
->
+        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
->
+        samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in,
->
+        samples/water/ssd/ssd.in, samples/water/ssd/ssd.md,
->
+        samples/water/ssd/water.md, samples/water/tip4p/tp4.in,
->
+        samples/water/tip4p/tp4.md, samples/water/tip4p/water.md,
->
+        samples/alkane/Makefile.in, samples/alkane/alkanes.md,
->
+        samples/alkane/butane.in, samples/alkane/butane.md,
->
+        samples/argon/500.in, samples/argon/500.md,
->
+        samples/argon/Makefile.in, samples/argon/ar864.in,
->
+        samples/argon/ar864.md, samples/argon/argonNVT.in,
->
+        samples/argon/argonNVT.md, samples/argon/lj.md,
->
+        samples/lipid/5x5.in, samples/lipid/5x5.md,
->
+        samples/lipid/Makefile.in, samples/lipid/lipid.md,
->
+        samples/lipid/water.md, samples/minimizer/Makefile.in,
->
+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
->
+        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in,
->
+        samples/minimizer/tip4p_two.md, samples/minimizer/water.md,
->
+        samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl,
->
+        forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl,
+        forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl,
+        forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl,
+        forceFields/DUFF.frc, forceFields/DipoleTest.frc,
+        forceFields/EAM.VC.frc, forceFields/EAM.frc,
+        forceFields/EAM.u3.frc, forceFields/EAM.u6.frc,
-<
+        forceFields/LJFF.frc, forceFields/Makefile,
-<
+        forceFields/Makefile.in, forceFields/Ni.VC.funcfl,
-<
+        forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl,
-<
+        forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl,
-<
+        forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl,
-<
+        forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl,
-<
+        forceFields/WATER.frc, libBASS/AtomStamp.cpp,
-<
+        libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp,
-<
+        libBASS/BASS_interface.h, libBASS/BASS_parse.c,
-<
+        libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y,
-<
+        libBASS/BendStamp.cpp, libBASS/BendStamp.hpp,
-<
+        libBASS/BondStamp.cpp, libBASS/BondStamp.hpp,
-<
+        libBASS/Component.cpp, libBASS/Component.hpp,
-<
+        libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp,
-<
+        libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp,
-<
+        libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp,
-<
+        libBASS/LinkedCommand.hpp, libBASS/Make.dep,
-<
+        libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile,
-<
+        libBASS/Makefile.in, libBASS/MoleculeStamp.cpp,
-<
+        libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp,
-<
+        libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp,
-<
+        libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp,
-<
+        libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c,
-<
+        libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h,
-<
+        libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h,
-<
+        libBASS/parse_interface.h, libBASS/parse_me.h,
-<
+        libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c,
-<
+        libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy,
-<
+        libBASS/obj/dummy, libmdtools/AbstractClasses.hpp,
-<
+        libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp,
-<
+        libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp,
-<
+        libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp,
-<
+        libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp,
-<
+        libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp,
-<
+        libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp,
-<
+        libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp,
-<
+        libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp,
-<
+        libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp,
-<
+        libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp,
-<
+        libmdtools/Euler3.cpp, libmdtools/Euler3.hpp,
-<
+        libmdtools/Exclude.cpp, libmdtools/Exclude.hpp,
-<
+        libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp,
-<
+        libmdtools/GenericData.cpp, libmdtools/GenericData.hpp,
-<
+        libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp,
-<
+        libmdtools/Integrator.cpp, libmdtools/Integrator.hpp,
-<
+        libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile,
-<
+        libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h,
-<
+        libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp,
-<
+        libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp,
-<
+        libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp,
-<
+        libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp,
-<
+        libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp,
-<
+        libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp,
-<
+        libmdtools/Restraints.cpp, libmdtools/Restraints.hpp,
-<
+        libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp,
-<
+        libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp,
-<
+        libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp,
-<
+        libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp,
-<
+        libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp,
-<
+        libmdtools/SimState.cpp, libmdtools/SimState.hpp,
-<
+        libmdtools/SkipList.cpp, libmdtools/SkipList.hpp,
-<
+        libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp,
-<
+        libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c,
-<
+        libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp,
-<
+        libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp,
-<
+        libmdtools/Thermo.hpp, libmdtools/Torsion.cpp,
-<
+        libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp,
-<
+        libmdtools/Utility.cpp, libmdtools/Utility.hpp,
-<
+        libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp,
-<
+        libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp,
-<
+        libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp,
-<
+        libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp,
-<
+        libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90,
-<
+        libmdtools/calc_charge_charge.F90,
-<
+        libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90,
-<
+        libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90,
-<
+        libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in,
-<
+        libmdtools/definitions_module.F90, libmdtools/do_Forces.F90,
-<
+        libmdtools/fForceField.h, libmdtools/fSimulation.h,
-<
+        libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp,
-<
+        libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp,
-<
+        libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp,
-<
+        libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp,
-<
+        libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c,
-<
+        libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp,
-<
+        libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90,
-<
+        libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90,
-<
+        libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp,
-<
+        libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90,
-<
+        libmdtools/status_module.F90, libmdtools/switch_module.F90,
-<
+        libmdtools/timing.F90, libmdtools/vector_class.F90,
-<
+        libmdtools/wrappers.F90, libmdtools/MPIobj/dummy,
-<
+        libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in,
-<
+        samples/alkane/Makefile, samples/alkane/Makefile.in,
-<
+        samples/alkane/alkanes.mdl, samples/alkane/butane.bass,
-<
+        samples/alkane/butane.eor, samples/alkane/init_butane.eor,
-<
+        samples/argon/500.bass, samples/argon/500.eor,
-<
+        samples/argon/500.in, samples/argon/Makefile,
-<
+        samples/argon/Makefile.in, samples/argon/NVT.bass,
-<
+        samples/argon/ar864.bass, samples/argon/ar864.eor,
-<
+        samples/argon/ar864.in, samples/argon/argon.bass,
-<
+        samples/argon/argon.eor, samples/argon/argonEM.bass,
-<
+        samples/argon/init_argon.eor, samples/argon/lj.mdl,
-<
+        samples/argon/machines, samples/lipid/5x5.bass,
-<
+        samples/lipid/5x5.eor, samples/lipid/Makefile,
-<
+        samples/lipid/Makefile.in, samples/lipid/init_5x5.eor,
-<
+        samples/lipid/lipid.mdl, samples/lipid/water.mdl,
-<
+        samples/metals/Au.bass, samples/metals/Au.eor,
-<
+        samples/metals/Makefile, samples/metals/Makefile.in,
-<
+        samples/metals/init_au.in, samples/metals/metals.mdl,
-<
+        samples/water/200.in, samples/water/Makefile,
-<
+        samples/water/Makefile.in, samples/water/init_ssd.eor,
-<
+        samples/water/spce.bass, samples/water/spce.eor,
-<
+        samples/water/ssd.bass, samples/water/ssd.eor,
-<
+        samples/water/tim.bass, samples/water/tim.eor,
-<
+        samples/water/tim.init, samples/water/tim.xyz,
-<
+        samples/water/tip3p.bass, samples/water/tip3p.eor,
-<
+        samples/water/tip3p.init, samples/water/two.bass,
-<
+        samples/water/two.eor, samples/water/two.init,
-<
+        samples/water/two.xyz, samples/water/water.mdl,
-<
+        samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass,
-<
+        samples/water/spce/water.mdl, samples/water/ssde/256init.in,
-<
+        samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl,
-<
+        samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass,
-<
+        samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl,
-<
+        scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in,
-<
+        src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy,
-<
+        third-party/Makefile, third-party/Makefile.in,
-<
+        third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo,
-<
+        utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep,
-<
+        utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub,
-<
+        utils/MPIobj/placeHolder, utils/obj/placeHolder,
-<
+        utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile,
-<
+        utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp,
-<
+        utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c,
-<
+        utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp,
-<
+        utils/sysbuilder/latticeBuilder.cpp,
-<
+        utils/sysbuilder/latticeBuilder.hpp,
-<
+        utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp,
-<
+        utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp,
-<
+        utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp,
-<
+        utils/sysbuilder/MPIobj/placeHolder,
-<
+        utils/sysbuilder/obj/placeHolder: Initial revision
->
+        forceFields/Makefile.in, forceFields/Ni.u3.funcfl,
->
+        forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl,
->
+        forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl,
->
+        forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc,
->
+        scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend,
->
+        ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess,
->
+        ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4,
->
+        ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf,
->
+        forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl,
->
+        forceFields/Au.u3.funcfl, forceFields/LJFF.frc,
->
+        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
->
+        forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0

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+Removed lines
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Comparing trunk/OOPSE-3.0/ChangeLog (file contents): Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs. Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC

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Comparing trunk/OOPSE-3.0/ChangeLog (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1644 by tim, Mon Oct 25 22:46:19 2004 UTC